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. 2006 Apr;15(4):935-41.
doi: 10.1110/ps.051958806. Epub 2006 Mar 7.

Evolutionary links between FliH/YscL-like proteins from bacterial type III secretion systems and second-stalk components of the FoF1 and vacuolar ATPases

Mark J Pallen  1 , Christopher M Bailey, Scott A Beatson
Affiliations

Evolutionary links between FliH/YscL-like proteins from bacterial type III secretion systems and second-stalk components of the FoF1 and vacuolar ATPases

Mark J Pallen et al. Protein Sci. 2006 Apr.

Abstract

Bacterial type III secretion drives flagellar biosynthesis and mediates bacterial-eukaryotic interactions. Type III secretion is driven by an ATPase that is homologous to the catalytic subunits of proton-translocating ATPases, such as the F(o)F(1) ATPase. Here we use PSI-BLAST searches to show that some noncalatytic components are also conserved between type III secretion systems and proton-translocating ATPases. In particular, we show that the FliH/YscL-like proteins and the E subunits of vacuolar ATPases represent fusions of domains homologous to second-stalk components of the F(o)F(1) ATPase (the b and delta subunits).

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Figures

Figure 1
Figure 1
(A) Diagrammatic depiction of proton-translocating and type III secretion ATPase complexes, highlighting homologous catalytic and noncatalytic components and interactions. (B,C) Multiple alignments of representative NF-T3SS, F-T3SS, F-type, and V-type ATPases. (B) N-proximal domains of NF-T3SS, F-T3SS, and V-type ATPases aligned with F-type B subunit proteins. (C) C-terminal domains of NF-T3SS, F-T3SS, and V-type ATPases aligned with C-terminal domains of F-type D subunit proteins. Alignments were generated using T-coffee (http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html) and a set of 32 representative sequences derived from the original YscL psiBLAST. For clarity, the final alignments contain only 3 NF-T3SS ATPases, 3 F-T3SS ATPases, 1 V-type ATPases, 3 F-type B subunits, and 4 F-type D subunits. Alignments were colored using CHROMA (http://www.lg.ndirect.co.uk/chroma/) with an 80% consensus threshold: aromatic (FHWY, blue lettering on a dark yellow background), big (EFHIKLMQRWY, blue on light yellow), hydrophobic (ACFGHILMTVWY, black on dark yellow), aliphatic (ILV, gray on dark yellow), polar (CDEHKNQRST, blue on white), small (ACDGNPSTV, dark green on white), tiny (AGS, light green on white), charged (DEKR, pink on white), and negatively charged (DE, red on white). Organism names are abbreviated as Ypest (Yersinia pestis), Bjapo (Bradyrhizobium japonicum), Psyri (Pseudomonas syringae), Styph (Salmonella typhimurium), Mjann (Methanococcus jannaschii), Chydro (Carboxydothermus hydrogenoformans), Ecoli (Escherichia coli), Efaec (Enterococcus faecium), Pmari (Prochlorococcus marinus), Avari (Anabaena variabilis), and Teryt (Trichodesmium erythraeum), respectively. Protein names are as stated in the respective GenBank record, except where no name is available (i.e., Efaec_AtpF, Pmari_AtpF, and Teryt_AtpF are EfaeDRAFT_0503, PMN2A_0982, and TeryDRAFT_3685, respectively). GenBank accession numbers (in alignment order) are 10955581, 27376926, 28868594, 16765309, 16122081, 28869164, 15668393, 78042703, 16131604, Efae021782, 75908826, 71674228, 72382820, 114580.
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