Crystal structures for short-chain pentraxin from zebrafish demonstrate a cyclic trimer with new recognition and effector faces

Chen, Rong; Qi, Jianxun; Yuan, Hongyu; Wu, Yanan; Hu, Wei; Xia, Chun

doi:10.1016/j.jsb.2015.01.001

Cited by 15 publications

(29 citation statements)

References 66 publications

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“…Bacterial CLPs all share a typical collagen domain with a repeating amino acid sequence [ 6 ]. The triplet repeat (Glycine-X-Threonine) n was identified from CLPs in the genome of B .…”

Section: Discussionmentioning

confidence: 99%

“…The occurrence of the (Glycine-X-Y) n pattern has also been demonstrated in many bacterial proteins but their functions have been discussed only rarely [ 6 ]. Most proteins that contain collagen-related structural motif (CSM) patterns are distributed in the Firmicutes group (including mycobacteria and Gram-positive bacteria) and in some cases a single genome encodes more than one CSM-containing protein [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

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Collagen-Like Proteins (ClpA, ClpB, ClpC, and ClpD) Are Required for Biofilm Formation and Adhesion to Plant Roots by Bacillus amyloliquefaciens FZB42

Zhao¹,

Wang

Shang³

et al. 2015

PLoS ONE

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The genes of collagen-like proteins (CLPs) have been identified in a broad range of bacteria, including some human pathogens. They are important for biofilm formation and bacterial adhesion to host cells in some human pathogenic bacteria, including several Bacillus spp. strains. Interestingly, some bacterial CLP-encoding genes (clps) have also been found in non-human pathogenic strains such as B. cereus and B. amyloliquefaciens, which are types of plant-growth promoting rhizobacteria (PGPR). In this study, we investigated a putative cluster of clps in B. amyloliquefaciens strain FZB42 and a collagen-related structural motif containing glycine-X-threonine repeats was found in the genes RBAM_007740, RBAM_007750, RBAM_007760, and RBAM_007770. Interestingly, biofilm formation was disrupted when these genes were inactivated separately. Scanning electron microscopy and hydrophobicity value detection were used to assess the bacterial cell shape morphology and cell surface architecture of clps mutant cells. The results showed that the CLPs appeared to have roles in bacterial autoaggregation, as well as adherence to the surface of abiotic materials and the roots of Arabidopsis thaliana. Thus, we suggest that the CLPs located in the outer layer of the bacterial cell (including the cell wall, outer membrane, flagella, or other associated structures) play important roles in biofilm formation and bacteria-plant interactions. This is the first study to analyze the function of a collagen-like motif-containing protein in a PGPR bacterium. Knocking out each clp gene produced distinctive morphological phenotypes, which demonstrated that each product may play specific roles in biofilm formation. Our in silico analysis suggested that these four tandemly ranked genes might not belong to an operon, but further studies are required at the molecular level to test this hypothesis. These results provide insights into the functions of clps during interactions between bacteria and plants.

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“…Bacterial CLPs all share a typical collagen domain with a repeating amino acid sequence [ 6 ]. The triplet repeat (Glycine-X-Threonine) n was identified from CLPs in the genome of B .…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Collagen-Like Proteins (ClpA, ClpB, ClpC, and ClpD) Are Required for Biofilm Formation and Adhesion to Plant Roots by Bacillus amyloliquefaciens FZB42

Zhao¹,

Wang

Shang³

et al. 2015

PLoS ONE

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“…These proteins are short-chain pentraxin proteins, where as PTX-3 is a long-chain pentraxin due to additional N-terminal domain. C-terminal domain (Pentraxin-domain) of PTX-3 is homologous to short-chain pentraxin proteins and are involved in recognition of pathogenic bacteria and fungi to activate the classical complement pathway via C1q, a complement pathway component (Inforzato et al, 2013 ; Chen et al, 2015 ). Predicted model structure of pentraxin-domain was submitted to structure refinement and energy minimization using ModRefiner and YASARA force field minimization server (Krieger et al, 2009 ; Xu and Zhang, 2011 ).…”

Section: Resultsmentioning

confidence: 99%

In silico Analysis Revealed High-risk Single Nucleotide Polymorphisms in Human Pentraxin-3 Gene and their Impact on Innate Immune Response against Microbial Pathogens

Thakur

Shankar

2016

Front. Microbiol.

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Pentraxin-3 (PTX-3) protein is an evolutionary conserved protein that acts as a soluble pattern-recognition receptor for pathogens and plays important role in innate immune response. It recognizes various pathogens by interacting with extracellular moieties such as glactomannan of conidia (Aspergillus fumigatus), lipopolysaccharide of Pseudomonas aeruginosa, Streptococcus pneumonia and Salmonella typhimurium. Thus, PTX-3 protein helps to clear these pathogens by activating downstream innate immune process. In this study, computational methods were used to analyze various non-synonymous single nucleotide polymorphisms (nsSNPs) in PTX-3 gene. Three different databases were used to retrieve SNP data sets followed by seven different in silico algorithms to screen nsSNPs in PTX-3 gene. Sequence homology based approach was used to identify nsSNPs. Conservation profile of PTX-3 protein amino acid residues were predicted by ConSurf web server. In total, 10 high-risk nsSNPs were identified in pentraxin-domain of PTX-3 gene. Out of these 10 high-risk nsSNPs, 4 were present in the conserved structural and functional residues of the pentraxin-domain, hence, selected for structural analyses. The results showed alteration in the putative structure of pentraxin-domain. Prediction of protein–protein interactions analysis showed association of PTX-3 protein with C1q component of complement pathway. Different functional and structural residues along with various putative phosphorylation sites and evolutionary relationship were also predicted for PTX-3 protein. This is the first extensive computational analyses of pentraxin protein family with nsSNPs and will serve as a valuable resource for future population based studies.

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“…Recently, an original Dare-C1q-CRP binding mode has been deduced in zebrafish, according to the resolved trimeric Dare-CRP. 21 The drifting of G-H loop may relate to the different interaction mode between Dare-C1qAgD and Dare-CRP. So the D-E Hydrophobic core is indicated in a purple box.…”

Section: Dare-c1qagd Shows Remarkable Differences With Hc1qagd In Thementioning

confidence: 99%

Crystal structure of zebrafish complement 1qA globular domain

et al. 2016

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C1q contains three globular domains (C1qgD) that are the key functional component of the classical complement system. C1qgD can interact with important immune molecules, including IgG and C-reactive protein (CRP) to form defense systems to protect animals. Here, the first nonmammalian structure, zebrafish C1qA globular domain (Dare-C1qAgD) was solved. Although the overall architecture of Dare-C1qAgD is similar to human C1qA, residues involved in C1qBgD, C1qCgD, and CRP binding are somewhat different while residues involved in IgG binding are not present in zebrafish. The structure gives insight into how human and fish C1qA evolved from an ancestral protein.

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Crystal structures for short-chain pentraxin from zebrafish demonstrate a cyclic trimer with new recognition and effector faces

Cited by 15 publications

References 66 publications

Collagen-Like Proteins (ClpA, ClpB, ClpC, and ClpD) Are Required for Biofilm Formation and Adhesion to Plant Roots by Bacillus amyloliquefaciens FZB42

Collagen-Like Proteins (ClpA, ClpB, ClpC, and ClpD) Are Required for Biofilm Formation and Adhesion to Plant Roots by Bacillus amyloliquefaciens FZB42

In silico Analysis Revealed High-risk Single Nucleotide Polymorphisms in Human Pentraxin-3 Gene and their Impact on Innate Immune Response against Microbial Pathogens

Crystal structure of zebrafish complement 1qA globular domain

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