Minimal Genome Project

• hard to identify all orthologs, especially for distantly related species

• same function can be performed by different genes/ functional analogs = NODs

  (Non-Ortologous gene Displacement)

-> results were prone to change as more species were sequenced and no evidence that this set alone is enough

Mushegian/ Koonin 1996

Find all genes conserved among the 3 complete bacterial genomes available at the time:

• H. influenzae, M. genitalium, E. coli)

• 256 genes in the minimal set

• 63 genes are common to all of life (Archaea, Bacteria, Eukaryotes)

• 91 genes are common to Archaea and Bacteria

• 217 genes are common to Bacteria (less than found by the bioinfo approach from ‘96)

COG:

It is a database that groups proteins from different organisms according to shared evolutionary origin and usually shared function.

For example, if several bacterial species contain genes descended from the same ancestral gene, those genes may be placed in the same COG.

M. genitalium, 580kbp, 480 protein coding genes

try to knock out genes from species with already little genes

use 2 species to estimate #genes not hit by chance vs #genes essential and led to death

start from:

M. genitalium: 580kbp — 480 prot coding genes

M. pneunomiae: 816kb — 480 orthologs + 197 genes (=677)

TE insertional mutagenesis to randomly knock out genes in both species, die if essential was hit

observed hits = non-essential genes

M. genitalium: 93 hits -> 480 -93 = 387 not observed hit (overestimation, some not hit by chance, no saturation screen)

M. pneunomiae: 57 ortholog, + 93 unique hits

final estimate: 265-350 essential genes

• 111 genes of unknown function undisrupted, many of these might be essential

• functional analogs: also some of the genes specific to a species can be essential

• synthetic lethals were not regarded

cases where two genes can be knocked out individually with no effect, but the cell dies if both genes are knocked out together

begin with bacillus subtilis, 4100 genes

• knock out individually with targeted homologous recombination (not random knockout like craig venter)

• combine with craig venters findings

• 271 genes (6% of total) were essential for growth under optimal laboratory conditions.

  The remaining 3,830 (94%) were non-essential

• BUT STILL only individual knock outs, synthetic lethals not regarded

• 50% DNA/ RNA synthesis or Protein Metabolism

  • more than 50% of these encode ribosomal proteins

• not all were completely conserved over all known genomes or even over all known bacterial genomes

  -> these essential genes would not show up

  as part of the minimal genome by the bioinformatic approach.

• well-conserved in other bacterial species

  -> Of the essential genes, ≈30% were conserved across 54 bacterial species

• many are also found in Archaea and/or Eukaryotes

  -> ≈20% were conserved across 18 Archaea and Eukaryotic

  
  

• 473 genes

• ransplant entire bacterial genomes and engineer

  synthetic life (paper 2008,2010)

negative correlation

• few genes-> high percentage essential

• many genes -> low percentage essentail