Appendix:
Regulation Genes Retained in Select Insect Mutualists
| Gene | Escherichia coli bnumber | Blochmannia pennsylvanicus | Blochmannia floridanus | Wigglesworthia brevipalpis | Buchnera–Acyrthosiphon pisum | Buchnera–Schizaphis graminum | Buchnera–Baizongia pistaciae | Function |
|---|---|---|---|---|---|---|---|---|
| alaS | b2697 | Bpen174 | Bfl168 | WGLp234 | BU403 | BUsg390 | Bbp364 | Alanyl-tRNA synthetase; transcriptional repressor |
| birA | b3973 | Bpen190 | Bfl184 | WGLp513 | – | – | – | Bifunctional biotin-[acetyl-CoA-carboxylase] ligase and transcriptional repressor |
| bolA | b0435 | – | – | – | BU473 | BUsg457 | Bbp418 | Transcriptional dual regulator |
| cgtA | b3183 | Bpen098 | Bfl095 | WGLp475 | BU389 | BUsg376 | Bbp352 | GTPase involved in DNA replication and ribosome assembly; transcriptional repressor |
| clpP | b0437 | Bpen253 | Bfl246 | WGLp155 | BU475 | BUsg459 | Bbp419 | Serine protease subunit; posttranscriptional regulator |
| cpxR | b3912 | – | – | WGLp538 | – | – | – | Transcriptional regulator in 2-component system |
| cspC | b1823 | Bpen462 | Bfl448 | – | BU322 | – | – | Predicted DNA-binding transcriptional regulator |
| cspE | b0623 | – | – | WGLp177 | BU489 | BUsg473 | Bbp433 | Transcription antiterminator and regulator of RNA stability |
| dksA | b0145 | Bpen154 | Bfl149 | – | BU198 | BUsg192 | Bbp184 | RNA polymerase-binding transcription factor |
| dnaA | b3702 | – | – | – | BU012 | BUsg012 | Bbp012 | Transcriptional dual regulator HU-alpha; (HU-2) |
| fis | b3261 | – | – | – | BU400 | BUsg387 | – | DNA-binding protein; a trans activator for transcription |
| flhC | b1891 | – | – | WGLp031 | – | – | – | Regulator of flagellar biosynthesis; transcription initiation factor |
| flhD | b1892 | – | – | WGLp030 | – | – | – | Regulator of flagellar biosynthesis; transcription initiation factor |
| fliA | b1922 | – | – | WGLp199 | – | – | – | Regulation of flagellar operons |
| frr | b0172 | Bpen282 | Bfl274 | WGLp389 | BU234 | BUsg228 | Bbp216 | Ribosome releasing factor |
| greA | b3181 | Bpen099 | Bfl096 | WGLp233 | BU384 | BUsg371 | Bbp347 | Transcription elongation factor |
| hflC | b4175 | Bpen085 | Bfl082 | WGLp186 | BU567 | BUsg547 | Bbp512 | Regulator of FtsH protease |
| hfq | b4172 | Bpen082 | – | WGLp184 | – | – | – | RNA-binding protein that affects many cellular processes |
| hha | b0460 | – | – | WGLp524 | – | – | – | Hemolysin expression modulating protein |
| hns | b1237 | Bpen448 | – | WGLp367 | BU272 | – | – | H-NS transcriptional dual regulator |
| hslK | b4174 | Bpen084 | Bfl081 | WGLp185 | BU568 | BUsg548 | Bbp513 | Regulator of FtsH protease |
| hslU | b3931 | – | – | WGLp277 | BU579 | BUsg558 | Bbp524 | ATPase component of the HslVU protease |
| hslV | b3932 | – | – | WGLp278 | BU578 | BUsg557 | Bbp523 | Peptidase component of the HslVU protease |
| hslX | b4173 | Bpen083 | Bfl080 | – | – | – | – | Putative GTPase; possible regulator of HflKC |
| hupA | b4000 | – | – | WGLp509 | BU032 | BUsg033 | Bbp033 | Transcriptional dual regulator HU-α (HU-2) |
| ihfA (himA) | b1712 | – | – | – | BU131 | BUsg123 | – | Integration host factor alpha |
| ihfB (himD) | b0912 | – | – | – | BU308 | BUsg298 | – | Integration host factor beta |
| ispH | b0029 | Bpen124 | – | – | – | – | – | Control of stringent response |
| lon | b0439 | Bpen307 | Bfl299 | WGLp153 | BU477 | BUsg461 | Bbp421 | ATP-dependent protease |
| metK | b2942 | Bpen259 | Bfl252 | WGLp316 | BU408 | BUsg393 | – | MetK S-adenosylmethionine synthetase monomer |
| metR | b3828 | – | – | – | – | BUsg030 | – | MetR transcriptional dual regulator |
| mntR | b0817 | Bpen403 | – | – | – | – | – | Putative toxin |
| nusA | b3169 | Bpen107 | Bfl103 | WGLp227 | BU378 | BUsg366 | Bbp341 | Transcription termination/antitermination L factor |
| ptsG | b1101 | – | – | – | BU356 | BUsg344 | Bbp326 | PTS system, glucose-specific IIBC component |
| putA | b1014 | – | – | WGLp434 | – | – | – | Proline dehydrogenase, P5C dehydrogenase |
| pyrI | b4244 | – | – | WGLp590 | BU370 | BUsg358 | – | Aspartate carbamoyltransferase, regulatory subunit |
| recA | b2699 | – | – | WGLp235 | – | – | – | DNA strand exchange and renaturation, DNA-dependent ATPase, DNA- and ATP-dependent coprotease |
| rho | b3783 | Bpen607 | Bfl586 | WGLp303 | BU596 | BUsg572 | Bbp538 | Transcription termination factor Rho monomer; polarity suppressor |
| rplA | b3984 | Bpen580 | Bfl560 | WGLp519 | BU037 | BUsg038 | Bbp038 | 50S ribosomal subunit protein L1; posttranscriptional regulation of ribosomal protein genes |
| rplD | b3319 | Bpen199 | Bfl192 | WGLp544 | BU523 | BUsg504 | Bbp466 | 50S ribosomal subunit protein L4; transcriptional and posttranscriptional regulation of ribosomal protein genes |
| rplJ | b3985 | Bpen579 | Bfl559 | WGLp520 | BU036 | BUsg037 | Bbp037 | 50S ribosomal subunit protein L10; posttranscriptional regulation of ribosomal protein genes |
| rplT | b1716 | Bpen365 | Bfl354 | WGLp084 | BU128 | BUsg120 | Bbp122 | 50S ribosomal subunit protein L20; autoregulates its own expression and that of L35 |
| rpmH | b3703 | Bpen014 | Bfl015 | WGLp014 | BU013 | BUsg013 | Bbp013 | 50S ribosomal subunit protein L34; inhibitor of the decarboxylases involved in polyamine biosynthesis |
| rpoD | b3067 | Bpen057 | Bfl056 | WGLp468 | BU055 | BUsg052 | Bbp052 | RNA polymerase, sigmaD factor; primary sigma factor during exponential growth |
| rpoH | b3461 | Bpen653 | Bfl626 | WGLp072 | BU025 | BUsg026 | Bbp027 | RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures |
| rpsH | b3306 | Bpen212 | Bfl205 | WGLp557 | BU510 | BUsg491 | Bbp453 | 30S ribosomal subunit protein S8; posttranscriptional regulation of ribosomal protein genes |
| rpsJ | b3321 | Bpen197 | Bfl190 | WGLp542 | BU525 | BUsg506 | Bbp468 | 30S ribosomal subunit protein S10; role in transcription antitermination |
| rpsT | b0023 | Bpen120 | Bfl116 | WGLp296 | BU151 | BUsg144 | Bbp140 | 30S ribosomal subunit protein S20; inhibitor of the decarboxylases involved in polyamine biosynthesis |
| rseP (yaeL) | b0176 | Bpen286 | Bfl278 | WGLp385 | – | – | – | Cleaves RseA, thereby activating sigmaE-mediated stress response |
| slyA | b1642 | Bpen380 | Bfl369 | WGLp336 | – | – | – | Transcriptional regulator for cryptic hemolysin |
| sufB (ynhE) | b1683 | Bpen370 | Bfl359 | WGLp360 | – | – | – | SufBCD complex activates the cysteine desulfurase; secondary pathway of iron-sulfur cluster assembly |
| sufC (ynhD) | b1682 | Bpen371 | Bfl360 | WGLp359 | – | – | – | Component of SufBCD complex |
| sufD (ynhC) | b1681 | Bpen372 | Bfl361 | WGLp358 | – | – | – | Component of SufBCD complex |
| sufE | b1679 | Bpen374 | Bfl363 | WGLp356 | – | – | – | Sulfur acceptor that activates SufS cysteine desulfurase |
| suhB | b2533 | Bpen555 | Bfl535 | WGLp285 | BU285 | BUsg274 | Bbp264 | Enhances synthesis of sigma32 in mutant; extragenic suppressor |
| thrS | b1719 | Bpen362 | Bfl351 | WGLp081 | BU125 | BUsg117 | Bbp119 | Threonyl-tRNA synthetase; translation attenuation and efficiency |
| uspA | b3495 | – | – | – | – | – | Bbp530 | Universal stress global stress response regulator |
| ychA | b1214 | – | – | – | BU173 | BUsg167 | Bbp163 | Predicted transcriptional regulator |
| ychF | b1203 | Bpen354 | Bfl344 | WGLp351 | BU191 | BUsg185 | Bbp180 | Putative GTP-binding protein; translation attenuation and efficiency |
| ydgL (rsxA) | b1627 | – | – | – | BU113 | – | Bbp108 | Integral membrane protein of SoxR-reducing complex; posttranscriptional regulation |
| ydgM (rsxB) | b1628 | – | – | – | BU114 | BUsg106 | Bbp109 | Member of SoxR-reducing complex; posttranscriptional regulation |
| ydgN (rsxC) | b1629 | – | – | – | BU115 | – | Bbp110 | Member of SoxR-reducing complex; posttranscriptional regulation |
| ydgO (rsxD) | b1630 | – | – | – | BU116 | BUsg108 | Bbp111 | Integral membrane protein of SoxR-reducing complex; posttranscriptional regulation |
| ydgP (rsxG) | b1631 | – | – | – | BU117 | BUsg109 | Bbp112 | Member of SoxR-reducing complex; posttranscriptional regulation |
| ydgQ (rsxE) | b1632 | – | – | – | BU118 | BUsg110 | Bbp113 | Integral membrane protein of SoxR-reducing complex; posttranscriptional regulation |
| yhdO | b3244 | Bpen305 | Bfl297 | – | BU398 | BUsg385 | Bbp361 | Protease involved in Microcin maturation and sensitivity to the DNA gyrase inhibitor |
| yidZ | b3711 | Bpen038 | Bfl038 | – | – | – | – | Putative transcriptional regulator LysR-type |
| yjeA | b4155 | – | – | – | BU582 | – | Bbp528 | Putative regulator of pyruvate oxidase |
| yqeI | b2847 | Bpen401 | Bfl390 | WGLp467 | – | – | – | Predicted transcriptional regulator |
| yrbA | b3190 | Bpen046 | Bfl045 | WGLp328 | BU385 | BUsg372 | Bbp348 | Predicted DNA-binding transcriptional regulator |
| zur | b4046 | Bpen026 | Bfl026 | – | – | – | – | Putative transcriptional repressor |
| 443 regulation genes | absent from the six mutualists above | |||||||
These gamma-Proteobacterial endosymbionts are closely related to E. coli, and their gene contents are generally a subset of the E. coli genome. To avoid inconsistencies in annotation methods, we first identified E. coli orthologs in each mutualist using the reciprocal smallest distance algorithm (Wall et al., 2003). M. H. Serres kindly provided a list of E. coli genes that have been assigned to Regulation category in the MultiFun catalog of roles (Serres et al., 2004). In addition to the genes listed above, E. coli possesses numerous (443) regulation genes that are absent from the six mutualists considered here. Reflecting their multiple functions in the cell, many genes (including the loci listed here) have more than one functional designation within Multifun. The table lists the primary annotation ID for the orthologs in mutualists.