Table 1. The operon structures of the riboflavin biosynthesis (RB) and transport genes in eubacteria.
| Genome | AB | RBS operons | Single RBS genes | Riboflavin transporters | ||
|---|---|---|---|---|---|---|
| α-Proteobacteria | ||||||
| Rhodobacter sphaeroides # | RS | ybaD-ribD/ribE2-X-ribBA-ribH-nusB | ||||
| Magnetospirillum magnetotacticum # | MMA | ybaD-ribD-ribE2-ribBA-ribH-nusB | ||||
| Rhodopseudomonas palustris # | RPA | ybaD-ribE2-ribD-ribH-nusB | ribBA | ribH2 | ||
| Mesorhizobium loti | MLO | ybaD-ribD-ribE2-ribH-nusB-rfnT | ribBA | & ^ ribH2 | ||
| Sinorhizobium meliloti | SM | ybaD-ribD-ribE2/ribH-nusB-rfnT | ribBA | & ^ ribH2 | ||
| Agrobacterium tumefaciens | AT | ybaD-ribD-ribE2/ribH-nusB-rfnT | ribBA | & ^ ribB | ||
| Brucella melitensis # | BME | ybaD-ribD-ribE2-ribH-nusB | ribBA | & ^ ribH2 | ||
| Caulobacter crescentus # | CC | ybaD-ribH1-nusB/ribD-ribE-ribBA-ribH2 | ||||
| β-Proteobacteria | ||||||
| (Neisseria) | (NM, NG) | ybaD-ribD/ribA=ribBA/ribH-nusB | ribE | |||
| (Bordetella) | (BP, BPA) | ribBA-ribH-nusB | ribD | ribE | & ^ ribB | |
| (Burkholderia), (Ralstonia) | (BU, BPS); (REU, RSO) | ribD-ribE2=ribBA-ribH-nusB | ribA | & ^ ribB | ||
| γ-Proteobacteria | ||||||
| (Enterobacteriaceae) | (EC, TY, KP, YP) | ybaD-ribD-ribH-nusB | ribA | ribE | & ^ ribB | |
| (Pasteurellaceae) | (HI, VK, AB) | ybaD-ribD/ribH-nusB | ribA | ribE | & ^ ribB | |
| ∼ Haemophilus ducreyi #, Actinobacillus pleuropneumoniae # | DU, AO | &* ribD-ribE-ribBA-ribH | ||||
| Pseudomonas aeruginosa | PA | ybaD-ribD=& ^ ribE2-ribBA-ribH-nusB | ribA | |||
| Pseudomonas fluorescens #, P.syringiae # | PU, Psy | ybaD-ribD-ribE2-ribBA=ribH-nusB | ribA/ribBA | & ^ ribH2 | ||
| Pseudomonas putida # | Ppu | ybaD-ribD-ribE2-ribBA=ribH-nusB | ribA/ribBA | ribE | & ^ ribB | |
| Shewanella putrefaciens # | Spu | ybaD-ribD-ribE2-ribBA-ribH-nusB | ribA | ribE | & ^ ribB | |
| Vibrio cholerae | VC | ybaD-ribD-ribE2-ribBA=ribH-nusB | ribA | & ^ ribB | ||
| Xylella fastidiosa | XFA | ybaD=ribD=ribE2-ribBA-ribH-nusB | ribA | |||
| Acinetobacter calcoaceticus # | AC | ybaD-ribD-X-ribE2/ribBA-ribH] | ribA | & ^ ribB | ||
| Buchnera sp. APS | BUC | mltA-ribH-thiL-ribD-nusB | ribA | ribE | ||
| ε-Proteobacteria | HP, CJ | ribBA-X-ribA/ribH-nusB | ribD | ribE | ||
| The Bacillus/Clostridium group | BS, BA, ZC, BE; SA; LLX; PN; CA, DF | &* ribD-ribE-ribBA-ribH | & ^ ypaA | |||
| ∼ Bacillus halodurans | HD | &* ribD-ribE-ribBA-ribH | None | |||
| ∼ Bacillus amyloliquefaciens | Bam | &* ribD-ribE-ribBA-ribH | ? | |||
| ∼ (Listeria), Streptococcus pyogenes | (LO, LI); ST | None | &* ypaA | |||
| ∼ Enterococcus faecalis #, Streptococcus mutans # | EF, MN | None? | & ^ ypaA | |||
| ∼ Desulfitobacterium halfniense # | DHA | ribD]/[ribE-ribBA-ribH | &* impX | |||
| Actinomycetes | ||||||
| (Mycobacterium) | (MT, ML) | ribE-X-ribBA-ribH | ribD | |||
| Corynebacterium diphtheriae # | DI | ribD-ribE-ribBA-ribH | X-pnuX | |||
| Corynebacterium glutamicum # | GLU | ribD-ribE-ribBA-ribH | & ^ pnuX | |||
| Streptomyces coelicolor # | SX | & ^ ribE-pnuX-ribBA-ribH/ribA-ribD | ||||
| Thermomonospora fusca # | TFU | & ^ ribE-pnuX-ribBA-ribH | ||||
| Atopobium minutum # | AMI | None? | & ^ ypaA | |||
| The Thermus/Deinococcus group | ||||||
| Deinococcus radiodurans | DR | & ^ ribD-ribE-ribBA-ribH | ||||
| Thermus thermophilus # | TQ | & ^ ribD-ribE-ribBA | ribH | |||
| Cyanobacteria | ribBA/ribD | ribE | ribH | |||
| Other groups of eubacteria | ||||||
| Thermotoga maritima | TM | &* ribD-ribE-ribBA-ribH | ypaA | |||
| Fusobacterium nucleatum # | FN | &* ribH-ribD-ribE-ribBA | &* impX | |||
| Chloroflexus aurantiacus # | CAU | & ^ ribD-ribE-ribBA-ribH | ribA | |||
| Aquifex aeolicus | AA | ribF-ribD/ribH-nusB | ribBA | ribE | ||
| (Chlamydia) | (QP, QT) | ybaD/ribE/ribD-ribBA=ribH | ||||
| Archaea | ||||||
| Pyrococcus furiosus | PF | ribBA-ribH-ribD-ribE | ||||
The standard E.coli names of the RB genes are used throughout (see the text for explanation and Fig. 1 for the B.subtilis equivalents). ribBA denotes the fusion gene encoding the protein consisting of two domains, RibB and RibA. Genes forming one candidate operon (with spacers <100 bp) are separated by ‘-’. Larger spacers between genes are marked by ‘=’. Operons from different loci, if shown in one column, are separated by slashes ‘/’. Non-RB genes are shown as X. The predicted RFN elements and possible terminators and sequestors are denoted by ‘&’, ‘*’ and ‘ ^’, respectively. The contig ends are marked by square brackets.
The genome abbreviations are given in column ‘AB’ with unfinished genomes marked by ‘#’. The names of taxonomic groups given in parentheses indicate similar operon structures of the RB genes in all available genomes from the group, the exclusions are listed in the table and marked ‘∼’. Additional genome abbreviations are: Neisseria meningitidis (NG), Neisseria gonorrhoeae (#, NG); Bordetella pertussis (#, BP), Bordetella bronchiseptica (#, BPA); Burkholderia cepacia (#, BU), Burkholderia pseudomallei (#, BPS); Ralstonia eutropha (#, REU), Ralstonia solanacearum (RSO); Escherichia coli (EC), Salmonella typhi (TY), Klebsiella pneumoniae (#, KP), Yersinia pestis (YP); Haemophilus influenzae (HI), Pasteurella multocida (VK), Actinobacillus actinomycetemcomitans (#, AB); Helicobacter pylori (HP), Campylobacter jejuni (CJ); Bacillus subtilis (BS), Bacillus anthracis (#, BA), Bacillus cereus (#, ZC), Bacillus stearothermophilus (#, BE), Staphylococcus aureus (SA), Lactococcus lactis (LLX), Streptococcus pneumoniae (PN), Clostridium acetobutylicum (CA), Clostridium difficile (#, DF); Listeria monocytogenes (LO), Listeria innocua (LI); Mycobacterium tuberculosis (MT), Mycobacterium leprae (ML); Chlamydia pneumoniae (QP), Chlamydia trachomatis (QT).