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Gupta AB, Seedorf H. Structural and functional insights from the sequences and complex domain architecture of adhesin-like proteins from Methanobrevibacter smithii and Methanosphaera stadtmanae. Front Microbiol 2024; 15:1463715. [PMID: 39498127 PMCID: PMC11532034 DOI: 10.3389/fmicb.2024.1463715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 09/03/2024] [Indexed: 11/07/2024] Open
Abstract
Methanogenic archaea, or methanogens, are crucial in guts and rumens, consuming hydrogen, carbon dioxide, and other fermentation products. While their molecular interactions with other microorganisms are not fully understood, genomic sequences provide information. The first genome sequences of human gut methanogens, Methanosphaera stadtmanae and Methanobrevibacter smithii, revealed genes encoding adhesin-like proteins (ALPs). These proteins were also found in other gut and rumen methanogens, but their characteristics and functions remain largely unknown. This study analyzes the ALP repertoire of M. stadtmanae and M. smithii using AI-guided protein structure predictions of unique ALP domains. Both genomes encode more than 40 ALPs each, comprising over 10% of their genomes. ALPs contain repetitive sequences, many of which are unmatched in protein domain databases. We present unique sequence signatures of conserved ABD repeats in ALPs and propose a classification based on domain architecture. Our study offers insights into ALP features and how methanogens may interact with other microorganisms.
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Affiliation(s)
- Anjali Bansal Gupta
- Temasek Life Sciences Laboratory Limited, 1 Research Link National University of Singapore, Singapore, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory Limited, 1 Research Link National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Yi Q, Li L, Wang H, Zhu C, Chen Y, Yang L, Zheng Y, Yang Y, Bao Y. A clade of Streptococcus pneumoniae clonal complex 320 with increased tolerance to β-lactam antibiotics in a Chinese metropolitan city. J Glob Antimicrob Resist 2024; 36:379-388. [PMID: 38307252 DOI: 10.1016/j.jgar.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVES We characterized the population structure and features of clinical Streptococcus pneumoniae isolates associated with invasive pneumococcal disease (IPD) from 2009 to 2017 in a Chinese metropolitan city using a whole-genome sequencing approach. METHODS Seventy-nine pneumococcal strains, including 60 serogroup-19 strains from children enduring IPD from a paediatric hospital in Shenzhen, were subjected to whole-genome sequencing. Population structure was characterized through phylogenetic analysis, sequence typing, serotyping, virulence factor, and antimicrobial drug resistance (AMR) gene profiling, combining the publicly available related WGS data. Clinical demography and antibiotic susceptibility profiles were compared among different populations to emphasize the higher-risk populations. Genetic regions associated with AMR gene mobilization were identified through comparative genomics. RESULTS These IPD strains mainly belonged to clonal complex 320 (CC320) and were composed of serotypes 19A and 19F. In addition to sporadic possible importation-related isolates (ST320), we identified an independent clade, CC320_SZpop (ST271), that predominantly circulated in Shenzhen and possibly expanded its range. Clinical features and antibiotic susceptibility analysis revealed that CC320_SZpop might manifest much higher pathogenicity and tolerance to β-lactams. Specific virulence factors in Shenzhen isolates of CC320_SZpop were identified. Furthermore, an ca. 40 kb hotspot genomic region enduring frequent recombination was identified, possibly associated with the divergence of S. pneumoniae strains. CONCLUSION A novel pneumococcal clade, CC320_SZpop, circulating in Shenzhen and other regions in China, possibly under expansion, was found and deserves more study and surveillance. Our study also emphasizes the importance of continuous genomic surveillance of clinical S. pneumoniae isolates, especially IPD isolates.
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Affiliation(s)
- Qiuwei Yi
- Shenzhen Children's Hospital, Guangdong, China
| | - Liqiang Li
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Guangdong Provincial Clinical Research Center for Infectious Diseases (Tuberculosis), Shenzhen Clinical Research Center for Tuberculosis, Shenzhen, China; Department of Clinical Laboratory, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, China.
| | - Heping Wang
- Shenzhen Children's Hospital, Guangdong, China
| | | | | | - Liang Yang
- Southern University of Science of and Technology, Guangdong, China
| | | | | | - Yanmin Bao
- Shenzhen Children's Hospital, Guangdong, China.
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Fernández-Pereira J, Alvarado M, Gómez-Molero E, Dekker HL, Blázquez-Muñoz MT, Eraso E, Bader O, de Groot PWJ. Characterization of Awp14, A Novel Cluster III Adhesin Identified in a High Biofilm-Forming Candida glabrata Isolate. Front Cell Infect Microbiol 2021; 11:790465. [PMID: 34869084 PMCID: PMC8634165 DOI: 10.3389/fcimb.2021.790465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/25/2021] [Indexed: 12/30/2022] Open
Abstract
Candida glabrata is among the most prevalent causes of candidiasis. Unlike Candida albicans, it is not capable of changing morphology between yeast and hyphal forms but instead has developed other virulence factors. An important feature is its unprecedented large repertoire of predicted cell wall adhesins, which are thought to enable adherence to a variety of surfaces under different conditions. Here, we analyzed the wall proteome of PEU1221, a high biofilm-forming clinical strain isolated from an infected central venous catheter, under biofilm-forming conditions. This isolate shows increased incorporation of putative adhesins, including eight proteins that were not detected in walls of reference strain ATCC 2001, and of which Epa22, Awp14, and Awp2e were identified for the first time. The proteomics data suggest that cluster III adhesin Awp14 is relatively abundant in PEU1221. Phenotypic studies with awp14Δ deletion mutants showed that Awp14 is not responsible for the high biofilm formation of PEU1221 onto polystyrene. However, awp14Δ mutant cells in PEU1221 background showed a slightly diminished binding to chitin and seemed to sediment slightly slower than the parental strain suggesting implication in fungal cell-cell interactions. By structural modeling, we further demonstrate similarity between the ligand-binding domains of cluster III adhesin Awp14 and those of cluster V and VI adhesins. In conclusion, our work confirms the increased incorporation of putative adhesins, such as Awp14, in high biofilm-forming isolates, and contributes to decipher the precise role of these proteins in the establishment of C. glabrata infections.
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Affiliation(s)
- Jordan Fernández-Pereira
- Albacete Regional Center for Biomedical Research, Castilla - La Mancha Science & Technology Park, University of Castilla-La Mancha, Albacete, Spain
| | - María Alvarado
- Albacete Regional Center for Biomedical Research, Castilla - La Mancha Science & Technology Park, University of Castilla-La Mancha, Albacete, Spain
| | - Emilia Gómez-Molero
- Albacete Regional Center for Biomedical Research, Castilla - La Mancha Science & Technology Park, University of Castilla-La Mancha, Albacete, Spain
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Henk L. Dekker
- Mass Spectrometry of Biomolecules, Swammerdam Institute for Life Sciences Amsterdam, University of Amsterdam, Amsterdam, Netherlands
| | - María Teresa Blázquez-Muñoz
- Albacete Regional Center for Biomedical Research, Castilla - La Mancha Science & Technology Park, University of Castilla-La Mancha, Albacete, Spain
| | - Elena Eraso
- Mass Spectrometry of Biomolecules, Swammerdam Institute for Life Sciences Amsterdam, University of Amsterdam, Amsterdam, Netherlands
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Piet W. J. de Groot
- Albacete Regional Center for Biomedical Research, Castilla - La Mancha Science & Technology Park, University of Castilla-La Mancha, Albacete, Spain
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4
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Vazquez-Lopez J, Navarro-Garcia F. In silico Analyses of Core Proteins and Putative Effector and Immunity Proteins for T6SS in Enterohemorrhagic E. coli. Front Cell Infect Microbiol 2020; 10:195. [PMID: 32432054 PMCID: PMC7216683 DOI: 10.3389/fcimb.2020.00195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/14/2020] [Indexed: 12/29/2022] Open
Abstract
Shiga-toxin-producing Escherichia coli (STEC) has become an important pathogen that can cause diarrhea, hemorrhagic colitis and hemolytic uremic syndrome (HUS) in humans. Recent reports show that the type VI secretion system (T6SS) from EHEC is required to produce infection in a murine model and its expression has been related to a higher prevalence of HUS. In this work, we use bioinformatics analyses to identify the core genes of the T6SS and compared the differences between these components among the two published genomes for EHEC O157:H7 strain EDL933. Prototype strain EDL933 was further compared with other O157:H7 genomes. Unlike other typical T6SS effectors found in E. coli, we identified that there are several rhs family genes in EHEC, which could serve as T6SS effectors. In-silico and PCR analyses of the differences between rhs genes in the two existing genomes, allowed us to determine that the most recently published genome is more reliable to study the rhs genes. Analyzing the putative tridimensional structure of Rhs proteins, as well as the motifs found in their C-terminal end, allowed us to predict their possible functions. A phylogenetic analysis showed that the orphan rhs genes are more closely related between them than the rhs genes belonging to vgrG islands and that they are divided into three clades. Analyses of the downstream region of the rhs genes for identifying hypothetical immunity proteins showed that every gene has an associated small ORF (129-609 nucleotides). These genes could serve as immunity proteins as they had several interaction motifs as well as structural homology with other known immunity proteins. Our findings highlight the relevance of the T6SS in EHEC as well as the possible function of the Rhs effectors of EHEC O157:H7 during pathogenesis and bacterial competition, and the identification of novel effectors for the T6SS using a structural approach.
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Affiliation(s)
- Jaime Vazquez-Lopez
- Department of Cell Biology, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Mexico City, Mexico
| | - Fernando Navarro-Garcia
- Department of Cell Biology, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Mexico City, Mexico
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Opening the OPK Assay Gatekeeper: Harnessing Multi-Modal Protection by Pneumococcal Vaccines. Pathogens 2019; 8:pathogens8040203. [PMID: 31652741 PMCID: PMC6963391 DOI: 10.3390/pathogens8040203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/14/2019] [Accepted: 10/21/2019] [Indexed: 11/16/2022] Open
Abstract
Pneumococcal vaccine development is driven by the achievement of high activity in a single gatekeeper assay: the bacterial opsonophagocytic killing (OPK) assay. New evidence challenges the dogma that anti-capsular antibodies have only a single function that predicts success. The emerging concept of multi-modal protection presents an array of questions that are fundamental to adopting a new vaccine design process. If antibodies have hidden non-opsonic functions that are protective, should these be optimized for better vaccines? What would protein antigens add to protective activity? Are cellular immune functions additive to antibodies for success? Do different organs benefit from different modes of protection? Can vaccine activities beyond OPK protect the immunocompromised host? This commentary raises these issues at a time when capsule-only OPK assay-based vaccines are increasingly seen as a limiting strategy.
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Yamaguchi M, Hirose Y, Takemura M, Ono M, Sumitomo T, Nakata M, Terao Y, Kawabata S. Streptococcus pneumoniae Evades Host Cell Phagocytosis and Limits Host Mortality Through Its Cell Wall Anchoring Protein PfbA. Front Cell Infect Microbiol 2019; 9:301. [PMID: 31482074 PMCID: PMC6710382 DOI: 10.3389/fcimb.2019.00301] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/05/2019] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pneumoniae is a Gram-positive bacterium belonging to the oral streptococcus species, mitis group. This pathogen is a leading cause of community-acquired pneumonia, which often evades host immunity and causes systemic diseases, such as sepsis and meningitis. Previously, we reported that PfbA is a β-helical cell surface protein contributing to pneumococcal adhesion to and invasion of human epithelial cells in addition to its survival in blood. In the present study, we investigated the role of PfbA in pneumococcal pathogenesis. Phylogenetic analysis indicated that the pfbA gene is highly conserved in S. pneumoniae and Streptococcus pseudopneumoniae within the mitis group. Our in vitro assays showed that PfbA inhibits neutrophil phagocytosis, leading to pneumococcal survival. We found that PfbA activates NF-κB through TLR2, but not TLR4. In addition, TLR2/4 inhibitor peptide treatment of neutrophils enhanced the survival of the S. pneumoniae ΔpfbA strain as compared to a control peptide treatment, whereas the treatment did not affect survival of a wild-type strain. In a mouse pneumonia model, the host mortality and level of TNF-α in bronchoalveolar lavage fluid were comparable between wild-type and ΔpfbA-infected mice, while deletion of pfbA decreased the bacterial burden in bronchoalveolar lavage fluid. In a mouse sepsis model, the ΔpfbA strain demonstrated significantly increased host mortality and TNF-α levels in plasma, but showed reduced bacterial burden in lung and liver. These results indicate that PfbA may contribute to the success of S. pneumoniae species by inhibiting host cell phagocytosis, excess inflammation, and mortality by interacting with TLR2.
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Affiliation(s)
- Masaya Yamaguchi
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Yujiro Hirose
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Moe Takemura
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan.,Department of Oral and Maxillofacial Surgery II, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Masayuki Ono
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan.,Department of Fixed Prosthodontics, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Tomoko Sumitomo
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Masanobu Nakata
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Yutaka Terao
- Division of Microbiology and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shigetada Kawabata
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
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Yan Z, Cui Y, Zhou W, Li W, Tan X, Chen W, Zhang J, Jiang Y. Molecular characterization of Streptococcus pneumoniae in children living in southwest China and assessment of a potential protein vaccine, rPfbA. Vaccine 2019; 37:721-731. [DOI: 10.1016/j.vaccine.2018.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/28/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
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8
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Radhakrishnan D, Yamaguchi M, Kawabata S, Ponnuraj K. Streptococcus pneumoniae surface adhesin PfbA and its interaction with erythrocytes and hemoglobin. Int J Biol Macromol 2018; 120:135-143. [PMID: 30125626 DOI: 10.1016/j.ijbiomac.2018.08.080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/14/2018] [Accepted: 08/14/2018] [Indexed: 12/19/2022]
Abstract
Streptococcus pneumoniae is one of the major colonizers of human nasopharynx and its surface protein PfbA interacts with host molecules like plasmin(ogen), fibrinogen and fibronectin for colonization. Most of the binding partners of PfbA are glycoproteins. Recently we found that PfbA exhibited high affinity towards carbohydrates. It was reported that S. pneumoniae invades erythrocytes and utilizes them to evade human innate immunity. The results of this study suggested that LPXTG motif containing pneumococcal surface proteins, erythrocyte lipid rafts and erythrocyte actin remodeling are all involved in the invasion mechanism. The erythrocyte cell membrane contains different glycoproteins and glycolipids. Therefore, to find out if PfbA plays any role in erythrocyte binding, we carried out the binding studies of rPfbA49-684 with human red blood cells (RBCs) especially with its surface molecules employing ELISA and Bio Layer Interferometry. The results from these experiments show that rPfbA49-684 has a broad specificity for carbohydrates and remarkable affinity towards RBCs and in particular with extracted surface glycolipids. Further rPfbA49-684 also exhibited moderate affinity towards hemoglobin. Thus the results of the present study provide clear evidence that PfbA can interact with RBCs and this could be one of the important factors in erythrocyte invasion of S. pneumoniae.
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Affiliation(s)
- Deepthi Radhakrishnan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - Masaya Yamaguchi
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka 565-0871, Japan
| | - Shigetada Kawabata
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka 565-0871, Japan
| | - Karthe Ponnuraj
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.
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9
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Synergistic findings from microbiological and evolutional analyses of virulence factors among pathogenic streptococcal species. J Oral Biosci 2018. [DOI: 10.1016/j.job.2018.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Beulin DSJ, Radhakrishnan D, Suresh SC, Sadasivan C, Yamaguchi M, Kawabata S, Ponnuraj K. Streptococcus pneumoniae
surface protein PfbA is a versatile multidomain and multiligand-binding adhesin employing different binding mechanisms. FEBS J 2017; 284:3404-3421. [DOI: 10.1111/febs.14200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/31/2017] [Accepted: 08/11/2017] [Indexed: 02/05/2023]
Affiliation(s)
| | - Deepthi Radhakrishnan
- Centre of Advanced Study in Crystallography and Biophysics; University of Madras; Chennai India
| | - Sharanya C. Suresh
- Department of Biotechnology & Microbiology; School of Life Sciences; Kannur University; Palayad India
| | - Chittalakottu Sadasivan
- Department of Biotechnology & Microbiology; School of Life Sciences; Kannur University; Palayad India
| | - Masaya Yamaguchi
- Department of Oral and Molecular Microbiology; Osaka University Graduate School of Dentistry; Suita Osaka Japan
| | - Shigetada Kawabata
- Department of Oral and Molecular Microbiology; Osaka University Graduate School of Dentistry; Suita Osaka Japan
| | - Karthe Ponnuraj
- Centre of Advanced Study in Crystallography and Biophysics; University of Madras; Chennai India
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Generic determinants of Streptococcus colonization and infection. INFECTION GENETICS AND EVOLUTION 2015; 33:361-70. [DOI: 10.1016/j.meegid.2014.09.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/10/2014] [Accepted: 09/14/2014] [Indexed: 11/20/2022]
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12
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Di Poto A, Papi M, Trivedi S, Maiorana A, Gavazzo P, Vassalli M, Lowy FD, De Spirito M, Montanaro L, Imbriani M, Arciola CR, Visai L. In vitro effect of temperature on the conformational structure and collagen binding of SdrF, a Staphylococcus epidermidis adhesin. Appl Microbiol Biotechnol 2015; 99:5593-603. [PMID: 25683665 DOI: 10.1007/s00253-015-6456-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 12/01/2022]
Abstract
Staphylococcus epidermidis is the leading etiologic agent of device-related infections. S. epidermidis is able to bind, by means of the adhesins of its cell wall, the host matrix proteins filming the artificial surfaces. Thence, bacteria cling to biomaterials and infection develops. The effect of temperature on integrity, structure, and biological activity of the collagen-binding adhesin (SdrF) of S. epidermidis has been here investigated. By cloning in E. coli XL1-Blue, a recombinant of the SdrF binding domain B (rSdrFB), carrying an N-terminal polyhistidine, was obtained. Purification was by HiTrap(TM) Chelating HP columns. Assessment of purity, molecular weight, and integrity was by SDS-PAGE. The rSdrFB-collagen binding was investigated by ELISA. A full three-dimensional reconstruction of rSdrFB was achieved by small-angle X-ray scattering (SAXS). At 25 °C, rSdrFB bound to type I collagen in a dose-dependent, saturable manner, with a Kd of 2.48 × 10(-7) M. When temperature increased from 25 to 37 °C, a strong conformational change occurred, together with the abolition of the rSdrFB-collagen binding. The rSdrFB integrity was not affected by temperature variation. SdrFB-collagen binding is switched on/off depending on the temperature. Implications with the infection pathogenesis are enlightened.
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Affiliation(s)
- Antonella Di Poto
- Department of Molecular Medicine, Center for Tissue Engineering (CIT), INSTM UdR of Pavia, University of Pavia, Viale Taramelli 3/b, 27100, Pavia, Italy
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Abbott DW, van Bueren AL. Using structure to inform carbohydrate binding module function. Curr Opin Struct Biol 2014; 28:32-40. [PMID: 25108190 DOI: 10.1016/j.sbi.2014.07.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/24/2014] [Accepted: 07/16/2014] [Indexed: 10/24/2022]
Abstract
Generally, non-catalytic carbohydrate binding module (CBM) specificity has been shown to parallel the catalytic activity of the carbohydrate active enzyme (CAZyme) module it is appended to. With the rapid expansion in metagenomic sequence space for the potential discovery of new CBMs in addition to the recent emergence of several new CBM families that display diverse binding profiles and novel functions, elucidating the function of these protein modules has become a much more challenging task. This review summarizes several approaches that have been reported for using primary structure to inform CBM specificity and streamlining their biophysical characterization. In addition we discuss general trends in binding site architecture and several newly identified functions for CBMs. Streams of investigation that will facilitate the development and refinement of sequence-based prediction tools are suggested.
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Affiliation(s)
- D Wade Abbott
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, 5403-1st Ave, Lethbridge, AB, Canada T1J4B1.
| | - Alicia Lammerts van Bueren
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747AG, The Netherlands
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Crystal structure of PfbA, a surface adhesin of Streptococcus pneumoniae, provides hints into its interaction with fibronectin. Int J Biol Macromol 2013; 64:168-73. [PMID: 24321492 DOI: 10.1016/j.ijbiomac.2013.11.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 12/27/2022]
Abstract
PfbA is a surface adhesin and invasin of Streptococcus pneumoniae that binds to human fibronectin and plasminogen of the host extracellular matrix. It is a virulence factor for its pathogenesis. The crystal structure of recombinant PfbA150-607 from S. pneumoniae strain R6, was determined using multiwavelength anomalous dispersion (MAD) method and refined to 1.90Å resolution. The structure of rPfbA150-607 revealed that residues Thr150 to Lys570 form a rigid parallel beta helix, followed by a short disordered region (571-607) that consists of beta hairpins. The structural organization of the beta helix resembles that of polysaccharide-modifying enzymes. The structural and sequence features essential for fibronectin-binding observed in the well characterized fibronectin-binding proteins such as FnBPA of Staphylococcus aureus, SfbI of Streptococcus pyogenes and BBK32 of Borrelia burgdorferi has been found in rPfbA150-607. Based on this, it is predicted that the disordered region following the beta helix could be the fibronectin-binding region in PfbA. PfbA150-607 contains relatively high number of surface exposed lysines and these residues are probably involved in binding plasmin(ogen) as observed in other plasminogen-binding proteins.
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