Term
| What are two approaches to study minimal genome size? |
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Definition
1) Bioinformatics
2) Experimental |
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Term
| Bioinformatics approach to study minimal genome |
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Definition
| Mushegian and Koonin in 1996: all genes conserved among the 3 complete bacterial genomes, 256 genes in minimal set |
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Term
| What are the problems of bioinformatics approach? |
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Definition
- with distantly-related species it is hard to identify orthologs
- some functions can be performed by functional analogs
-results may change with each new genome
- no evidence that minimal set alone is sufficient for life |
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Term
| Experimental approach I to study minimal genome |
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Definition
| Craig Venter in 1999, used transposable element (TE) insertion mutagenesis to randomly knock out genes in two species. Only surviving cells could be detected, so “hit” genes must be non-essential.Final estimate = 265 – 350 essential genes. |
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Term
| What are the problems of experimental approach I? |
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Definition
-Not all 197 M.pneumoniae-specific genes may be non-essential in M.pneumoniae (“new”genes can become essential)
-Genes were knocked-out individually. |
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Term
| Experimental approach II to study minimal genome |
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Definition
| Kobayashi in 2003, Bacillus subtilis,knocked-out genes using a targeted, homologous recombination approach, 271 genes,50% - DNA/RNA metabolism or protein synthesis),50% protein synthesis genes encode ribosomal proteins |
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Term
| What are the correlations between genome size and the number of minimal genes |
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Definition
| The number of essential genes is not strongly correlated with the total number of genes in the genome. However, there is a negative correlation between the percentage of essential genes and the total number of genes in the genome. In organisms with few genes, such as M.genitalium, a high proportion of the genes are essential. |
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