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Chen B, Liu G, Chen Q, Wang H, Liu L, Tang K. Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes. Comput Struct Biotechnol J 2024; 23:406-416. [PMID: 38235362 PMCID: PMC10792170 DOI: 10.1016/j.csbj.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024] Open
Abstract
Members of the phylum Bacteroidetes play a key role in the marine carbon cycle through their degradation of polysaccharides via carbohydrate-active enzymes (CAZymes) and polysaccharide utilization loci (PULs). The discovery of novel CAZymes and PULs is important for our understanding of the marine carbon cycle. In this study, we isolated and identified a potential new genus of the family Catalimonadaceae, in the phylum Bacteroidetes, from the southwest Indian Ocean. Strain TK19036, the type strain of the new genus, is predicted to encode CAZymes that are relatively abundant in marine Bacteroidetes genomes. Tunicatimonas pelagia NBRC 107804T, Porifericola rhodea NBRC 107748T and Catalinimonas niigatensis NBRC 109829T, which exhibit 16 S rRNA similarities exceeding 90% with strain TK19036, and belong to the same family, were selected as reference strains. These organisms possess a highly diverse repertoire of CAZymes and PULs, which may enable them to degrade a wide range of polysaccharides, especially pectin and alginate. In addition, some secretory CAZymes in strain TK19036 and its relatives were predicted to be transported by type IX secretion system (T9SS). Further, to the best of our knowledge, we propose the first reported "hybrid" PUL targeting alginates in T. pelagia NBRC 107804T. Our findings provide new insights into the polysaccharide degradation capacity of marine Bacteroidetes, and suggest that T9SS may play a more important role in this process than previously believed.
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Affiliation(s)
- Beihan Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Guohua Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Huanyu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Le Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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2
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Kumari K, Dey J, Mahapatra SR, Ma Y, Sharma PK, Misra N, Singh RP. Protein profiling and immunoinformatic analysis of the secretome of a metal-resistant environmental isolate Pseudomonas aeruginosa S-8. Folia Microbiol (Praha) 2024; 69:1095-1122. [PMID: 38457114 DOI: 10.1007/s12223-024-01152-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 02/03/2024] [Indexed: 03/09/2024]
Abstract
The bacterial secretome represents a comprehensive catalog of proteins released extracellularly that have multiple important roles in virulence and intercellular communication. This study aimed to characterize the secretome of an environmental isolate Pseudomonas aeruginosa S-8 by analyzing trypsin-digested culture supernatant proteins using nano-LC-MS/MS tool. Using a combined approach of bioinformatics and mass spectrometry, 1088 proteins in the secretome were analyzed by PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb tool for their subcellular localization and further categorization of secretome proteins according to signal peptides. Using the gene ontology tool, secretome proteins were categorized into different functional categories. KEGG pathway analysis identified the secreted proteins into different metabolic functional pathways. Moreover, our LC-MS/MS data revealed the secretion of various CAZymes into the extracellular milieu, which suggests its strong biotechnological applications to breakdown complex carbohydrate polymers. The identified immunodominant epitopes from the secretome of P. aeruginosa showed the characteristic of being non-allergenic, highly antigenic, nontoxic, and having a low risk of triggering autoimmune responses, which highlights their potential as successful vaccine targets. Overall, the identification of secreted proteins of P. aeruginosa could be important for both diagnostic purposes and the development of an effective candidate vaccine.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, 835215, India
| | - Jyotirmayee Dey
- School of Biotechnology, Deemed to Be University, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, 751024, India
| | - Soumya Ranjan Mahapatra
- School of Biotechnology, Deemed to Be University, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, 751024, India
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Namrata Misra
- School of Biotechnology, Deemed to Be University, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, 751024, India
| | - Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, 201309, India.
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3
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Saravanan V, Gopalakrishnan V, Mahendran MIMS, Vaithianathan R, Srinivasan S, Boopathy V, Krishnamurthy S. Biofilm mediated integrin activation and directing acceleration of colorectal cancer. APMIS 2024. [PMID: 39246244 DOI: 10.1111/apm.13466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 08/15/2024] [Indexed: 09/10/2024]
Abstract
Bacterial biofilm plays a vital role in influencing several diseases, infections, metabolic pathways and communication channels. Biofilm influence over colorectal cancer (CRC) has been a booming area of research interest. The virulence factors of bacterial pathogen have a high tendency to induce metabolic pathway to accelerate CRC. The bacterial species biofilm may induce cancer through regulating the major signalling pathways responsible for cell proliferation, differentiation, survival and growth. Activation of cancer signals may get initiated from the chronic infections through bacterial biofilm species. Integrin mediates in the activation of major pathway promoting cancer. Integrin-mediated signals are expected to be greatly influenced by biofilm. Integrins are identified as an important dimer, whose dysfunction may alter the signalling cascade specially focusing on TGF-β, PI3K/Akt/mToR, MAPK and Wnt pathway. Along with biofilm shield, the tumour gains greater resistance from radiation, chemotherapy and also from other antibiotics. The biofilm barrier is known to cause challenges for CRC patients undergoing treatment.
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Affiliation(s)
- Vaijayanthi Saravanan
- MGM Advanced Research Institute, Sri Balaji Vidhyapeeth (Deemed to be University), Pondicherry, Tamil Nadu, India
| | - Vinoj Gopalakrishnan
- MGM Advanced Research Institute, Sri Balaji Vidhyapeeth (Deemed to be University), Pondicherry, Tamil Nadu, India
| | | | - Rajan Vaithianathan
- Mahatma Gandhi Medical College and Research Institute, Sri Balaji Vidhyapeeth (Deemed to be University), Pondicherry, Tamil Nadu, India
| | - Sowmya Srinivasan
- Mahatma Gandhi Medical College and Research Institute, Sri Balaji Vidhyapeeth (Deemed to be University), Pondicherry, Tamil Nadu, India
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Srinivasan S. Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture. Genes (Basel) 2024; 15:1048. [PMID: 39202408 PMCID: PMC11354047 DOI: 10.3390/genes15081048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 09/03/2024] Open
Abstract
The rhizosphere of plants contains a wide range of microorganisms that can be cultivated and used for the benefit of agricultural practices. From garden soil near the rhizosphere region, Strain ES10-3-2-2 was isolated, and the cells were Gram-negative, aerobic, non-spore-forming rods that were 0.3-0.8 µm in diameter and 1.5-2.5 µm in length. The neighbor-joining method on 16S rDNA similarity revealed that the strain exhibited the highest sequence similarities with "Fibrivirga algicola JA-25" (99.2%) and Fibrella forsythia HMF5405T (97.3%). To further explore its biotechnological potentialities, we sequenced the complete genome of this strain employing the PacBio RSII sequencing platform. The genome of Strain ES10-3-2-2 comprises a 6,408,035 bp circular chromosome with a 52.8% GC content, including 5038 protein-coding genes and 52 RNA genes. The sequencing also identified three plasmids measuring 212,574 bp, 175,683 bp, and 81,564 bp. Intriguingly, annotations derived from the NCBI-PGAP, eggnog, and KEGG databases indicated the presence of genes affiliated with radiation-resistance pathway genes and plant-growth promotor key/biofertilization-related genes regarding Fe acquisition, K and P assimilation, CO2 fixation, and Fe solubilization, with essential roles in agroecosystems, as well as genes related to siderophore regulation. Additionally, T1SS, T6SS, and T9SS secretion systems are present in this species, like plant-associated bacteria. The inoculation of Strain ES10-3-2-2 to Arabidopsis significantly increases the fresh shoot and root biomass, thereby maintaining the plant quality compared to uninoculated controls. This work represents a link between radiation tolerance and the plant-growth mechanism of Strain ES10-3-2-2 based on in vitro experiments and bioinformatic approaches. Overall, the radiation-tolerant bacteria might enable the development of microbiological preparations that are extremely effective at increasing plant biomass and soil fertility, both of which are crucial for sustainable agriculture.
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Affiliation(s)
- Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 01797, Republic of Korea
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Saran A, Kim HM, Manning I, Hancock MA, Schmitz C, Madej M, Potempa J, Sola M, Trempe JF, Zhu Y, Davey ME, Zeytuni N. Unveiling the molecular mechanisms of the type IX secretion system's response regulator: Structural and functional insights. PNAS NEXUS 2024; 3:pgae316. [PMID: 39139265 PMCID: PMC11320123 DOI: 10.1093/pnasnexus/pgae316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 07/22/2024] [Indexed: 08/15/2024]
Abstract
The type IX secretion system (T9SS) is a nanomachinery utilized by bacterial pathogens to facilitate infection. The system is regulated by a signaling cascade serving as its activation switch. A pivotal member in this cascade, the response regulator protein PorX, represents a promising drug target to prevent the secretion of virulence factors. Here, we provide a comprehensive characterization of PorX both in vitro and in vivo. First, our structural studies revealed PorX harbors a unique enzymatic effector domain, which, surprisingly, shares structural similarities with the alkaline phosphatase superfamily, involved in nucleotide and lipid signaling pathways. Importantly, such pathways have not been associated with the T9SS until now. Enzymatic characterization of PorX's effector domain revealed a zinc-dependent phosphodiesterase activity, with active site dimensions suitable to accommodate a large substrate. Unlike typical response regulators that dimerize via their receiver domain upon phosphorylation, we found that zinc can also induce conformational changes and promote PorX's dimerization via an unexpected interface. These findings suggest that PorX can serve as a cellular zinc sensor, broadening our understanding of its regulatory mechanisms. Despite the strict conservation of PorX in T9SS-utilizing bacteria, we demonstrate that PorX is essential for virulence factors secretion in Porphyromonas gingivalis and affects metabolic enzymes secretion in the nonpathogenic Flavobacterium johnsoniae, but not for the secretion of gliding adhesins. Overall, this study advances our structural and functional understanding of PorX, highlighting its potential as a druggable target for intervention strategies aimed at disrupting the T9SS and mitigating virulence in pathogenic species.
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Affiliation(s)
- Anshu Saran
- Department of Anatomy and Cell Biology, McGill University, 3640 Rue University, Montreal, QC H3A 0C7, Canada
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, 3649 Promenade Sir William Olser, Montreal, QC H3G 0B1, Canada
| | - Hey-Min Kim
- Department of Microbiology, The Forsyth Institute, 245 First St, Cambridge, MA 02142, USA
| | - Ireland Manning
- Department of Biological Sciences, Minnesota State University Mankato, 242 Trafton Science Center South, Mankato, MN 56001, USA
| | - Mark A Hancock
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, 3649 Promenade Sir William Olser, Montreal, QC H3G 0B1, Canada
- Department of Pharmacology & Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Montreal, QC H3G 1Y6, Canada
| | - Claus Schmitz
- Department of Structural Biology, Molecular Biology Institute of Barcelona, Spanish Research Council, Barcelona Science Park, Barcelona E-08028, Spain
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków PL-30-387, Poland
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków PL-30-387, Poland
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, 501 S Preston St, Louisville, KY 40202, USA
| | - Maria Sola
- Department of Structural Biology, Molecular Biology Institute of Barcelona, Spanish Research Council, Barcelona Science Park, Barcelona E-08028, Spain
| | - Jean-François Trempe
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, 3649 Promenade Sir William Olser, Montreal, QC H3G 0B1, Canada
- Department of Pharmacology & Therapeutics, McGill University, 3655 Promenade Sir-William-Osler, Montreal, QC H3G 1Y6, Canada
| | - Yongtao Zhu
- Department of Biological Sciences, Minnesota State University Mankato, 242 Trafton Science Center South, Mankato, MN 56001, USA
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou Dushu Lake Science and Education Innovation District, Suzhou Industrial Park, Suzhou, Jiangsu 215123, China
| | - Mary Ellen Davey
- Department of Microbiology, The Forsyth Institute, 245 First St, Cambridge, MA 02142, USA
| | - Natalie Zeytuni
- Department of Anatomy and Cell Biology, McGill University, 3640 Rue University, Montreal, QC H3A 0C7, Canada
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, 3649 Promenade Sir William Olser, Montreal, QC H3G 0B1, Canada
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Romanenko L, Bystritskaya E, Savicheva Y, Eremeev V, Otstavnykh N, Kurilenko V, Velansky P, Isaeva M. Description and Whole-Genome Sequencing of Mariniflexile litorale sp. nov., Isolated from the Shallow Sediments of the Sea of Japan. Microorganisms 2024; 12:1413. [PMID: 39065181 PMCID: PMC11278836 DOI: 10.3390/microorganisms12071413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
A Gram-negative, aerobic, rod-shaped, non-motile, yellow-pigmented bacterium, KMM 9835T, was isolated from the sediment sample obtained from the Amur Bay of the Sea of Japan seashore, Russia. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences positioned the novel strain KMM 9835T in the genus Mariniflexile as a separate line sharing the highest 16S rRNA gene sequence similarities of 96.6% and 96.2% with Mariniflexile soesokkakense RSSK-9T and Mariniflexile fucanivorans SW5T, respectively, and similarity values of <96% to other recognized Mariniflexile species. The average nucleotide identity and digital DNA-DNA hybridization values between strain KMM 9835T and M. soesokkakense KCTC 32427T, Mariniflexile gromovii KCTC 12570T, M. fucanivorans DSM 18792T, and M. maritimum M5A1MT were 83.0%, 82.5%, 83.4%, and 78.3% and 30.7%, 29.6%, 29.5%, and 24.4%, respectively. The genomic DNA GC content of strain KMM 9835T was 32.5 mol%. The dominant menaquinone was MK-6, and the major fatty acids were iso-C15:0, iso-C15:1ω10c, and C15:0. The polar lipids of strain KMM 9835T consisted of phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, and six unidentified lipids. A pan-genome analysis showed that the KMM 9835T genome encoded 753 singletons. The annotated singletons were more often related to transport protein systems (SusC), transcriptional regulators (AraC, LytTR, LacI), and enzymes (glycosylases). The KMM 9835T genome was highly enriched in CAZyme-encoding genes, the proportion of which reached 7.3%. Moreover, the KMM 9835T genome was characterized by a high abundance of CAZyme gene families (GH43, GH28, PL1, PL10, CE8, and CE12), indicating its potential to catabolize pectin. This may represent part of an adaptation strategy facilitating microbial consumption of plant polymeric substrates in aquatic environments near shorelines and freshwater sources. Based on the combination of phylogenetic and phenotypic characterization, the marine sediment strain KMM 9835T (=KCTC 92792T) represents a novel species of the genus Mariniflexile, for which the name Mariniflexile litorale sp. nov. is proposed.
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Affiliation(s)
- Lyudmila Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Evgeniya Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Yuliya Savicheva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Viacheslav Eremeev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Nadezhda Otstavnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Valeriya Kurilenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
| | - Peter Velansky
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia;
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (E.B.); (Y.S.); (V.E.); (N.O.); (V.K.)
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Han J, Balasubramanian I, Flores JA, Bandyopadhyay S, Yang J, Liu Y, Singh R, Setty P, Kiela P, Ferraris R, Gao N. Intestinal lysozyme engagement of Salmonella Typhimurium stimulates the release of barrier-impairing InvE and Lpp1. J Biol Chem 2024; 300:107424. [PMID: 38823640 PMCID: PMC11255904 DOI: 10.1016/j.jbc.2024.107424] [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: 02/28/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 06/03/2024] Open
Abstract
Lysozyme is a β-1,4-glycosidase that hydrolyzes the polysaccharide backbone of bacterial cell walls. With an additional bactericidal function mediated by a separate protein domain, lysozyme is considered a uniquely important antimicrobial molecule contributing to the host's innate immune response to infection. Elevated lysozyme production is found in various inflammatory conditions while patients with genetic risks for inflammatory bowel diseases demonstrate abnormal lysozyme expression, granule packaging, and secretion in Paneth cells. However, it remains unclear how a gain- or loss-of-function in host lysozyme may impact the host inflammatory responses to pathogenic infection. We challenged Lyz1-/- and ectopic Lyz1-expressing (Villin-Lyz1TG) mice with S. Typhimurium and then comprehensively assessed the inflammatory disease progression. We conducted proteomics analysis to identify molecules derived from human lysozyme-mediated processing of live Salmonella. We examined the barrier-impairing effects of these identified molecules in human intestinal epithelial cell monolayer and enteroids. Lyz1-/- mice are protected from infection in terms of morbidity, mortality, and barrier integrity, whereas Villin-Lyz1TG mice demonstrate exacerbated infection and inflammation. The growth and invasion of Salmonella in vitro are not affected by human or chicken lysozyme, whereas lysozyme encountering of live Salmonella stimulates the release of barrier-disrupting factors, InvE-sipC and Lpp1, which directly or indirectly impair the tight junctions. The direct engagement of host intestinal lysozyme with an enteric pathogen such as Salmonella promotes the release of virulence factors that are barrier-impairing and pro-inflammatory. Controlling lysozyme function may help alleviate the inflammatory progression.
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Affiliation(s)
- Jiangmeng Han
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | | | - Juan A Flores
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | | | - Jiaxing Yang
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | - Yue Liu
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | - Rajbir Singh
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | - Prashanth Setty
- Department of Pediatrics, Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children's Research Center, University of Arizona, Tucson, Arizona, USA
| | - Pawel Kiela
- Department of Pediatrics, Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children's Research Center, University of Arizona, Tucson, Arizona, USA
| | - Ronaldo Ferraris
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA; Department of Pharmacology, Physiology, and Neuroscience, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA.
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Rothenberger CM, Yu M, Kim HM, Cheung YW, Chang YW, Davey ME. An outer membrane vesicle specific lipoprotein promotes Porphyromonas gingivalis aggregation on red blood cells. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100249. [PMID: 38974668 PMCID: PMC11225709 DOI: 10.1016/j.crmicr.2024.100249] [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] [Indexed: 07/09/2024] Open
Abstract
Porphyromonas gingivalis uses a variety of mechanisms to actively interact with and promote the hydrolysis of red blood cells (RBCs) to obtain iron in the form of heme. In this study, we investigated the function of lipoprotein PG1881 which was previously shown to be up-regulated during subsurface growth and selectively enriched on outer membrane vesicles (OMVs). Our results show that wildtype strain W83 formed large aggregates encompassing RBCs whereas the PG1881 deletion mutant remained predominately as individual cells. Using a PG1881 antibody, immunofluorescence revealed that the wildtype strain's aggregation to RBCs involves an extracellular matrix enriched with PG1881. Our findings discover that RBCs elicit cell aggregation and matrix formation by P. gingivalis and that this process is promoted by an OMV-specific lipoprotein. We propose this strategy is advantageous for nutrient acquisition as well as dissemination from the oral cavity and survival of this periodontal pathogen.
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Affiliation(s)
- Christina M. Rothenberger
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
- Department of Oral Microbiology, University of Florida College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Manda Yu
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
| | - Hey-Min Kim
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
| | - Yee-Wai Cheung
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mary Ellen Davey
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
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9
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Rocha ST, Shah DD, Shrivastava A. Ecological, beneficial, and pathogenic functions of the Type 9 Secretion System. Microb Biotechnol 2024; 17:e14516. [PMID: 38924452 PMCID: PMC11205867 DOI: 10.1111/1751-7915.14516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The recently discovered Type 9 Secretion System (T9SS) is present in bacteria of the Fibrobacteres-Bacteroidetes-Chlorobi superphylum, which are key constituents of diverse microbiomes. T9SS is instrumental in the extracellular secretion of over 270,000 proteins, including peptidases, sugar hydrolases, metal ion-binding proteins, and metalloenzymes. These proteins are essential for the interaction of bacteria with their environment. This mini-review explores the extensive array of proteins secreted by the T9SS. It highlights the diverse functions of these proteins, emphasizing their roles in pathogenesis, bacterial interactions, host colonization, and the overall health of the ecosystems inhabited by T9SS-containing bacteria.
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Affiliation(s)
- Sofia T. Rocha
- Biodesign InstituteArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Dhara D. Shah
- Biodesign InstituteArizona State UniversityTempeArizonaUSA
- School of Mathematical and Natural SciencesArizona State UniversityGlendaleArizonaUSA
| | - Abhishek Shrivastava
- Biodesign InstituteArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
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Younker IT, Molnar N, Scorza K, Weed R, Light SH, Pfister CA. Bacteria on the foundational kelp in kelp forest ecosystems: Insights from culturing, whole genome sequencing and metabolic assays. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13270. [PMID: 38778582 PMCID: PMC11112141 DOI: 10.1111/1758-2229.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/06/2024] [Indexed: 05/25/2024]
Abstract
In coastal marine ecosystems, kelp forests serve as a vital habitat for numerous species and significantly influence local nutrient cycles. Bull kelp, or Nereocystis luetkeana, is a foundational species in the iconic kelp forests of the northeast Pacific Ocean and harbours a complex microbial community with potential implications for kelp health. Here, we report the isolation and functional characterisation of 16 Nereocystis-associated bacterial species, comprising 13 Gammaproteobacteria, 2 Flavobacteriia and 1 Actinomycetia. Genome analyses of these isolates highlight metabolisms potentially beneficial to the host, such as B vitamin synthesis and nitrogen retention. Assays revealed that kelp-associated bacteria thrive on amino acids found in high concentrations in the ocean and in the kelp (glutamine and asparagine), generating ammonium that may facilitate host nitrogen acquisition. Multiple isolates have genes indicative of interactions with key elemental cycles in the ocean, including carbon, nitrogen and sulphur. We thus report a collection of kelp-associated microbial isolates that provide functional insight for the future study of kelp-microbe interactions.
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Affiliation(s)
- Isaac T. Younker
- Committee on MicrobiologyThe University of ChicagoChicagoIllinoisUSA
| | - Nichos Molnar
- The CollegeThe University of ChicagoChicagoIllinoisUSA
| | - Kaylie Scorza
- The CollegeThe University of ChicagoChicagoIllinoisUSA
| | - Roo Weed
- The Graduate Program in Biophysical SciencesThe University of ChicagoChicagoIllinoisUSA
| | - Samuel H. Light
- Department of MicrobiologyThe University of ChicagoChicagoIllinoisUSA
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11
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Mizgalska D, Rodríguez-Banqueri A, Veillard F, Książęk M, Goulas T, Guevara T, Eckhard U, Potempa J, Gomis-Rüth FX. Structural and functional insights into the C-terminal signal domain of the Bacteroidetes type-IX secretion system. Open Biol 2024; 14:230448. [PMID: 38862016 DOI: 10.1098/rsob.230448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/20/2024] [Indexed: 06/13/2024] Open
Abstract
Gram-negative bacteria from the Bacteroidota phylum possess a type-IX secretion system (T9SS) for protein secretion, which requires cargoes to have a C-terminal domain (CTD). Structurally analysed CTDs are from Porphyromonas gingivalis proteins RgpB, HBP35, PorU and PorZ, which share a compact immunoglobulin-like antiparallel 3+4 β-sandwich (β1-β7). This architecture is essential as a P. gingivalis strain with a single-point mutant of RgpB disrupting the interaction of the CTD with its preceding domain prevented secretion of the protein. Next, we identified the C-terminus ('motif C-t.') and the loop connecting strands β3 and β4 ('motif Lβ3β4') as conserved. We generated two strains with insertion and replacement mutants of PorU, as well as three strains with ablation and point mutants of RgpB, which revealed both motifs to be relevant for T9SS function. Furthermore, we determined the crystal structure of the CTD of mirolase, a cargo of the Tannerella forsythia T9SS, which shares the same general topology as in Porphyromonas CTDs. However, motif Lβ3β4 was not conserved. Consistently, P. gingivalis could not properly secrete a chimaeric protein with the CTD of peptidylarginine deiminase replaced with this foreign CTD. Thus, the incompatibility of the CTDs between these species prevents potential interference between their T9SSs.
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Affiliation(s)
- Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Arturo Rodríguez-Banqueri
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Catalonia 08028, Spain
| | - Florian Veillard
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Mirosław Książęk
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Theodoros Goulas
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Thessaly, Karditsa 43100, Greece
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Catalonia 08028, Spain
| | - Ulrich Eckhard
- Synthetic Structural Biology Group, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Catalonia 08028, Spain
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY 40202, USA
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Catalonia 08028, Spain
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12
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Saran A, Kim HM, Manning I, Hancock MA, Schmitz C, Madej M, Potempa J, Sola M, Trempe JF, Zhu Y, Davey ME, Zeytuni N. Unveiling the Molecular Mechanisms of the Type-IX Secretion System's Response Regulator: Structural and Functional Insights. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594396. [PMID: 38798656 PMCID: PMC11118453 DOI: 10.1101/2024.05.15.594396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The Type-IX secretion system (T9SS) is a nanomachinery utilized by bacterial pathogens to facilitate infection. The system is regulated by a signaling cascade serving as its activation switch. A pivotal member in this cascade, the response regulator protein PorX, represents a promising drug target to prevent the secretion of virulence factors. Here, we provide a comprehensive characterization of PorX both in vitro and in vivo . First, our structural studies revealed PorX harbours a unique enzymatic effector domain, which, surprisingly, shares structural similarities with the alkaline phosphatase superfamily, involved in nucleotide and lipid signaling pathways. Importantly, such pathways have not been associated with the T9SS until now. Enzymatic characterization of PorX's effector domain revealed a zinc-dependent phosphodiesterase activity, with active site dimensions suitable to accommodate a large substrate. Unlike typical response regulators that dimerize via their receiver domain upon phosphorylation, we found that zinc can also induce conformational changes and promote PorX's dimerization via an unexpected interface. These findings suggest that PorX can serve as a cellular zinc sensor, broadening our understanding of its regulatory mechanisms. Despite the strict conservation of PorX in T9SS-utilizing bacteria, we demonstrate that PorX is essential for virulence factors secretion in Porphyromonas gingivalis and affects metabolic enzymes secretion in the non-pathogenic Flavobacterium johnsoniae , but not for the secretion of gliding adhesins. Overall, this study advances our structural and functional understanding of PorX, highlighting its potential as a druggable target for intervention strategies aimed at disrupting the T9SS and mitigating virulence in pathogenic species.
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13
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Miranda-López DC, Pérez-Rueda E, Rojas-Vargas J, Cortez CH, Saldaña-Padilla A, Castelán-Sánchez HG, Castro-Escarpulli G. Comprehensive comparative analysis of the periodontal pathogen Porphyromonas gingivalis: exploring the pan-genome, the reconstruction of the gene regulatory network and genome-scale metabolic network. Lett Appl Microbiol 2024; 77:ovae048. [PMID: 38769598 DOI: 10.1093/lambio/ovae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/23/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Porphyromonas gingivalis is a nonmotile, obligate anaerobic, Gram-negative bacterium known for its association with periodontal disease and its involvement in systemic diseases such as atherosclerosis, cardiovascular disease, colon cancer, and Alzheimer's disease. This bacterium produces several virulence factors, including capsules, fimbriae, lipopolysaccharides, proteolytic enzymes, and hemagglutinins. A comparative genomic analysis revealed the open pangenome of P. gingivalis and identified complete type IV secretion systems in strain KCOM2805 and almost complete type VI secretion systems in strains KCOM2798 and ATCC49417, which is a new discovery as previous studies did not find the proteins involved in secretion systems IV and VI. Conservation of some virulence factors between different strains was observed, regardless of their genetic diversity and origin. In addition, we performed for the first time a reconstruction analysis of the gene regulatory network, identifying transcription factors and proteins involved in the regulatory mechanisms of bacterial pathogenesis. In particular, QseB regulates the expression of hemagglutinin and arginine deaminase, while Rex may suppress the release of gingipain through interactions with PorV and the formatum/nitrate transporter. Our study highlights the central role of conserved virulence factors and regulatory pathways, particularly QseB and Rex, in P. gingivalis and provides insights into potential therapeutic targets.
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Affiliation(s)
- Diana C Miranda-López
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, México
| | - Ernesto Pérez-Rueda
- Unidad Académica del Estado de Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mérida 97357, México
| | - Jorge Rojas-Vargas
- Department of Biology, University of Western, London, Ontario N6A 3K7, Canada
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western, London, Ontario N6A 3K7, Canada
| | - Cecilia Hernández Cortez
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, México
| | - Andres Saldaña-Padilla
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, México
| | - Hugo G Castelán-Sánchez
- Programa de Investigadoras e Investigadores por México. Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Humanidades, Ciencias y Tecnologías, Ciudad de México 03940, México
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario N6A 3K7, Canada
| | - Graciela Castro-Escarpulli
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, México
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14
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Hao MS, Mazurkewich S, Li H, Kvammen A, Saha S, Koskela S, Inman AR, Nakajima M, Tanaka N, Nakai H, Brändén G, Bulone V, Larsbrink J, McKee LS. Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to β-glucans. Nat Commun 2024; 15:3429. [PMID: 38653764 PMCID: PMC11039641 DOI: 10.1038/s41467-024-47584-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Carbohydrate-binding modules (CBMs) are non-catalytic proteins found appended to carbohydrate-active enzymes. Soil and marine bacteria secrete such enzymes to scavenge nutrition, and they often use CBMs to improve reaction rates and retention of released sugars. Here we present a structural and functional analysis of the recently established CBM family 92. All proteins analysed bind preferentially to β-1,6-glucans. This contrasts with the diversity of predicted substrates among the enzymes attached to CBM92 domains. We present crystal structures for two proteins, and confirm by mutagenesis that tryptophan residues permit ligand binding at three distinct functional binding sites on each protein. Multivalent CBM families are uncommon, so the establishment and structural characterisation of CBM92 enriches the classification database and will facilitate functional prediction in future projects. We propose that CBM92 proteins may cross-link polysaccharides in nature, and might have use in novel strategies for enzyme immobilisation.
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Affiliation(s)
- Meng-Shu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Scott Mazurkewich
- Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden
| | - He Li
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Alma Kvammen
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Srijani Saha
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Salla Koskela
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Nobukiyo Tanaka
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Hiroyuki Nakai
- Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
- College of Medicine and Public Health, Flinders University, Bedford Park Campus, Sturt Road, SA, 5042, Australia
| | - Johan Larsbrink
- Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden.
- Wallenberg Wood Science Center, Teknikringen 56-58, 10044, Stockholm, Sweden.
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15
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Lauber F, Deme JC, Liu X, Kjær A, Miller HL, Alcock F, Lea SM, Berks BC. Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon. Nat Microbiol 2024; 9:1089-1102. [PMID: 38538833 PMCID: PMC10994853 DOI: 10.1038/s41564-024-01644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/19/2024] [Indexed: 04/06/2024]
Abstract
Secretion systems are protein export machines that enable bacteria to exploit their environment through the release of protein effectors. The Type 9 Secretion System (T9SS) is responsible for protein export across the outer membrane (OM) of bacteria of the phylum Bacteroidota. Here we trap the T9SS of Flavobacterium johnsoniae in the process of substrate transport by disrupting the T9SS motor complex. Cryo-EM analysis of purified substrate-bound T9SS translocons reveals an extended translocon structure in which the previously described translocon core is augmented by a periplasmic structure incorporating the proteins SprE, PorD and a homologue of the canonical periplasmic chaperone Skp. Substrate proteins bind to the extracellular loops of a carrier protein within the translocon pore. As transport intermediates accumulate on the translocon when energetic input is removed, we deduce that release of the substrate-carrier protein complex from the translocon is the energy-requiring step in T9SS transport.
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Affiliation(s)
- Frédéric Lauber
- Department of Biochemistry, University of Oxford, Oxford, UK
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK
| | - Xiaolong Liu
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andreas Kjær
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Helen L Miller
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK
- Newcastle University Biosciences Institute, Newcastle University, Newcastle, UK
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK.
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK.
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16
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Michnik ML, Semple SL, Joshi RN, Whittaker P, Barreda DR. The use of salmonid epithelial cells to characterize the toxicity of Tenacibaculum maritimum soluble extracellular products. J Appl Microbiol 2024; 135:lxae049. [PMID: 38409849 DOI: 10.1093/jambio/lxae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/07/2024] [Accepted: 02/24/2024] [Indexed: 02/28/2024]
Abstract
AIMS This study assessed how the etiological agent of mouth rot in farmed Atlantic salmon, Tenacibaculum maritimum, induces toxicity in host salmonid barrier cells, and determined whether environmental changes are relevant for these effects. METHODS AND RESULTS Tenacibaculum maritimum soluble extracellular products (ECPs) were collected and used to treat Atlantic salmon and rainbow trout intestinal barrier cell lines as a comparative model of bacterial-salmonid cell interactions. Cellular assays that examine cell membrane integrity, marker expression, and metabolic activity revealed that T. maritimum ECPs induced salmonid epithelial cell death through an apoptosis mechanism. Changes in salinity (25, 29, and 33 ppt) and temperature (12°C, 18°C, and 24°C) within the natural ranges observed in Pacific Northwest aquaculture facilities affected bacterial growth and cytotoxicity of T. maritimum ECPs. CONCLUSIONS Our results suggest epithelial barriers as targets of T. maritimum-mediated toxicity in farmed mouth rot-infected Atlantic salmon. The induction of apoptosis by T. maritimum soluble ECPs may also help to explain the absence of overt inflammation typically reported for these fish.
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Affiliation(s)
- Matthew L Michnik
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Shawna L Semple
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Reema N Joshi
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Patrick Whittaker
- Grieg Seafood BC Ltd, Campbell River, British Columbia, V9W 5P7, Canada
| | - Daniel R Barreda
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
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17
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Doi K, Mitani A, Nakakita SI, Higuchi Y, Takegawa K. Characterization of novel endo-β-N-acetylglucosaminidases from intestinal Barnesiella intestinihominis that hydrolyze multi-branched complex-type N-glycans. J Biosci Bioeng 2024; 137:101-107. [PMID: 38142217 DOI: 10.1016/j.jbiosc.2023.12.004] [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: 09/06/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/25/2023]
Abstract
Endo-β-N-acetylglucosaminidases (ENGases) are enzymes that hydrolyze N-linked glycans. Many ENGases have been characterized, but few have been identified with hydrolytic activity towards multi-branched complex-type N-glycans. In this study, three candidate ENGases were identified from Barnesiella intestinihominis based on database searches and phylogenetic analysis. A domain search identified the N x E motif in all three candidates, suggesting that they were members of glycosyl hydrolase family 85 (GH85). The three candidate ENGases, named Endo-BIN1, Endo-BIN2, and Endo-BIN3, were expressed in Escherichia coli cells, and their hydrolytic activity towards N-glycans and glycoproteins was measured by high performance liquid chromatography analysis and SDS-PAGE analysis. All ENGases showed hydrolytic activity towards glycoproteins, but only Endo-BIN2 and Endo-BIN3 showed hydrolytic activity towards pyridylaminated N-glycans. The optimum pH of Endo-BIN1, Endo-BIN2, and End-BIN3 was pH 6.5, 4.0, and 7.0, respectively. We measured substrate specificities of Endo-BIN2 and Endo-BIN3 towards pyridylaminated N-glycans, and found that the two Endo-BIN enzymes showed similar substrate specificity, preferring bi-antennary complex-type N-glycans with galactose or α2,6-linked sialic acid residues at the non-reducing ends. Endo-BIN2 and Endo-BIN3 were also able to hydrolyze multi-branched complex-type N-glycans. SDS-PAGE analysis revealed that all Endo-BIN enzymes were capable of releasing complex-type N-glycans from glycoproteins such as rituximab, transferrin, and fetuin. We expect that B. intestinihominis possesses ENGases to facilitate the utilization of complex-type N-glycans from host cells. These findings will have applications in N-glycan remodeling of glycoproteins and the development of pharmaceuticals.
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Affiliation(s)
- Kanako Doi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ai Mitani
- Fushimi Pharmaceutical Co. Ltd., Marugame, Kagawa 763-8605, Japan
| | | | - Yujiro Higuchi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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18
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Abby SS, Denise R, Rocha EPC. Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder Version 2. Methods Mol Biol 2024; 2715:1-25. [PMID: 37930518 DOI: 10.1007/978-1-0716-3445-5_1] [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] [Indexed: 11/07/2023]
Abstract
Protein secretion systems are complex molecular machineries that translocate proteins through the outer membrane and sometimes through multiple other barriers. They have evolved by co-option of components from other envelope-associated cellular machineries, making them sometimes difficult to identify and discriminate. Here, we describe how to identify protein secretion systems in bacterial genomes using the MacSyFinder program. This flexible computational tool uses the knowledge gathered from experimental studies to identify homologous systems in genome data. It can be used with a set of predefined MacSyFinder models, "TXSScan," to identify all major secretion systems of diderm bacteria (i.e., with inner and LPS-containing outer membranes) as well as evolutionarily related cell appendages (pili and flagella). For this, it identifies and clusters co-localized genes encoding proteins of secretion systems using sequence similarity search with Hidden Markov Model (HMM) protein profiles. Finally, it checks if the clusters' genetic content and genomic organization satisfy the constraints of the model. TXSScan models can be altered in the command line or customized to search for variants of known secretion systems. Models can also be built from scratch to identify novel systems. In this chapter, we describe a complete pipeline of analysis, starting from (i) the integration of information from a reference set of experimentally studied systems, (ii) the identification of conserved proteins and the construction of their HMM protein profiles, (iii) the definition and optimization of "macsy-models," and (iv) their use and online distribution as tools to search genomic data for secretion systems of interest. MacSyFinder is available here: https://github.com/gem-pasteur/macsyfinder, and MacSyFinder models here: https://github.com/macsy-models .
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Affiliation(s)
- Sophie S Abby
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble, France.
| | - Rémi Denise
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
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19
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Richter I, Uzum Z, Wein P, Molloy EM, Moebius N, Stinear TP, Pidot SJ, Hertweck C. Transcription activator-like effectors from endosymbiotic bacteria control the reproduction of their fungal host. mBio 2023; 14:e0182423. [PMID: 37971247 PMCID: PMC10746252 DOI: 10.1128/mbio.01824-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Interactions between fungi and bacteria are critically important in ecology, medicine, and biotechnology. In this study, we shed light on factors that promote the persistence of a toxin-producing, phytopathogenic Rhizopus-Mycetohabitans symbiosis that causes severe crop losses in Asia. We present an unprecedented case where bacterially produced transcription activator-like (TAL) effectors are key to maintaining a stable endosymbiosis. In their absence, fungal sporulation is abrogated, leading to collapse of the phytopathogenic alliance. The Mycetohabitans TAL (MTAL)-mediated mechanism of host control illustrates a unique role of bacterial effector molecules that has broader implications, potentially serving as a model to understand how prokaryotic symbionts interact with their eukaryotic hosts.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Evelyn M. Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Nadine Moebius
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute, Melbourne, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute, Melbourne, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
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20
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Sahoo A, Vivek-Ananth RP, Chivukula N, Rajaram SV, Mohanraj K, Khare D, Acharya C, Samal A. T9GPred: A Comprehensive Computational Tool for the Prediction of Type 9 Secretion System, Gliding Motility, and the Associated Secreted Proteins. ACS OMEGA 2023; 8:34091-34102. [PMID: 37744817 PMCID: PMC10515386 DOI: 10.1021/acsomega.3c05155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023]
Abstract
Type 9 secretion system (T9SS) is one of the least characterized secretion systems exclusively found in the Bacteroidetes phylum, which comprises various environmental and economically relevant bacteria. While T9SS plays a central role in bacterial movement termed gliding motility, survival, and pathogenicity, there is an unmet need for a comprehensive tool that predicts T9SS, gliding motility, and proteins secreted via T9SS. In this study, we develop such a computational tool, Type 9 secretion system and Gliding motility Prediction (T9GPred). To build this tool, we manually curated published experimental evidence and identified mandatory components for T9SS and gliding motility prediction. We also compiled experimentally characterized proteins secreted via T9SS and determined the presence of three unique types of C-terminal domain signals, and these insights were leveraged to predict proteins secreted via T9SS. Notably, using recently published experimental evidence, we show that T9GPred has high predictive power. Thus, we used T9GPred to predict the presence of T9SS, gliding motility, and associated secreted proteins across 693 completely sequenced Bacteroidetes strains. T9GPred predicted 402 strains to have T9SS, of which 327 strains are also predicted to exhibit gliding motility. Further, T9GPred also predicted putative secreted proteins for the 402 strains. In a nutshell, T9GPred is a novel computational tool for systems-level prediction of T9SS and streamlining future experimentation. The source code of the computational tool is available in our GitHub repository: https://github.com/asamallab/T9GPred. The tool and its predicted results are compiled in a web server available at: https://cb.imsc.res.in/t9gpred/.
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Affiliation(s)
- Ajaya
Kumar Sahoo
- The
Institute of Mathematical Sciences (IMSc), Chennai 600113, India
- Homi
Bhabha National Institute (HBNI), Mumbai 400094, India
| | - R. P. Vivek-Ananth
- The
Institute of Mathematical Sciences (IMSc), Chennai 600113, India
- Homi
Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Nikhil Chivukula
- The
Institute of Mathematical Sciences (IMSc), Chennai 600113, India
- Homi
Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Shri Vishalini Rajaram
- The
Institute of Mathematical Sciences (IMSc), Chennai 600113, India
- Centre
for Biotechnology, Anna University, Chennai 600025, India
| | - Karthikeyan Mohanraj
- Institute
for Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Dresden 01307, Germany
| | - Devanshi Khare
- Molecular
Biology Division, Bhabha Atomic Research
Centre, Mumbai 400085, India
- Homi
Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Celin Acharya
- Molecular
Biology Division, Bhabha Atomic Research
Centre, Mumbai 400085, India
- Homi
Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Areejit Samal
- The
Institute of Mathematical Sciences (IMSc), Chennai 600113, India
- Homi
Bhabha National Institute (HBNI), Mumbai 400094, India
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21
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Li H, Lu Z, Hao MS, Kvammen A, Inman AR, Srivastava V, Bulone V, McKee LS. Family 92 carbohydrate-binding modules specific for β-1,6-glucans increase the thermostability of a bacterial chitinase. Biochimie 2023; 212:153-160. [PMID: 37121306 DOI: 10.1016/j.biochi.2023.04.019] [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: 02/15/2023] [Revised: 03/30/2023] [Accepted: 04/28/2023] [Indexed: 05/02/2023]
Abstract
In biomass-processing industries there is a need for enzymes that can withstand high temperatures. Extensive research efforts have been dedicated to finding new thermostable enzymes as well as developing new means of stabilising existing enzymes. The attachment of a stable non-catalytic domain to an enzyme can, in some instances, protect a biocatalyst from thermal denaturation. Carbohydrate-binding modules (CBMs) are non-catalytic domains typically found appended to biomass-degrading or modifying enzymes, such as glycoside hydrolases (GHs). Most often, CBMs interact with the same polysaccharide as their enzyme partners, leading to an enhanced reaction rate via the promotion of enzyme-substrate interactions. Contradictory to this general concept, we show an example of a chitin-degrading enzyme from GH family 18 that is appended to two CBM domains from family 92, both of which bind preferentially to the non-substrate polysaccharide β-1,6-glucan. During chitin hydrolysis, the CBMs do not contribute to enzyme-substrate interactions but instead confer a 10-15 °C increase in enzyme thermal stability. We propose that CBM92 domains may have a natural enzyme stabilisation role in some cases, which may be relevant to enzyme design for high-temperature applications in biorefinery.
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Affiliation(s)
- He Li
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Zijia Lu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Meng-Shu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Alma Kvammen
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden; College of Medicine & Public Health, Flinders University, Bedford Park Campus, Sturt Road, SA, 5042, Australia
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91, Stockholm, Sweden; Wallenberg Wood Science Center, Teknikringen 56-58, 100 44, Stockholm, Sweden.
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22
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Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol 2023; 31:959-971. [PMID: 37173204 DOI: 10.1016/j.tim.2023.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023]
Abstract
Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.
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Affiliation(s)
- Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain; Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Málaga, Spain.
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23
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Costeira R, Aduse-Opoku J, Vernon JJ, Rodriguez-Algarra F, Joseph S, Devine DA, Marsh PD, Rakyan V, Curtis MA, Bell JT. Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis. mSystems 2023; 8:e0119322. [PMID: 37436062 PMCID: PMC10470040 DOI: 10.1128/msystems.01193-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/12/2023] [Indexed: 07/13/2023] Open
Abstract
Periodontal disease is a chronic inflammatory disease in which the oral pathogen Porphyromonas gingivalis plays an important role. Porphyromonas gingivalis expresses virulence determinants in response to higher hemin concentrations, but the underlying regulatory processes remain unclear. Bacterial DNA methylation has the potential to fulfil this mechanistic role. We characterized the methylome of P. gingivalis, and compared its variation to transcriptome changes in response to hemin availability. Porphyromonas gingivalis W50 was grown in chemostat continuous culture with excess or limited hemin, prior to whole-methylome and transcriptome profiling using Nanopore and Illumina RNA-Seq. DNA methylation was quantified for Dam/Dcm motifs and all-context N6-methyladenine (6mA) and 5-methylcytosine (5mC). Of all 1,992 genes analyzed, 161 and 268 were respectively over- and under-expressed with excess hemin. Notably, we detected differential DNA methylation signatures for the Dam "GATC" motif and both all-context 6mA and 5mC in response to hemin availability. Joint analyses identified a subset of coordinated changes in gene expression, 6mA, and 5mC methylation that target genes involved in lactate utilization and ABC transporters. The results identify altered methylation and expression responses to hemin availability in P. gingivalis, with insights into mechanisms regulating its virulence in periodontal disease. IMPORTANCE DNA methylation has important roles in bacteria, including in the regulation of transcription. Porphyromonas gingivalis, an oral pathogen in periodontitis, exhibits well-established gene expression changes in response to hemin availability. However, the regulatory processes underlying these effects remain unknown. We profiled the novel P. gingivalis epigenome, and assessed epigenetic and transcriptome variation under limited and excess hemin conditions. As expected, multiple gene expression changes were detected in response to limited and excess hemin that reflect health and disease, respectively. Notably, we also detected differential DNA methylation signatures for the Dam "GATC" motif and both all-context 6mA and 5mC in response to hemin. Joint analyses identified coordinated changes in gene expression, 6mA, and 5mC methylation that target genes involved in lactate utilization and ABC transporters. The results identify novel regulatory processes underlying the mechanism of hemin regulated gene expression in P. gingivalis, with phenotypic impacts on its virulence in periodontal disease.
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Affiliation(s)
- Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Joseph Aduse-Opoku
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Jon J. Vernon
- Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | - Francisco Rodriguez-Algarra
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Susan Joseph
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Deirdre A. Devine
- Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | - Philip D. Marsh
- Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, United Kingdom
| | - Vardhman Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Michael A. Curtis
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, United Kingdom
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
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24
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Lu Z, Kvammen A, Li H, Hao M, Inman AR, Bulone V, McKee LS. A polysaccharide utilization locus from Chitinophaga pinensis simultaneously targets chitin and β-glucans found in fungal cell walls. mSphere 2023; 8:e0024423. [PMID: 37493618 PMCID: PMC10449523 DOI: 10.1128/msphere.00244-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/06/2023] [Indexed: 07/27/2023] Open
Abstract
In nature, complex carbohydrates are rarely found as pure isolated polysaccharides. Instead, bacteria in competitive environments are presented with glycans embedded in heterogeneous matrices such as plant or microbial cell walls. Members of the Bacteroidota phylum thrive in such ecosystems because they are efficient at extracting nutrients from complex substrates, secreting consortia of synergistic enzymes to release metabolizable sugars. Carbohydrate-binding modules (CBMs) are used to target enzymes to substrates, enhancing reaction rate and product release. Additionally, genome organizational tools like polysaccharide utilization loci (PULs) ensure that the appropriate set of enzymes is produced when needed. In this study, we show that the soil bacterium Chitinophaga pinensis uses a PUL and several CBMs to coordinate the activities of enzymes targeting two distinct polysaccharides found in fungal cell walls. We describe the enzymatic activities and carbohydrate-binding behaviors of components of the fungal cell wall utilization locus (FCWUL), which uses multiple chitinases and one β-1,3-glucanase to hydrolyze two different substrates. Unusually, one of the chitinases is appended to a β-glucan-binding CBM, implying targeting to a bulk cell wall substrate rather than to the specific polysaccharide being hydrolyzed. Based on our characterization of the PUL's outer membrane sensor protein, we suggest that the FCWUL is activated by β-1,3-glucans, even though most of its enzymes are chitin-degrading. Our data showcase the complexity of polysaccharide deconstruction in nature and highlight an elegant solution for how multiple different glycans can be accessed using one enzymatic cascade. IMPORTANCE We report that the genome of the soil bacterium Chitinophaga pinensis encodes three multi-modular carbohydrate-active enzymes that work together to hydrolyze the major polysaccharide components found in fungal cell walls (FCWs). The enzymes are all encoded by one polysaccharide utilization locus and are co-expressed, potentially induced in the presence of β-1,3-glucans. We present biochemical characterization of each enzyme, including the appended carbohydrate-binding modules that likely tether the enzymes to a FCW substrate. Finally, we propose a model for how this so-called fungal cell wall utilization locus might enable C. pinensis to metabolize both chitin and β-1,3-glucans found in complex biomass in the soil.
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Affiliation(s)
- Zijia Lu
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alma Kvammen
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - He Li
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mengshu Hao
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Annie R. Inman
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vincent Bulone
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Lauren S. McKee
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, Stockholm, Sweden
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25
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Brown HA, DeVeaux AL, Juliano BR, Photenhauer AL, Boulinguiez M, Bornschein RE, Wawrzak Z, Ruotolo BT, Terrapon N, Koropatkin NM. BoGH13A Sus from Bacteroides ovatus represents a novel α-amylase used for Bacteroides starch breakdown in the human gut. Cell Mol Life Sci 2023; 80:232. [PMID: 37500984 PMCID: PMC10540511 DOI: 10.1007/s00018-023-04812-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 07/29/2023]
Abstract
Members of the Bacteroidetes phylum in the human colon deploy an extensive number of proteins to capture and degrade polysaccharides. Operons devoted to glycan breakdown and uptake are termed polysaccharide utilization loci or PUL. The starch utilization system (Sus) is one such PUL and was initially described in Bacteroides thetaiotaomicron (Bt). BtSus is highly conserved across many species, except for its extracellular α-amylase, SusG. In this work, we show that the Bacteroides ovatus (Bo) extracellular α-amylase, BoGH13ASus, is distinguished from SusG in its evolutionary origin and its domain architecture and by being the most prevalent form in Bacteroidetes Sus. BoGH13ASus is the founding member of both a novel subfamily in the glycoside hydrolase family 13, GH13_47, and a novel carbohydrate-binding module, CBM98. The BoGH13ASus CBM98-CBM48-GH13_47 architecture differs from the CBM58 embedded within the GH13_36 of SusG. These domains adopt a distinct spatial orientation and invoke a different association with the outer membrane. The BoCBM98 binding site is required for Bo growth on polysaccharides and optimal enzymatic degradation thereof. Finally, the BoGH13ASus structure features bound Ca2+ and Mn2+ ions, the latter of which is novel for an α-amylase. Little is known about the impact of Mn2+ on gut bacterial function, much less on polysaccharide consumption, but Mn2+ addition to Bt expressing BoGH13ASus specifically enhances growth on starch. Further understanding of bacterial starch degradation signatures will enable more tailored prebiotic and pharmaceutical approaches that increase starch flux to the gut.
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Affiliation(s)
- Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Anna L DeVeaux
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Amanda L Photenhauer
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Matthieu Boulinguiez
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS AMU; USC1408 INRAE, 13288, Marseille, France
| | | | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Lemont, IL, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS AMU; USC1408 INRAE, 13288, Marseille, France
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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26
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Morales-Olavarría M, Nuñez-Belmar J, González D, Vicencio E, Rivas-Pardo JA, Cortez C, Cárdenas JP. Phylogenomic analysis of the Porphyromonas gingivalis - Porphyromonas gulae duo: approaches to the origin of periodontitis. Front Microbiol 2023; 14:1226166. [PMID: 37538845 PMCID: PMC10394638 DOI: 10.3389/fmicb.2023.1226166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
Porphyromonas gingivalis is an oral human pathogen associated with the onset and progression of periodontitis, a chronic immune-inflammatory disease characterized by the destruction of the teeth-supporting tissue. P. gingivalis belongs to the genus Porphyromonas, which is characterized by being composed of Gram-negative, asaccharolytic, non-spore-forming, non-motile, obligatory anaerobic species, inhabiting niches such as the oral cavity, urogenital tract, gastrointestinal tract and infected wound from different mammals including humans. Among the Porphyromonas genus, P. gingivalis stands out for its specificity in colonizing the human oral cavity and its keystone pathogen role in periodontitis pathogenesis. To understand the evolutionary process behind P. gingivalis in the context of the Pophyoromonas genus, in this study, we performed a comparative genomics study with publicly available Porphyromonas genomes, focused on four main objectives: (A) to confirm the phylogenetic position of P. gingivalis in the Porphyromonas genus by phylogenomic analysis; (B) the definition and comparison of the pangenomes of P. gingivalis and its relative P. gulae; and (C) the evaluation of the gene family gain/loss events during the divergence of P. gingivalis and P. gulae; (D) the evaluation of the evolutionary pressure (represented by the calculation of Tajima-D values and dN/dS ratios) comparing gene families of P. gingivalis and P. gulae. Our analysis found 84 high-quality assemblies representing P. gingivalis and 14 P. gulae strains (from a total of 233 Porphyromonas genomes). Phylogenomic analysis confirmed that P. gingivalis and P. gulae are highly related lineages, close to P. loveana. Both organisms harbored open pangenomes, with a strong core-to-accessory ratio for housekeeping genes and a negative ratio for unknown function genes. Our analyses also characterized the gene set differentiating P. gulae from P. gingivalis, mainly associated with unknown functions. Relevant virulence factors, such as the FimA, Mfa1, and the hemagglutinins, are conserved in P. gulae, P. gingivalis, and P. loveana, suggesting that the origin of those factors occurred previous to the P. gulae - P. gingivalis divergence. These results suggest an unexpected evolutionary relationship between the P. gulae - P. gingivalis duo and P. loveana, showing more clues about the origin of the role of those organisms in periodontitis.
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Affiliation(s)
- Mauricio Morales-Olavarría
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Josefa Nuñez-Belmar
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Dámariz González
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Emiliano Vicencio
- Escuela de Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jaime Andres Rivas-Pardo
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Cristian Cortez
- Escuela de Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Juan P. Cárdenas
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
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27
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Rocha ST, Shah DD, Zhu Q, Shrivastava A. The prevalence of motility within the human oral microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549387. [PMID: 37503047 PMCID: PMC10370060 DOI: 10.1101/2023.07.17.549387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The human oral and nasal microbiota contains approximately 770 cultivable bacterial species. More than 2000 genome sequences of these bacteria can be found in the expanded Human Oral Microbiome Database (eHOMD). We developed HOMDscrape, a freely available Python software tool to programmatically retrieve and process amino acid sequences and sequence identifiers from BLAST results acquired from the eHOMD website. Using the data obtained through HOMDscrape, the phylogeny of proteins involved in bacterial flagellar motility, Type 4 pilus driven twitching motility, and Type 9 Secretion system (T9SS) driven gliding motility was constructed. A comprehensive phylogenetic analysis was conducted for all components of the rotary T9SS, a machinery responsible for secreting various enzymes, virulence factors, and enabling bacterial gliding motility. Results revealed that the T9SS outer membrane ß-barrel protein SprA of human oral microbes underwent horizontal evolution. Overall, we catalog motile microbes that inhabit the human oral microbiota and document their evolutionary connections. These results will serve as a guide for further studies exploring the impact of motility on shaping of the human oral microbiota.
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28
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Treerat P, Anderson D, Giacaman RA, Merritt J, Kreth J. Glycerol metabolism supports oral commensal interactions. THE ISME JOURNAL 2023; 17:1116-1127. [PMID: 37169870 PMCID: PMC10284889 DOI: 10.1038/s41396-023-01426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
During oral biofilm development, interspecies interactions drive species distribution and biofilm architecture. To understand what molecular mechanisms determine these interactions, we used information gained from recent biogeographical investigations demonstrating an association of corynebacteria with streptococci. We previously reported that Streptococcus sanguinis and Corynebacterium durum have a close relationship through the production of membrane vesicle and fatty acids leading to S. sanguinis chain elongation and overall increased fitness supporting their commensal state. Here we present the molecular mechanisms of this interspecies interaction. Coculture experiments for transcriptomic analysis identified several differentially expressed genes in S. sanguinis. Due to its connection to fatty acid synthesis, we focused on the glycerol-operon. We further explored the differentially expressed type IV pili genes due to their connection to motility and biofilm adhesion. Gene inactivation of the glycerol kinase glpK had a profound impact on the ability of S. sanguinis to metabolize C. durum secreted glycerol and impaired chain elongation important for their interaction. Investigations on the effect of type IV pili revealed a reduction of S. sanguinis twitching motility in the presence of C. durum, which was caused by a decrease in type IV pili abundance on the surface of S. sanguinis as determined by SEM. In conclusion, we identified that the ability to metabolize C. durum produced glycerol is crucial for the interaction of C. durum and S. sanguinis. Reduced twitching motility could lead to a closer interaction of both species, supporting niche development in the oral cavity and potentially shaping symbiotic health-associated biofilm communities.
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Affiliation(s)
- Puthayalai Treerat
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA.
| | - David Anderson
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
| | - Rodrigo A Giacaman
- Cariology Unit, Department of Oral Rehabilitation, Faculty of Dentistry, University of Talca, Talca, Chile
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA.
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Qin Z, Yu S, Zhang K, Wei X, Li J, Zhang Z, Wan S, Gao H. Characterization of a Glycoside Hydrolase Family 157 Endo-β-1,3-Glucanase That Displays Antifungal Activity against Phytopathogens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37376774 DOI: 10.1021/acs.jafc.3c02083] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
β-1,3-Glucan-degrading enzymes are widely used in fields such as food processing, plant protection, and breweries. In this work, we identified a glycoside hydrolase (GH) family 157 endo-β-1,3-glucanase (BsGlc157A) from Bacteroides sp. M27 and characterized its biochemical properties, structural model, and antifungal activity. Enzymological characterization indicated that BsGlc157A performs its optimal catalytic activity at pH 6.0 and 40 °C. BsGlc157A adopted the classic (β/α)8 TIM-barrel structure. Two catalytic residues, the nucleophile (Glu215) and the proton donor (Glu123), were confirmed via structural modeling and site-directed mutagenesis. Moreover, BsGlc157A hydrolyzed curdlan into a series of oligosaccharides with polymerization degrees 2-5 and exhibited inhibitory effects on the hyphal growth of typical fruit pathogenic fungi (Monilinia fructicola, Alternaria alternata, and Colletotrichum gloeosporioides), thereby illustrating effective biocontrol activity. These results revealed the catalytic properties and the application potential of GH family 157 β-1,3-glucanase, thus providing valuable biochemistry information about the group of carbohydrate-active enzymes.
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Affiliation(s)
- Zhen Qin
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Sainan Yu
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Kemin Zhang
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Xiasen Wei
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Junjie Li
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Zheyi Zhang
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Sibao Wan
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Haiyan Gao
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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Shen Y, Gao S, Fan Q, Zuo J, Wang Y, Yi L, Wang Y. New antibacterial targets: Regulation of quorum sensing and secretory systems in zoonotic bacteria. Microbiol Res 2023; 274:127436. [PMID: 37343493 DOI: 10.1016/j.micres.2023.127436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023]
Abstract
Quorum sensing (QS) is a communication mechanism that controls bacterial communication and can influence the transcriptional expression of multiple genes through one or more signaling molecules, thereby coordinating the population response of multiple bacterial pathogens. Secretion systems (SS) play an equally important role in bacterial information exchange, relying on the secretory systems to secrete proteins that act as virulence factors to promote adhesion to host cells. Eight highly efficient SS have been described, all of which are involved in the secretion or transfer of virulence factors, and the effector proteins they secrete play a key role in the virulence and pathogenicity of bacteria. It has been shown that many bacterial SS are directly or indirectly regulated by QS and thus influence bacterial virulence and antibiotic resistance. This review describes the relationship between QS and SS of several common zoonotic pathogenic bacteria and outlines the molecular mechanisms of how QS systems regulate SS, to provide a theoretical basis for the study of bacterial pathogenicity and the development of novel antibacterial drugs.
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Affiliation(s)
- Yamin Shen
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China
| | - Shuji Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Qingying Fan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China
| | - Jing Zuo
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China
| | - Yuxin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China
| | - Li Yi
- Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China; College of Life Science, Luoyang Normal University, Luoyang, China.
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China.
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Wang G, Yin X, Feng Z, Chen C, Chen D, Wu B, Liu C, Morel JL, Jiang Y, Yu H, He H, Chao Y, Tang Y, Qiu R, Wang S. Novel biological aqua crust enhances in situ metal(loid) bioremediation driven by phototrophic/diazotrophic biofilm. MICROBIOME 2023; 11:110. [PMID: 37202810 DOI: 10.1186/s40168-023-01549-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/13/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Understanding the ecological and environmental functions of phototrophic biofilms in the biological crust is crucial for improving metal(loid) (e.g. Cd, As) bioremediation in mining ecosystems. In this study, in combination with metal(loid) monitoring and metagenomic analysis, we systematically evaluated the effect of biofilm in a novel biological aqua crust (biogenic aqua crust-BAC) on in situ metal(loid) bioremediation of a representative Pb/Zn tailing pond. RESULTS We observed strong accumulation of potentially bioavailable metal(loid)s and visible phototrophic biofilms in the BAC. Furthermore, dominating taxa Leptolyngbyaceae (10.2-10.4%, Cyanobacteria) and Cytophagales (12.3-22.1%, Bacteroidota) were enriched in biofilm. Along with predominant heterotrophs (e.g. Cytophagales sp.) as well as diazotrophs (e.g. Hyphomonadaceae sp.), autotrophs/diazotrophs (e.g. Leptolyngbyaceae sp.) in phototrophic biofilm enriched the genes encoding extracellular peptidase (e.g. family S9, S1), CAZymes (e.g. CBM50, GT2) and biofilm formation (e.g. OmpR, CRP and LuxS), thus enhancing the capacity of nutrient accumulation and metal(loid) bioremediation in BAC system. CONCLUSIONS Our study demonstrated that a phototrophic/diazotrophic biofilm constitutes the structured communities containing specific autotrophs (e.g. Leptolyngbyaceae sp.) and heterotrophs (e.g. Cytophagales sp.), which effectively control metal(loid) and nutrient input using solar energy in aquatic environments. Elucidation of the mechanisms of biofilm formation coupled with metal(loid) immobilization in BAC expands the fundamental understanding of the geochemical fate of metal(loid)s, which may be harnessed to enhance in situ metal(loid) bioremediation in the aquatic ecosystem of the mining area. Video Abstract.
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Affiliation(s)
- Guobao Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xiuran Yin
- Microbial Ecophysiology Group, University of Bremen, Bremen, Germany
| | - Zekai Feng
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Chiyu Chen
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Daijie Chen
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Bo Wu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chong Liu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jean Louis Morel
- Laboratoire Sols Et Environnement, UMR 1120, Université de Lorraine, INRAE, 54518, Vandoeuvre-Lès-Nancy, France
| | - Yuanyuan Jiang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Hang Yu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Huan He
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yetao Tang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China.
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The AtoC family response regulator upregulates an operon encoding putative outer membrane proteins sorted by type IX secretion system in Porphyromonas gingivalis. J Oral Biosci 2023; 65:80-87. [PMID: 36375735 DOI: 10.1016/j.job.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/02/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Porphyromonas gingivalis, a keystone periodontopathogen, has multiple two-component systems that are thought to modulate virulence. In this study, we focused on PGN_0775 response regulator (RR), an AtoC homolog, and attempted to identify the target gene that it regulates in P. gingivalis. METHODS Comparative proteomic analyses comprising two-dimensional electrophoresis and peptide mass fingerprinting were applied to total protein samples from parent (WT) and atoC gene knockout (KO) strains to screen for affected protein spots. Fluctuations in the expression of corresponding genes were further confirmed using relative quantitative real-time polymerase chain reaction (RQPCR). RESULTS Five protein spots with fluctuating expression levels were identified in pgn_0775 KO strains along with their masses and physiological features, which contained two hypothetical proteins with higher expression levels in the WT than in the KO strains. RQPCR analysis confirmed that mRNA levels were consistently decreased in KO and recovered in pgn_0775-complemented KO strains. The two hypothetical proteins appeared to be the products of an operon that comprises four genes encoding three hypothetical but putative type IX secretion system sorting domain-containing proteins and an N-terminal region of the C25 cysteine peptidase. CONCLUSIONS The AtoC RR homolog in P. gingivalis upregulates the expression of the operon encoding potentially antigenic proteins retained on the cell surface; thus, it could be a promising target for P. gingivalis-specific antivirulence therapy.
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Gorasia DG, Veith PD, Reynolds EC. Protein interactome mapping of Porphyromonas gingivalis provides insights into the formation of the PorQ-Z complex of the type IX secretion system. Mol Oral Microbiol 2023; 38:34-40. [PMID: 35862235 PMCID: PMC10947112 DOI: 10.1111/omi.12383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022]
Abstract
Porphyromonas gingivalis is an anaerobic Gram-negative human oral pathogen highly associated with the more severe forms of periodontal disease. Porphyromonas gingivalis utilises the type IX secretion system (T9SS) to transport ∼30 cargo proteins, including multiple virulence factors, to the cell surface. The T9SS is a multiprotein system consisting of at least 20 proteins, and recently, we characterised the protein interactome of these components. Similar to the T9SS, almost all biological processes are mediated through protein-protein interactions (PPIs). Therefore, mapping PPIs is important to understand the biological functions of many proteins in P. gingivalis. Herein, we provide native migration profiles of over 1000 P. gingivalis proteins. Using the T9SS, we demonstrate that our dataset is a useful resource for identifying novel protein interactions. Using this dataset and further analysis of T9SS P. gingivalis mutants, we discover new mechanistic insights into the formation of the PorQ-Z complex of the T9SS. This dataset is a valuable resource for studies of P. gingivalis.
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Affiliation(s)
- Dhana G. Gorasia
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 InstituteThe University of MelbourneParkvilleAustralia
| | - Paul D. Veith
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 InstituteThe University of MelbourneParkvilleAustralia
| | - Eric C. Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 InstituteThe University of MelbourneParkvilleAustralia
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Fujita M, Chiu CH, Nagano K. Transcriptional analysis of the mfa-cluster genes in Porphyromonas gingivalis strains with one and two mfa5 genes. Mol Oral Microbiol 2023; 38:41-47. [PMID: 36333926 DOI: 10.1111/omi.12399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/08/2022]
Abstract
The Porphyromonas gingivalis Mfa1 fimbria is composed of the Mfa1 to Mfa5 proteins, encoded by the mfa1 to mfa5 genes, respectively, which are tandemly arranged on chromosomes. A recent study discovered that many P. gingivalis strains possess two mfa5 genes (called herein mfa5-1 and mfa5-2), which are also in tandem. This study examined the transcriptional unit and activity of mfa-cluster genes in strains with one (the ATCC 33277 and TDC60 strains) and two (the HG66 and A7436 strains) mfa5 genes. Complementary DNA was prepared from the total RNA extracted from the bacterial cells in the logarithmic growth phase using a random primer. PCR analysis for the intergenic regions from mfa1 to mfa5 or mfa5-2 showed that mfa1 to mfa5 or mfa5-2 formed a polycistronic gene cluster. Quantitative real-time PCR showed that the mfa1 transcription was 5-10 times higher than that of mfa2 in all the strains. However, mfa2 to mfa5 mostly showed a comparable expression. Both mfa5 genes were comparably transcribed in HG66 and A7436 strains. The transcriptional levels were almost consistent with the respective protein expression levels. In silico analysis identified a transcriptional terminator structure in the intergenic region between mfa1 and mfa2 that was probably responsible for the decreased transcription rate of mfa2 and the downstream genes.
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Affiliation(s)
- Mari Fujita
- Division of Microbiology, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - Chen-Hsuan Chiu
- Division of Microbiology, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - Keiji Nagano
- Division of Microbiology, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Tobetsu, Japan
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Książek M, Goulas T, Mizgalska D, Rodríguez-Banqueri A, Eckhard U, Veillard F, Waligórska I, Benedyk-Machaczka M, Sochaj-Gregorczyk AM, Madej M, Thøgersen IB, Enghild JJ, Cuppari A, Arolas JL, de Diego I, López-Pelegrín M, Garcia-Ferrer I, Guevara T, Dive V, Zani ML, Moreau T, Potempa J, Gomis-Rüth FX. A unique network of attack, defence and competence on the outer membrane of the periodontitis pathogen Tannerella forsythia. Chem Sci 2023; 14:869-888. [PMID: 36755705 PMCID: PMC9890683 DOI: 10.1039/d2sc04166a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Periodontopathogenic Tannerella forsythia uniquely secretes six peptidases of disparate catalytic classes and families that operate as virulence factors during infection of the gums, the KLIKK-peptidases. Their coding genes are immediately downstream of novel ORFs encoding the 98-132 residue potempins (Pot) A, B1, B2, C, D and E. These are outer-membrane-anchored lipoproteins that specifically and potently inhibit the respective downstream peptidase through stable complexes that protect the outer membrane of T. forsythia, as shown in vivo. Remarkably, PotA also contributes to bacterial fitness in vivo and specifically inhibits matrix metallopeptidase (MMP) 12, a major defence component of oral macrophages, thus featuring a novel and highly-specific physiological MMP inhibitor. Information from 11 structures and high-confidence homology models showed that the potempins are distinct β-barrels with either a five-stranded OB-fold (PotA, PotC and PotD) or an eight-stranded up-and-down fold (PotE, PotB1 and PotB2), which are novel for peptidase inhibitors. Particular loops insert like wedges into the active-site cleft of the genetically-linked peptidases to specifically block them either via a new "bilobal" or the classic "standard" mechanism of inhibition. These results discover a unique, tightly-regulated proteolytic armamentarium for virulence and competence, the KLIKK-peptidase/potempin system.
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Affiliation(s)
- Mirosław Książek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland .,Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry Louisville 40202 KY USA
| | - Theodoros Goulas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain .,Department of Food Science and Nutrition, School of Agricultural Sciences, University of Thessaly Temponera str. Karditsa 43100 Greece
| | - Danuta Mizgalska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Arturo Rodríguez-Banqueri
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Ulrich Eckhard
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Florian Veillard
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Irena Waligórska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Małgorzata Benedyk-Machaczka
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Alicja M. Sochaj-Gregorczyk
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityGronostajowa 7Kraków 30-387Poland
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland
| | - Ida B. Thøgersen
- Department of Molecular Biology and Genetics, Aarhus UniversityUniversitetsbyen 81Aarhus C 8000Denmark
| | - Jan J. Enghild
- Department of Molecular Biology and Genetics, Aarhus UniversityUniversitetsbyen 81Aarhus C 8000Denmark
| | - Anna Cuppari
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Joan L. Arolas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Parkc/Baldiri Reixac, 15-21Barcelona 08028CataloniaSpain
| | - Iñaki de Diego
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain .,Sample Environment and Characterization Group, European XFEL GmbH Holzkoppel 4 Schenefeld 22869 Germany
| | - Mar López-Pelegrín
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Irene Garcia-Ferrer
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park c/Baldiri Reixac, 15-21 Barcelona 08028 Catalonia Spain
| | - Vincent Dive
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), ERL CNRS 9004Gif-sur-Yvette 91191France
| | - Marie-Louise Zani
- Departement de Biochimie, Université de Tours10 Bd. TonelléTours Cedex 37032France
| | | | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland .,Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry Louisville 40202 KY USA
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Parkc/Baldiri Reixac, 15-21Barcelona 08028CataloniaSpain
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Shibata S, Tahara YO, Katayama E, Kawamoto A, Kato T, Zhu Y, Nakane D, Namba K, Miyata M, McBride MJ, Nakayama K. Filamentous structures in the cell envelope are associated with bacteroidetes gliding machinery. Commun Biol 2023; 6:94. [PMID: 36690840 PMCID: PMC9870892 DOI: 10.1038/s42003-023-04472-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/12/2023] [Indexed: 01/24/2023] Open
Abstract
Many bacteria belonging to the phylum Bacteroidetes move on solid surfaces, called gliding motility. In our previous study with the Bacteroidetes gliding bacterium Flavobacterium johnsoniae, we proposed a helical loop track model, where adhesive SprB filaments are propelled along a helical loop on the cell surface. In this study, we observed the gliding cell rotating counterclockwise about its axis when viewed from the rear to the advancing direction of the cell and revealed that one labeled SprB focus sometimes overtook and passed another SprB focus that was moving in the same direction. Several electron microscopic analyses revealed the presence of a possible multi-rail structure underneath the outer membrane, which was associated with SprB filaments and contained GldJ protein. These results provide insights into the mechanism of Bacteroidetes gliding motility, in which the SprB filaments are propelled along tracks that may form a multi-rail system underneath the outer membrane. The insights may give clues as to how the SprB filaments get their driving force.
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Affiliation(s)
- Satoshi Shibata
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
- Division of Bacteriology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan.
| | - Yuhei O Tahara
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka Metropolitan University, Sumiyoshi-ku, Osaka, Japan
- Graduate School of Science, Osaka Metropolitan University, Sumiyoshi-ku, Osaka, Japan
| | - Eisaku Katayama
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka Metropolitan University, Sumiyoshi-ku, Osaka, Japan
- Waseda Research Institute for Science and Engineering, Okubo Shinjyuku, Tokyo, Japan
| | - Akihiro Kawamoto
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yongtao Zhu
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Daisuke Nakane
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Makoto Miyata
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka Metropolitan University, Sumiyoshi-ku, Osaka, Japan
- Graduate School of Science, Osaka Metropolitan University, Sumiyoshi-ku, Osaka, Japan
| | - Mark J McBride
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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Lu Z, Rämgård C, Ergenlioğlu İ, Sandin L, Hammar H, Andersson H, King K, Inman AR, Hao M, Bulone V, McKee LS. Multiple enzymatic approaches to hydrolysis of fungal β-glucans by the soil bacterium Chitinophaga pinensis. FEBS J 2023. [PMID: 36610032 DOI: 10.1111/febs.16720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/26/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
The genome of the soil Bacteroidota Chitinophaga pinensis encodes a large number of glycoside hydrolases (GHs) with noteworthy features and potentially novel functions. Several are predicted to be active on polysaccharide components of fungal and oomycete cell walls, such as chitin, β-1,3-glucan and β-1,6-glucan. While several fungal β-1,6-glucanase enzymes are known, relatively few bacterial examples have been characterised to date. We have previously demonstrated that C. pinensis shows strong growth using β-1,6-glucan as the sole carbon source, with the efficient release of oligosaccharides from the polymer. We here characterise the capacity of the C. pinensis secretome to hydrolyse the β-1,6-glucan pustulan and describe three distinct enzymes encoded by its genome, all of which show different levels of β-1,6-glucanase activity and which are classified into different GH families. Our data show that C. pinensis has multiple tools to deconstruct pustulan, allowing the species' broad utility of this substrate, with potential implications for bacterial biocontrol of pathogens via cell wall disruption. Oligosaccharides derived from fungal β-1,6-glucans are valuable in biomedical research and drug synthesis, and these enzymes could be useful tools for releasing such molecules from microbial biomass, an underexploited source of complex carbohydrates.
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Affiliation(s)
- Zijia Lu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Carl Rämgård
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - İrem Ergenlioğlu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Lova Sandin
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Hugo Hammar
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Helena Andersson
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Katharine King
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Mengshu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,College of Medicine & Public Health, Flinders University, Adelaide, SA, Australia
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,Wallenberg Wood Science Centre, Stockholm, Sweden
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SurA-like and Skp-like Proteins as Important Virulence Determinants of the Gram Negative Bacterial Pathogens. Int J Mol Sci 2022; 24:ijms24010295. [PMID: 36613738 PMCID: PMC9820271 DOI: 10.3390/ijms24010295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
In the Gram-negative bacteria, many important virulence factors reach their destination via two-step export systems, and they must traverse the periplasmic space before reaching the outer membrane. Since these proteins must be maintained in a structure competent for transport into or across the membrane, they frequently require the assistance of chaperones. Based on the results obtained for the model bacterium Escherichia coli and related species, it is assumed that in the biogenesis of the outer membrane proteins and the periplasmic transit of secretory proteins, the SurA peptidyl-prolyl isomerase/chaperone plays a leading role, while the Skp chaperone is rather of secondary importance. However, detailed studies carried out on several other Gram-negative pathogens indicate that the importance of individual chaperones in the folding and transport processes depends on the properties of client proteins and is species-specific. Taking into account the importance of SurA functions in bacterial virulence and severity of phenotypes due to surA mutations, this folding factor is considered as a putative therapeutic target to combat microbial infections. In this review, we present recent findings regarding SurA and Skp proteins: their mechanisms of action, involvement in processes related to virulence, and perspectives to use them as therapeutic targets.
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Dorgan B, Liu Y, Wang S, Aduse-Opoku J, Whittaker SBM, Roberts MAJ, Lorenz CD, Curtis MA, Garnett JA. Structural Model of a Porphyromonas gingivalis type IX Secretion System Shuttle Complex. J Mol Biol 2022; 434:167871. [PMID: 36404438 DOI: 10.1016/j.jmb.2022.167871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
Porphyromonas gingivalis is a gram-negative oral anaerobic pathogen and is one of the key causative agents of periodontitis. P. gingivalis utilises a range of virulence factors, including the cysteine protease RgpB, to drive pathogenesis and these are exported and attached to the cell surface via the type IX secretion system (T9SS). All cargo proteins possess a conserved C-terminal signal domain (CTD) which is recognised by the T9SS, and the outer membrane β-barrel protein PorV (PG0027/LptO) can interact with cargo proteins as they are exported to the bacterial surface. Using a combination of solution nuclear magnetic resonance (NMR) spectroscopy, biochemical analyses, machine-learning-based modelling and molecular dynamics (MD) simulations, we present a structural model of a PorV:RgpB-CTD complex from P. gingivalis. This is the first structural insight into CTD recognition by the T9SS and shows how the conserved motifs in the CTD are the primary sites that mediate binding. In PorV, interactions with extracellular surface loops are important for binding the CTD, and together these appear to cradle and lock RgpB-CTD in place. This work provides insight into cargo recognition by PorV but may also have important implications for understanding other aspects of type-IX dependent secretion.
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Affiliation(s)
- Ben Dorgan
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK; School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yichao Liu
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sunjun Wang
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Joseph Aduse-Opoku
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sara B-M Whittaker
- Institute of Cancer & Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Mark A J Roberts
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Christian D Lorenz
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Michael A Curtis
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
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40
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Gao H, Ma K, Ji G, Pan L, Zhou Q. Lipid transfer proteins involved in plant-pathogen interactions and their molecular mechanisms. MOLECULAR PLANT PATHOLOGY 2022; 23:1815-1829. [PMID: 36052490 PMCID: PMC9644281 DOI: 10.1111/mpp.13264] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/05/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Nonspecific lipid transfer proteins (LTPs) are small, cysteine-rich proteins that play numerous functional roles in plant growth and development, including cutin wax formation, pollen tube adhesion, cell expansion, seed development, germination, and adaptation to changing environmental conditions. LTPs contain eight conserved cysteine residues and a hydrophobic cavity that provides a wide variety of lipid-binding specificities. As members of the pathogenesis-related protein 14 family (PR14), many LTPs inhibit fungal or bacterial growth, and act as positive regulators in plant disease resistance. Over the past decade, these essential immunity-related roles of LTPs in plant immune processes have been documented in a growing body of literature. In this review, we summarize the roles of LTPs in plant-pathogen interactions, emphasizing the underlying molecular mechanisms in plant immune responses and specific LTP functions.
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Affiliation(s)
- Hang Gao
- College of Biology and FoodShangqiu Normal UniversityShangqiuHenanChina
| | - Kang Ma
- College of Biology and FoodShangqiu Normal UniversityShangqiuHenanChina
| | - Guojie Ji
- Experimental Teaching Center of Biology and Basic MedicineSanquan College of Xinxiang Medical UniversityXinxiangHenanChina
| | - Liying Pan
- College of Biology and FoodShangqiu Normal UniversityShangqiuHenanChina
| | - Qingfeng Zhou
- College of Biology and FoodShangqiu Normal UniversityShangqiuHenanChina
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Schmitz C, Madej M, Nowakowska Z, Cuppari A, Jacula A, Ksiazek M, Mikruta K, Wisniewski J, Pudelko-Malik N, Saran A, Zeytuni N, Mlynarz P, Lamont RJ, Usón I, Siksnys V, Potempa J, Solà M. Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors. Nucleic Acids Res 2022; 50:12558-12577. [PMID: 36464236 PMCID: PMC9757075 DOI: 10.1093/nar/gkac1103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 12/07/2022] Open
Abstract
The PglZ family of proteins belongs to the alkaline phosphatase superfamily, which consists of metallohydrolases with limited sequence identity but similar metal-coordination architectures in otherwise divergent active sites. Proteins with a well-defined PglZ domain are ubiquitous among prokaryotes as essential components of BREX phage defence systems and two-component systems (TCSs). Whereas other members of the alkaline phosphatase superfamily are well characterized, the activity, structure and biological function of PglZ family proteins remain unclear. We therefore investigated the structure and function of PorX, an orphan response regulator of the Porphyromonas gingivalis TCS containing a putative PglZ effector domain. The crystal structure of PorX revealed a canonical receiver domain, a helical bundle, and an unprecedented PglZ domain, similar to the general organization of the phylogenetically related BREX-PglZ proteins. The PglZ domain of PorX features an active site cleft suitable for large substrates. An extensive search for substrates revealed that PorX is a phosphodiesterase that acts on cyclic and linear oligonucleotides, including signalling molecules such as cyclic oligoadenylates. These results, combined with mutagenesis, biophysical and enzymatic analysis, suggest that PorX coordinates oligonucleotide signalling pathways and indirectly regulates gene expression to control the secretion of virulence factors.
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Affiliation(s)
- Claus Schmitz
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Zuzanna Nowakowska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Anna Cuppari
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
| | - Anna Jacula
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Miroslaw Ksiazek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Katarzyna Mikruta
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Jerzy Wisniewski
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw PL-50-370, Poland
| | - Natalia Pudelko-Malik
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw PL-50-370, Poland
| | - Anshu Saran
- Department of Anatomy and Cell Biology, McGill University, Montréal, Quebec H3A 0C7, Canada
| | - Natalie Zeytuni
- Department of Anatomy and Cell Biology, McGill University, Montréal, Quebec H3A 0C7, Canada
| | - Piotr Mlynarz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw PL-50-370, Poland
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - Isabel Usón
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
- ICREA Institució Catalana de Recerca i Estudis Avançats, Barcelona E-08010, Spain
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - Maria Solà
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
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Phillips PL, Wu XJ, Reyes L. Differential affinity chromatography reveals a link between Porphyromonas gingivalis-induced changes in vascular smooth muscle cell differentiation and the type 9 secretion system. Front Cell Infect Microbiol 2022; 12:983247. [PMID: 36483452 PMCID: PMC9722745 DOI: 10.3389/fcimb.2022.983247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/24/2022] [Indexed: 11/23/2022] Open
Abstract
Porphyromonas gingivalis is implicated in adverse pregnancy outcome. We previously demonstrated that intrauterine infection with various strains of P. gingivalis impairs the physiologic remodeling of the uterine spiral arteries (IRSA) during pregnancy, which underlies the major obstetrical syndromes. Women diagnosed with IRSA also have a greater risk for premature cardiovascular disease in later life. The dysregulated plasticity of vascular smooth muscle cells (VSMCs) is present in both IRSA and premature cardiovascular events. We hypothesized that VSMCs could serve as a bait to identify P. gingivalis proteins associated with dysregulated VSMC plasticity as seen in IRSA. We first confirmed that dams with P. gingivalis A7UF-induced IRSA also show perturbed aortic smooth muscle cell (AoSMC) plasticity along with the P. gingivalis colonization of the tissue. The in vitro infection of AoSMCs with IRSA-inducing strain A7UF also perturbed AoSMC plasticity that did not occur with infection by non-IRSA-inducing strain W83. Far-Western blotting with strain W83 and strain A7UF showed a differential binding pattern to the rat aorta and primary rat AoSMCs. The affinity chromatography/pull-down assay combined with mass spectrometry was used to identify P. gingivalis/AoSMC protein interactions specific to IRSA. Membrane proteins with a high binding affinity to AoSMCs were identified in the A7UF pull-down but not in the W83 pull-down, most of which were the outer membrane components of the Type 9 secretion system (T9SS) and T9SS cargo proteins. Additional T9SS cargo proteins were detected in greater abundance in the A7UF pull-down eluate compared to W83. None of the proteins enriched in the W83 eluate were T9SS components nor T9SS cargo proteins despite their presence in the prey preparations used in the pull-down assay. In summary, differential affinity chromatography established that the components of IRSA-inducing P. gingivalis T9SS as well as its cargo directly interact with AoSMCs, which may play a role in the infection-induced dysregulation of VSMC plasticity. The possibility that the T9SS is involved in the microbial manipulation of host cell events important for cell differentiation and tissue remodeling would constitute a new virulence function for this system.
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Affiliation(s)
- Priscilla L. Phillips
- Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville College of Osteopathic Medicine, Kirksville, MO, United States
| | - Xiao-jun Wu
- Department of Pathobiological Sciences, University of Wisconsin - Madison, School of Veterinary Medicine, Madison, WI, United States
| | - Leticia Reyes
- Department of Pathobiological Sciences, University of Wisconsin - Madison, School of Veterinary Medicine, Madison, WI, United States,*Correspondence: Leticia Reyes,
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Astafyeva Y, Gurschke M, Streit WR, Krohn I. Interplay between the microalgae Micrasterias radians and its symbiont Dyadobacter sp. HH091. Front Microbiol 2022; 13:1006609. [PMID: 36312980 PMCID: PMC9606717 DOI: 10.3389/fmicb.2022.1006609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Based on previous research, related to detailed insight into mutualistic collaboration of microalga and its microbiome, we established an artificial plant-bacteria system of the microalga Micrasterias radians MZCH 672 and the bacterial isolate Dyadobacter sp. HH091. The bacteria, affiliated with the phylum Bacteroidota, strongly stimulated growth of the microalga when it was added to axenic algal cultures. For further advances, we studied the isolate HH091 and its interaction with the microalga M. radians using transcriptome and extensive genome analyses. The genome of HH091 contains predicted polysaccharide utilizing gene clusters co-working with the type IX secretion system (T9SS) and conceivably involved in the algae-bacteria liaison. Here, we focus on characterizing the mechanism of T9SS, implementing the attachment and invasion of microalga by Dyadobacter sp. HH091. Omics analysis exposed T9SS genes: gldK, gldL, gldM, gldN, sprA, sprE, sprF, sprT, porU and porV. Besides, gld genes not considered as the T9SS components but required for gliding motility and protein secretion (gldA, gldB, gldD, gldF, gldG, gldH, gldI, gldJ), were also identified at this analysis. A first model of T9SS apparatus of Dyadobacter was proposed in a course of this research. Using the combination of fluorescence labeling of Dyadobacter sp. HH091, we examined the bacterial colonisation and penetration into the cell wall of the algal host M. radians MZCH 672.
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Glycosyltransferase-Related Protein GtrA Is Essential for Localization of Type IX Secretion System Cargo Protein Cellulase Cel9A and Affects Cellulose Degradation in Cytophaga hutchinsonii. Appl Environ Microbiol 2022; 88:e0107622. [PMID: 36197104 PMCID: PMC9599414 DOI: 10.1128/aem.01076-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gram-negative bacterium Cytophaga hutchinsonii digests cellulose through a novel cellulose degradation mechanism. It possesses the lately characterized type IX secretion system (T9SS). We recently discovered that N-glycosylation of the C-terminal domain (CTD) of a hypothetical T9SS substrate protein in the periplasmic space of C. hutchinsonii affects protein secretion and localization. In this study, green fluorescent protein (GFP)-CTDCel9A recombinant protein was found with increased molecular weight in the periplasm of C. hutchinsonii. Site-directed mutagenesis studies on the CTD of cellulase Cel9A demonstrated that asparagine residue 900 in the D-X-N-X-S motif is important for the processing of the recombinant protein. We found that the glycosyltransferase-related protein GtrA (CHU_0012) located in the cytoplasm of C. hutchinsonii is essential for outer membrane localization of the recombinant protein. The deletion of gtrA decreased the abundance of the outer membrane proteins and affected cellulose degradation by C. hutchinsonii. This study provided a link between the glycosylation system and cellulose degradation in C. hutchinsonii. IMPORTANCE N-Glycosylation systems are generally limited to some pathogenic bacteria in prokaryotes. The disruption of the N-glycosylation pathway is related to adherence, invasion, colonization, and other phenotypic characteristics. We recently found that the cellulolytic bacterium Cytophaga hutchinsonii also has an N-glycosylation system. The cellulose degradation mechanism of C. hutchinsonii is novel and mysterious; cellulases and other proteins on the cell surface are involved in utilizing cellulose. In this study, we identified an asparagine residue in the C-terminal domain of cellulase Cel9A that is necessary for the processing of the T9SS cargo protein. Moreover, the glycosyltransferase-related protein GtrA is essential for the localization of the GFP-CTDCel9A recombinant protein. Deletion of gtrA affected cellulose degradation and the abundance of outer membrane proteins. This study enriched the understanding of the N-glycosylation system in C. hutchinsonii and provided a link between N-glycosylation and cellulose degradation, which also expanded the role of the N-glycosylation system in bacteria.
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Hudson J, Egan S. Opportunistic diseases in marine eukaryotes: Could Bacteroidota be the next threat to ocean life? Environ Microbiol 2022; 24:4505-4518. [PMID: 35706128 PMCID: PMC9804302 DOI: 10.1111/1462-2920.16094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 01/05/2023]
Abstract
Bacteria within the phylum Bacteroidota (Bacteroidetes) are known to cause devastating and widespread disease outbreaks in marine eukaryotic hosts. However, with few pathogens described in detail, their prevalence and virulence strategies remain largely unknown. Here, we systematically reviewed the literature to evaluate the current understanding of Bacteroidota that cause disease in marine hosts. Isolates affiliated with the genera Tenacibaculum and Aquimarina (Flavobacteriaceae) were the most widely reported and characterized pathogens. Although cultured isolates were predominantly Flavobacteriia, culture-independent studies also found classes Bacteroidia, Cytophagia and Sphingobacteriia associated with disease. We found that pathogenic marine Bacteroidota largely conformed to an opportunistic lifestyle but could also act as secondary pathogens or were involved in polymicrobial diseases. Many diseases were also associated with an environmental stressor, especially those affecting coral, macroalgae and fish. Key virulence traits included the production of adhesins and host tissue-degrading enzymes. Overall, the nature of disease involving Bacteroidota pathogens appears to be an outcome of complex host-pathogen-environment interactions; however, our understanding of virulence remains limited by the lack of functional characterization studies. This is concerning as Bacteroidota have the potential to emerge as a serious threat to marine ecosystems and aquaculture industries, driven by global changes in ocean conditions.
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Affiliation(s)
- Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyAustralia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyAustralia
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Saran A, Weerasinghe N, Thibodeaux CJ, Zeytuni N. Purification, crystallization and crystallographic analysis of the PorX response regulator associated with the type IX secretion system. Acta Crystallogr F Struct Biol Commun 2022; 78:354-362. [PMID: 36189719 PMCID: PMC9527653 DOI: 10.1107/s2053230x22008500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
Pathogenic bacteria utilize specialized macromolecular secretion systems to transport virulence factors across membrane(s) and manipulate their infected host. To date, 11 secretion systems have been identified, including the type IX secretion system (T9SS) associated with human, avian and farmed-fish diseases. As a bacterial secretion system, the T9SS also facilitates gliding motility and the degradation of different macromolecules by the secretion of metabolic enzymes in nonpathogenic bacteria. PorX is a highly conserved protein that regulates the transcription of essential T9SS components and additionally mediates the function of T9SS via direct interaction with PorL, the rotary motor protein of the T9SS. PorX is also a member of a two-component system regulatory cascade, where it serves as the response regulator that relays a signal transduced from a conserved sensor histidine kinase, PorY, to a designated sigma factor. Here, the recombinant expression and purification of PorX homologous proteins from the pathogenic bacterium Porphyromonas gingivalis and the nonpathogenic bacterium Flavobacterium johnsoniae are reported. A bioinformatical characterization of the different domains comprising the PorX protein is also provided, and the crystallization and X-ray analysis of PorX from F. johnsoniae are reported.
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Affiliation(s)
- Anshu Saran
- The Department of Anatomy and Cell Biology and the Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Nuwani Weerasinghe
- The Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | | | - Natalie Zeytuni
- The Department of Anatomy and Cell Biology and the Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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Identification of trypsin-degrading commensals in the large intestine. Nature 2022; 609:582-589. [PMID: 36071157 PMCID: PMC9477747 DOI: 10.1038/s41586-022-05181-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 08/02/2022] [Indexed: 11/23/2022]
Abstract
Increased levels of proteases, such as trypsin, in the distal intestine have been implicated in intestinal pathological conditions1–3. However, the players and mechanisms that underlie protease regulation in the intestinal lumen have remained unclear. Here we show that Paraprevotella strains isolated from the faecal microbiome of healthy human donors are potent trypsin-degrading commensals. Mechanistically, Paraprevotella recruit trypsin to the bacterial surface through type IX secretion system-dependent polysaccharide-anchoring proteins to promote trypsin autolysis. Paraprevotella colonization protects IgA from trypsin degradation and enhances the effectiveness of oral vaccines against Citrobacter rodentium. Moreover, Paraprevotella colonization inhibits lethal infection with murine hepatitis virus-2, a mouse coronavirus that is dependent on trypsin and trypsin-like proteases for entry into host cells4,5. Consistently, carriage of putative genes involved in trypsin degradation in the gut microbiome was associated with reduced severity of diarrhoea in patients with SARS-CoV-2 infection. Thus, trypsin-degrading commensal colonization may contribute to the maintenance of intestinal homeostasis and protection from pathogen infection. Colonization of trypsin-degrading commensal bacteria may contribute to the maintenance of intestinal homeostasis and protection against pathogen infection in humans and mice.
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Insertional Inactivation and Gene Complementation of Prevotella intermedia Type IX Secretion System Reveals Its Indispensable Roles in Black Pigmentation, Hemagglutination, Protease Activity of Interpain A, and Biofilm Formation. J Bacteriol 2022; 204:e0020322. [PMID: 35862729 PMCID: PMC9380532 DOI: 10.1128/jb.00203-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Prevotella intermedia, a Gram-negative oral anaerobic bacterium, is frequently isolated from the periodontal pockets of patients with chronic periodontitis. In recent years, the involvement of the bacterium in respiratory tract infections as well as in oral infections has been revealed. P. intermedia possesses several potent virulence factors, such as cysteine proteinase interpain A encoded by the inpA gene. The genome of P. intermedia carries genes of the type IX secretion system (T9SS), which enables the translocation of virulence factors across the outer membrane in several pathogens belonging to the phylum Bacteroidetes; however, it is still unclear whether the T9SS is functional in this microorganism. Recently, we performed targeted mutagenesis in the strain OMA14 of P. intermedia. Here, we successfully obtained mutants deficient in inpA and the T9SS component genes porK and porT. None of the mutants exhibited protease activity of interpain A. The porK and porT mutants, but not the inpA mutant, showed defects in colony pigmentation, hemagglutination, and biofilm formation. We also obtained a complemented strain for the porK gene that recovered all the above abilities. These results indicate that T9SS functions in P. intermedia and that interpain A is one of the T9SS cargo proteins. IMPORTANCE The virulence factors of periodontal pathogens such as Prevotella intermedia have not been elucidated. Using our established procedure, we succeeded in generating type IX secretion system mutants and gene complementation strains that might transfer virulence factors to the bacterial surface. The generated strains clearly indicate that T9SS in P. intermedia is essential for colonial pigmentation, hemagglutination, and biofilm formation. These results indicated that interpain A is a T9SS cargo protein.
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Sharma G, Garg N, Hasan S, Shirodkar S. Prevotella: An insight into its characteristics and associated virulence factors. Microb Pathog 2022; 169:105673. [PMID: 35843443 DOI: 10.1016/j.micpath.2022.105673] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/04/2022] [Accepted: 07/06/2022] [Indexed: 10/17/2022]
Abstract
Prevotella species, a gram-negative obligate anaerobe, is commonly associated with human infections such as dental caries and periodontitis, as well as other conditions such as chronic osteomyelitis, bite-related infections, rheumatoid arthritis and intestinal diseases like ulcerative colitis. This generally harmless commensal possesses virulence factors such as adhesins, hemolysins, secretion systems exopolysaccharide, LPS, proteases, quorum sensing molecules and antibiotic resistance to evolve into a well-adapted pathogen capable of causing successful infection and proliferation in the host tissue. This review describes several of these virulence factors and their advantage to Prevotella spp. in causing inflammatory diseases like periodontitis. In addition, using genome analysis of Prevotella reference strains, we examined other putative virulence determinants which can provide insights as biomarkers and be the targets for effective interventions in Prevotella related diseases like periodontitis.
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Affiliation(s)
- Geetika Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida Campus, Noida, 201313, India
| | - Nancy Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida Campus, Noida, 201313, India
| | - Shamimul Hasan
- Department of Oral Medicine and Radiology, Faculty of Dentistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sheetal Shirodkar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida Campus, Noida, 201313, India.
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Clarke KR, Hor L, Pilapitiya A, Luirink J, Paxman JJ, Heras B. Phylogenetic Classification and Functional Review of Autotransporters. Front Immunol 2022; 13:921272. [PMID: 35860281 PMCID: PMC9289746 DOI: 10.3389/fimmu.2022.921272] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022] Open
Abstract
Autotransporters are the core component of a molecular nano-machine that delivers cargo proteins across the outer membrane of Gram-negative bacteria. Part of the type V secretion system, this large family of proteins play a central role in controlling bacterial interactions with their environment by promoting adhesion to surfaces, biofilm formation, host colonization and invasion as well as cytotoxicity and immunomodulation. As such, autotransporters are key facilitators of fitness and pathogenesis and enable co-operation or competition with other bacteria. Recent years have witnessed a dramatic increase in the number of autotransporter sequences reported and a steady rise in functional studies, which further link these proteins to multiple virulence phenotypes. In this review we provide an overview of our current knowledge on classical autotransporter proteins, the archetype of this protein superfamily. We also carry out a phylogenetic analysis of their functional domains and present a new classification system for this exquisitely diverse group of bacterial proteins. The sixteen phylogenetic divisions identified establish sensible relationships between well characterized autotransporters and inform structural and functional predictions of uncharacterized proteins, which may guide future research aimed at addressing multiple unanswered aspects in this group of therapeutically important bacterial factors.
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Affiliation(s)
- Kaitlin R. Clarke
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Lilian Hor
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Akila Pilapitiya
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Joen Luirink
- Department of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit, Amsterdam, Netherlands
| | - Jason J. Paxman
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
- *Correspondence: Begoña Heras, ; Jason J. Paxman,
| | - Begoña Heras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
- *Correspondence: Begoña Heras, ; Jason J. Paxman,
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