gene name, catagory of proposed ORF comments/references function MP MG
DNA replication/repair: DNA polymerase III, dnaE, A19_orf 872 MG261 highest similarity to Gram-negative bacteria, no [[alpha]] subunit 3'-5' exonuclease (5, 44) [[alpha]] subunit, dnaE B01_orf1443 MG031 highest similarity to Gram-posititve bacteria, 3'-5' exonuclease DNA polymerase, polA, A19_orf291 MG262 no polymerase specific domain, 5'-3' exonuclease domain RNaseH, rnhA - - not identified (45)* Mismatch-repair system, mutS, - - not identified mutL, mutH
Transcription: RNA polymerase, sigma H91_orf499 MG249 one sigma factor only factor, sigA Transcription termination - - not identified factor Rho
Translation: Ribosomal protein, rpl, rps 50 ribosomal rpS1 not identified proteins tRNA synthetases 19 different glutaminyl-tRNA synthetase not identified, both synthetases proteins are missing in other Gram-positive bacteria transfer RNAs 33 tRNAs identical set of tRNAs (2, 46), UGA codon is read as tryptophan 10Sa small stable RNA Peptide + - + - proposed function in transtranslation (47) RF-2 not chain release factor RF-2, identified, RF-2 recognizes UGA, RF-2 has to be prfB deleted to avoid premature translation stop
Protein secretion: the machinery for protein A05_orf348 MG297 Simplified version, some of the channel-forming or secretion is rather complex (ftsY) MG048 + associated proteins (secD,E,F,G) and secB were not and consists in E.coli of 12 D09_orf450 4.5S RNA identified (48) Remarkable is the failure to detect components, of which only a (ffh) + MG072 signal peptidaseI (SPaseI) fraction is found in 4.5SRNA MG170 mycoplasmas G07_orf808 MG238 (secA) MG305 GT9_orf477 (secY) F10_orf444 (tig) A05_orf595 (dnaK)
Transport systems: ABC transporter for The substrate binding protein was not identified by oligopeptides similariy search 1 substrate binding domain - - (49)*, this protein seems to be essential unless oppA the bacterium receives the substrate by close contact from host directly
Cell surface, lipoproteins: - - A transacylase linking a third fatty acid to the N after cleavage of the terminal Cys was not identified; this type of signal-peptide a lipid acylation has not yet been shown to occur in modified Cys is the first mycoplasmas amino acid. For modification of this Cys in E.coli a transacylase is required.
Fatty acid, phospho- and A65_orf272 MG114 Only three genes were identified by DNA sequence glycolipid metabolism: About (pgsA) E30_ MG437 analysis in both bacteria, e.g. 10 genes are required for orf395 (cdsA) MG212 glucosyl-transferases are missing synthesis of the H10_orf266 experimentally identified (plsB) phospho- and glyco-lipids of M.pneumoniae
Nucleotide synthesis: Purine and pyrimidine salvage +/- + /- Salvage pathway complete but nucleoside diphosphate pathway kinase (ndk) not identified (41)*, (45) *, the reaction is essential
Energy metabolism: Glycolysis, pentose phosphate + +/- - - + +/- - - Glycolysis is complete in both mycoplasmas, pentose pathway, tricarboxylic acid phosphate pathway only truncated, no cytochromes. cycle, cytochromes See the difference between M.pneumoniae and M.genitalium: arginine dihydrolase pathway for generation of ATP only in M.pneumoniae.
Table 4: Common genes of M.pneumoniae and M.genitalium
References marked with asterics ()*: the authors proposed ORFs in M.genitalium which should code for the "not identified" proteins. Since in our opinion the evidence is not convincing enough we consider these functions still as not identified.