The<i>yrpAB</i>operon of<i>Yersinia ruckeri</i>encoding two putative U32 peptidases is involved in virulence and induced under microaerobic conditions

Navais, Roberto; Méndez, Jessica; Pérez-Pascual, David; Cascales, Desirée; Guijarro, José A.

doi:10.4161/viru.29363

Cited by 25 publications

(21 citation statements)

References 28 publications

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“…RlhA contains peptidase U32 and DUF3656 motifs. The former motif is present in bacterial collagenases, which in general contribute to bacterial infection ( 82 – 84 ). Porphyromonas gingivalis PrtC is a well-characterized peptidase U32 protein with proteolytic activity against a specific type of collagen, which allows the bacteria to exert virulence in gingival tissue ( 64 ).…”

Section: Discussionmentioning

confidence: 99%

Biogenesis and iron-dependency of ribosomal RNA hydroxylation

Kimura

Sakai

Ishiguro

et al. 2017

Nucleic Acids Research

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Post-transcriptional modifications of ribosomal RNAs (rRNAs) are involved in ribosome biogenesis and fine-tuning of translation. 5-Hydroxycytidine (ho5C), a modification of unknown biogenesis and function, is present at position 2501 of Escherichia coli 23S rRNA. We conducted a genome-wide screen in E. coli to identify genes required for ho5C2501 formation, and found a previously-uncharacterized gene, ydcP (renamed rlhA), iron-sulfur cluster (isc) genes, and a series of genes responsible for prephenate biosynthesis, indicating that iron-sulfur clusters and prephenate are required for ho5C2501 formation. RlhA interacted with precursors of the 50S ribosomal subunit, suggesting that this protein is directly involved in formation of ho5C2501. RlhA belongs to a family of enzymes with an uncharacterized peptidase U32 motif and conserved Cys residues in the C-terminal region. These elements were essential for ho5C2501 formation. We also found that the frequency of ho5C2501 is modulated by environmental iron concentration. Together, our results reveal a novel biosynthetic pathway for RNA hydroxylation and its response to iron.

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Section: Discussionmentioning

confidence: 99%

Biogenesis and iron-dependency of ribosomal RNA hydroxylation

Kimura

Sakai

Ishiguro

et al. 2017

Nucleic Acids Research

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“…Multiple molecules are known to contribute to the virulence of these ECP, for example: the iron-regulated Serratia -like haemolysin YhlA, which has cytolytic and haemolytic activity [ 44 ], an azocasein protease [ 45 ], and the 47 kDa metalloprotease Yrp1, which has a wide range of targets and is particularly efficacious at degrading fibronectin, actin and myosin [ 46 , 47 ]. Recently, yrpA and yrpB have been demonstrated to be induced in the gut of rainbow trout [ 48 ]. In addition, genes involved in the catecholate siderophore ruckerbactin iron acquisition system were shown to be over-expressed by the bacterium during the infection process in fish.…”

Section: Virulence Factorsmentioning

confidence: 99%

Yersinia ruckeri, the causative agent of enteric redmouth disease in fish

Kumar

Menanteau–Ledouble

Saleh

et al. 2015

Vet Res

158

136

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Enteric redmouth disease (ERM) is a serious septicemic bacterial disease of salmonid fish species. It is caused by Yersinia ruckeri, a Gram-negative rod-shaped enterobacterium. It has a wide host range, broad geographical distribution, and causes significant economic losses in the fish aquaculture industry. The disease gets its name from the subcutaneous hemorrhages, it can cause at the corners of the mouth and in gums and tongue. Other clinical signs include exophthalmia, darkening of the skin, splenomegaly and inflammation of the lower intestine with accumulation of thick yellow fluid. The bacterium enters the fish via the secondary gill lamellae and from there it spreads to the blood and internal organs. Y. ruckeri can be detected by conventional biochemical, serological and molecular methods. Its genome is 3.7 Mb with 3406–3530 coding sequences. Several important virulence factors of Y. ruckeri have been discovered, including haemolyin YhlA and metalloprotease Yrp1. Both non-specific and specific immune responses of fish during the course of Y. ruckeri infection have been well characterized. Several methods of vaccination have been developed for controlling both biotype 1 and biotype 2 Y. ruckeri strains in fish. This review summarizes the current state of knowledge regarding enteric redmouth disease and Y. ruckeri: diagnosis, genome, virulence factors, interaction with the host immune responses, and the development of vaccines against this pathogen.

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“…It should also be stressed that the published proteolytic activities of PrtC and H. pylori HP0169 have never been confirmed in the literature. Interestingly, for at least some members of the U32 peptidase family a role in anaerobic or microaerobic growth has been suggested, but without further characterization of the function of these proteins (Filiatrault et al, 2006;Navais et al, 2014).…”

Section: Figurementioning

confidence: 99%

“…Many of the U32 members are implicated in pathogenicity, such as the yegQ gene of Salmonella enterica (Wu et al, 2002;Xiong et al, 2011) or the operon-encoded proteins YprA and YprB from Yersina ruckeri, which increase virulence in a fish model (Navais et al, 2014). Furthermore, a gene encoding a U32 member was found on a plasmid conferring antibiotic resistance in a Providencia stuartii strain (McGann et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

The first crystal structure of the peptidase domain of the U32 peptidase family

Schacherl

Montada

Brunstein

et al. 2015

Acta Cryst D Biol Crystallogr

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The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins from Helicobacter and Salmonella. The first crystal structure analysis of a U32 catalytic domain from Methanopyrus kandleri (gene mk0906) reveals a modified (βα)8 TIM-barrel fold with some unique features. The connecting segment between strands β7 and β8 is extended and helix α7 is located on top of the C-terminal end of the barrel body. The protein exhibits a dimeric quaternary structure in which a zinc ion is symmetrically bound by histidine and cysteine side chains from both monomers. These residues reside in conserved sequence motifs. No typical proteolytic motifs are discernible in the three-dimensional structure, and biochemical assays failed to demonstrate proteolytic activity. A tunnel in which an acetate ion is bound is located in the C-terminal part of the β-barrel. Two hydrophobic grooves lead to a tunnel at the C-terminal end of the barrel in which an acetate ion is bound. One of the grooves binds to a Strep-Tag II of another dimer in the crystal lattice. Thus, these grooves may be binding sites for hydrophobic peptides or other ligands.

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TheyrpABoperon ofYersinia ruckeriencoding two putative U32 peptidases is involved in virulence and induced under microaerobic conditions

Cited by 25 publications

References 28 publications

Biogenesis and iron-dependency of ribosomal RNA hydroxylation

Biogenesis and iron-dependency of ribosomal RNA hydroxylation

Yersinia ruckeri, the causative agent of enteric redmouth disease in fish

The first crystal structure of the peptidase domain of the U32 peptidase family

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