Table 3Members of the original minimal gene set that show scattered phylogenetic patterns and are predicted to be dispensable (examples)

M. genitalium geneFunction/activityPhylogenetic patternaTransposon insertion knockout reported?
MG012Ribosomal protein S6 modificationam-k---ce--h--gp-----No
Enzyme (glutaminyl transferase)
MG104Exoribonuclease (RNase B family)----yqvceb-hujgp-lin-No
MG346rRNA methylase (SpoU class)-------cebrh--gp--in-Yes
MG278Guanosine polyphosphate-----qvcebrhujgpo----Yes
Pyrophosphohydrolase (SpoT)
MG097Uracil DNA glycosylase----y---ebrhujgpo-in-No
MG262.1Formamidopyrimidine-DNA glycosylase-------cebrh--gp-----No
MG408Peptide methionine sulfoxide reductase--t-yqvcebrhujgp-l---Yes
MG448Conserved domain frequently associated with peptide--t-yqvcebrhujgp-l---No
Methionine sulfoxide reductase
MG049Purine-nucleoside phosphorylase--------eb-huj-------Yes
MG052Cytidine deaminase----y-v-ebrh--gpo----Yes
MG127Arsenate reductase--------eb-h--gp-----No
MG033Glycerol uptake facilitatora-t-y-vceb-h--gpo----Yes
MG038Glycerol kinasea---yqvcebrh--gpo----No

Pattern notation: a letter indicates presence of the respective species in the given cluster of orthologous groups of proteins, and a hyphen in the corresponding position indicates its absence. Species abbreviations: a, Archeoglobus fulgidus; m, Methanococcus jannaschii, t, Methanobacterium thermoautotrophicum; k, Pysococcus horikoshii; y, S. cerevisiae; q, Aquifex aeolicus; v, Thermotoga maritima; c, Synechocystis sp.; e, E. coli; b, B. subtilis; r, Mycobacterium tuberculosis; h, H. influenzae; u, Helicobacter pylori; j, H. pylori J strain; g, M. genitalium; p, M. pneumoniae; o, Borrelia burgdorferi; l, Treponema pallidum; I, Chlamydia trachomatis; n, C. pneumoniae; x, Rickettsia prowazekii.

From: How Many Genes Can Make a Cell: The Minimal-Gene-Set Concept

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