|
Global Transposon Mutagenesis and a Minimal Mycoplasma Genome
Clyde A. Hutchison III, Scott N. Peterson, Steven R. Gill, Robin T. Cline, Owen White, Claire M. Fraser, Hamilton O. Smith, and J. Craig Venter
|
Supplementary Material
Disrupted
Mycoplasma genitalium genes (or
M. pneumoniae homologs)
This table lists transposon insertion sites more than 9 bases downstream of the first base in the initiation codon, and located in the 5´-most 80% of the coding sequence (hits in the COOH-terminal 20% of proteins are considered potentially nondisruptive; see text). An M. genitalium gene is listed (MGXXX) if a presumptively disruptive hit has been identified in M. genitalium (g), its M. pneumoniae ortholog (p), or both (g/p). The second column lists the M. pneumoniae ortholog of the gene (MPYYY) where YYY corresponds to the gene designation in Fig. 2. The number of distinct sites in M. genitalium and M. pneumoniae (X and Y) at which such insertions have been observed are indicated by gX and/or pY in the column "Disrupted species". Entries for genes in which we have observed more that one independent disruptive event are shown in red. If the gene is a member of the proposed minimal gene set of Mushegian and Koonin (1), then the gene designation is underlined. Gene functions are from the current TIGR version of the M. genitalium annotation
(www.tigr.org/~clyde/Mgengenes99.html).
If the assignment of a gene to the minimal gene set (1) is based on a different functional assignment, then that assignment is also shown in square brackets, i.e., [alternate assignment]. The name of each functional class is followed by a fraction in parentheses. This fraction indicates the number of putative dispensable genes observed over the total number of genes within that functional class. For this analysis we have pooled the functional classes "Unknown" and "Hypothetical" into a class we call "Unknown function".
Mycoplasma genes with Tn4001 insertions
M.gen. M.pn. Disrupted Gene function
gene gene species
Purines, pyrimidines, nucleosides, and nucleotides (5/19)
2'-Deoxyribonucleotide metabolism
MG231 MP513 p1 ribonucleoside-diphosphate reductase,
alpha chain (nrdE)
MG227 MP517 p1 thymidylate synthase (thyA)
Salvage of nucleosides and nucleotides
MG049 MP092 g1 purine-nucleoside phosphorylase (deoD)
MG051 MP090 g1 thymidine phosphorylase (deoA)
MG052 MP089 g2 cytidine deaminase (cdd)
Fatty acid and phospholipid
metabolism (1/8)
Degradation
MG310 MP395 g5 lipase/esterase, putative
Biosynthesis of cofactors, prosthetic groups, and carriers (1/4)
Lipoate
MG270 MP450 p1 lipoate protein ligase (lplA)
Central intermediary metabolism (3/7)
Other
MG293 MP420 g6 glycerophosphoryl diester phosphodiesterase, putative
MG299 MP412 p1 phosphotransacetylase (pta)
MG394 MP266 g1 serine hydroxymethyltransferase (glyA)
Energy metabolism (1/33)
Sugars
MG118 MP577 p1 UDP-glucose 4-epimerase (galE)
Transport and binding proteins(8/33)
Anions
MG410 MP233 g1/p2 phosphate ABC transporter, ATP-binding protein (pstB)
MG411 MP232 g4 phosphate ABC transporter, permease protein (pstA)
Carbohydrates, organic alcohols, and acids
MG033 MP111 g2 glycerol uptake facilitator (glpF)
MG062 MP077 g4/p1 PTS system, fructose-specific IIABC component (fruA)
Unknown substrate
MG014 MP136 g1 ABC transporter, ATP-binding protein
MG467 MP159 g1 ABC transporter, ATP-binding protein
MG390 MP271 g1/p2 ABC transporter, ATP-binding protein
MG291 MP422 g1 transport system permease protein P69
DNA metabolism (6/29)
DNA replication, recombination, and repair
MG244 MP496 p2 DNA helicase II, putative
MG261 MP460 p1 DNA polymerase III, subunit alpha (polC-2)
MG339 MP351 g3 recA protein (recA)
MG380 MP284 g1 glucose-inhibited division protein B gidB)
MG421 MP223 g1/p1 excinuclease ABC subunit A (uvrA)
MG469 MP156 p1 chromosomal replication initiator protein
(dnaA)
Transcription (3/13)
Transcription factors
MG249 MP485 p1 RNA polymerase sigma-43 factor (rpoD)
RNA processing
MG017 MP134 g2 ATP-dependent RNA helicase, putative
MG308 MP397 g1 ATP-dependent RNA helicase, putative
Protein synthesis (6/90)
tRNA aminoacylation
MG345 MP322 g1 isoleucyl-tRNA synthetase (ileS)
MG455 MP173 p1 tyrosyl-tRNA synthetase (tyrS)
Ribosomal proteins: synthesis and modification
MG426 MP218 g1 ribosomal protein L28 (rpL28)
tRNA and rRNA base modification
MG182 MP636 g5 pseudouridylate synthase I (hisT)
MG252 MP482 p1 rRNA methylase, putative
MG346 MP321 g1/p2 rRNA methylase, putative
Protein fate (4/21)
Protein modification and repair
MG106 MP588 g1 polypeptide deformylase (def)
Protein folding and stabilization
MG392 MP269 p2 heat shock protein (groEL)
Degradation of proteins, peptides, and glycopeptides
MG183 MP635 g1 oligoendopeptidase F (pepF)
MG355 MP311 p3 ATP-dependent Clp protease, ATPase subunit (clpB)
Regulatory functions (3/5)
Other
MG085 MP609 g1 hpr(ser) kinase, putative
MG278 MP442 p7 guanosine-3',5'- bis(diphosphate) 3'- pyrophosphohydrolase (spoT)
MG408 MP235 g2 peptide methionine sulfoxide reductase (pmsR)
Cell envelope (18/29)
Lipoproteins
MG040 MP102 p1 lipoprotein, putative
MG045 MP096 p1 lipoprotein, putative [spermidine/putrescine periplasmic binding protein]
MG067 MP256 g3 lipoprotein, putative
MG068 MP255 p1 lipoprotein, putative
MG149 MP670 g1 lipoprotein, putative
MG185 MP633 g1 lipoprotein, putative
MG186 MP022 g2 lipoprotein, putative
MG260 MP552 p2 lipoprotein, putative
MG307 MP404 p1 lipoprotein, putative
MG338 MP352 g1 lipoprotein, putative
MG395 MP250 g40 lipoprotein, putative
MG412 MP231 g3 lipoprotein, putative
MG440 MP199 g2 lipoprotein, putative
Surface structures
MG191 MP014 g1/p1 adhesin P1 (mgpB)
MG192 MP013 g1/p2 mgpC protein (mgpC)
MG218 MP527 p4 cytadherence accessory protein (hmw2)
MG317 MP388 g1 cytadherence accessory protein (hmw3)
Biosynthesis of surface polysaccharides and lipopolysaccharides
MG137 MP558 p2 UDP-galactopyranose mutase (glf)
Cellular processes (1/6)
Adaptations to atypical conditions
MG470 MP154 g2 soj protein (soj)
Unknown function (69/180)
MG002 MP152 g1 Unknown function (dnaJ-like protein)
MG009 MP145 g9 Unknown function [uncharacterized ACR (metal-utilizing enzyme?)]
MG010 MP140 g1 Unknown function
MG011 MP139 g8 Unknown function
MG024 MP128 p2 Unknown function (GTP-binding protein, putative)
MG025 MP126 g1 Unknown function
MG029 MP122 g5 Unknown function
MG032 MP112 g5 Unknown function
MG039 MP103 p2 Unknown function
MG055 MP086 p1 Unknown function [preprotein translocase subunit (secE)]
MG059 MP081 p1 Unknown function (small protein (smpB))[LPS-heptosyl-2-transferase]
MG074 MP620 p1 Unknown function
MG096 MP598 g4 Unknown function
MG103 MP591 g1 Unknown function
MG110 MP584 g1 Unknown function
MG116 MP579 p4 Unknown function
MG130 MP565 g1 Unknown function
MG131 ---- g1 Unknown function
MG132 MP563 g6 Unknown function (hit protein, putative)
MG140 MP002 g4/p1 Unknown function
MG202 MP034 g1/p1 Unknown function
MG207 MP209 g4/p1 Unknown function
MG208 MP545 p2 Unknown function
MG209 MP544 g1/p1 Unknown function(sfhB protein, putative)[pseudouridylate synthase(YceC)]
MG213 MP537 g1 Unknown function
MG226 MP518 g2/p2 Unknown function
MG236 MP508 p4 Unknown function
MG237 MP507 g1/p1 Unknown function
MG241 MP500 p1 Unknown function
MG255 MP479 g4 Unknown function
MG255.1 MP479 g3 Unknown function
MG256 MP478 g2 Unknown function
MG263 MP457 p2 Unknown function
MG264 MP456 g3 Unknown function
MG268 MP452 g1 Unknown function [dG-dA kinase I]
MG269 MP451 g40 Unknown function
MG279 MP441 g8/p3 Unknown function
MG280 MP440 g10/p13 Unknown function
MG281 MP439 g28/p5 Unknown function
MG284 MP436 p1 Unknown function
MG285 MP435 g3 Unknown function
MG286 MP434 g1 Unknown function
MG288 ---- g4 Unknown function (authentic frameshift)
MG294 MP419 g5/p1 Unknown function
MG295 MP418 g1 Unknown function [ATP-utilizing enzyme (Gua family)]
MG296 MP417 g2 Unknown function
MG306 MP405 p1 Unknown function
MG316 MP389 g3 Unknown function
MG320 MP385 p1 Unknown function
MG320.1 ---- g1 Unknown function
MG323.1 MP371 g1 Unknown function
MG328 MP366 g9 Unknown function
MG335 MP359 g1 Unknown function (GTP-binding protein)[GTPase]
MG343 MP324 g1 Unknown function
MG352 ---- g1 Unknown function
MG366 MP298 g1 Unknown function
MG370 MP294 g5 Unknown function
MG372 MP292 g1/p1 Unknown function
MG385 MP276 g4/p3 Unknown function
MG389 MP272 p1 Unknown function
MG414 MP230 g2/p9 Unknown function
MG415 MP229 g1/p2 Unknown function
MG423 MP221 g1 Unknown function
MG428 MP216 g1 Unknown function
MG438 MP204 g2/p1 Unknown function
MG442 MP186 g1 Unknown function
MG443 MP185 p1 Unknown function
MG452 MP176 g2 Unknown function
MG468 MP158 g1 Unknown function
Reference
1. A. R. Mushegian and E. V. Koonin, Proc. Natl. Acad. Sci. U.S.A. 93, 1026 (1996).
