Table 3.

Complex relationships between genes of C. acetobutylicum and B. subtilis—nonorthologous and xenologous gene displacement and differences in domain architecturesa

C.a. gene IDB.s. gene productCommentb
CAC0039, CAC0408YukADNA segregation ATPase FtsK/SpoIIIE; both contain 3 ATPase domains; C.a. protein in addition contains C-terminal FHA domain
CAC0578YitJMethionine synthase I; same domain organization as in E.c., D.r., Syn., and M.t. but not B.s.
CAC0459, CAC3088RocRArginine degradation positive regulator; AAA-ATPase domain (NtrC family) fused to PAS domains; C.a. proteins contain an unknown domain at the N terminus similar to the N-terminal domain of PrpR E.c.
CAC0538-40, CAC2556YdhTBeta-mannanase ManB; C.a. proteins have more complex domain organization
CAC0577YxiAEndo-arabinase-related enzyme (family 43, glycosyl hydrolase domain); C.a. contains additional ricin B-like domain
CAP0120XynDXylanase; C.a. contains additional ricin B-like domain
CAC1655PurQ and PurLPhosphoribosylformylglycinamidine synthase; C.a. has PurL/PurQ fusion; B.s.—separate proteins
CAC1847YqfP and YpfDC.a. has fusion of LytB protein and S1 RNA-binding domain; B.s.—separate proteins
CAC1793LexAC.a. has fusion of P-loop ATPase and LexA; B.s. has only a LexA protein and has no ortholog of the ATPase domain
CAC2927FolA and FolKFolate biosynthesis enzymes; C.a. has fusion FolA and FolK; B.s.—separate proteins
CAC0404YbdMC.a. has fusion Pkn2 protein kinase with TPR repeats; B.s. has only a Pkn2 ortholog without the TPR domain.
CAC32458 one-domain proteinsC.a. has fusion of two B. subtilis domains; B.s. has only separate proteins
CAC3195GlyQ, GlySGlycyl-tRNA synthetase; typical bacterial version (two subunits) in B.s.; eukaryotic version (one subunit) in C.a.
CAC0219, CAC2997UngUracil-DNA glycosylase; typical bacterial version in B.s.; archaeal version in C.a.
CAC1256, CAC1909RphC.a. encodes RNase D and RNAse E/G, whereas B.s. encodes the unrelated RNAse PH; it can be predicted that these RNases complement each other's functions.
CAC0752YoqV, YoqUATP-dependent DNA ligases; B.s. encodes two copies of a typical ATP-dependent ligase strongly similar to archaeal homologs (one fused to a eukaryotic-type DNA primase); in contrast, C.a. has an extremely diverged version with significant similarity only to predicted ligases from D.r.
CAC1041ArgSArginyl-tRNA synthetase; eukaryotic version in C.a.
CAC0935, CAC2740HisS, HisZHistidyl-tRNA synthetase; B.s. encodes two recently diverged copies of the typical bacterial enzyme; C.a. possesses an archaeal-eukaryotic version and a distinct bacterial variant shared with D.r. and Syn
CAC3038IleSIsoleucyl-tRNA synthetase; archaeal-eukaryotic version in C.a.
CAC1047YosORibonucleotide reductase in B.s. contains an intein; there is no ortholog of this in C.a.; instead, C.a. contains a distinct ribonucleotide reductase with an archaeal evolutionary affinity
  • a See the Table 1a footnote for abbreviations. Additional abbreviations of bacterial species are as follows: D.r., Deinococcus radiodurans; Syn,Synechocystis sp.

  • b The first 12 comparisons relate to different domain organization; the last 8 relate to nonorthologous and xenologous gene displacement.