Structural and functional characterization of DUF1471 domains of Salmonella proteins SrfN, YdgH/SssB, and YahO.

Alexander Eletsky,Adelinda Yee,Scott Houliston,Thomas Szyperski,Michael D Daily,Maite Garcia,Kristen M Meyer,Joshua N Adkins,Uma K Aryal,Charles Ansong,Hong Cui,Alexander Lemak,Rong Xiao,Meagan C Burnet,Gaetano T Montelione,Octavio Sanchez,Alexei Savchenko,Bin Wu,Qi Zhang,Xiaohui Xu,Thomas Acton ,A Joachimiak ,K Michalska ,C.h Arrowsmith ,John Cort

doi:10.1371/journal.pone.0101787

Abstract

Bacterial species in the Enterobacteriaceae typically contain multiple paralogues of a small domain of unknown function (DUF1471) from a family of conserved proteins also known as YhcN or BhsA/McbA. Proteins containing DUF1471 may have a single or three copies of this domain. Representatives of this family have been demonstrated to play roles in several cellular processes including stress response, biofilm formation, and pathogenesis. We have conducted NMR and X-ray crystallographic studies of four DUF1471 domains from Salmonella representing three different paralogous DUF1471 subfamilies: SrfN, YahO, and SssB/YdgH (two of its three DUF1471 domains: the N-terminal domain I (residues 21–91), and the C-terminal domain III (residues 244–314)). Notably, SrfN has been shown to have a role in intracellular infection by Salmonella Typhimurium. These domains share less than 35% pairwise sequence identity. Structures of all four domains show a mixed α+β fold that is most similar to that of bacterial lipoprotein RcsF. However, all four DUF1471 sequences lack the redox sensitive cysteine residues essential for RcsF activity in a phospho-relay pathway, suggesting that DUF1471 domains perform a different function(s). SrfN forms a dimer in contrast to YahO and SssB domains I and III, which are monomers in solution. A putative binding site for oxyanions such as phosphate and sulfate was identified in SrfN, and an interaction between the SrfN dimer and sulfated polysaccharides was demonstrated, suggesting a direct role for this DUF1471 domain at the host-pathogen interface.

Highlights

Many of the basic features of sequences in the family of conserved proteins from Enterobacteriaceae known as DUF1471 (PF07338, alternatively, the YhcN or BhsA/McbA family) were recognized [1] soon after release of the first E. coli genome sequence
Structures of Salmonella SrfN, YahO, and SssB-I proteins from the DUF1471 protein family were determined with solution state NMR spectroscopy by the Northeast Structural Genomics Consortium
In E. coli, the DUF1471 proteins YcfR/BhsA, YbiM/McbA, YjfO/BsmA, and YhcN appear to be involved in the bacterial response to extracellular stress

Summary

Introduction

Many of the basic features of sequences in the family of conserved proteins from Enterobacteriaceae known as DUF1471 (PF07338, alternatively, the YhcN or BhsA/McbA family) were recognized [1] soon after release of the first E. coli genome sequence. These proteins are characteristically small, single domain proteins of around 90 residues; though one subfamily has three repeated DUF1471 domains. By sequence analysis the DUF1471 family members can be divided into around twelve paralogous subfamilies with high (greater than 50%) intra- and low (20–40%) inter-subfamily sequence identity and few residues that are conserved across all DUF1471 subfamilies (Fig. 1). There are eleven paralogues each in Salmonella and Klebsiella pneumoniae–the largest repertoire of DUF1471 proteins found in bacterial genomes–whereas there are ten paralogues in E

Methods

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Conclusion