Ancient origins of flagellar operons

Morgan N. Price
November, 2007


The bacterial flagellum, which allows many bacteria to swim, is enabled by about two dozen conserved proteins that form its structure and/or aid in its assembly. Flagellar genes from several phyla of bacteria are found in giant operons with consistent gene order, albeit with various insertions of other flagellar genes. Thus, the ancestral bacterial flagellum was probably encoded by a giant operon that contained the sequence fliEFGHILMNOPQR-flhBA. The type III secretion systems, which are distant relatives of the flagellum, also have the gene order fliMPQR-flhBA.


A recent analysis proposed that the ancestor of Bacteria had small, usually two-gene flagellar operons, and that there was an evolutionary trend towards increasing cluster size (Liu and Ochman 2007). However, this analysis only considered operons that are present in the well-studied bacterium Escherichia coli. Flagellar genes are often clustered together, and I suspected that these huge clusters contained large operons, but with a different ordering or combination of genes than in E. coli, so that the operons were not recognized in the previous analysis.

Experimentally Characterized Flagellar Operons

As a preliminary test of this hypothesis, I searched for experimental data on the operon structures for flagellar genes across the bacteria. I found experimental evidence for large operons in several lineages, as listed in the table below. Within each operon, "*" indicates that adjacent genes are in the same operon in this organism, but are in different operons in E. coli. Genes that are not core flagellar genes (as defined by Liu and Ochman 2007) are in parentheses. In B. subtilis and E. coli, "|" indicates internal promoters.

Organism Phylogenetic Group Operon structures References
Bacillus subtilis Firmicutes flgBC*(fliE)fliFG
|*fliA(ylxL) 1 operon, 3 internal promoters
Estacio98, West00, deHoon05
Borrelia burgerdorferi Spirochaete flgBC*(fliE)fliFGHI(flbABC)*flgDE(flbD)*motAB
*fliL*fliM*fliNOPQR*flhBA(flhF-flbE) 1 operon
Treponema pallidum Spirochaete (tap1)flgDE(flgEa)*motAB*fliL*fliM Limberger96
Treponema denticola Spirochaete flgBC*(fliE)FGHIJ Heinzerling97
Caulobacter crescentus alpha-Proteobacteria ("group I") fliFG(flbE)*fliN(flbD),
(fliO)fliP 4 operons
Boyd01, Ramakrishnan94
Rhodobacter sphaeroides alpha-Proteobacteria ("group II") flgBC*flgD*flgE*flgF,
Ballado01, Gonzalez-Predajo02
Sinorhizobium meliloti alpha-Proteobacteria ("group II") motA*fliMN*fliG,
Sourjik00, Rotter06
Vibrio parahaemolyticus gamma-Proteobacteria (non-enteric "main" polar flagellum) flgA(flgMN),
Escherichia coli gamma-Proteobacteria (enteric) flgA|MN,

Caveat: In S. meliloti, direct evidence for co-transcription is lacking. However, the regulation of these genes has been studied, and some promoters have been identified. The huge size of this gene cluster (51 genes), which is largely conserved in other alpha-Proteobacteria (e.g., Agrobacterium tumefaciens), also suggests that large operons are present.

The B. subtilis and B. burgerdorferi giant operons contain 18 genes in common that are in the same order. 13 of those genes are in the same order and co-transcribed in the gamma-Proteobacterium Vibrio parahaemolyticus as well (fliE*FGHI*..L..MNOPQR*flhB). Although these 13 genes seem to be spread across 4 operons in E. coli, they are all adjacent except for flhB.

Furthermore, a similar gene order fliMPQR-flhBA is found in putative Type III secretion systems. For example, Myxococcus xanthus DK 1622, beginning with MXAN_5649, contains the genes fliM-?-escR-fliQ-escT-flhB-escV. (The gene names are from their COG assignments, see here.) escR is a distant homolog of fliP, and similarly escT=fliR, escV=flhA (and fliM is also known as hrcQ, and flhBis known as hrpN).


T. Ballado et al., J. Bact. (2001) The hook gene (flgE) is expressed from the flgBCDEF operon in Rhodobacter sphaeroides: study of an flgE mutant. J Bact. 183:1680-7

C. H. Boyd and J. W. Gober (2001) Temporal regulation of genes encoding the flagellar proximal rod in Caulobacter crescentus. J Bact. 183:725-35

M. de Hoon et al. (2005) Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comp. Bio. 1:e25

W. Estacio et al. (1998) Dual promoters are responsible for transcription initiation of the fla/che operon in Bacillus subtilis. J Bact. 180:3548-55

Y. Ge et al. (1997) Molecular characterization of a large Borrelia burgdorferi motility operon which is initiated by a consensus sigma70 promoter. J Bact. 179:2289-99

Y. Ge and N.W. Charon (1997) Identification of a large motility operon in Borrelia burgdorferi by semi-random PCR chromosome walking. Gene 189:195-201

B. Gonzalez-Pedrajo et al. (2002) Characterization of the flgG operon of Rhodobacter sphaeroides WS8 and its role in flagellum biosynthesis. Biochim Biophys Acta 1579:55-63

H.F. Heinzerling et al. (1997) Genetic and transcriptional analysis of flgB flagellar operon constituents in the oral spirochete Treponema denticola and their heterologous expression in enteric bacteria. Infect Immun. 65:2041-51

I.M. Keseler et al. (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33:D334-D337

R. Limberger et al. (1996) Organization, transcription, and expression of the 5' region of the fla operon of Treponema phagedenis and Treponema pallidum. J Bact. 178:4628-34

R. Liu and H. Ochman (2007) Origins of flagellar gene operons and secondary flagellar systems. J Bact. 189:7098-104

L. McCarter et al. (2001) Polar flagellar motility of the Vibrionaceae. Microbiol. Mol. Biol. Rev. 65:445-62

G. Ramakrishnan et al. (1994) Multiple structural proteins are required for both transcriptional activation and negative autoregulation of Caulobacter crescentus flagellar genes. J Bact. 176:7587-600

C. Rotter et al. (2006) Rem, a new transcriptional activator of motility and chemotaxis in Sinorhizobium meliloti. J Bact. 188:6932-42

V. Sourjik et al. (2000) VisN and VisR are global regulators of chemotaxis, flagellar, and motility genes in Sinorhizobium (Rhizobium) meliloti. J Bact. 182:782-8

J.T. West et al. (2000) Relative roles of the fla/che P(A), P(D-3), and P(sigD) promoters in regulating motility and sigD expression in Bacillus subtilis. J Bact. 182:4841-8