Term
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Definition
| A mutant of Ralstonia solanacearum. An auxotroph that requires at least 15 μM of putrescine. Growth is poorly complemented by other polyamines. Did not grow after direct inoculation in the xylem. Unable to grow in tomato stems, suggesting that the wildtype R. solanacearum produces putrescine in the xylem sap, rather than the host. Co-inoculation with wildtype partially rescued in planta growth. Plant putrescine synthesis could not rescue its auxotrophy, even though it induces tomato ADC1. |
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Term
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Definition
| A phytohormone. Regulates interacting signalling pathways. Involved in drought, salt, and cold stress, as well as growth and development. Regulates stress-inducible gene expression. In shoots it is downregulated by jasmonic and salicylic acid, but upregulated by itself and ethylene. In roots it is upregulated by itself and jasmonic acid, but downregulated by ethylene. Antagonistic with ethylene in roots. During salt stress, it is transported into guard cells by specialized reporters. Leads to ROS accumulation and signalling. |
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Term
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Definition
| Secreted by endophytic bacteria to reduce ethylene levels in the plants. Allows the plant to recover faster after the stress is gone. A well-studied form of hormone adjustment. |
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Term
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Definition
| CRIPSR/Cas technologies may be able to produce a transgenic resistance gene that can adapt to new pathogens. This may have unintended consequences. |
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Term
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Definition
| A gene in tomato that is induced by Ralstonia solanacearum. Requires a functional T3SS, suggesting that one or more effector targets host polyamine synthesis. |
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Term
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Definition
| A (n+n) stage of MLP in larch. Produced by pycniospores. Produces aeciospores. Aecial stage occurs from 10 days onward. Collected from larch needles. Has weak correlation with expression in basidial stage, and strong correlation with expression in pycnial stage. There were 48 transcripts found only in the aecial stage. Of DEGs, 39.8% (617) were overexpressed. |
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Term
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Definition
| The third stage in MLP lifecycle. Produced by aecia. Travel from larch to poplar in the summer. Produce uredinia in larch. |
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Term
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Definition
| Transformed Agrobacterium tumefaciens is injected into the plant with a needleless syringe. Induces transient expression of constructs in the plant. Transformed plants are viable in selective media. |
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Term
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Definition
| A bacterial phytotoxin that blocks DNA replication in the chloroplasts and mitochondria, resulting in chlorosis and weakening of the plant cell. |
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Term
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Definition
| A trait that helps competent endophytes colonize the plant. The inside of a plant root is anaerobic. Harmful alcohols can build up in the endophyte. Alcohol dehydrogenase enables the bacteria to use these alcohols as an energy source. |
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Term
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Definition
| The second step in metabolomics data analysis. For each sample, the presence of each metabolite is measured. Uses all available information, including retention index and spectral match. Software includes MetPP, Guineu, or MetAlign. Typical results from high quality raw data produce 200 - 400 peaks in 80% of samples. Missing values represent 2 - 5% of data. |
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Term
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Definition
| A substrate of glutamine synthase. A byproduct of photosynthesis. Without active glutamine synthase, it will accumulate in the cell. Degrades membranes, proteins, and other components. Can break down the chloroplast. |
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Term
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Definition
| A soil enzyme. Detected in a buffer containing starch, arsenomolybdate reagent, and Somogyi's micro reagent. Found in higher levels when Paenibacillus yonginensis DCY84T is present, regardless of salt stress. |
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Term
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Definition
Oxo-epoxidecanoic acid
A non-protein amino acid. A key component of the HC toxin. |
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Term
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Definition
| The space outside of plant cell membranes, in the cell wall and middle lamella. Biotrophs live in the apoplast to prevent host cell death. There is not much nutrition for pathogens in the apoplast. Pathogen PAMPs can be detected in the apoplast by membrane receptors. |
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Term
| Arabidopsis thaliana (At) |
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Definition
| A model organism in plant science. Although it is in the same family as Brassica sp., the marker gene responsiveness activation of specific hormonal pathways might show important differences. It does not have the same hormone signalling pathways as B. rapa. |
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Term
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Definition
| A CWDE produced by pathogenic fungi. Produced in smaller amounts than pectinase, and is less plant-toxic. Degrades half of arabinogalactose, but causes no structural damage. |
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Term
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Definition
| A component of the cell wall. A polymer of arabinose and galactose. Degraded by arabinase. |
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Term
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Definition
| The first stage of bacterial pathogen infection. Cells multiply to form colonies and microcolonies on the surface of the plant. Secreted extracellular polysaccharides help bacteria stick to the plant. |
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Term
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Definition
Indole-3-acetic acid
A pant hormone. Some bacterial endophytes release analogs. Includes formation of secondary roots. Causes a larger root ball. Can change the shape of ginseng roots. |
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Term
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Definition
| A fungal effector. Inhibits host cysteine proteases, a plant defence response. |
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Term
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Definition
| A fungal effector. Binds to chitin, protecting it from host chitinases. |
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Term
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Definition
| A defence compound which can be detoxified by Gaeumannomyces graminis. Found only in oats. |
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Term
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Definition
| A transcriptional activator. An unusual effector that enters the nucleus and activates the transcription of genes involved in susceptibility. An example of an effector that binds to DNA. |
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Term
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Definition
| A bacterial effector. A protein kinase inhibitor. Inhibits kinase domains of plant receptors. An effector that targets the kinase cascade. |
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Term
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Definition
| A bacterial effector. An analog of ubiquitin ligase. Marks proteins for degradation, including MAPK, and other important proteins. An example of an effector that degrades proteins. |
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Term
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Definition
| A bacterial effector. A cysteine protease. Degrades proteins in the host cyctoplasm. An effector that degrades proteins. |
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Term
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Definition
| An endophytic bacteria which is marketed as a product to trigger ISR, protecting plants from pathogens. |
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Term
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Definition
| Biotrophic bacteria which are non-pathogenic. Can be acquired from roots (most common), leaves, stems, tubers, fruits, natural openings, wounds, and seeds infected during development or germination. Enter at root wounds, lateral root formations, roots at intact surfaces, or wounds or natural openings in leaves. Have low diversity. Includes actinobacteria, firmicutes, and proteobacteria. Includes gram-negative and -positive bacteria. Approximately 219 culturable species are found in 71 genera. Some species may not be culturable. There are 788 species inside Arabidopsis roots, based on 16S rRNA analysis. The bacteria move to the plant roots passively with water uptake, or actively via chemotaxis, seeking out plant signals including malic and citric acid secreted by roots. May have non-specific absorption by sticking to the root surface. Divide and form a colony in the apoplast. Spread through the vascular system. Classified into three groups based on function, not phylogeny: passenger, opportunistic, and competent endophytes. In the roots, populations can range from 105 to 107 cfu/g fresh weight, but in localized areas can be as high as 1010 cfu/g. Populations in the shoots are lower and less diverse, including only competent endophytes; 103 - 104 cfu/g fresh weight. Population in seeds is even lower: 101 - 103 cfu/g. Population cannot exceed a certain amount without becoming pathogenic to the plant. There are often several species inside a plant at once. The bacteria may lack some types of PAMPs, but still have some, however PTI response is not as strong as with pathogens. |
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Term
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Definition
| The stages of infection of a bacterial pathogen are the same as for fungal pathogens: attachment, penetration, and invasion. Lack hyphae. Cells multiply to form colonies and microcolonies, which are held together by EPS and pili. Grows in the apoplast of the plant host. Cells are much smaller than plant cells, and can fit in between them. Do not have a vegetative stage; only exist as bacterial cells. |
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Term
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Definition
| One of the major diseases of tomatoes and other Solanaceous plants. Caused by Ralstonia solanacearum race 1 or 3, but rarely 2. Symptoms include wilting of the youngest leaves and the ends of branches during the hottest part of the day. Only one or half a leaflet may wilt, and the plants may appear to recover at night. The entire plant may wilt quickly and desiccate although dried leaves remain green, leading to general wilting and yellowing of foliage, and eventually plant death. Cross-sections of stems reveal brown discolouration in well-established infections. |
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Term
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Definition
| A (n) stage of MLP in poplar. Produced by teliospores. Undergo meiosis to produce basidiospores. Basidial stage occurs from 0 - 5 days. Collected from telia on overwintered poplar leaves. Has weak correlation with expression in aecial and pycnial stages. There were 230 transcripts found only in the basidial stage. Of DEGs, 38.8% (661) were overexpressed. |
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Term
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Definition
| The first stage in MLP lifecycle. Produced by basidia in poplar. Infect larch leaves through stomatal openings. Produces pycnia in larch. |
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Term
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Definition
β-galactosidase
A reporter system. A product of yeast when histidine cannot be transcribed in a yeast two hybrid assay. |
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Term
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Definition
| A hypothesis for how CDWEs kill plant cells. The CWDE creates shortened oligo galacturonates of different sizes, 10 - 13 sugars long, depending on where bonds are attacked. These act as DAMPs, and plant defences are activated. |
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Term
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Definition
| An antimicrobial compound secreted by some endophytes. Solubilizes the biofilm of other endophytes, reducing the numbers of their microcolonies. |
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Term
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Definition
| Pathogens which do not kill their host. Limited in the types of CWDEs it can have, because they kill the cell easily. However, it needs some CWDEs to grow in the apoplast. In bacteria, includes only crown gall bacterium; biotrophic bacterial pathogens are rare. Cannot feed if the host dies. To prevent host cell death, it grows in the apoplast and/or releases effectors to stop defence responses. Forms haustoria in the host cell to feed. |
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Term
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Definition
Field mustard
A model organism with a sequenced genome, fast reproduction, and simple cultivation. Closely related to Arabidopsis. Plants mature 4 weeks after germination, at 5-leaf stage. |
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Term
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Definition
BR-C, ttk, and bab/pox virus and zinc finger
A homodimerization domain found in NRL1. Mutated in NRL1NQ. |
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Term
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Definition
| Guanidine hydrochloride. Lyses cells with β-mercaptoethanol. |
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Term
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Definition
| Ethanol buffer. Used to wash RNA samples. |
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Term
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Definition
| Guanidine salt and ethanol. Used to wash RNA shamples. |
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Term
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Definition
| May directly influence and regulate osmotolerance of membranes under salt stress. |
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Term
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Definition
| The mass of EPS that encases bacteria within a microcolony with strong attachment. |
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Term
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Definition
| CRISPR-associated proteins. Encode proteins that have roles in CRIPSR functioning. Includes nucleases, helicases, and nucleotide-binding proteins. Guided by crRNA. There are 4 - 7 Cas proteins. Includes effector modules. |
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Term
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Definition
| A class 2 effector. Contains an HNH domain. Activated when RNA binds and causes a conformational change. Cleaves target DNA that is complementary to the guide RNA. Widely characterized. Includes types II, V, and VI. |
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Term
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Definition
| A class 2, type VI effector. A Cas protein containing HEPN domains. Has RNase activity. May be a single RNA-guided RNA targeting effector. Interaction with crRNA is mediated with the protospacer flanking sequence. Conformational change upon RNA binding places arginine and histidine together, allowing cleavage activity. Predominantly cleaves at U residues in secondary structures formed by the RNA target sequence. Has a distinct RNase mechanism. Has collateral RNA degradation when the catalytic site is exposed; can cleave ssRNAs outside of the crRNA binding site. Leads to programmed cell death, induction of dormancy, and sensing of viruses. Has applications in biotechnology (engineering programmed cell death) and diagnostics (binding specificity, collateral cleavage). Removing rare codons aids in expression and optimizes activity. |
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Term
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Definition
| A step in RNA sequencing. Primers and reverse transcriptase generate dsDNA. |
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Term
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Definition
| Made up of cellulose, xyloglucan, arabinogalactose, and pectin. All components are digestible by microorganisms. Fibres are interlinked with cellulose, and other components. Some fungi can grow directly through the cell wall. |
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Term
| Cell wall degrading enzymes (CWDE) |
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Definition
| Enzymes which degrade cell wall components. Includes pectinase, cellulase, arabinase, galactanase, and glucanase. There are two hypotheses for how they kill the plant cell: physical effects and biochemical effects. Pectinase is the most important CWDE, causing plant cell death; other CWDEs are used for nutrition of the pathogen. Secreted by all plant pathogenic bacteria. More are expressed when infecting certain types of plants than others. Can attack a variety of plant species. In endophytes they help colonize the plant, but do not break the cell wall so much that it is detrimental. Allow bacteria to break the cell in the exo-and endodermis. Ralstonia solanacearum secretes CWDEs via a highly conserved type II protein secretion system. Causes release of cellulose-derived metabolites including cellobiose, gentiobiose, and sugars. Facilitates leakage of metabolites into the xylem from adjacent tissue. |
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Term
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Definition
| A CWDE that degrades cellulose. Does not kill the cell. Not the most important CWDE, even though cellulose is the most abundant cell wall component. |
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Term
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Definition
| A fungal phytotoxin. Not toxic without light. When it absorbs UV light, the toxin produces ROS as it releases the energy. The ROS then binds and damages host cell membranes and other components. |
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Term
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Definition
| Proteins that bind onto something in order to control when it is active and not active. Can stop effectors from acting until they need to, protecting it from detection and degradation. |
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Term
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Definition
| A multi-subunit crRNA effector complex. Accounts for 90% of CRISPR-Cas loci. Includes 4 - 7 Cas proteins. |
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Term
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Definition
| A single-subunit crRNA effector complex. Accounts for 10% of CRISPR-Cas loci. RNA-guided endonuclease domains cleave dsDNA. Includes RuvC and Cas9. |
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Term
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Definition
| A protein tagging system. Allows detection with immunoprecipitation. |
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Term
| Co-immunoprecipitation (Co-IP) |
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Definition
| A technique for precipitating a protein and its associated subunits out of a solution using an antibody. |
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Term
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Definition
| A pathogen which produces HC toxin. Some races are non-toxic. Causes northern corn leaf blight, a disease which affects areas north of the Mississippi Valley. Symptoms include leaf spots and necrotic areas. |
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Term
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Definition
| Measures the absorbance of particular wavelengths of light. |
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Term
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Definition
| A group of bacterial endophytes. Found in the rhizosphere. Have adaptations for being endophytes. The most competent type of endophytes. Colonize roots and enter through wounds. Extensively colonize the apoplast. Colonize roots and enter through wounds. Extensively colonize the apoplast. Can enter the pericycle through the endodermis, and get into the xylem to spread quickly throughout the whole plant. The exo- and endodermis is penetrated using enzymes. Traits that allow them to colonize the plant include: flagella, lipopolysaccharides, CWDEs, pili, detoxification, alcohol dehydrogenase, TonB-dependent receptors, and type III, IV, and VI secretion systems. |
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Term
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Definition
| The second step in untargeted metabolomics. Determines the chemical structure of the discovered metabolites. |
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Term
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Definition
| A metabolite secreted by Pseudomonas syringae to subvert host plant immunity. |
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Term
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Definition
| A bacterial phytotoxin that mimics jasmonic acid, stopping jasmonate-related responses such as stomatal closure. Causes stomata to stay open as an entry point for the bacterial pathogen. |
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Term
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Definition
Clustered regularly interspaced short palindromic repeats
Includes a leader sequence, direct repeats, and spacer sequences. |
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Term
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Definition
| Found in all archaea and some bacteria. A nucleic acid-based adaptive immune system. A mobile system that moves intracellularly, attacking invading viruses and plasmids. Similar to RNAi in eukaryotes. |
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Term
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Definition
| A class 2, type VI effector module. TRV plasmids were electroporated into Agrobacterium tumefaciens, and then agroinfiltrated into Nicotiana benthamiana. Successfully interfered with TuMV-GFP. Interference is pCas13a-dependent and RNAi-independent. Expression of only cRNAs in wildtype did not mediate interference with TuMP-GFP. Has specific RNA targeting in planta. Efficiency is higher for HC-Pro and GFP2 target sequences, and lower for CP or GFP1 target sequences. RNA target accessibility is affected by secondary structures in the TuMV crRNA. Provides a defence against invading nucleic acids in archaea and bacteria. Has applications in biology, biotechnology, and medicine. Can be engineered to provide selective interference and immunity against plant RNA viruses; only one protein is needed to silence a whole library of RNAs. Has no collateral RNA cleavage in eukaryotes. Future research into this system could lead to multiplex targeting of virus genomes, variants with enhanced RNA-guided RNase activity, and protein stability fusions such as monomeric superfolder GFP (msfGFP). |
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Term
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Definition
| The antagonistic and synergistic interactions between jasmonic and salicylic acid. A complex network that fine-tunes defence responses to multiple stimuli. The majority of Brassica rapa genes are similar to those in Arabidopsis. |
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Term
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Definition
| Single-stranded RNA which is copied from foreign ssRNA. Includes a 28 nt spacer and a 28 nt direct repeat. |
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Term
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Definition
| A type of fungal effector. The cysteines form disulphide bonds which make it resistance to decay by proteases. Secreted into the apoplast, where proteases are found. |
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Term
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Definition
| A plant hormone. Some bacterial endophytes release analogs, leading to production of more root hairs and growth. |
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Term
| Damage-associated molecular pattern (DAMP) |
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Definition
| A molecule which can only have been produced by damage from a pathogen. Acts like an effector or PAMP, triggering defence, possibly HR. Includes shortened oligo galacturonates, 10 - 13 sugars in length. |
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Term
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Definition
| A mutated Cas13a with an arginine mutation in the HEPN domain. Catalytically inactive. Can still bind to the RNA target, but cannot cleave it. |
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Term
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Definition
| A soil enzyme. Detected with triphenyltetrazolium chloride dyes, which are colourless, and then red when dehydrogenated. Found in higher levels when Paenibacillus yonginensis DCY84T is present, regardless of salt stress. |
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Term
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Definition
| A trait that helps competent endophytes colonize the plant. Many genes help detoxify ROS which are harmful to the bacteria. Deals with the PTI reaction of the plant. |
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Term
| Differentially expressed genes (DEG) |
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Definition
| Genes with observed changes in transcript read counts. Either upregulated or downregulated. |
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Term
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Definition
| An element of CRISPR. Palindromic sequences, 21 - 48 bp in length. Conserved within species, but not between species. Allows for binding with Cas13a. |
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Term
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Definition
| Enzymes that degrade DNA. Eliminates genomic DNA. |
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Term
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Definition
| A Cas protein that targets and cleaves foreign nucleic acids. Guided by crRNA. 90% class 1, and 10% are class 2. |
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Term
| Effector-triggered immunity (ETI) |
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Definition
| There is no ETI reaction against beneficial endophytes; this would be detrimental to the plant. |
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Term
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Definition
| Secreted by fungal pathogens to suppress PTI. Pathogen-produced proteins that alter the plant cell or its environment to cause disease and/or to trigger defences. Bacteria have large numbers of effectors; a strain can have 20 - 30. Multiple effectors attack multiple plant components. Classified into cysteine rich, and non-cysteine rich effectors. Includes Av2, Av4, HopAL1, AvrPto, ArRpt2, AvrPtoB, and AvrBs3. |
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Term
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Definition
| Cells are electrified to create pores in the cell membrane. Introduces a vector into Agrobacterium tumefaciens. |
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Term
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Definition
| Biotrophic bacteria or fungi that live in the plant tissue, but have no apparent negative impact on the plant. Isolated from surface-disinfected plant tissue, or extracted from within the plant in order to be identified. Not all endophytes are culturable. Found in all plants. Includes obligate and facultative endophytes. Diversity can be affected by plant genotype when inside the plant (nutrients, PTI response), as well as in the soil. The latter is the main factor for most endophytes. Do better with intermediate soil moisture and pH: no drought or water-logging. Soil with high organic matter and/or conservation tillage will have greater endophyte diversity. The population size inside the plant is less than that of a pathogen. Benefits to the endophyte include more environmental niches, N and C sources, and TCA substrates including malate, succinate, and ketoglutarate. Benefits to the plant includes higher N, P, and Fe nutrient availability, plant hormone adjustments, and antimicrobial compounds that may defend against pathogens (ISR). Some endophytes have no apparent benefit or detriment to the plant. Endophytes may consume each other, and there is competition for space, nutrients, and iron. They may secrete antimicrobial compounds to protect themselves from other bacteria such as biosurfactants, hydrolytic enzymes, chitinases, glucanases, and proteinases; these might trigger ISR. |
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Term
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Definition
| A gene in Arabidopsis activated by the jasmonic acid pathway. Coregulated by ethylene. Involved in necrotrophic pathogen defence. Requires both jasmonic acid and ethylene signaling. Regulated by AP2/ERF transcription factors. Regulates expression of marker genes PDF1.2 and ERF1. Antagonistic with MYC. |
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Term
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Definition
Ethylene response factor 1
A marker gene in the ethylene branch of the jasmonic acid pathway, and the ethylene pathway. Regulates expression of PR genes. A marker for root-induced responses in Brassica rapa. In shoots it is upregulated by ethylene; activated by ethylene or jasmonic acid pathways synergistically. In the roots it is downregulated by jasmonic and abscisic acid but upregulated by ethylene. A suitable marker for ethylene in shoots and roots. Antagonistic with MYC only in roots. |
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Term
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Definition
| A pathogenic bacteria with five major and three minor pectate lyases. |
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Term
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Definition
| Helps precipitate out RNA from samples. |
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Term
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Definition
| Converted into ethylene in plants. A gas treatment. |
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Term
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Definition
| A gaseous stress phytohormone. Involved in fruit ripening, stem thickening, and apical hook response. Induced by disease. The pant adjusts to stress by slowing its growth when it senses ethylene. The gaseous hormone can linger even after the stress is gone. ACC deaminase secreted by some endophytic bacteria reduces stress-induced ethyene, allowing the plant to resume growth faster. Synergistic with jasmonic acid, inducing defence genes including PR1b, PR5, and PDF1.2. Antagonistic with abscisic acid in the roots. |
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Term
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Definition
Ethylene receptor 1
A marker gene in the ethylene pathway. Encodes an ethylene receptor. Dependent on other defence genes. Activated upon pathogen attack. |
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Term
| Eukaryotic orthologous genes (KOG) |
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Definition
| A database that clusters proteins together. Secreted proteins were the most abundant type of transcript in MLP. |
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Term
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Definition
| Ions that bind to soil particles. Cation amount is a measure of soil fertility. Includes calcium, magnesium, sodium, and potassium. Determined by displacing the ions from soil colloids with NH4. The soil is mixed with ammonium acetate and pH is adjusted to 7.0, then diluted with Lanthanum. Measured with a spectrophotometer. |
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Term
| Extracellular polysaccharide (EPS) |
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Definition
| Secreted by bacterial pathogens in order to stick to the plant surface and to each other in a microcolony. Prevents the bacteria from drying out. Helps form the capsule and slime layer of the microcolony. Causes the first symptoms in the plant, water soaking. Of EPS secreted by Ralstonia solanacearum, 90% is EPS1; 85% is released unbound in cell-free slime, and 15% is released in capsular form, cell surface bound. Minimizes recognition of bacterial surface pili or lipopolysaccharides by plant defence mechanisms. |
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Term
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Definition
| Endophytes that may live outside a plant. Includes most endophytes. Found in the soil, plant surface, and in the environment. Grows in plant tissue if entry and space are available. |
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Term
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Definition
| The first step in metabolomics data analysis. Peaks originating from derivation reagents from solvent are filtered. |
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Term
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Definition
| A trait that helps competent endophytes colonize the plant. Allows for chemotaxis, in which bacteria move towards wounds and through the host apoplast. |
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Term
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Definition
| A component of sucrose. Cannot be used by the plant cell, but can be used by fungal pathogens. |
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Term
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Definition
| Found in necrotrophic pathogens. The fungus is able to degrade host defence molecules. |
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Term
| Fusarium solani f.sp. pisi |
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Definition
| A pathogen with 4 PL genes. Can diverge the regulation of genes for different situations. Two of the PLs are constitutive, always produced. The third can be turned off or on depending on whether the substrate is dead or alive. The fourth is host-specific, only expressed when attacking a live plant. The amount of pectin is controlled by the pathogen to allow its growth. |
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Term
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Definition
| A fungal phytotoxin. One of the only toxins which can cause wilting. It enters the guard cells of stomata, and turns on ATPase. |
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Term
|
Definition
| A pathogen of wheat and oats. Can detoxify avenacin. |
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Term
|
Definition
| A CWDE produced by pathogenic fungi. Produced in smaller amounts than pectinase, and is less plant-toxic. |
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Term
| Gas chromatography-mass spectrometry (GC-MS) |
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Definition
| A common method in metabolomics. An effective system for sensing volatile metabolites. Few metabolites are truly volatile. Adding methoxamine (methoximation) stabilizes ketones, and adding a silyl group (silylation) to polar functional groups including -COOH, -OH, -NH, and -SH; both are necessary to reduce polarity and increase thermal stability and volatility of metabolites. Most instruments use proprietary software to do peak deconvolution. During data analysis overlap peaks are decomposed. Software includes Metlin, XCMS, and ChromaTOF. Derived the metabolite extracts into volatile and thermally stable derivatives. Detects small, non-molar organic acids and fatty acids short to medium in size. Highly reproducible retention indices. Metabolites are identified in libraries. Performed on sap from soil-soaked inoculated plants. |
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Term
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Definition
| Includes Korean ginseng (Panax ginseng), South China ginseng (P. notoginseng), and American ginseng (P. quinquefolius). Takes 4 - 6 years to cultivate. A high value, but sensitive crop. Produces soil phytotoxins that kill its own self; it cannot be cultivated in the same plot twice. Contains ginsenosides and gintonin, which have antioxidant, anti-Alzheimer's and anti-cancer properties. Human-shaped roots are the most prized. Sold as a dry product, often consumed as tea. |
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Term
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Definition
| A CWDE produced by pathogenic fungi. Produced in smaller amounts than pectinase, and is less plant-toxic. |
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Term
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Definition
| A component of sucrose. Cannot be used by the plant cell, but can be used by fungal pathogens. Inside the pathogen it is converted into sugar alcohols, including mannitol, sorbitol, and trehalose, which are used for nutrition. |
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Term
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Definition
| An enzyme deactivated by tabtoxin. Converts ammonia and glutamate into glutamine, using ATP. Without it, the cell cannot make the essential amino acid glutamine, and ammonia produced as a byproduct of photosynthesis builds up in the cell. |
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Term
| Green fluorescent protein (GFP) |
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Definition
| A fluorescent marker gene. Fluoresces green under UV light. |
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Term
|
Definition
| A protein tag that allows for detection in Western blot. |
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Term
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Definition
| Salt-tolerant plants. Adaptations include ion pumps, abscisic acid responses, osmoprotectants, and/or ROS scavenging. |
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Term
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Definition
| A protein that incorporates into the membranes of the host cell, making them leaky and less functional. Provides more water and nutrients for the bacterial pathogen. |
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Term
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Definition
| A structure formed by some pathogens, mostly biotrophs. Found in ascomycetes, basidiomycetes, and oomycetes. An invagination into a living host cell. A side branch of the pathogen hyphae that penetrates the cell wall, but avoids breaking the host cell membrane. The plant cell membrane expands as the haustoria grows. Increases surface area of pathogen and host interface, the matrix. Secretes invertase into the matrix. ATPase-coupled transporters pump sugars and amino acids from the matrix into the pathogen; the energy expanded is less than what is absorbed. The cytoskeleton of the host plant cell is changed entirely, and the nucleus is moved to right up against the haustoria. |
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Term
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Definition
| A fungal phytotoxin produced by Cochliobolus carbonum. The name comes from when this organism was known as Helminthosporium carbonum. A cyclopeptide, forming a circle. Some of the amino acids are non-protein amino acids, including Aoe. Deactivates histone acetylase. Without histone deacetylase, the cell cannot change its DNA expression, so it cannot activate any defence responses. Host specific; works only in corn. |
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Term
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Definition
| Pathogens with both biotrophic and necrotrophic stages. In bacteria, includes leaf spot bacteria. Most bacterial pathogens are hemibiotrophs. |
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Term
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Definition
Higher eukaryotes and prokaryotes nucleotide-binding domains
A domain in Cas13a. Has conserved arginine and histidine residues. Mutated in dCas13a. Required for the cleavage of target RNA. |
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Term
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Definition
Histidine
An essential amino acid. Used in a yeast two hybrid assay. When the transcription factor is disabled, an essential synthesis enzyme is absent, and the yeast cannot survive in histidine-negative medium. |
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Term
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Definition
| A plant enzyme which is deactivated by HC toxin. An important enzyme. Uncoils heterochromatin in the nucleus, so that DNA may be affected by transcription factors and expressed as mRNA. Triggers gene expression, including when defence responses are activated. |
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Term
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Definition
HC toxin reductase
A gene in corn. Detoxifies HC toxin by cleaving a part of it. Follows gene-for-gene resistance patterns, but is not a receptor. |
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Term
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Definition
Histidine-asparagine-histidine
A domain of Cas9. |
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Term
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Definition
| A bacterial effector. A phosphothreonine lyase. Dephosphorylates kinases. An effector that targets the kinase cascade. |
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Term
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Definition
| A constitutive gene. Used as a baseline to compare other genes. |
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Term
| Hypersensitive response (HR) |
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Definition
| Cell death defence response, preventing spread of the pathogen. Not effective against necrotrophs, which can feed on dead cells. |
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Term
| Hypersensitive response and pathogenicity (HRP) |
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Definition
| Controls type III secretion systems in gram-negative bacteria. Name comes from the fact that genes from this region can trigger ETI in the host, but is also necessary for the bacteria's pathogenicity. Knocks out genes and limits disease. |
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Term
| Induced systemic resistance (ISR) |
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Definition
| Can be triggered by endophytic bacteria. There are several species of bacteria that can cause ISR in a variety of plants, for defence against the variety of disease including viruses and fungi. Some of these cases are well-studied, such as Bacillus pumilus INR7. |
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Term
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Definition
| A PAMP of Phytophthora infestans. Activates SWAP70, which then promotes INF1-triggered cell death. |
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Term
| INF1-triggered cell death (ICD) |
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Definition
| A type of HR caused by the PAMP of Phytophthora infestans INF1. A defence mechanism that inhibits the development of late blight disease. |
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Term
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Definition
| The third step in untargeted metabolomics. Uncovers biological connections of the results. |
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Term
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Definition
| The third stage of a bacterial pathogen infection. Bacteria multiply within the host apoplast, forming microcolonies inside the plant tissue. Secreted EPS forms the capsule and slime layer. The bacteria absorb water and Ca2+, inhibiting the calcium burst, suppressing PTI. |
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Term
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Definition
| An enzyme secreted into the matrix by pathogens with haustoria. Breaks sucrose into glucose and fructose, which can be absorbed by the pathogen. A soil enzyme. Detected in a buffer containing sucrose. Found in higher levels when Paenibacillus yonginensis DCY84T is present, regardless of salt stress. |
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Term
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Definition
Ion-accumulation response
The second stage of plant response to salinity. Occurs over a longer period than the osmotic phase. Ions build up to toxic concentrations in the shoot, particularly in older leaves. Leaves senesce prematurely, yield decreases, and the plant may die. |
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Term
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Definition
| A limiting nutrient for endophytic and pathogenic bacteria. Endophytic bacteria may secrete siderophores into the soil and re-uptake them with chelated iron. This gives the plant higher Fe nutrient availability. |
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Term
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Definition
| A phytohormone. A key regulator of plant defence. Synergistic with ethylene. Induced by necrotrophic pathogens, chewing insects, and wound response. Part of the backbone of the plant immune system. In shoots it is upregulated by itself, and downregulated by salicylic acid. In roots it is upregulated by itself. |
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Term
| Kyoto eukaryotic genes and genomes (KEGG) |
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Definition
| A database with complete genomes. |
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Term
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Definition
| Measures nitrogen and phosphorus content. The soil is mixed with HCl, glacial acetic acid, malonic acid, and ammonium fluoride. The mixture is filtered through a porosity filter, then measured with inductively coupled argon plasma spectroscopy. |
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Term
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Definition
Larix sp.
The aecial host of MLP. A deciduous conifer tree, 50 - 60 m tall. Includes 10 - 12 species. Important for forestry industries worldwide. Produces durable, waterproof wood. Used to make boats, fencing, and building exteriors. There were more secreted proteins found during the larch in planta stage of MLP. |
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Term
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Definition
| A disease of potatoes, tomatoes, and Nicotiana benthamiana caused by the oomycete pathogen Phytophthora infestans. Contributed greatly to the Irish potato famine. |
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Term
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Definition
| When lateral roots form, they always break through the exoderm, forming a wound. Bacterial endophytes and pathogens commonly enter through these wounds. |
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Term
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Definition
Late embryogenesis abundant 4
An Arabidopsis-derived novel marker gene in the abscisic acid pathway. A protein that accumulates during seed development and water deficit. Involved in seed maturation. Highly responsive to abscisic acid in vegetative tissue. An early inducible gene and marker for root-induced responses in Brassica rapa. BrLEA4 has 100% similarity to AtLEA4-5. In shoots it is downregulated by jasmonic and salicylic acid, but upregulated by abscisic acid. In roots it is downregulated by jasmonic acid, salicylic acid, and ethylene; abscisic acid upregulates it at first, and then downregulates it. Involved in the abscisic acid pathway in both shoots and roots. |
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Term
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Definition
| An element of CRISPR. The promoter element. Rich in A and T. It is 300 - 500 bp in length. Conserved within species, but not between species. |
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Term
| Leptotrichia shahii Cas13a (LshCas13a) |
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Definition
| The Cas13a of the bacteria L. shahii. It was reconstituted in E. coli to mediate RNA-guided interference of the RNA phage MS1 in vitro and in vivo. A programmable RNA-guided ssRNA ribonuclease. Induces defence to the virus. Guided to knockdown RFP mRNA in E. coli. Caused nonspecific cleavage of RNAs, reducing E. coli growth. Requires a target and functional Cas13a. |
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Term
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Definition
| A trait that helps competent endophytes colonize the plant. Help the bacteria stick to the root surface and to each other, forming microcolonies. |
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Term
| Liquid chromatography mass spectrometry (LC-MS) |
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Definition
| A common method in metabolomics. Offers the broadest coverage due to the ability to work with different column chemistries. Hydrophobic interaction liquid chromatography (HIC) separates molecules based on their hydrophobicity. Common compounds detected include lipids, polyamines, and alcohols. Detects medium to large, polar nucleotides and lipids. Chromatography is less critical. Metabolites are identified by composition by accurate mass. Showed that Ralstonia solanacearum exports putrescine. |
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Term
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Definition
| A lipid oxidation product. Increased in salt-stressed plants. |
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Term
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Definition
| A mapped gene with known characteristics. Used to investigate genes. Links pathway with defence response. Indicators of activated pathways. The majority of Arabidopsis studies look into shoot tissues, expression patterns after exogenous hormone application, marker gene responsiveness, and pathway interactions. Information is implemented in other plant species such as Brassica sp. The majority of marker genes in B. rapa are similar to those in Arabidopsis. Some markers are not unique to the pathway. The response of marker genes to certain pathways can differ between shoots and roots. Includes PR1, MYC2, VSP2, ERF1, PDF1.2, ETR1, and LEA4. |
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Term
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Definition
| The space between the host plant cell membrane and the membrane of a pathogen haustoria. Nutrients, including photosynthates, cross the matrix into the pathogen, either following a concentration gradient, or actively pumped by ATPases of the pathogen. The pathogen secretes invertase into the matrix. |
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Term
| Melampsora larici-populina (MLP) |
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Definition
| A basidiomycete, macrocyclic, heteroecious rust pathogen. A devastating disease of poplars and larch (Populus sp. and Larix sp., respectively) in Europe. Secretes effectors and toxins that interfere with physiological defence and immune response. Has five stages: uredinia, telia, basidia, pycnia, and aecia. RNA transcript analysis found that 62% of all transcripts were found across basidial, pycnial, and aecial stages, while 5.94% of transcripts were found exclusively in one of these three stages. |
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Term
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Definition
| An intermediate to the end product of metabolism. A small molecule. May be involved in nutrition, structure, signalling, or stimulation. Includes primary and secondary metabolites. The metabolome comprises all the metabolites in a biological cell, tissue, or organism. Microbial pathogens produce metabolites that manipulate and damage their host. Includes coratine and oxalate. |
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Term
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Definition
| The omic technology of sugars, nucleotides, amino acids, and lipids. Samples are broken down into their smallest components. Cellular processes are analyzed based on the chemical traces that they leaves behind. Provides insight into the physiological state of the organism. Can be used in food production, medical research, and plant science. creates a picture of what is or is not happening in plants at the most fundamental cellular level. Most common methods include GC-MS, LC-MS, NMR, and untargeted metabolomics. During data analysis, steps are filtering, alignment, normalization, and statistical analysis. |
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Term
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Definition
| A liquid which works as a jasmonic acid treatment. Less volatile than jasmonic acid, and easier to work with. |
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Term
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Definition
| A treatment which inhibits the activity of 26S proteasomes. |
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Term
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Definition
| A gene in Arabidopsis activated by the jasmonic acid pathway. Regulated by abscisic acid. Involved in wounding and insect herbivory stress. Controlled by MYC-type transcription factors and marker genes MYC2 and VSP2. Antagonistic with ERF. |
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Term
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Definition
| A marker gene in the abscisic acid branch of the jasmonic acid pathway. A transcription factor induced by light, abscisic acid, and jasmonic acid signalling pathways. Has a basic helix-loop-helix leucine zipper. Antagonistic with ERF1. |
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Term
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Definition
| Pathogens which feed on dead plant hosts. May kill the plant so quickly that there are no triggered responses. May produce a lot of CWDEs. In bacteria, includes soft rot bacteria, the only group of necrotrophic bacterial pathogens. |
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Term
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Definition
| A fungal pathogen of peas. Produces hydrogen demethylase, encoded on an SDC, which demethylates pisatin, making it less toxic to the pathogen. |
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Term
| Nicotiana benthamiana (Nb) |
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Definition
| A model organism for transgenic plants. A host of TRV, and works well with VIGS. |
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Term
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Definition
| Free-living nitrogen-fixing bacteria can convert atmospheric N into forms that are usable by plants. When living as endophytes, they give the plant higher N nutrient availability. |
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Term
| Non-cysteine rich effector |
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Definition
| A type of fungal effector. Unlike cysteine rich effectors, it is susceptible to proteases. More likely to be secreted into the host symplasm. |
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Term
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Definition
| The third step in metabolomics data analysis. A common practice. Injection control. Normalization by SUM; the total area under the curve. Critical samples are normalized by creatine or other specific analytes. |
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Term
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Definition
NPH3/RPT2-LIKE1 protein
A Phytophthora infestans S factor in potatoes and tomatoes. A substrate adaptor for the E3 ubiquitin ligase CUL3. Causes proteasome-dependent degradation of SWAP70, preventing ICD defence response. Promoted by the pathogen effector Pi02860. Contains a BTB/POZ homodimerization domain, which prevents activity when mutated. |
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Term
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Definition
| A mutant of NRL1 in which aspartate 28 (D) is turned into asparagine (N), and lysine 42 (K) is turned into glutamine (Q), in the BTB/POZ homodimerization domain. Unable to dimerize, and cannot inhibit SWAP70. |
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Term
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Definition
| A crRNA with four 28 nt direct repeats interspaced between three non-specific crRNAs. Inserted via the pUC19 plasmid. |
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Term
| Nuclear magnetic resonance (NMR) |
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Definition
| A common method in metabolomics. A fast and highly reproducible spectroscopic technique based on the energy absorption and re-emission of the atom nuclei due to variations in external magnetic field. Resulting spectral data allows quantification of concentration of metabolites, and provides information about their chemical structure. |
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Term
| Nucleic acid extracellular traps (NET) |
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Definition
| An extracellular matrix of proteins, polysaccharides, and DNA that immobilizes the pathogens. A defence mechanism that Ralstonia solanacearum can evade by encoding two putative extracellular DNases expressed during pathogenesis, enabling the bacteria to degrade and escape root border cell traps. |
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Term
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Definition
| Endophytes which can only live inside a plant. |
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Term
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Definition
| Primarily aimed at the universal detection of molecules in a specific biological sample. Has a broad range of applications. Includes genomics (DNA), transcriptomics (RNA), proteomics (proteins), and metabolomics (sugars, nucleotides, amino acids, and lipids). |
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Term
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Definition
| A group of bacterial endophytes. Found in the rhizosphere. Have some adaptations for being endophytes. Good colonizers of the root surface, occasionally entering through wounds. Grow in the apoplast. Have a higher population inside the plant than passenger endophytes. Growth is limited. The "medium"-good bacterial endophyte. |
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Term
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Definition
| A small organic molecule with a neutral charge. Gives salt tolerance to halophytes. |
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Term
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Definition
Shoot ion-dependent phase
The first stage of plant response to salinity. Occurs minutes to days after exposure to salt. Stomata close, and leaf expansion is inhibited. |
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Term
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Definition
| A metabolite secreted by fungal pathogen Sclerotinia sclerotium to subvert host plant immunity. |
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Term
| Paenibacillus polymyxa KACC10485T |
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Definition
| A commercialized plant growth promoting bacteria. Promotes growth in Arabidopsis. |
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Term
| Paenibacillus yonginensis DCY84T |
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Definition
| A plant growth-promoting bacteria found in soil from Yongin forest in Korea. Has the highest auxin production of all bacteria in the soil screening. Produces siderophores. Has phosphate solubilization ability, and no antifungal activity against pathogenic fungi. May exhibit more biocompatibility in a real ecosystem than in vivo. Populations in the rhizospheres is not reduced during salinity stress. Provides soil nutrition, water retention, metabolites, and gene expression in ginseng. Upregulates ginseng ion pump SOS1. Enriches soil system nutrients and increases plant nitrogen and phosphorus content. Plants do not exhibit water loss during salt stress. Increases K+ and decreases Na+ stressed ginseng, but doesn't change Mg2+. Seedlings recover from salt stress better, and have less ROS accumulation. Can be used as a microbial inoculant to protect ginseng plants against salinity stress, root rot, water retention, growth promotion, iron and soluble phosphorus uptake, and expression of defence-related genes. |
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Term
| PAMP-triggered immunity (PTI) |
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Definition
| Immunity triggered by conserved pathogen PAMPs. Cannot be avoided, even against beneficial endophytes. The reaction to beneficial endophytes is localized and with lower intensity. Competent endophytes may detoxify factors, helping it avoid PTI. An endophyte may trigger PTI that then helps the plant defend itself from a pathogen that invades later on. |
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Term
| Partial least squares discriminate analysis (PLS-DA) |
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Definition
| A statistical analysis procedure used to find fundamental relationships between two matrices. Performed to sharpen the separation between groups of observations. Uses rotating PCA components. Decomposes both the design matrix X and Y by taking information from each other into account. The matrices are decomposed into latent structures in an iterative process. The latent structure corresponding to the most variation of Y is extracted and explained by the latent structure of X that explains it the best. |
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Term
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Definition
| A group of bacterial endophytes. Found in the rhizosphere. Have no adaptations for being endophytes. Poor colonizers of the root surface. Enter the plant accidentally through wounds. Population inside the plant is very low. Has limited growth inside the plant; usually stays near the wound site. |
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Term
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Definition
| Populations in the plant are much higher than that of endophytes: 107 - 1010 cfu/g fresh weight. Populations can reach 1010 cfu/g in susceptible plants. |
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Term
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Definition
Plant defensin 1.2
A marker gene in the ethylene branch of the jasmonic acid pathway. In previous studies it was found to induce distinct organ-specific expression patterns in leaves. In shoots it is upregulated by salicylic acid. In roots it is upregulated by salicylic acid and downregulated by ethylene. |
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Term
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Definition
| A component of the cell wall. A polymer of galacturonic acid. The "glue" which holds the cell wall together. Adjacent sugars are linked by oxygen. Degraded by pectinase. A great food source for pathogens. |
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Term
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Definition
Pectate
A type of pectinase. Breaks pectin polymers. A double bond is created in the galacturonate. Does not use a water molecule. It can kill plant cells. Includes endo- and exo-PLs, which can break bonds anywhere in the polymer, or only from the end, respectively. |
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Term
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Definition
| An enzyme which degrades pectin. The most important CWDE; the first produced by the pathogen, and in the largest amounts. Can kill plant cells. Includes pectinesterases, polygalacturonases, and pectin lyase. |
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Term
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Definition
| A type of pectinase. Doesn't degrade pectin directly; it converts its bonds into ester bonds. |
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Term
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Definition
| The second stage of a bacterial pathogen infection. Bacteria do not have appressoria; they have passive penetration only, through natural openings or wounds. Rain may wash bacteria into these openings. If the bacteria have flagella, they may be able to swim through water on the plant surface into an opening close by; they cannot swim very far. |
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Term
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Definition
| Some endophytes can digest petroleum, and help plants survive in oil-contaminated soil. |
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Term
| Phenotypic conversion (PC) type cells |
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Definition
| A form that Ralstonia solanacearum may take in the soil. A mucoid produced by accumulation of exopolysaccharides with typical irregularities on the surface. Linked to reduction in disease-inducing capacity. |
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Term
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Definition
| A plate screening method for detecting phosphorus solubilization ability. Media formulated by Pikovksaya is opaque, but turns clear when phosphates are dissolved. |
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Term
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Definition
| A nutrient which is insoluble for plants. Endophytic bacteria may secrete organic acids that solubilize phosphorus, giving the plant higher P nutrient availability. |
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Term
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Definition
| A hypothesis for how CWDEs kill plant cells. Pectinases degrade the middle lamella, and the cell wall is loosened. Water pressure turgidity in the cell increases, causing the cell wall to rupture, and the cell dies. Attacks the physical integrity of the wall only. Cellulose would not work. |
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Term
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Definition
| Signalling molecules that regulate plant responses. Includes jasmonic acid, salicylic acid, ethylene, and abscisic acid. |
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Term
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Definition
| An oomycetes pathogen which causes late blight disease. Produces the effector Pi02860 which activates the host S factor NRL1. |
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Term
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Definition
| A chemical which quickly kills plant tissues, and has a low molecular weight. Does not includes enzymes. Produced by pathogens. Damage the host plant, and are involved in disease development, benefiting the pathogen. Causes chlorosis, necrosis, and/or wilting. Can be isolated and purified, and still produce symptoms, following the same virulence patterns as the pathogen. Often has an "odd" molecular structure, with rings. An anti-metabolite that jams up the plant's metabolic pathways. May bind to plant enzymes and never release, compete with normal enzyme substrates, or insert into membranes where they shouldn't be. Secreted by fungal pathogens which are usually non-host-specific, and can attack outside of their host range. It is more important for competition with other microbes, especially necrotrophs. Toxins have trivial names based on the organism they come from, as well as chemical names. Many toxins are related to each other. Fungal pathogens cannot avoid releasing PAMPs, but it can produce toxins that stop plant PTI defence reactions. All are non-host specific; can attack many different species of plants and microorganisms. Includes T-toxin, victorin, cercosporin, fusicoccin, coronatine, albicidin, syringomycin, and tabtoxin. |
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Term
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Definition
| An RXLR effector produced by the oomycetes pathogen Phytophthora infestans. Activates the host S factor NRL1. |
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Term
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Definition
| Protrusions on bacterial cells. Help hold bacterial colonies together. A tube that allows plasmids to be exchanged between bacteria. A modified pilus may be used to secrete effectors in plant pathogenic bacteria. Conserved in bacteria. Black plague uses a pilus to attack humans. A trait that helps competent endophytes colonize the plant. Gives bacteria "twitching" movement that allows for directional movement through the xylem. |
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Term
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Definition
| A defence compound produced by peas. A phytoalexin from the phenylpropanoid pathway. |
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Term
| Plant growth-promoting bacteria (PGPB) |
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Definition
| Bacteria which indirectly activate various antioxidant enzymes that scavenge ROS, including superoxide dismutase (SOD), peroxidase, and catalase. Aid the plant in acquisition of nutrients, phosphorus solubilization, siderophores, fixation of atmospheric nitrogen, hydrocyanic acid production, regulation of plant hormones, and defensive action against biotic pathogens. Modulate root architecture by increasing auxin levels. Allows more nutrients to be taken up during salinity stress. |
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Term
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Definition
| A crRNA with four 28 nt direct repeats interspaced between GFP1, GFP2, and HC-Pro. Successfully reduced expression of GFP in planta. Processed into multiple mature, functional crRNAs by CRISPR/pCas13a. |
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Term
|
Definition
| A type of pectinase. Breaks pectin polymers. Includes endo- and exo-PGLs, which break bonds in the middle of the polymer or at the end of the polymer, respectively. Breaks bonds between sugars with hydrolysis; adds a water molecule to break the compound. |
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Term
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Definition
Populus sp.
The telial host of MLP. A deciduous broadleaf tree, 15 - 50 m tall. Includes 25 - 35 species. Important for the paper industry, as well as for making pallets and snowboards. Produces lower quality, flexible wood. |
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Term
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Definition
| The second largest genus of plant viruses, including 158 species. Has a wide host range. Contains positive sense ssRNA, 10,000 nt long. Filamentous particles 700 - 750 nm long. Includes TuMV. |
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Term
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Definition
Pathogenesis-related protein 1
An Arabidopsis-derived marker gene in the salicylic acid pathway. A group of PR proteins induced by pathogens or salicylic acid. Has antimicrobial properties, and amplifies defence signals. Used as a marker for SAR and root-induced responses in Brassica rapa. In shoots it is a unique marker for the salicylic acid pathway. Not induced by jasmonic acid, abscisic acid, or ethylene pathways. Has similar responses in Arabidopsis, Brassica, tomato, corn, and soybean. In roots it is upregualted by salicylic acid and ethylene. Does not require salicylic acid accumulation. Involved in salicylic acid pathway in roots, and salicylic acid and ethylene pathways in roots. |
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Term
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Definition
| A metabolite involved in growth, development, and reproduction. Includes ethylene. |
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Term
| Principal component analysis (PCA) |
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Definition
| An orthogonal transformation statistical analysis technique. Possibly correlated variables are converted into a set of linearly uncorrelated variables. Principle components are graphed as the X and Y axes. Similar datapoints group together on the graph. |
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Term
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Definition
| The first step in untargeted metabolomics. Finds metabolites with statistically significant variations, of the control and test sample. |
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Term
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Definition
| Found in increased levels in salt-stressed and PGPB-primed plants. A defence mechanism against osmotic stress. Enhances water retention. Accumulation leads to increased transcription of PgP5CS. |
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Term
| Protospacer flanking sequence (PFS) |
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Definition
| A single nucleotide in the ssRNA which is made into crRNA: A, U, or C (never G). Mediates Cas13a-crRNA interactions by binding with the spacer sequence. |
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Term
| Pseudomonas putida WCS358 |
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Definition
| A bacterial endophyte found in tomato seeds and roots. |
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Term
| Pseudomonas syringae pv. tomato DC3000 |
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Definition
| A pathogen of tomato and Arabidopsis. A model strain of P. syringae. There are more papers on this strain than many other plant pathogens. Has an unusually large number of effectors, over 50. Has a large host range. |
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Term
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Definition
| The required diamine for the biosynthesis of polyamines, spermine, and spermidine, the essential components for DNA packaging during the cell cycle. Synthesized by Ralstonia solanacearum via SpeC ornithine decarboxylase. Accumulates during drought, or after a soil-soak inoculation. Expression is induced by infection in several plants. Exogenous putrescine application accelerates bacterial wilt progress. Cannot be used as a sole carbon or nitrogen source by the bacteria. Synthesis in the host plant is altered by infection, to artificially synchronize bacterial wilt disease and polyamine biosynthesis over time. Soil treatment increased expression of tomato PR1b and ACO5, markers for salicylic acid and ethylene defence signalling pathways. Increased growth of tobacco pathogenic R. solanacearum strain K60 in the leaf apoplast. Must alter tomato physiology in a way that increases bacterial growth in the xylem. A pathogen-produced virulence metabolite. |
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Term
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Definition
| A (n) stage of MLP in larch. Produced by basidiospores. Produces pycniospores in the spring. Collected from larch needles. Pycnial stage occurs from 5 - 10 days. Has weak correlation with expression in basidial stage. Has strong correlation with expression in aecial stage. There were 696 transcripts found only in the pycnial stage. Of DEGs, 21.3% (330) were overexpressed. |
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Term
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Definition
| The second stage in the MLP lifecycle. Produced by pycnia. Undergo plasmogamy to produce aecia in larch. |
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Term
| Quantitative real time RT-PCR |
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Definition
| A variant of PCR. RNA from the plant tissue is treated with DNase I, purified into RNA, and treated with reverse transcriptase. The primer oligo(dT)20 and enzymes are added to create undiluted cDNA. After 10-fold serial dilutions of cDNA the standard curve indicates the PCR efficiency. Amplifies target DNA sequences, and measures amplification using fluorescent dyes. The accumulation of amplification product is measured as the reaction progresses in real time, with product quantification after each cycle. A fluorescent reporter molecule is proportional to the amount of DNA product. |
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Term
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Definition
| Different strains of a pathogen based on resistance pathogens within its host range. Can be conferred by effectors. |
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Term
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Definition
| Several genus names are used. An aerobic non-spore-forming gram - proteobacteria. A soil-borne, motile pathogen. Colonizes the xylem of its host, causing devastating lethality. Threatens global food security. Host range includes 450 plant species, includes potato, tomato, eggplant, banana, ginger, tobacco, sweet pepper, olive, rose, and soybean. Evades root defences such as NET. Enters through wounds and natural openings. Forms biofilms in the xylem vessel walls that restrict sap flow, protecting from host defences, and causing wilt. Filters nutrients from the flow of xylem fluid. Lives as a saprophyte in the soil or other environments. Survives until contact with a new host. Survives for 40 years in water at 20 - 25ºC. Bacterial populations are reduced in extreme conditions. May exist as VBNS, starved cells, or PC-type cells. Deploys virulence factors including CWDE, EPS, and T3SS. No single factor completely explains bacterial wilt virulence. Alters the xylem sap physical and chemical conditions to favour its own growth. There is increase in trehalose, 3-hydroxybutyrate, alanine, gluconate, mannitol, and galactose; there are 22 enriched metabolites in total, but this may exclude metabolites consumed at the same rate as they enter the xylem. Putrescine is highly enriched. Decreases pipecolate. Not all enriched compounds were nutrients for the bacteria. Cannot use putrescine as a sole carbon or nitrogen source. Does not produce spermidine, but absolutely requires putrescine. Grows better ex vivo on sap from infected plants than healthy plants |
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Term
| Ralstonia solanacearum race 1 |
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Definition
| Causes bacterial wilt in eggplant, pepper, potato, tobacco, and tomato. Endemic to the USA. |
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Term
| Red fluorescent protein (RFP) |
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Definition
| A fluorescent marker gene. Fluoresces red under UV light. |
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Term
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Definition
| Beneficial bacterial endophytes which have type VI secretion systems. |
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Definition
| The soil adjacent to plant roots. Rich with nutrients. Many types of bacteria live in the rhizosphere. A small portion of these bacteria are able to be plant endophytes. |
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Definition
| Steps include RNA fragmentation, cDNA synthesis, adding sequence adaptors, PCR amplification, and sequencing using a reference genome. |
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Term
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Definition
| A positive-sense ssRNA in TRV. Causes post-transcriptional gene silencing. Can be used for genome engineering. |
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Term
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Definition
| Plant roots interact with the rhizosphere. Responses to hormone elicitation can differ shoots and roots of the same plant. |
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Term
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Definition
| A salinity defence in halophytes. Nanomaterials with redox properties eliminate ROS. ROS accumulation activates cell-to-cell signalling and significantly increases transcription of antioxidant genes. PGPB-primed plants have increased activity of antioxidant enzymes. |
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Definition
| Pathogenic fungi in the order Pucciniales. Includes around 8,000 species. Obligate biotrophs with a wide host range including ferns, gymnosperms, and angiosperms. Has heteroecism, with macro- or microcyclic life stages; 5 or 2 spore stages, respectively. Includes white pine blister rust, cedar apple rust, and wheat leaf rust. Few studies have looked at expression levels of secreted proteins throughout the entire rust life cycle. |
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Term
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Definition
RNase H-like fold
A class 2 effector. |
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Term
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Definition
| Effectors produced by Phytophthora infestans. Contain the motif arginine (R) - [any amino acid] - leucine (L) - arginine (R), which is required for entry into the host cell. Target host S factors. Includes Pi02860. |
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Term
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Definition
| A phytohormone. A key regulator of plant defence. Induced by biotrophic pathogens and phloem-sucking insects. Part of the backbone of the plant immune system. Upregulated by itself in both roots and shoots. |
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Term
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Definition
| Allows for detection of auxin (IAA). Medium is cultured with Salkowski's agent. Bacterial cultures are mixed with the reagent, and colour indicates the auxin levels. |
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Definition
| Can be caused by incorrect fertilizer application, water management, and weather conditions. Prevents uptake of essential nutrients, and causes ionic toxicity, osmotic stress, ROS production, nutrient imbalance, and deficiency of Ca2+ and K+. Plant response occurs in two phases: osmotic phase and ionic phase. Stressed plants have lower nitrogen and phosphorus content. Symptoms include wilting, shrinking, discolouration, yield decrease, and decreased chlorophyll and carotenoids. Salt stressed ginseng has less relative water content in aerial parts. There is increased hydrogen peroxide and malondialdehyde. Can halt growth of seedlings. |
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Definition
| A metabolite not directly involved in growth, development, or reproduction, but has an important ecological function. Includes antibiotics and pigments. |
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Term
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Definition
| Any protein secreted from the pathogen. Includes small secreted proteins. The most abundant known gene category in MLP during infection of both its hosts, but more so in the larch infection stage. Preferentially expressed in both hosts. Very important during infection. Of preferentially expressed genes, 18% were secreted proteins. Of other genes, 10% were secreted proteins. |
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Term
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Definition
| Involved in bacterial pathogenicity. Secrete different classes of extracellular enzymes. Includes types I - IV. |
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Definition
| A compound that has a high affinity or chelating with iron. Secreted by bacteria, and then taken up chelated with iron by TonB-dependent receptors. Secreted by plant growth-promoting bacteria. Transports iron across cell membranes. Produced by Pseudomonas under iron-limiting conditions. |
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Term
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Definition
| The mass of EPS that encases bacteria within a microcolony with loose attachment. |
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Term
| Small secreted protein (SSP) |
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Definition
| Any secreted protein less than 250 bp. Preferentially expressed by MLP during poplar and larch infection. Overall, 205 small proteins were preferentially expressed in planta on larch, and 351 were preferentially expressed in planta on poplar. Roughly 75% were detected in all four life stages analyzed. Detected in larch more so than in poplar. Includes SSP families 1, 7, and 9. There is host-specific expression across these gene families. Different sets are expressed depending on the stage of disease cycle. Indicates that different proteins are secreted during different stages of the disease cycle. |
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Definition
| A membrane protein ion pump. The most commonly expressed ion pump. Upregulated in PGPB-primed plants. Secretes ions from the cell for salt stress tolerance. |
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Term
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Definition
| An element of CRISPR. Non-coding sequences, 27 - 72 bp in length. Integrated into the CRISPR locus. Contains the target RNA sequences. Bind to the protospacer flanker sequence in the invading RNA. |
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Term
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Definition
| Leaf tissue is ground and acetone is added, then the mixture is centrifuged. The supernatant is measured with a spectrophotometer. There is a specific calculation for each molecule, including proline, sugar, chlorophyll, and carotenoids. |
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Term
| Small dispensable chromosomes (SDC) |
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Definition
| Found in many fungal pathogens. Smaller than regular chromosomes. The fungus can survive without an SDC, but it will lose its pathogenicity, and must live as a saprophyte. Encodes genes for virulence. Some fungi can fuse hyphae and pick up SDCs from other fungi. Not found in animals. |
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Term
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Definition
| A group of small secreted proteins. Expressed specifically at the basidial and larch stages of MLP. Includes 24 genes. Only 4 were expressed specifically in urediniospore and poplar stages, and the remaining genes showed a higher expression in the basidial and larch stages. |
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Term
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Definition
| A group of small secreted proteins. Roughly half were expressed specifically in the larch in planta stage, and half in the poplar in planta stage. |
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Term
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Definition
| A group of small secreted proteins. Includes 11 genes. Of these, 9 were expressed specifically in the poplar in planta stage, and 2 had increased expression in the larch in planta stage. |
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Term
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Definition
| A form that Ralstonia solanacearum may take in the soil. A survival mechanism in energy-deficient systems. Bacterial populations manage to maintain in a non-growing but culturable state. |
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Definition
| The fourth step in metabolomics data analysis. A wide variety of tools and packages are available. An R-package in web-based apps includes Metaboanalyst. Aligned data is uploaded in .cs or .txt format. Goes through normalization, missing data, and filtering steps, then allows a variety of analyses. Can produce heat maps, clustering, PCA, PLS-DA, T-tests (paired and unpaired), and some pathway analysis. |
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Term
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Definition
| The photosynthate most commonly secreted by plant cells. Cannot be used by fungi directly. A disaccharide of glucose and fructose. Broken by invertase. |
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Term
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Definition
S factor
Elements endogenous to the host which promote development of the disease. Housekeeping genes which are taken advantage of by the pathogen. |
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Term
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Definition
| An R factor that induces INF1-triggered cell death in response to Phytophthora infestans. A guanine exchange factor that can activate GTPases. Associates with endosomes. |
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Term
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Definition
| A fungal phytotoxin which affects corn, wheat, and other fungi. It inserts itself into the inner membrane of mitochondria, creating pores that disturb the electron transport cycle. The cell loses ATP synthesis and dies. A host-specific toxin. |
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Term
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Definition
| A bacterial phytotoxin secreted by Pseudomonas syringae pv. tabaci, as well as other pathovars. Non-toxic when formed in a dipeptide of threonine and tantoxinin-β-lactam, and activated when the dipeptide is cleaved inside the host. Active tabtoxin irreversibly binds to glutamine synthetase, deactivating it. This leads to ammonia buildup, casing foliar chlorosis. Can bind to glutamine synthase in any organism, including humans. |
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Term
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Definition
| A bacterial phytotoxin that makes pores in the plant membranes at low concentrations, and lyses membranes at high concentrations. |
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Term
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Definition
| A (n+n) stage in MLP. Produced by urediniospores. Produces teliospores in the winter. Collected from fallen poplar leaves. The overwintering structure of MLP. |
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Term
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Definition
| The fifth stage in MLP lifecycle. Produced by telia. Undergoes karyogamy to produce basidia in poplar. |
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Term
| Threonine and tabtoxinin-β-lactam |
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Definition
| A dipeptide that detoxifies tabtoxin. Secreted by Pseudomonas syringae pv. tabaci, and is broken by peptidase (aminopeptidase cleavage), releasing active tabtoxin into the plant cell. |
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Term
| Time-of-flight mass spectrometry |
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Definition
| Uses a gas chromatograph which measures the content of various components in a sample. Each compound has a unique spectrum, including chlorophyll a and myoglobin. |
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Term
| Tobacco rattle virus (TRV) |
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Definition
| A Tobravirus. A vector or virus-induced gene silencing. Used to create transgenic plants. Contains 2 positive-sense ssRNAs: RNA1 and RNA2. Both RNAs are necessary for expression of the crRNA. |
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Term
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Definition
| A trait that helps competent endophytes colonize the plant. An outer membrane receptor that re-uptakes secreted siderophores chelated with iron. Inside the plant, bacteria have an iron deficiency. Gives the plant higher Fe nutrient availability. |
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Term
| Total soluble sugar (TSS) |
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Definition
| Increases in salt-stressed ginseng. Maintains homeostasis. Does not increase with PGPB-priming. |
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Term
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Definition
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Term
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Definition
| Transgenic plants that express viral genes or RNA sequences, or resistance genes; may provide resistance against plant viruses. Created by electroporating plasmids into Agrobacterium tumefaciens, and then agroinfiltrating the bacteria into Nicotiana benthamiana. The cells are cultured on kanamycin medium to kill untransformed plants. Expression of the construct is confirmed with Western and Northern blot. |
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Term
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Definition
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Term
| Turnip mosaic virus (TuMV) |
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Definition
| A Potyvirus. RNA contains an open reading frame that translates into a single polyprotein, which is then hydrolyzed by proteinase into at least 10 proteins. |
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Term
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Definition
| Found in gram-negative bacterial pathogens, including Erwinia. Secretes proteases and lipases into the intercellular space. Common in endophytes and other types of bacteria. |
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Term
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Definition
| Found in gram-negative bacterial pathogens, including Erwinia. Secretes pectinase and cellulase into the intercellular space. Common in endophytes and other types of bacteria. |
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Term
| Type III secretion system (T3SS) |
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Definition
| Found in many bacterial pathogens. Secretes effectors into the host cell. Controlled by HRP. Associated with chaperones and harpins. Rare, usually found only in endophytes. A virulence factor of Ralstonia solanacearum. Secretes infection-promoting effector proteins into the host cell. There are 74 suspected or confirmed T3SS. No effector significantly alters pathogenicity. |
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Term
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Definition
| Found in Agrobacterium. Secretes T-DNA and proteins into the host cell. Rare, usually found only in endophytes. Allows the PAMPs of the bacteria to avoid detection by PTI receptors. |
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Term
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Definition
| Class 2 effectors that affect cleavage and expression. Includes Cas13a. |
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Term
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Definition
| Delivers effectors into the host from biotrophic bacteria. A rare secretion system, more common in beneficial endophytes than pathogens. Allows for mutualistic relationships. Found in Rhizobium. |
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Definition
| Involved comparing the metabolome of control and test groups to identify differences between their metabolite profiles. Differences may be relevant to specific biological conditions. There are three steps: profiling, compound identification, and interpretation. Used to compare the chemical composition of sap from healthy Ralstonia solanacearum-infected plants. |
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Definition
| A (n+n) stage of MLP in poplar. Produced by aeciospores. Produces urediniospores in the summer. |
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Term
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Definition
| The fourth stage in MLP lifecycle. Produced by uredinia. Produces telia in poplar. Infect poplar leaves through stomatal openings during MLP's asexual cycle. |
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Term
| Viable but non-culture form (VBNS) |
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Definition
| A form that Ralstonia solanacearum may take in the soil. Dormant cells that are metabolically active and viable. Unable to grow in solid media. A survival mechanism of non-sporulating bacteria exposed to extreme environmental conditions. Survive for less than a month at 4ºC. Reported in planta during infections, and increases under extensive necrosis. |
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Term
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Definition
| A fungal phytotoxin. Cleaves or binds to rubisco and other key proteins of photosynthesis and photorespiration, inhibiting their function. |
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Term
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Definition
| A plant hormone. A plant-growth promoting compound. Secreted by some bacterial endophytes. |
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Term
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Definition
Vegetative storage protein 2
An Arabidopsis-derived marker gene in the abscisic acid-regulated MYC branch of the jasmonic acid pathway. An acid phosphatase. Induced by wounding, MeJA, and insect herbivory. Upregulated in response to jasmonic acid. A marker for root-induced responses in Brassica rapa. In the shoots it is upregulated by jasmonic and abscisic acid, but downregulated by salicylic acid and ethylene. In the roots it is upregulated by jasmonic acid, but downregulated by salicylic acid and ethylene. Responsiveness is conserved in Brassicaceae. In B. rapa it is elicited independently of jasmonic acid. Time-dependent; organs process it differently. Involved in jasmonic and abscisic acid pathways in shoots, and jasmonic acid pathway in roots. |
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Term
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Definition
| The first symptom seen in host plants with a bacterial infection. Spots on the leaf appear to be filled with water. Caused by microcolonies filling the apoplast with bacterial cells and EPS. Water is retained for use by the bacteria. |
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Definition
| A component of the cell wall in monocots. A polymer of xylose. |
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Term
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Definition
| Nutrient-poor and hypoxic in comparison to the phloem. Metabolites are 10 - 100 fold less than in the leaf apoplast. Poses further metabolic limits for Ralstonia solanacearum growth, however the bacteria grows to high cell densities. |
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Term
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Definition
| A component of the cell wall. A polymer of xylose and glucose. |
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Term
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Definition
| A technique for determining whether to proteins bind to each other or not. The bait and prey are attached to two separate parts of a transcription factor and expressed in yeast. If the two components do not bind naturally, the transcription factor is unable to activate a histidine synthesis enzyme. If this is the case, the yeast cells will not survive in histidine-negative medium. |
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