Genes encoding Cher-TPR fusion proteins are predominantly found in gene clusters encoding chemosensory pathways with alternative cellular functions

PLoS One. 2012;7(9):e45810. doi: 10.1371/journal.pone.0045810. Epub 2012 Sep 20.

Abstract

Chemosensory pathways correspond to major signal transduction mechanisms and can be classified into the functional families flagellum-mediated taxis, type four pili-mediated taxis or pathways with alternative cellular functions (ACF). CheR methyltransferases are core enzymes in all of these families. CheR proteins fused to tetratricopeptide repeat (TPR) domains have been reported and we present an analysis of this uncharacterized family. We show that CheR-TPRs are widely distributed in GRAM-negative but almost absent from GRAM-positive bacteria. Most strains contain a single CheR-TPR and its abundance does not correlate with the number of chemoreceptors. The TPR domain fused to CheR is comparatively short and frequently composed of 2 repeats. The majority of CheR-TPR genes were found in gene clusters that harbor multidomain response regulators in which the REC domain is fused to different output domains like HK, GGDEF, EAL, HPT, AAA, PAS, GAF, additional REC, HTH, phosphatase or combinations thereof. The response regulator architectures coincide with those reported for the ACF family of pathways. Since the presence of multidomain response regulators is a distinctive feature of this pathway family, we conclude that CheR-TPR proteins form part of ACF type pathways. The diversity of response regulator output domains suggests that the ACF pathways form a superfamily which regroups many different regulatory mechanisms, in which all CheR-TPR proteins appear to participate. In the second part we characterize WspC of Pseudomonas putida, a representative example of CheR-TPR. The affinities of WspC-Pp for S-adenosylmethionine and S-adenosylhomocysteine were comparable to those of prototypal CheR, indicating that WspC-Pp activity is in analogy to prototypal CheRs controlled by product feed-back inhibition. The removal of the TPR domain did not impact significantly on the binding constants and consequently not on the product feed-back inhibition. WspC-Pp was found to be monomeric, which rules out a role of the TPR domain in self-association.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics*
  • Conserved Sequence
  • Genes, Bacterial
  • Gram-Negative Bacteria / genetics
  • Gram-Positive Bacteria / genetics*
  • Membrane Proteins / genetics
  • Methyl-Accepting Chemotaxis Proteins
  • Methyltransferases / chemistry
  • Methyltransferases / genetics*
  • Molecular Sequence Data
  • Multigene Family
  • Phylogeny
  • Protein Binding
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary / genetics
  • Pseudomonas putida / genetics*
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / genetics*
  • Repetitive Sequences, Amino Acid / genetics
  • S-Adenosylhomocysteine / chemistry
  • S-Adenosylmethionine / chemistry
  • Thermodynamics

Substances

  • Bacterial Proteins
  • Membrane Proteins
  • Methyl-Accepting Chemotaxis Proteins
  • Recombinant Fusion Proteins
  • S-Adenosylmethionine
  • S-Adenosylhomocysteine
  • Methyltransferases

Grant support

This work has been funded by research projects from the Andalusian regional government Junta de Andalucía (grants P09-RNM-4509 and CVI-7335 to T.K.), the Spanish Ministry for Economy and Competitiveness (grant Bio2010-16937 to T.K.) and from the BBVA Foundation (grant BIOCON08 185/09 to T.K.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.