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Zhao Y, Zhang Y, Lu W, Sun R, Guo R, Cao X, Liu X, Lyu C, Zhao M. The diagnostic/prognostic roles and biological function of the IFIT family members in acute myeloid leukemia. BMC Med Genomics 2023; 16:296. [PMID: 37980495 PMCID: PMC10657597 DOI: 10.1186/s12920-023-01735-0] [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: 07/06/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND The Interferon-induced protein with tetratricopeptide repeat (IFIT) family, IFIT1/2/3/5, play an important role in different tumors progression. However, the prognosis significance and biological role of IFIT family members in acute myeloid leukemia (AML) remains unclear. METHODS We obtained the gene expression data and clinical information of 173 AML patients from The Cancer Genome Atlas (TCGA) database. Several databases were used in our study, including GEPIA, MethSurv, STRING, GSCA and GeneMANIA database. RESULTS The mRNA expression of IFIT1/2/3/5 was elevated in AML patients and had a high ability to distinguish AML from controls based on the receiver operating characteristic (ROC) curve (AUC > 0.9). Kaplan-Meier survival analysis showed that higher levels of IFIT2/3/5 expression predict poor prognosis in AML patients. Besides, the DNA methylation analysis suggested that 7 CpG sites of IFIT2, 4 CpG sites of IFIT3 and 10 CpG sites of IFIT5 were significantly associated with the prognosis of AML patients. In addition, IFIT2/3/5 expression was significantly positively associated with the immune cell infiltration and immune checkpoint expression, such as CTLA4, PDCD1, LAG3, and TIGIT. Finally, drug sensitivity analysis revealed that AML patients with high expression of IFIT2/3/5 were resistant to multiple drugs, but sensitive to dasatinib. CONCLUSION IFIT family genes might serve as biomarkers for diagnosis, prognosis and drug sensitivity in AML patients. The activation or blocking of IFIT-related signaling pathways may provide novel insights into immunotherapy for patients with AML.
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Affiliation(s)
- YiFan Zhao
- First Center Clinic College of Tianjin Medical University, Tianjin, People's Republic of China
| | - Yi Zhang
- First Center Clinic College of Tianjin Medical University, Tianjin, People's Republic of China
| | - WenYi Lu
- Department of Hematology, Tianjin First Central Hospital, Tianjin, People's Republic of China
| | - Rui Sun
- School of Medicine, Nankai University, Tianjin, People's Republic of China
| | - RuiTing Guo
- First Center Clinic College of Tianjin Medical University, Tianjin, People's Republic of China
| | - XinPing Cao
- First Center Clinic College of Tianjin Medical University, Tianjin, People's Republic of China
| | - Xingzhong Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, People's Republic of China
| | - Cuicui Lyu
- Department of Hematology, Tianjin First Central Hospital, Tianjin, People's Republic of China.
| | - MingFeng Zhao
- First Center Clinic College of Tianjin Medical University, Tianjin, People's Republic of China.
- Department of Hematology, Tianjin First Central Hospital, Tianjin, People's Republic of China.
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2
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Gheorghita AA, Wozniak DJ, Parsek MR, Howell PL. Pseudomonas aeruginosa biofilm exopolysaccharides: assembly, function, and degradation. FEMS Microbiol Rev 2023; 47:fuad060. [PMID: 37884397 PMCID: PMC10644985 DOI: 10.1093/femsre/fuad060] [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: 04/21/2023] [Revised: 10/04/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023] Open
Abstract
The biofilm matrix is a fortress; sheltering bacteria in a protective and nourishing barrier that allows for growth and adaptation to various surroundings. A variety of different components are found within the matrix including water, lipids, proteins, extracellular DNA, RNA, membrane vesicles, phages, and exopolysaccharides. As part of its biofilm matrix, Pseudomonas aeruginosa is genetically capable of producing three chemically distinct exopolysaccharides - alginate, Pel, and Psl - each of which has a distinct role in biofilm formation and immune evasion during infection. The polymers are produced by highly conserved mechanisms of secretion, involving many proteins that span both the inner and outer bacterial membranes. Experimentally determined structures, predictive modelling of proteins whose structures are yet to be solved, and structural homology comparisons give us insight into the molecular mechanisms of these secretion systems, from polymer synthesis to modification and export. Here, we review recent advances that enhance our understanding of P. aeruginosa multiprotein exopolysaccharide biosynthetic complexes, and how the glycoside hydrolases/lyases within these systems have been commandeered for antimicrobial applications.
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Affiliation(s)
- Andreea A Gheorghita
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Medical Science Building, 1 King's College Cir, Toronto, ON M5S 1A8, Canada
| | - Daniel J Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, 776 Biomedical Research Tower, 460 W 12th Ave, Columbus, OH 43210, United States
- Department of Microbiology, The Ohio State University College, Biological Sciences Bldg, 105, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Health Sciences Bldg, 1705 NE Pacific St, Seattle, WA 98195-7735, United States
| | - P Lynne Howell
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Medical Science Building, 1 King's College Cir, Toronto, ON M5S 1A8, Canada
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3
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Low KE, Gheorghita AA, Tammam SD, Whitfield GB, Li YE, Riley LM, Weadge JT, Caldwell SJ, Chong PA, Walvoort MTC, Kitova EN, Klassen JS, Codée JDC, Howell PL. Pseudomonas aeruginosa AlgF is a protein-protein interaction mediator required for acetylation of the alginate exopolysaccharide. J Biol Chem 2023; 299:105314. [PMID: 37797696 PMCID: PMC10641220 DOI: 10.1016/j.jbc.2023.105314] [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: 07/26/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
Enzymatic modifications of bacterial exopolysaccharides enhance immune evasion and persistence during infection. In the Gram-negative opportunistic pathogen Pseudomonas aeruginosa, acetylation of alginate reduces opsonic killing by phagocytes and improves reactive oxygen species scavenging. Although it is well known that alginate acetylation in P. aeruginosa requires AlgI, AlgJ, AlgF, and AlgX, how these proteins coordinate polymer modification at a molecular level remains unclear. Here, we describe the structural characterization of AlgF and its protein interaction network. We characterize direct interactions between AlgF and both AlgJ and AlgX in vitro and demonstrate an association between AlgF and AlgX, as well as AlgJ and AlgI, in P. aeruginosa. We determine that AlgF does not exhibit acetylesterase activity and is unable to bind to polymannuronate in vitro. Therefore, we propose that AlgF functions to mediate protein-protein interactions between alginate acetylation enzymes, forming the periplasmic AlgJFXK (AlgJ-AlgF-AlgX-AlgK) acetylation and export complex required for robust biofilm formation.
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Affiliation(s)
- Kristin E Low
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andreea A Gheorghita
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie D Tammam
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gregory B Whitfield
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yancheng E Li
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Laura M Riley
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joel T Weadge
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shane J Caldwell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - P Andrew Chong
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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4
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Srimahaeak T, Thongdee N, Chittrakanwong J, Atichartpongkul S, Jaroensuk J, Phatinuwat K, Phaonakrop N, Jaresitthikunchai J, Roytrakul S, Mongkolsuk S, Fuangthong M. Pseudomonas aeruginosa GidA modulates the expression of catalases at the posttranscriptional level and plays a role in virulence. Front Microbiol 2023; 13:1079710. [PMID: 36726575 PMCID: PMC9884967 DOI: 10.3389/fmicb.2022.1079710] [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: 10/25/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
Pseudomonas aeruginosa gidA, which encodes a putative tRNA-modifying enzyme, is associated with a variety of virulence phenotypes. Here, we demonstrated that P. aeruginosa gidA is responsible for the modifications of uridine in tRNAs in vivo. Loss of gidA was found to have no impact on the mRNA levels of katA and katB, but it decreased KatA and KatB protein levels, resulting in decreased total catalase activity and a hydrogen peroxide-sensitive phenotype. Furthermore, gidA was found to affect flagella-mediated motility and biofilm formation; and it was required for the full virulence of P. aeruginosa in both Caenorhabditis elegans and macrophage models. Together, these observations reveal the posttranscriptional impact of gidA on the oxidative stress response, highlight the complexity of catalase gene expression regulation, and further support the involvement of gidA in the virulence of P. aeruginosa.
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Affiliation(s)
- Thanyaporn Srimahaeak
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand,Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Sanamchandra Palace Campus, Nakhon Pathom, Thailand
| | - Narumon Thongdee
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand
| | | | | | - Juthamas Jaroensuk
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Kamonwan Phatinuwat
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Narumon Phaonakrop
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Janthima Jaresitthikunchai
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Skorn Mongkolsuk
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand,Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Mayuree Fuangthong
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand,Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand,*Correspondence: Mayuree Fuangthong, ✉
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5
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Gheorghita AA, Li YE, Kitova EN, Bui DT, Pfoh R, Low KE, Whitfield GB, Walvoort MTC, Zhang Q, Codée JDC, Klassen JS, Howell PL. Structure of the AlgKX modification and secretion complex required for alginate production and biofilm attachment in Pseudomonas aeruginosa. Nat Commun 2022; 13:7631. [PMID: 36494359 PMCID: PMC9734138 DOI: 10.1038/s41467-022-35131-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Synthase-dependent secretion systems are a conserved mechanism for producing exopolysaccharides in Gram-negative bacteria. Although widely studied, it is not well understood how these systems are organized to coordinate polymer biosynthesis, modification, and export across both membranes and the peptidoglycan. To investigate how synthase-dependent secretion systems produce polymer at a molecular level, we determined the crystal structure of the AlgK-AlgX (AlgKX) complex involved in Pseudomonas aeruginosa alginate exopolysaccharide acetylation and export. We demonstrate that AlgKX directly binds alginate oligosaccharides and that formation of the complex is vital for polymer production and biofilm attachment. Finally, we propose a structural model for the AlgEKX outer membrane modification and secretion complex. Together, our study provides insight into how alginate biosynthesis proteins coordinate production of a key exopolysaccharide involved in establishing persistent Pseudomonas lung infections.
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Affiliation(s)
- Andreea A. Gheorghita
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada
| | - Yancheng E. Li
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada ,grid.20861.3d0000000107068890Present Address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA USA
| | - Elena N. Kitova
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - Duong T. Bui
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - Roland Pfoh
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada
| | - Kristin E. Low
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.55614.330000 0001 1302 4958Present Address: Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Gregory B. Whitfield
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada ,grid.14848.310000 0001 2292 3357Present Address: Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC Canada
| | - Marthe T. C. Walvoort
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands ,grid.4830.f0000 0004 0407 1981Present Address: Department of Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | - Qingju Zhang
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands ,grid.411862.80000 0000 8732 9757Present Address: National Research Centre for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang, China
| | - Jeroen D. C. Codée
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - John S. Klassen
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - P. Lynne Howell
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada
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6
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Role of Exopolysaccharides of Pseudomonas in Heavy Metal Removal and Other Remediation Strategies. Polymers (Basel) 2022; 14:polym14204253. [PMID: 36297831 PMCID: PMC9609410 DOI: 10.3390/polym14204253] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/30/2022] Open
Abstract
Pseudomonas biofilms have been studied intensively for several decades and research outcomes have been successfully implemented in various medical and agricultural applications. Research on biofilm synthesis and composition has also overlapped with the objectives of environmental sciences, since biofilm components show exceptional physicochemical properties applicable to remediation techniques. Especially, exopolysaccharides (ExPs) have been at the center of scientific interest, indicating their potential in solving the environmental issues of heavy metal land and water contamination via sorptive interactions and flocculation. Since exposure to heavy metal via contaminated water or soil poses an imminent risk to the environment and human health, ExPs provide an interesting and viable solution to this issue, alongside other effective and green remedial techniques (e.g., phytostabilization, implementation of biosolids, and biosorption using agricultural wastes) aiming to restore contaminated sites to their natural, pollution-free state, or to ameliorate the negative impact of heavy metals on the environment. Thus, we discuss the plausible role and performance of Pseudomonas ExPs in remediation techniques, aiming to provide the relevant available and comprehensive information on ExPs’ biosynthesis and their usage in heavy metal remediation or other environmental applications, such as wastewater treatment via bioflocculation and soil remediation.
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7
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Vandana, Das S. Genetic regulation, biosynthesis and applications of extracellular polysaccharides of the biofilm matrix of bacteria. Carbohydr Polym 2022; 291:119536. [DOI: 10.1016/j.carbpol.2022.119536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 11/02/2022]
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8
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Boron Derivatives Accelerate Biofilm Formation of Recombinant Escherichia coli via Increasing Quorum Sensing System Autoinducer-2 Activity. Int J Mol Sci 2022; 23:ijms23158059. [PMID: 35897636 PMCID: PMC9332218 DOI: 10.3390/ijms23158059] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Boron is an essential element for autoinducer-2 (AI-2) synthesis of quorum sensing (QS) system, which affects bacterial collective behavior. As a living biocatalyst, biofilms can stably catalyze the activity of intracellular enzymes. However, it is unclear how boron affects biofilm formation in E. coli, particularly recombinant E. coli with intracellular enzymes. This study screened different boron derivatives to explore their effect on biofilm formation. The stress response of biofilm formation to boron was illuminated by analyzing AI-2 activity, extracellular polymeric substances (EPS) composition, gene expression levels, etc. Results showed that boron derivatives promote AI-2 activity in QS system. After treatment with H3BO3 (0.6 mM), the AI-2 activity increased by 65.99%, while boron derivatives increased the biomass biofilms in the order H3BO3 > NaBO2 > Na2B4O7 > NaBO3. Moreover, treatment with H3BO3 (0.6 mM) increased biomass by 88.54%. Meanwhile, AI-2 activity had a linear correlation with polysaccharides and protein of EPS at 0−0.6 mM H3BO3 and NaBO2 (R2 > 0.8). Furthermore, H3BO3 upregulated the expression levels of biofilm formation genes, quorum sensing genes, and flagellar movement genes. These findings demonstrated that boron promoted biofilm formation by upregulating the expression levels of biofilm-related genes, improving the QS system AI-2 activity, and increasing EPS secretion in E. coli.
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9
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Balmuri SR, Phandanouvong-Lozano V, House SD, Yang JC, Niepa TH. Mucoid Coating Provides a Growth Advantage to Pseudomonas aeruginosa at Oil–Water Interfaces. ACS APPLIED BIO MATERIALS 2022; 5:1868-1878. [DOI: 10.1021/acsabm.1c01198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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Gheorghita AA, Wolfram F, Whitfield GB, Jacobs HM, Pfoh R, Wong SSY, Guitor AK, Goodyear MC, Berezuk AM, Khursigara CM, Parsek MR, Howell PL. The Pseudomonas aeruginosa homeostasis enzyme AlgL clears the periplasmic space of accumulated alginate during polymer biosynthesis. J Biol Chem 2022; 298:101560. [PMID: 34990713 PMCID: PMC8829089 DOI: 10.1016/j.jbc.2021.101560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen and a leading cause of chronic infection in the lungs of individuals with cystic fibrosis. After colonization, P. aeruginosa often undergoes a phenotypic conversion to mucoidy, characterized by overproduction of the alginate exopolysaccharide. This conversion is correlated with poorer patient prognoses. The majority of genes required for alginate synthesis, including the alginate lyase, algL, are located in a single operon. Previous investigations of AlgL have resulted in several divergent hypotheses regarding the protein’s role in alginate production. To address these discrepancies, we determined the structure of AlgL and, using multiple sequence alignments, identified key active site residues involved in alginate binding and catalysis. In vitro enzymatic analysis of active site mutants highlights R249 and Y256 as key residues required for alginate lyase activity. In a genetically engineered P. aeruginosa strain where alginate biosynthesis is under arabinose control, we found that AlgL is required for cell viability and maintaining membrane integrity during alginate production. We demonstrate that AlgL functions as a homeostasis enzyme to clear the periplasmic space of accumulated polymer. Constitutive expression of the AlgU/T sigma factor mitigates the effects of an algL deletion during alginate production, suggesting that an AlgU/T-regulated protein or proteins can compensate for an algL deletion. Together, our study demonstrates the role of AlgL in alginate biosynthesis, explains the discrepancies observed previously across other P. aeruginosa ΔalgL genetic backgrounds, and clarifies the existing divergent data regarding the function of AlgL as an alginate degrading enzyme.
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Affiliation(s)
- Andreea A Gheorghita
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Francis Wolfram
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gregory B Whitfield
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Holly M Jacobs
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
| | - Roland Pfoh
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Steven S Y Wong
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Allison K Guitor
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mara C Goodyear
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Alison M Berezuk
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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11
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Cell Envelope Stress Response in Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:147-184. [DOI: 10.1007/978-3-031-08491-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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A New Sugar for an Old Phage: a c-di-GMP-Dependent Polysaccharide Pathway Sensitizes Escherichia coli for Bacteriophage Infection. mBio 2021; 12:e0324621. [PMID: 34903045 PMCID: PMC8669472 DOI: 10.1128/mbio.03246-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Bacteriophages are ubiquitous parasites of bacteria and major drivers of bacterial ecology and evolution. Despite an ever-growing interest in their biotechnological and therapeutic applications, detailed knowledge of the molecular mechanisms underlying phage-host interactions remains scarce. Here, we show that bacteriophage N4 exploits a novel surface glycan (NGR) as a receptor to infect its host Escherichia coli. We demonstrate that this process is regulated by the second messenger c-di-GMP and that N4 infection is specifically stimulated by the diguanylate cyclase DgcJ, while the phosphodiesterase PdeL effectively protects E. coli from N4-mediated killing. PdeL-mediated protection requires its catalytic activity to reduce c-di-GMP and includes a secondary role as a transcriptional repressor. We demonstrate that PdeL binds to and represses the promoter of the wec operon, which encodes components of the enterobacterial common antigen (ECA) exopolysaccharide pathway. However, only the acetylglucosamine epimerase WecB but none of the other ECA components is required for N4 infection. Based on this, we postulate that NGR is an N-acetylmannosamine-based carbohydrate polymer that is produced and exported to the cell surface of E. coli in a c-di-GMP-dependent manner, where it serves as a receptor for N4. This novel carbohydrate pathway is conserved in E. coli and other bacterial pathogens, serves as the primary receptor for various bacteriophages, and is induced at elevated temperature and by specific amino acid-based nutrients. These studies provide an entry point into understanding how bacteria use specific regulatory mechanisms to balance costs and benefits of highly conserved surface structures.
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13
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Dharshini RS, Manickam R, Curtis WR, Rathinasabapathi P, Ramya M. Genome analysis of alginate synthesizing Pseudomonas aeruginosa strain SW1 isolated from degraded seaweeds. Antonie van Leeuwenhoek 2021; 114:2205-2217. [PMID: 34661815 DOI: 10.1007/s10482-021-01673-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/07/2021] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa strain SW1 is an aerobic, motile, Gram-negative, and rod-shaped bacterium isolated from degraded seaweeds. Based on the 16S rRNA gene sequence and MALDI TOF analysis, strain SW1 exhibits 100% similarity to P. aeruginosa DSM 50,071, its closest phylogenetic neighbor. The complete genome of strain SW1 consists of a single circular chromosome with 23,258,857 bp (G + C content of 66%), including 6734 protein-coding sequences, 8 rRNA, and 63 tRNA sequences. The genome of the P. aeruginosa SW1 contains at least 27 genes for the biosynthesis of alginate and other exopolysaccharide involved in biofilm formation. KAAS and GO analysis and functional annotation by COG and CAZymes are consistent with the biosynthesis of alginate. In addition, the presence of antimicrobial resistance, multi-efflux operon, and antibiotic inactivation genes indicate a pathogenic potential similar to strain DSM50071. The high-quality genome and associated annotation provide a starting point to exploit the potential for P. aeruginosa to produce alginate.
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Affiliation(s)
- Rajathirajan Siva Dharshini
- Faculty of Engineering and Technology, Molecular Genetics Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, 603203, India
| | - Ranjani Manickam
- SRM-DBT Platform for Advanced Life Science Technologies, SRMIST, Chengalpattu, Chennai, Tamil Nadu, 603203, India
| | - Wayne R Curtis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Pasupathi Rathinasabapathi
- Faculty of Engineering and Technology, Molecular Genetics Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, 603203, India
| | - Mohandass Ramya
- Faculty of Engineering and Technology, Molecular Genetics Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, 603203, India.
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14
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Abstract
Microbes are hardly seen as planktonic species and are most commonly found as biofilm communities in cases of chronic infections. Biofilms are regarded as a biological condition, where a large group of microorganisms gets adhered to a biotic or abiotic surface. In this context, Pseudomonas aeruginosa, a Gram-negative nosocomial pathogen is the main causative organism responsible for life-threatening and persistent infections in individuals affected with cystic fibrosis and other lung ailments. The bacteria can form a strong biofilm structure when it adheres to a surface suitable for the development of a biofilm matrix. These bacterial biofilms pose higher natural resistance to conventional antibiotic therapy due to their multiple tolerance mechanisms. This prevailing condition has led to an increasing rate of treatment failures associated with P. aeruginosa biofilm infections. A better understanding of the effect of a diverse group of antibiotics on established biofilms would be necessary to avoid inappropriate treatment strategies. Hence, the search for other alternative strategies as effective biofilm treatment options has become a growing area of research. The current review aims to give an overview of the mechanisms governing biofilm formation and the different strategies employed so far in the control of biofilm infections caused by P. aeruginosa. Moreover, this review can also help researchers to search for new antibiofilm agents to tackle the effect of biofilm infections that are currently imprudent to conventional antibiotics.
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15
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Kim SK, Ngo HX, Dennis EK, Thamban Chandrika N, DeShong P, Garneau-Tsodikova S, Lee VT. Inhibition of Pseudomonas aeruginosa Alginate Synthesis by Ebselen Oxide and Its Analogues. ACS Infect Dis 2021; 7:1713-1726. [PMID: 33871968 DOI: 10.1021/acsinfecdis.1c00045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that is frequently found in the airways of cystic fibrosis (CF) patients due to the dehydrated mucus that collapses the underlying cilia and prevents mucociliary clearance. During this life-long chronic infection, P. aeruginosa cell accumulates mutations that lead to inactivation of the mucA gene that results in the constitutive expression of algD-algA operon and the production of alginate exopolysaccharide. The viscous alginate polysaccharide further occludes the airways of CF patients and serves as a protective matrix to shield P. aeruginosa from host immune cells and antibiotic therapy. Development of inhibitors of alginate production by P. aeruginosa would reduce the negative impact from this viscous polysaccharide. In addition to transcriptional regulation, alginate biosynthesis requires allosteric activation by bis (3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) binding to an Alg44 protein. Previously, we found that ebselen (Eb) and ebselen oxide (EbO) inhibited diguanylate cyclase from synthesizing c-di-GMP. In this study, we show that EbO, Eb, ebsulfur (EbS), and their analogues inhibit alginate production. Eb and EbS can covalently modify the cysteine 98 (C98) residue of Alg44 and prevent its ability to bind c-di-GMP. However, P. aeruginosa with Alg44 C98 substituted with alanine or serine was still inhibited for alginate production by Eb and EbS. Our results indicate that EbO, Eb, and EbS are lead compounds for reducing alginate production by P. aeruginosa. Future development of these inhibitors could provide a potential treatment for CF patients infected with mucoid P. aeruginosa.
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Affiliation(s)
- Soo-Kyoung Kim
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, Maryland 20742, United States
| | - Huy X. Ngo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Emily K. Dennis
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Philip DeShong
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, Maryland 20742, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Vincent T. Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, Maryland 20742, United States
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16
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Cooper B, Beard HS, Yang R, Garrett WM, Campbell KB. Bacterial Immobilization and Toxicity Induced by a Bean Plant Immune System. J Proteome Res 2021; 20:3664-3677. [PMID: 34097416 DOI: 10.1021/acs.jproteome.1c00232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudomonas savastanoi pv. phaseolicola causes halo blight disease in the common bean Phaseolus vulgaris. The bacterium invades the leaf apoplast and uses a type III secretion system to inject effector proteins into a bean cell to interfere with the bean immune system. Beans counter with resistance proteins that can detect effectors and coordinate effector-triggered immunity responses transduced by salicylic acid, the primary defense hormone. Effector-triggered immunity halts bacterial spread, but its direct effect on the bacterium is not known. In this study, mass spectrometry of bacterial infections from immune and susceptible beans revealed that immune beans inhibited the accumulation of bacterial proteins required for virulence, secretion, motility, chemotaxis, quorum sensing, and alginate production. Sets of genes encoding these proteins appeared to function in operons, which implies that immunity altered the coregulated genes in the bacterium. Immunity also reduced amounts of bacterial methylglyoxal detoxification enzymes and their transcripts. Treatment of bacteria with salicylic acid, the plant hormone produced during immunity, reduced bacterial growth, decreased gene expression for methylglyoxal detoxification enzymes, and increased bacterial methylglyoxal concentrations in vitro. Increased methylglyoxal concentrations reduced bacterial reproduction. These findings support the hypothesis that plant immunity involves the chemical induction of adverse changes to the bacterial proteome to reduce pathogenicity and to cause bacterial self-toxicity.
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Affiliation(s)
- Bret Cooper
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville 20705, Maryland, United States
| | - Hunter S Beard
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville 20705, Maryland, United States
| | - Ronghui Yang
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville 20705, Maryland, United States
| | - Wesley M Garrett
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville 20705, Maryland, United States
| | - Kimberly B Campbell
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville 20705, Maryland, United States
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17
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Ageorges V, Monteiro R, Leroy S, Burgess CM, Pizza M, Chaucheyras-Durand F, Desvaux M. Molecular determinants of surface colonisation in diarrhoeagenic Escherichia coli (DEC): from bacterial adhesion to biofilm formation. FEMS Microbiol Rev 2021; 44:314-350. [PMID: 32239203 DOI: 10.1093/femsre/fuaa008] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/31/2020] [Indexed: 12/11/2022] Open
Abstract
Escherichia coli is primarily known as a commensal colonising the gastrointestinal tract of infants very early in life but some strains being responsible for diarrhoea, which can be especially severe in young children. Intestinal pathogenic E. coli include six pathotypes of diarrhoeagenic E. coli (DEC), namely, the (i) enterotoxigenic E. coli, (ii) enteroaggregative E. coli, (iii) enteropathogenic E. coli, (iv) enterohemorragic E. coli, (v) enteroinvasive E. coli and (vi) diffusely adherent E. coli. Prior to human infection, DEC can be found in natural environments, animal reservoirs, food processing environments and contaminated food matrices. From an ecophysiological point of view, DEC thus deal with very different biotopes and biocoenoses all along the food chain. In this context, this review focuses on the wide range of surface molecular determinants acting as surface colonisation factors (SCFs) in DEC. In the first instance, SCFs can be broadly discriminated into (i) extracellular polysaccharides, (ii) extracellular DNA and (iii) surface proteins. Surface proteins constitute the most diverse group of SCFs broadly discriminated into (i) monomeric SCFs, such as autotransporter (AT) adhesins, inverted ATs, heat-resistant agglutinins or some moonlighting proteins, (ii) oligomeric SCFs, namely, the trimeric ATs and (iii) supramolecular SCFs, including flagella and numerous pili, e.g. the injectisome, type 4 pili, curli chaperone-usher pili or conjugative pili. This review also details the gene regulatory network of these numerous SCFs at the various stages as it occurs from pre-transcriptional to post-translocational levels, which remains to be fully elucidated in many cases.
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Affiliation(s)
- Valentin Ageorges
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Ricardo Monteiro
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,GSK, Via Fiorentina 1, 53100 Siena, Italy
| | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Catherine M Burgess
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | | | - Frédérique Chaucheyras-Durand
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,Lallemand Animal Nutrition SAS, F-31702 Blagnac Cedex, France
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
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18
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Structure of the Bacterial Cellulose Ribbon and Its Assembly-Guiding Cytoskeleton by Electron Cryotomography. J Bacteriol 2021; 203:JB.00371-20. [PMID: 33199282 PMCID: PMC7811197 DOI: 10.1128/jb.00371-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/26/2020] [Indexed: 12/20/2022] Open
Abstract
This work’s relevance for the microbiology community is twofold. It delivers for the first time high-resolution near-native snapshots of Gluconacetobacter spp. (previously Komagataeibacter spp.) in the process of cellulose ribbon synthesis, in their native biofilm environment. Cellulose is a widespread component of bacterial biofilms, where its properties of exceptional water retention, high tensile strength, and stiffness prevent dehydration and mechanical disruption of the biofilm. Bacteria in the genus Gluconacetobacter secrete crystalline cellulose, with a structure very similar to that found in plant cell walls. How this higher-order structure is produced is poorly understood. We used cryo-electron tomography and focused-ion-beam milling of native bacterial biofilms to image cellulose-synthesizing Gluconacetobacter hansenii and Gluconacetobacter xylinus bacteria in a frozen-hydrated, near-native state. We confirm previous results suggesting that cellulose crystallization occurs serially following its secretion along one side of the cell, leading to a cellulose ribbon that can reach several micrometers in length and combine with ribbons from other cells to form a robust biofilm matrix. We were able to take direct measurements in a near-native state of the cellulose sheets. Our results also reveal a novel cytoskeletal structure, which we have named the cortical belt, adjacent to the inner membrane and underlying the sites where cellulose is seen emerging from the cell. We found that this structure is not present in other cellulose-synthesizing bacterial species, Agrobacterium tumefaciens and Escherichia coli 1094, which do not produce organized cellulose ribbons. We therefore propose that the cortical belt holds the cellulose synthase complexes in a line to form higher-order cellulose structures, such as sheets and ribbons. IMPORTANCE This work’s relevance for the microbiology community is twofold. It delivers for the first time high-resolution near-native snapshots of Gluconacetobacter spp. (previously Komagataeibacter spp.) in the process of cellulose ribbon synthesis, in their native biofilm environment. It puts forward a noncharacterized cytoskeleton element associated with the side of the cell where the cellulose synthesis occurs. This represents a step forward in the understanding of the cell-guided process of crystalline cellulose synthesis, studied specifically in the Gluconacetobacter genus and still not fully understood. Additionally, our successful attempt to use cryo-focused-ion-beam milling through biofilms to image the cells in their native environment will drive the community to use this tool for the morphological characterization of other studied biofilms.
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19
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Liston SD, Willis LM. Racing to build a wall: glycoconjugate assembly in Gram-positive and Gram-negative bacteria. Curr Opin Struct Biol 2021; 68:55-65. [PMID: 33429200 DOI: 10.1016/j.sbi.2020.11.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/17/2022]
Abstract
The last two years have seen major advances in understanding the structural basis of bacterial cell envelope glycoconjugate biosynthesis, including capsules, lipopolysaccharide, teichoic acid, cellulose, and peptidoglycan. The recent crystal and cryo-electron microscopy structures of proteins involved in the initial glycosyltransferase steps in the cytoplasm, the transport of large and small lipid-linked glycoconjugates across the inner membrane, the polymerization of glycans in the periplasm, and the export of molecules from the cell have shed light on the mechanisms by which cell envelope glycoconjugates are made. We discuss these recent advances and highlight remaining unanswered questions.
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Affiliation(s)
- Sean D Liston
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G1M1, Canada
| | - Lisa M Willis
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G2T2, Canada; Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G2T2, Canada; Women and Children's Health Research Institute, Edmonton, AB, T6G2T2, Canada.
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20
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Scott W, Lowrance B, Anderson AC, Weadge JT. Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ. PLoS One 2020; 15:e0242686. [PMID: 33264329 PMCID: PMC7710045 DOI: 10.1371/journal.pone.0242686] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 11/09/2020] [Indexed: 01/10/2023] Open
Abstract
Biofilms are community structures of bacteria enmeshed in a self-produced matrix of exopolysaccharides. The biofilm matrix serves numerous roles, including resilience and persistence, making biofilms a subject of research interest among persistent clinical pathogens of global health importance. Our current understanding of the underlying biochemical pathways responsible for biosynthesis of these exopolysaccharides is largely limited to Gram-negative bacteria. Clostridia are a class of Gram-positive, anaerobic and spore-forming bacteria and include the important human pathogens Clostridium perfringens, Clostridium botulinum and Clostridioides difficile, among numerous others. Several species of Clostridia have been reported to produce a biofilm matrix that contains an acetylated glucan linked to a series of hypothetical genes. Here, we propose a model for the function of these hypothetical genes, which, using homology modelling, we show plausibly encode a synthase complex responsible for polymerization, modification and export of an O-acetylated cellulose exopolysaccharide. Specifically, the cellulose synthase is homologous to that of the known exopolysaccharide synthases in Gram-negative bacteria. The remaining proteins represent a mosaic of evolutionary lineages that differ from the described Gram-negative cellulose exopolysaccharide synthases, but their predicted functions satisfy all criteria required for a functional cellulose synthase operon. Accordingly, we named these hypothetical genes ccsZABHI, for the Clostridial cellulose synthase (Ccs), in keeping with naming conventions for exopolysaccharide synthase subunits and to distinguish it from the Gram-negative Bcs locus with which it shares only a single one-to-one ortholog. To test our model and assess the identity of the exopolysaccharide, we subcloned the putative glycoside hydrolase encoded by ccsZ and solved the X-ray crystal structure of both apo- and product-bound CcsZ, which belongs to glycoside hydrolase family 5 (GH-5). Although not homologous to the Gram-negative cellulose synthase, which instead encodes the structurally distinct BcsZ belonging to GH-8, we show CcsZ displays specificity for cellulosic materials. This specificity of the synthase-associated glycosyl hydrolase validates our proposal that these hypothetical genes are responsible for biosynthesis of a cellulose exopolysaccharide. The data we present here allowed us to propose a model for Clostridial cellulose synthesis and serves as an entry point to an understanding of cellulose biofilm formation among class Clostridia.
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Affiliation(s)
- William Scott
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Brian Lowrance
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
| | | | - Joel T. Weadge
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
- * E-mail:
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21
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Whitfield C, Wear SS, Sande C. Assembly of Bacterial Capsular Polysaccharides and Exopolysaccharides. Annu Rev Microbiol 2020; 74:521-543. [PMID: 32680453 DOI: 10.1146/annurev-micro-011420-075607] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polysaccharides are dominant features of most bacterial surfaces and are displayed in different formats. Many bacteria produce abundant long-chain capsular polysaccharides, which can maintain a strong association and form a capsule structure enveloping the cell and/or take the form of exopolysaccharides that are mostly secreted into the immediate environment. These polymers afford the producing bacteria protection from a wide range of physical, chemical, and biological stresses, support biofilms, and play critical roles in interactions between bacteria and their immediate environments. Their biological and physical properties also drive a variety of industrial and biomedical applications. Despite the immense variation in capsular polysaccharide and exopolysaccharide structures, patterns are evident in strategies used for their assembly and export. This review describes recent advances in understanding those strategies, based on a wealth of biochemical investigations of select prototypes, supported by complementary insight from expanding structural biology initiatives. This provides a framework to identify and distinguish new systems emanating from genomic studies.
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Affiliation(s)
- Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada;
| | - Samantha S Wear
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada;
| | - Caitlin Sande
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada;
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22
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Anderson AC, Burnett AJN, Hiscock L, Maly KE, Weadge JT. The Escherichia coli cellulose synthase subunit G (BcsG) is a Zn 2+-dependent phosphoethanolamine transferase. J Biol Chem 2020; 295:6225-6235. [PMID: 32152228 DOI: 10.1074/jbc.ra119.011668] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/05/2020] [Indexed: 01/08/2023] Open
Abstract
Bacterial biofilms are cellular communities that produce an adherent matrix. Exopolysaccharides are key structural components of this matrix and are required for the assembly and architecture of biofilms produced by a wide variety of microorganisms. The human bacterial pathogens Escherichia coli and Salmonella enterica produce a biofilm matrix composed primarily of the exopolysaccharide phosphoethanolamine (pEtN) cellulose. Once thought to be composed of only underivatized cellulose, the pEtN modification present in these matrices has been implicated in the overall architecture and integrity of the biofilm. However, an understanding of the mechanism underlying pEtN derivatization of the cellulose exopolysaccharide remains elusive. The bacterial cellulose synthase subunit G (BcsG) is a predicted inner membrane-localized metalloenzyme that has been proposed to catalyze the transfer of the pEtN group from membrane phospholipids to cellulose. Here we present evidence that the C-terminal domain of BcsG from E. coli (EcBcsGΔN) functions as a phosphoethanolamine transferase in vitro with substrate preference for cellulosic materials. Structural characterization of EcBcsGΔN revealed that it belongs to the alkaline phosphatase superfamily, contains a Zn2+ ion at its active center, and is structurally similar to characterized enzymes that confer colistin resistance in Gram-negative bacteria. Informed by our structural studies, we present a functional complementation experiment in E. coli AR3110, indicating that the activity of the BcsG C-terminal domain is essential for integrity of the pellicular biofilm. Furthermore, our results established a similar but distinct active-site architecture and catalytic mechanism shared between BcsG and the colistin resistance enzymes.
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Affiliation(s)
- Alexander C Anderson
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Alysha J N Burnett
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Lana Hiscock
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada; Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Kenneth E Maly
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Joel T Weadge
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada.
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23
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Brunkard JO, Xu M, Scarpin MR, Chatterjee S, Shemyakina EA, Goodman HM, Zambryski P. TOR dynamically regulates plant cell-cell transport. Proc Natl Acad Sci U S A 2020; 117:5049-5058. [PMID: 32051250 PMCID: PMC7060719 DOI: 10.1073/pnas.1919196117] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The coordinated redistribution of sugars from mature "source" leaves to developing "sink" leaves requires tight regulation of sugar transport between cells via plasmodesmata (PD). Although fundamental to plant physiology, the mechanisms that control PD transport and thereby support development of new leaves have remained elusive. From a forward genetic screen for altered PD transport, we discovered that the conserved eukaryotic glucose-TOR (TARGET OF RAPAMYCIN) metabolic signaling network restricts PD transport in leaves. Genetic approaches and chemical or physiological treatments to either promote or disrupt TOR activity demonstrate that glucose-activated TOR decreases PD transport in leaves. We further found that TOR is significantly more active in mature leaves photosynthesizing excess sugars than in young, growing leaves, and that this increase in TOR activity correlates with decreased rates of PD transport. We conclude that leaf cells regulate PD trafficking in response to changing carbohydrate availability monitored by the TOR pathway.
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Affiliation(s)
- Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720;
- Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710
- Innovative Genomics Institute, Berkeley, CA 94720
| | - Min Xu
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720
- Department of Biology, Northwest University, 710069 Xi'an, China
| | - M Regina Scarpin
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720
- Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710
| | - Snigdha Chatterjee
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720
- Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710
- Innovative Genomics Institute, Berkeley, CA 94720
| | - Elena A Shemyakina
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720
- Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710
| | - Howard M Goodman
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720
| | - Patricia Zambryski
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720;
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24
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Acheson JF, Derewenda ZS, Zimmer J. Architecture of the Cellulose Synthase Outer Membrane Channel and Its Association with the Periplasmic TPR Domain. Structure 2019; 27:1855-1861.e3. [PMID: 31604608 PMCID: PMC6939607 DOI: 10.1016/j.str.2019.09.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/12/2019] [Accepted: 09/16/2019] [Indexed: 02/06/2023]
Abstract
Extracellular bacterial cellulose contributes to biofilm stability and to the integrity of the bacterial cell envelope. In Gram-negative bacteria, cellulose is synthesized and secreted by a multi-component cellulose synthase complex. The BcsA subunit synthesizes cellulose and also transports the polymer across the inner membrane. Translocation across the outer membrane occurs through the BcsC porin, which extends into the periplasm via 19 tetra-tricopeptide repeats (TPR). We present the crystal structure of a truncated BcsC, encompassing the last TPR repeat and the complete outer membrane channel domain, revealing a 16-stranded, β barrel pore architecture. The pore is blocked by an extracellular gating loop, while the extended C terminus inserts deeply into the channel and positions a conserved Trp residue near its extracellular exit. The channel is lined with hydrophilic and aromatic residues suggesting a mechanism for facilitated cellulose diffusion based on aromatic stacking and hydrogen bonding.
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Affiliation(s)
- Justin F Acheson
- University of Virginia, School of Medicine, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22903, USA
| | - Zygmunt S Derewenda
- University of Virginia, School of Medicine, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22903, USA
| | - Jochen Zimmer
- University of Virginia, School of Medicine, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22903, USA.
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25
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Salgado L, Blank S, Esfahani RAM, Strap JL, Bonetta D. Missense mutations in a transmembrane domain of the Komagataeibacter xylinus BcsA lead to changes in cellulose synthesis. BMC Microbiol 2019; 19:216. [PMID: 31514737 PMCID: PMC6740014 DOI: 10.1186/s12866-019-1577-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cellulose is synthesized by an array of bacterial species. Komagataeibacter xylinus is the best characterized as it produces copious amounts of the polymer extracellularly. Despite many advances in the past decade, the mechanisms underlying cellulose biosynthesis are not completely understood. Elucidation of these mechanisms is essential for efficient cellulose production in industrial applications. RESULTS In an effort to gain a better understanding of cellulose biosynthesis and its regulation, cellulose crystallization was investigated in K. xylinus mutants resistant to an inhibitor of cellulose I formation, pellicin. Through the use of forward genetics and site-directed mutagenesis, A449T and A449V mutations in the K. xylinus BcsA protein were found to be important for conferring high levels of pellicin resistance. Phenotypic analysis of the bcsAA449T and bcsAA449V cultures revealed that the mutations affect cellulose synthesis rates and that cellulose crystallinity is affected in wet pellicles but not dry ones. CONCLUSIONS A449 is located in a predicted transmembrane domain of the BcsA protein suggesting that the structure of the transmembrane domain influences cellulose crystallization either by affecting the translocation of the nascent glucan chain or by allosterically altering protein-protein interactions.
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Affiliation(s)
- Luis Salgado
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Canada
| | - Silvia Blank
- Evonik Industries AG, Rellinghauser Straße 1-11 45128, Essen, Germany
| | | | - Janice L Strap
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Canada
| | - Dario Bonetta
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Canada.
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26
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Taweecheep P, Naloka K, Matsutani M, Yakushi T, Matsushita K, Theeragool G. Superfine bacterial nanocellulose produced by reverse mutations in the bcsC gene during adaptive breeding of Komagataeibacter oboediens. Carbohydr Polym 2019; 226:115243. [PMID: 31582059 DOI: 10.1016/j.carbpol.2019.115243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 12/30/2022]
Abstract
Nonsense mutation in the bcsC gene occurred in the ethanol-adapted strain of Komagataeibacter oboediens MSKU 3, E3 strain, resulting in the loss of the function to produce BNC. In this study, we tried to restore the BNC-producing ability of E3 strain by the following adaptive mutation through repetitive static culture, and obtained four BNC-producing revertant strains, of which the bcsC gene had InDel mutations near the frameshift mutation region in E3 strain, resulting in several amino acid alterations compared with the BcsC of MSKU 3. Each revertant produced BNCs with different productivity on the static culture. Interestingly, one of the revertants, R37-9, produced BNC with a finer structure and narrower range of fibrils width, compared to others. The genome of R37-9 strain revealed only one amino acid substitution in the bcsC gene. Thus, we concluded that N713D mutation occurred in the bcsC gene is responsible for the finer fibrils structure.
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Affiliation(s)
- Pornchanok Taweecheep
- Interdisciplinary Graduate Program in Genetic Engineering, The Graduate School, Kasetsart University, Bangkok 10900, Thailand.
| | - Kallayanee Naloka
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Minenosuke Matsutani
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | - Toshiharu Yakushi
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | - Kazunobu Matsushita
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | - Gunjana Theeragool
- Interdisciplinary Graduate Program in Genetic Engineering, The Graduate School, Kasetsart University, Bangkok 10900, Thailand; Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
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27
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Zimmer J. Structural features underlying recognition and translocation of extracellular polysaccharides. Interface Focus 2019; 9:20180060. [PMID: 30842868 DOI: 10.1098/rsfs.2018.0060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2019] [Indexed: 12/31/2022] Open
Abstract
Essentially all living systems produce complex carbohydrates as an energy source, structural component, protective coat or adhesive for cell attachment. Many polysaccharides are displayed on the cell surface or are threaded through proteinaceous tunnels for degradation. Dictated by their chemical composition and mode of polymerization, the physical properties of complex carbohydrates differ substantially, from amphipathic water-insoluble polymers to highly hydrated hydrogel-forming macromolecules. Accordingly, diverse recognition and translocation mechanisms evolved to transport polysaccharides to their final destinations. This review will summarize and compare diverse polysaccharide transport mechanisms implicated in the biosynthesis and degradation of cell surface polymers in pro- and eukaryotes.
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Affiliation(s)
- Jochen Zimmer
- University of Virginia, 480 Ray C. Hunt Dr., Charlottesville, VA 22903, USA
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28
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Low KE, Howell PL. Gram-negative synthase-dependent exopolysaccharide biosynthetic machines. Curr Opin Struct Biol 2018; 53:32-44. [DOI: 10.1016/j.sbi.2018.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/03/2018] [Accepted: 05/07/2018] [Indexed: 11/16/2022]
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29
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Gullo M, La China S, Falcone PM, Giudici P. Biotechnological production of cellulose by acetic acid bacteria: current state and perspectives. Appl Microbiol Biotechnol 2018; 102:6885-6898. [PMID: 29926141 DOI: 10.1007/s00253-018-9164-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 12/17/2022]
Abstract
Bacterial cellulose is an attractive biopolymer for a number of applications including food, biomedical, cosmetics, and engineering fields. In addition to renewability and biodegradability, its unique structure and properties such as chemical purity, nanoscale fibrous 3D network, high water-holding capacity, high degree of polymerization, high crystallinity index, light transparency, biocompatibility, and mechanical features offer several advantages when it is used as native polymer or in composite materials. Structure and properties play a functional role in both the biofilm life cycle and biotechnological applications. Among all the cellulose-producing bacteria, acetic acid bacteria of the Komagataeibacter xylinus species play the most important role because they are considered the highest producers. Bacterial cellulose from acetic acid bacteria is widely investigated as native and modified biopolymer in functionalized materials, as well as in terms of differences arising from the static or submerged production system. In this paper, the huge amount of knowledge on basic and applied aspects of bacterial cellulose is reviewed to the aim to provide a comprehensive viewpoint on the intriguing interplay between the biological machinery of synthesis, the native structure, and the factors determining its nanostructure and applications. Since in acetic acid bacteria biofilm and cellulose production are two main phenotypes with industrial impact, new insights into biofilm production are provided.
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Affiliation(s)
- Maria Gullo
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Amendola, 2, Pad. Besta, 42122, Reggio Emilia, Italy.
| | - Salvatore La China
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Amendola, 2, Pad. Besta, 42122, Reggio Emilia, Italy
| | - Pasquale Massimiliano Falcone
- Department of Agricultural, Food and Environmental Sciences, University Polytechnical of Marche, Brecce Bianche 2, Ancona, Italy
| | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Amendola, 2, Pad. Besta, 42122, Reggio Emilia, Italy
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30
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Lotfy WA, Atalla RG, Sabra WA, El-Helow ER. Expression of extracellular polysaccharides and proteins by clinical isolates of Pseudomonas aeruginosa in response to environmental conditions. Int Microbiol 2018; 21:129-142. [PMID: 30810953 DOI: 10.1007/s10123-018-0010-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 11/25/2022]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa causes chronic respiratory infections in patients with cystic fibrosis (CF). Persistence of this bacterium is attributed to its ability to form biofilms which rely on an extracellular polymeric substance matrix. Extracellular polysaccharides (EPS) and secreted proteins are key matrix components of P. aeruginosa biofilms. Recently, nebulized magnesium sulfate has been reported as a significant bronchodilator for asthmatic patients including CF. However, the impact of magnesium sulfate on the virulence effect of P. aeruginosa is lacking. In this report, we investigated the influence of magnesium sulfate and other environmental factors on the synthesis of alginate and secretion of proteins by a mucoid and a non-mucoid strain of P. aeruginosa, respectively. By applying the Plackett-Burman and Box-Behnken experimental designs, we found that phosphates (6.0 g/l), ammonium sulfate (4.0 g/l), and trace elements (0.6 mg/l) markedly supported alginate production by the mucoid strain. However, ferrous sulfate (0.3 mg/l), magnesium sulfate (0.02 g/l), and phosphates (6.0 g/l) reinforced the secretion of proteins by the non-mucoid strain.
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Affiliation(s)
- Walid A Lotfy
- Microbiology Department, Faculty of Dentistry, Pharos University in Alexandria, Alexandria, Egypt.
| | - Ramy G Atalla
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Wael A Sabra
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Ehab R El-Helow
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, Egypt
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31
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Gao N, Xia M, Dai J, Yu D, An W, Li S, Liu S, He P, Zhang L, Wu Z, Bi X, Chen S, Haft DH, Qiu D. Both widespread PEP-CTERM proteins and exopolysaccharides are required for floc formation of Zoogloea resiniphila and other activated sludge bacteria. Environ Microbiol 2018; 20:1677-1692. [PMID: 29473278 DOI: 10.1111/1462-2920.14080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/12/2018] [Accepted: 02/19/2018] [Indexed: 12/28/2022]
Abstract
Bacterial floc formation plays a central role in the activated sludge (AS) process, which has been widely utilized for sewage and wastewater treatment. The formation of AS flocs has long been known to require exopolysaccharide biosynthesis. This study demonstrates an additional requirement for a PEP-CTERM protein in Zoogloea resiniphila, a dominant AS bacterium harboring a large exopolysaccharide biosynthesis gene cluster. Two members of a wide-spread family of high copy number-per-genome PEP-CTERM genes, transcriptionally regulated by the RpoN sigma factor and accessory PrsK-PrsR two-component system and at least one of these, pepA, must be expressed for Zoogloea to build the floc structures that allow gravitational sludge settling and recycling. Without PrsK or PrsR, Zoogloea cells were planktonic rather than flocculated and secreted exopolysaccharides were released into the growth broth in soluble form. Overexpression of PepA could circumvent the requirement of rpoN, prsK and prsR for the floc-forming phenotype by fixing the exopolysaccharides to bacterial cells. However, overexpression of PepA, which underwent post-translational modifications, could not rescue the long-rod morphology of the rpoN mutant. Consistently, PEP-CTERM genes and exopolysaccharide biosynthesis gene cluster are present in the genome of the floc-forming Nitrospira comammox and Mitsuaria strain as well as many other AS bacteria.
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Affiliation(s)
- Na Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dianzhen Yu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Weixing An
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shuyang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shuangyuan Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Penghui He
- College of Life Sciences, Hubei University, Wuhan 430070, China
| | - Liping Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhenbin Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xuezhi Bi
- Agency for Science, Technology and Research, Bioprocessing Technology Institute, Singapore 138668, Singapore
| | - Shouwen Chen
- College of Life Sciences, Hubei University, Wuhan 430070, China
| | - Daniel H Haft
- National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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32
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Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum T. Appl Environ Microbiol 2018; 84:AEM.02091-17. [PMID: 29150517 PMCID: PMC5772234 DOI: 10.1128/aem.02091-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/09/2017] [Indexed: 11/20/2022] Open
Abstract
Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647T (here referred to as Leptospirillum ferriphilum T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum T obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS2). Adaptations of Leptospirillum ferriphilum T to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCE Leptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilum T coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilum T for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction.
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33
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Abstract
Agrobacterium exopolysaccharides play a major role in the life of the cell. Exopolysaccharides are required for bacterial growth as a biofilm and they protect the bacteria against environmental stresses. Five of the exopolysaccharides made by A. tumefaciens have been characterized extensively with respect to their structure, synthesis, regulation, and role in the life of the bacteria. These are cyclic-β-(1, 2)-glucan, cellulose, curdlan, succinoglycan, and the unipolar polysaccharide (UPP). This chapter describes the structure, synthesis, regulation, and function of these five exopolysaccharides.
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34
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Nojima S, Fujishima A, Kato K, Ohuchi K, Shimizu N, Yonezawa K, Tajima K, Yao M. Crystal structure of the flexible tandem repeat domain of bacterial cellulose synthesis subunit C. Sci Rep 2017; 7:13018. [PMID: 29026093 PMCID: PMC5638805 DOI: 10.1038/s41598-017-12530-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/12/2017] [Indexed: 01/20/2023] Open
Abstract
Bacterial cellulose (BC) is synthesized and exported through the cell membrane via a large protein complex (terminal complex) that consists of three or four subunits. BcsC is a little-studied subunit considered to export BC to the extracellular matrix. It is predicted to have two domains: a tetratrico peptide repeat (TPR) domain and a β-barrelled outer membrane domain. Here we report the crystal structure of the N-terminal part of BcsC-TPR domain (Asp24-Arg272) derived from Enterobacter CJF-002. Unlike most TPR-containing proteins which have continuous TPR motifs, this structure has an extra α-helix between two clusters of TPR motifs. Five independent molecules in the crystal had three different conformations that varied at the hinge of the inserted α-helix. Such structural feature indicates that the inserted α-helix confers flexibility to the chain and changes the direction of the TPR super-helix, which was also suggested by structural analysis of BcsC-TPR (Asp24-Leu664) in solution by size exclusion chromatography-small-angle X-ray scattering. The flexibility at the α-helical hinge may play important role for exporting glucan chains.
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Affiliation(s)
- Shingo Nojima
- Graduate school of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Ayumi Fujishima
- Graduate school of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Koji Kato
- Graduate school of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Kayoko Ohuchi
- Graduate school of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Kento Yonezawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Kenji Tajima
- Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
| | - Min Yao
- Graduate school of Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan. .,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
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35
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Marmont LS, Whitfield GB, Rich JD, Yip P, Giesbrecht LB, Stremick CA, Whitney JC, Parsek MR, Harrison JJ, Howell PL. PelA and PelB proteins form a modification and secretion complex essential for Pel polysaccharide-dependent biofilm formation in Pseudomonas aeruginosa. J Biol Chem 2017; 292:19411-19422. [PMID: 28972168 DOI: 10.1074/jbc.m117.812842] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/14/2017] [Indexed: 11/06/2022] Open
Abstract
The pellicle (PEL) polysaccharide is synthesized by the opportunistic pathogen Pseudomonas aeruginosa and is an important biofilm constituent critical for bacterial virulence and persistence. PEL is a cationic polymer that promotes cell-cell interactions within the biofilm matrix through electrostatic interactions with extracellular DNA. Translocation of PEL across the outer membrane is proposed to occur via PelB, a membrane-embedded porin with a large periplasmic domain predicted to contain 19 tetratricopeptide repeats (TPRs). TPR-containing domains are typically involved in protein-protein interactions, and we therefore sought to determine whether PelB serves as a periplasmic scaffold that recruits other components of the PEL secretion apparatus. In this study, we show that the TPR domain of PelB interacts with PelA, an enzyme with PEL deacetylase and hydrolase activities. Structure determination of PelB TPRs 8-11 enabled us to design systematic deletions of individual TPRs and revealed that repeats 9-14, which are required for the cellular localization of PelA with PelB are also essential for PEL-dependent biofilm formation. Copurification experiments indicated that the interaction between PelA and PelB is direct and that the deacetylase activity of PelA increases and its hydrolase activity decreases when these proteins interact. Combined, our results indicate that the TPR-containing domain of PelB localizes PelA to the PEL secretion apparatus within the periplasm and that this may allow for efficient deacetylation of PEL before its export from the cell.
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Affiliation(s)
- Lindsey S Marmont
- From the Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Gregory B Whitfield
- From the Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jacquelyn D Rich
- the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada, and
| | - Patrick Yip
- From the Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Laura B Giesbrecht
- From the Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Carol A Stremick
- the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada, and
| | - John C Whitney
- From the Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Matthew R Parsek
- the Department of Microbiology, University of Washington, Seattle, Washington 98195-7242
| | - Joe J Harrison
- the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada, and
| | - P Lynne Howell
- From the Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada, .,the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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36
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Gao JX, Li P, Du XJ, Han ZH, Xue R, Liang B, Wang S. A Negative Regulator of Cellulose Biosynthesis, bcsR, Affects Biofilm Formation, and Adhesion/Invasion Ability of Cronobacter sakazakii. Front Microbiol 2017; 8:1839. [PMID: 29085341 PMCID: PMC5649176 DOI: 10.3389/fmicb.2017.01839] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/08/2017] [Indexed: 12/17/2022] Open
Abstract
Cronobacter sakazakii is an important foodborne pathogen that causes neonatal meningitis and sepsis, with high mortality in neonates. However, very little information is available regarding the pathogenesis of C. sakazakii at the genetic level. In our previous study, a cellulose biosynthesis-related gene (bcsR) was shown to be involved in C. sakazakii adhesion/invasion into epithelial cells. In this study, the detailed functions of this gene were investigated using a gene knockout technique. A bcsR knockout mutant (ΔbcsR) of C. sakazakii ATCC BAA-894 showed decreased adhesion/invasion (3.9-fold) in human epithelial cell line HCT-8. Biofilm formation by the mutant was reduced to 50% of that exhibited by the wild-type (WT) strain. Raman spectrometry was used to detect variations in biofilm components caused by bcsR knockout, and certain components, including carotenoids, fatty acids, and amides, were significantly reduced. However, another biofilm component, cellulose, was increased in ΔbcsR, suggesting that bcsR negatively affects cellulose biosynthesis. This result was also verified via RT-PCR, which demonstrated up-regulation of five crucial cellulose synthesis genes (bcsA, B, C, E, Q) in ΔbcsR. Furthermore, the expression of other virulence or biofilm-related genes, including flagellar assembly genes (fliA, C, D) and toxicity-related genes (ompA, ompX, hfq), was studied. The expression of fliC and ompA in the ΔbcsR mutant was found to be remarkably reduced compared with that in the wild-type and the others were also affected excepted ompX. In summary, bcsR is a negative regulator of cellulose biosynthesis but positively regulates biofilm formation and the adhesion/invasion ability of C. sakazakii.
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Affiliation(s)
- Jian-Xin Gao
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
| | - Ping Li
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
| | - Xin-Jun Du
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
| | - Zhong-Hui Han
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
| | - Rui Xue
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
| | - Bin Liang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, China
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37
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Yang J, Toyofuku M, Sakai R, Nomura N. Influence of the alginate production on cell-to-cell communication in Pseudomonas aeruginosa PAO1. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:239-249. [PMID: 28120378 DOI: 10.1111/1758-2229.12521] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/13/2017] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
Many bacteria communicate with each other through signalling molecules, a process known as cell-to-cell communication. During this process, it is important for the signalling molecules to: (1) reach the target cells; and (2) to be received by the cognate receptor. Barriers such as the presence of extracellular matrix may prevent signals from reaching their targets; however, the influence of the extracellular matrix on cell-to-cell communication has scarcely been studied. Here, we demonstrate that the overproduction of an extracellular matrix, alginate, in a Pseudomonas aeruginosa mucoid variant, alters cell-to-cell communication by interfering with the response to quinolone signals while having no effect on N-acyl-L-homoserine lactones. The inhibition of quinolone signalling by alginate is limited to the alginate overproducer and has no effect on neighbour cells that do not produce alginate. Our study indicates that alginate overproduction affects the cell-to-cell communication of the mucoid variant, which may results in different downstream behaviours when it emerges in the presence of the wild-type (WT).
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Affiliation(s)
- Jiayue Yang
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Masanori Toyofuku
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Department of Plant and Microbial Biology, University of Zurich, Zürich, 8008, Switzerland
| | - Ryosuke Sakai
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Nobuhiko Nomura
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
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38
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Oligomeric lipoprotein PelC guides Pel polysaccharide export across the outer membrane of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2017; 114:2892-2897. [PMID: 28242707 DOI: 10.1073/pnas.1613606114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Secreted polysaccharides are important functional and structural components of bacterial biofilms. The opportunistic pathogen Pseudomonas aeruginosa produces the cationic exopolysaccharide Pel, which protects bacteria from aminoglycoside antibiotics and contributes to biofilm architecture through ionic interactions with extracellular DNA. A bioinformatics analysis of genome databases suggests that gene clusters for Pel biosynthesis are present in >125 bacterial species, yet little is known about how this biofilm exopolysaccharide is synthesized and exported from the cell. In this work, we characterize PelC, an outer membrane lipoprotein essential for Pel production. Crystal structures of PelC from Geobacter metallireducens and Paraburkholderia phytofirmans coupled with structure-guided disulfide cross-linking in P. aeruginosa suggest that PelC assembles into a 12- subunit ring-shaped oligomer. In this arrangement, an aromatic belt in proximity to its lipidation site positions the highly electronegative surface of PelC toward the periplasm. PelC is structurally similar to the Escherichia coli amyloid exporter CsgG; however, unlike CsgG, PelC does not possess membrane-spanning segments required for polymer export across the outer membrane. We show that the multidomain protein PelB with a predicted C-terminal β-barrel porin localizes to the outer membrane, and propose that PelC functions as an electronegative funnel to guide the positively charged Pel polysaccharide toward an exit channel formed by PelB. Together, our findings provide insight into the unique molecular architecture and export mechanism of the Pel apparatus, a widespread exopolysaccharide secretion system found in environmental and pathogenic bacteria.
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Chen L, Liu S, Xu F, Kong Y, Wan L, Zhang Y, Zhang Z. Inhibition of Proteasome Activity Induces Aggregation of IFIT2 in the Centrosome and Enhances IFIT2-Induced Cell Apoptosis. Int J Biol Sci 2017; 13:383-390. [PMID: 28367102 PMCID: PMC5370445 DOI: 10.7150/ijbs.17236] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/27/2016] [Indexed: 01/18/2023] Open
Abstract
IFN-induced protein with tetratricopeptide repeats 2 (IFIT2), one of the most highly responsive interferon-stimulated genes, inhibits the proliferation and migration of cancer cells and regulates viral replication. IFIT2 has been demonstrated to be a cytoskeleton-associated protein that becomes enriched in the mitotic spindle of cells. However, the molecular mechanisms by which IFIT2 executes biological functions are largely unclear. The findings of this study showed that inhibiting the activation of proteasome led to the enrichment of IFIT2 and induced the aggregation of IFIT2 protein in the centrosome. Microtubule inhibitor colchicine and dynein inhibitor ciliobrevin inhibited the proteasome inhibitor-induced aggregation of IFIT2 protein in the centrosome. Intriguingly, IFIT2 and proteasome inhibitor worked together to induce the apoptosis of cancer cells. The results of the present study revealed that the inhibition of proteasome activity blocked the degradation of IFIT2 and promoted the aggregation of IFIT2 in the centrosome, which in turn induced cell apoptosis. In short, IFIT2 may be a potential target for cancer therapeutics.
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Affiliation(s)
- Limin Chen
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China;; Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Shuyuan Liu
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Fen Xu
- Department of Clinical Laboratory Technology, Jiangxi Medical College, Shangrao, Jiangxi 334000, China
| | - Yunyuan Kong
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Lagen Wan
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yonglu Zhang
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zhanglin Zhang
- Department of Clinical laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
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Zhu H, Sepulveda E, Hartmann MD, Kogenaru M, Ursinus A, Sulz E, Albrecht R, Coles M, Martin J, Lupas AN. Origin of a folded repeat protein from an intrinsically disordered ancestor. eLife 2016; 5:e16761. [PMID: 27623012 PMCID: PMC5074805 DOI: 10.7554/elife.16761] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/09/2016] [Indexed: 01/03/2023] Open
Abstract
Repetitive proteins are thought to have arisen through the amplification of subdomain-sized peptides. Many of these originated in a non-repetitive context as cofactors of RNA-based replication and catalysis, and required the RNA to assume their active conformation. In search of the origins of one of the most widespread repeat protein families, the tetratricopeptide repeat (TPR), we identified several potential homologs of its repeated helical hairpin in non-repetitive proteins, including the putatively ancient ribosomal protein S20 (RPS20), which only becomes structured in the context of the ribosome. We evaluated the ability of the RPS20 hairpin to form a TPR fold by amplification and obtained structures identical to natural TPRs for variants with 2-5 point mutations per repeat. The mutations were neutral in the parent organism, suggesting that they could have been sampled in the course of evolution. TPRs could thus have plausibly arisen by amplification from an ancestral helical hairpin.
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Affiliation(s)
- Hongbo Zhu
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Edgardo Sepulveda
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Manjunatha Kogenaru
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Astrid Ursinus
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eva Sulz
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Characterization of Cellulose Synthesis in Plant Cells. ScientificWorldJournal 2016; 2016:8641373. [PMID: 27314060 PMCID: PMC4897727 DOI: 10.1155/2016/8641373] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/02/2016] [Accepted: 04/28/2016] [Indexed: 12/22/2022] Open
Abstract
Cellulose is the most significant structural component of plant cell wall. Cellulose, polysaccharide containing repeated unbranched β (1-4) D-glucose units, is synthesized at the plasma membrane by the cellulose synthase complex (CSC) from bacteria to plants. The CSC is involved in biosynthesis of cellulose microfibrils containing 18 cellulose synthase (CesA) proteins. Macrofibrils can be formed with side by side arrangement of microfibrils. In addition, beside CesA, various proteins like the KORRIGAN, sucrose synthase, cytoskeletal components, and COBRA-like proteins have been involved in cellulose biosynthesis. Understanding the mechanisms of cellulose biosynthesis is of great importance not only for improving wood production in economically important forest trees to mankind but also for plant development. This review article covers the current knowledge about the cellulose biosynthesis-related gene family.
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Structure of the Cellulose Synthase Complex of Gluconacetobacter hansenii at 23.4 Å Resolution. PLoS One 2016; 11:e0155886. [PMID: 27214134 PMCID: PMC4877109 DOI: 10.1371/journal.pone.0155886] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 05/05/2016] [Indexed: 01/08/2023] Open
Abstract
Bacterial crystalline cellulose is used in biomedical and industrial applications, but the molecular mechanisms of synthesis are unclear. Unlike most bacteria, which make non-crystalline cellulose, Gluconacetobacter hansenii extrudes profuse amounts of crystalline cellulose. Its cellulose synthase (AcsA) exists as a complex with accessory protein AcsB, forming a 'terminal complex' (TC) that has been visualized by freeze-fracture TEM at the base of ribbons of crystalline cellulose. The catalytic AcsAB complex is embedded in the cytoplasmic membrane. The C-terminal portion of AcsC is predicted to form a translocation channel in the outer membrane, with the rest of AcsC possibly interacting with AcsD in the periplasm. It is thus believed that synthesis from an organized array of TCs coordinated with extrusion by AcsC and AcsD enable this bacterium to make crystalline cellulose. The only structural data that exist for this system are the above mentioned freeze-fracture TEM images, fluorescence microscopy images revealing that TCs align in a row, a crystal structure of AcsD bound to cellopentaose, and a crystal structure of PilZ domain of AcsA. Here we advance our understanding of the structural basis for crystalline cellulose production by bacterial cellulose synthase by determining a negative stain structure resolved to 23.4 Å for highly purified AcsAB complex that catalyzed incorporation of UDP-glucose into β-1,4-glucan chains, and responded to the presence of allosteric activator cyclic diguanylate. Although the AcsAB complex was functional in vitro, the synthesized cellulose was not visible in TEM. The negative stain structure revealed that AcsAB is very similar to that of the BcsAB synthase of Rhodobacter sphaeroides, a non-crystalline cellulose producing bacterium. The results indicate that the crystalline cellulose producing and non-crystalline cellulose producing bacteria share conserved catalytic and membrane translocation components, and support the hypothesis that it is the extrusion mechanism and order in linearly arrayed TCs that enables production of crystalline cellulose.
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Morgan JL, McNamara JT, Fischer M, Rich J, Chen HM, Withers SG, Zimmer J. Observing cellulose biosynthesis and membrane translocation in crystallo. Nature 2016; 531:329-34. [PMID: 26958837 PMCID: PMC4843519 DOI: 10.1038/nature16966] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 01/05/2016] [Indexed: 12/18/2022]
Abstract
Many biopolymers, including polysaccharides, must be translocated across at least one membrane to reach their site of biological function. Cellulose is a linear glucose polymer synthesized and secreted by a membrane-integrated cellulose synthase. Here, in crystallo enzymology with the catalytically active bacterial cellulose synthase BcsA-BcsB complex reveals structural snapshots of a complete cellulose biosynthesis cycle, from substrate binding to polymer translocation. Substrate- and product-bound structures of BcsA provide the basis for substrate recognition and demonstrate the stepwise elongation of cellulose. Furthermore, the structural snapshots show that BcsA translocates cellulose via a ratcheting mechanism involving a 'finger helix' that contacts the polymer's terminal glucose. Cooperating with BcsA's gating loop, the finger helix moves 'up' and 'down' in response to substrate binding and polymer elongation, respectively, thereby pushing the elongated polymer into BcsA's transmembrane channel. This mechanism is validated experimentally by tethering BcsA's finger helix, which inhibits polymer translocation but not elongation.
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Affiliation(s)
- Jacob L.W. Morgan
- University of Virginia School of Medicine, Center for Membrane Biology, Molecular Physiology and Biological Physics, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
| | - Joshua T. McNamara
- University of Virginia School of Medicine, Center for Membrane Biology, Molecular Physiology and Biological Physics, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
| | - Michael Fischer
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada V6T 1Z1
| | - Jamie Rich
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada V6T 1Z1
| | - Hong-Ming Chen
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada V6T 1Z1
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada V6T 1Z1
| | - Jochen Zimmer
- University of Virginia School of Medicine, Center for Membrane Biology, Molecular Physiology and Biological Physics, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
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Wang Y, Andole Pannuri A, Ni D, Zhou H, Cao X, Lu X, Romeo T, Huang Y. Structural Basis for Translocation of a Biofilm-supporting Exopolysaccharide across the Bacterial Outer Membrane. J Biol Chem 2016; 291:10046-57. [PMID: 26957546 DOI: 10.1074/jbc.m115.711762] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 12/14/2022] Open
Abstract
The partially de-N-acetylated poly-β-1,6-N-acetyl-d-glucosamine (dPNAG) polymer serves as an intercellular biofilm adhesin that plays an essential role for the development and maintenance of integrity of biofilms of diverse bacterial species. Translocation of dPNAG across the bacterial outer membrane is mediated by a tetratricopeptide repeat-containing outer membrane protein, PgaA. To understand the molecular basis of dPNAG translocation, we determined the crystal structure of the C-terminal transmembrane domain of PgaA (residues 513-807). The structure reveals that PgaA forms a 16-strand transmembrane β-barrel, closed by four loops on the extracellular surface. Half of the interior surface of the barrel that lies parallel to the translocation pathway is electronegative, suggesting that the corresponding negatively charged residues may assist the secretion of the positively charged dPNAG polymer. In vivo complementation assays in a pgaA deletion bacterial strain showed that a cluster of negatively charged residues proximal to the periplasm is necessary for biofilm formation. Biochemical analyses further revealed that the tetratricopeptide repeat domain of PgaA binds directly to the N-deacetylase PgaB and is critical for biofilm formation. Our studies support a model in which the positively charged PgaB-bound dPNAG polymer is delivered to PgaA through the PgaA-PgaB interaction and is further targeted to the β-barrel lumen of PgaA potentially via a charge complementarity mechanism, thus priming the translocation of dPNAG across the bacterial outer membrane.
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Affiliation(s)
- Yan Wang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Archana Andole Pannuri
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611-0700
| | - Dongchun Ni
- Department of Cardiovascular Diseases, Tianjin Xiqing Hospital, Tianjin 300380, China
| | - Haizhen Zhou
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiou Cao
- School of Life Sciences, Peking University, Beijing 100871, China, and
| | - Xiaomei Lu
- Dongguan Institute of Pediatrics, the Eighth People's Hospital of Dongguan, Dongguan 523325, Guangdong Province, China
| | - Tony Romeo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611-0700,
| | - Yihua Huang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China,
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Alginate Biosynthesis Factories in Pseudomonas fluorescens: Localization and Correlation with Alginate Production Level. Appl Environ Microbiol 2015; 82:1227-1236. [PMID: 26655760 DOI: 10.1128/aem.03114-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/03/2015] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas fluorescens is able to produce the medically and industrially important exopolysaccharide alginate. The proteins involved in alginate biosynthesis and secretion form a multiprotein complex spanning the inner and outer membranes. In the present study, we developed a method by which the porin AlgE was detected by immunogold labeling and transmission electron microscopy. Localization of the AlgE protein was found to depend on the presence of other proteins in the multiprotein complex. No correlation was found between the number of alginate factories and the alginate production level, nor were the numbers of these factories affected in an algC mutant that is unable to produce the precursor needed for alginate biosynthesis. Precursor availability and growth phase thus seem to be the main determinants for the alginate production rate in our strain. Clustering analysis demonstrated that the alginate multiprotein complexes were not distributed randomly over the entire outer cell membrane surface.
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Römling U, Galperin MY. Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. Trends Microbiol 2015; 23:545-57. [PMID: 26077867 DOI: 10.1016/j.tim.2015.05.005] [Citation(s) in RCA: 307] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/05/2015] [Accepted: 05/18/2015] [Indexed: 12/30/2022]
Abstract
Recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. In most studied bacteria, just two subunits, BcsA and BcsB, are necessary and sufficient for the formation of the polysaccharide chain in vitro. Other subunits - which differ among various taxa - affect the enzymatic activity and product yield in vivo by modulating (i) the expression of the biosynthesis apparatus, (ii) the export of the nascent β-D-glucan polymer to the cell surface, and (iii) the organization of cellulose fibers into a higher-order structure. These auxiliary subunits play key roles in determining the quantity and structure of resulting biofilms, which is particularly important for the interactions of bacteria with higher organisms - leading to rhizosphere colonization and modulating the virulence of cellulose-producing bacterial pathogens inside and outside of host cells. We review the organization of four principal types of cellulose synthase operon found in various bacterial genomes, identify additional bcs genes that encode components of the cellulose biosynthesis and secretion machinery, and propose a unified nomenclature for these genes and subunits. We also discuss the role of cellulose as a key component of biofilms and in the choice between acute infection and persistence in the host.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Abstract
The molecular mechanisms of alginate polymerization/modification/secretion by a proposed envelope-spanning multiprotein complex are unknown. Here, bacterial two-hybrid assays and pulldown experiments showed that the catalytic subunit Alg8 directly interacts with the proposed copolymerase Alg44 while embedded in the cytoplasmic membrane. Alg44 additionally interacts with the lipoprotein AlgK bridging the periplasmic space. Site-specific mutagenesis of Alg44 showed that protein-protein interactions and stability were independent of conserved amino acid residues R17 and R21, which are involved in c-di-GMP binding, the N-terminal PilZ domain, and the C-terminal 26 amino acids. Site-specific mutagenesis was employed to investigate the c-di-GMP-mediated activation of alginate polymerization by the PilZAlg44 domain and Alg8. Activation was found to be different from the proposed activation mechanism for cellulose synthesis. The interactive role of Alg8, Alg44, AlgG (epimerase), and AlgX (acetyltransferase) on alginate polymerization and modification was studied by using site-specific deletion mutants, inactive variants, and overproduction of subunits. The compositions, molecular masses, and material properties of resulting novel alginates were analyzed. The molecular mass was reduced by epimerization, while it was increased by acetylation. Interestingly, when overproduced, Alg44, AlgG, and the nonepimerizing variant AlgG(D324A) increased the degree of acetylation, while epimerization was enhanced by AlgX and its nonacetylating variant AlgX(S269A). Biofilm architecture analysis showed that acetyl groups promoted cell aggregation while nonacetylated polymannuronate alginate promoted stigmergy. Overall, this study sheds new light on the arrangement of the multiprotein complex involved in alginate production. Furthermore, the activation mechanism and the interplay between polymerization and modification of alginate were elucidated. This study provides new insights into the molecular mechanisms of the synthesis of the unique polysaccharide, alginate, which not only is an important virulence factor of the opportunistic human pathogen Pseudomonas aeruginosa but also has, due to its material properties, many applications in medicine and industry. Unraveling the assembly and composition of the alginate-synthesizing and envelope-spanning multiprotein complex will be of tremendous significance for the scientific community. We identified a protein-protein interaction network inside the multiprotein complex and studied its relevance with respect to alginate polymerization/modification as well as the c-di-GMP-mediated activation mechanism. A relationship between alginate polymerization and modification was shown. Due to the role of alginate in pathogenesis as well as its unique material properties harnessed in numerous applications, results obtained in this study will aid the design and development of inhibitory drugs as well as the commercial bacterial production of tailor-made alginates.
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Simm S, Keller M, Selymesi M, Schleiff E. The composition of the global and feature specific cyanobacterial core-genomes. Front Microbiol 2015; 6:219. [PMID: 25852675 PMCID: PMC4365693 DOI: 10.3389/fmicb.2015.00219] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/04/2015] [Indexed: 12/21/2022] Open
Abstract
Cyanobacteria are photosynthetic prokaryotes important for many ecosystems with a high potential for biotechnological usage e.g., in the production of bioactive molecules. Either asks for a deep understanding of the functionality of cyanobacteria and their interaction with the environment. This in part can be inferred from the analysis of their genomes or proteomes. Today, many cyanobacterial genomes have been sequenced and annotated. This information can be used to identify biological pathways present in all cyanobacteria as proteins involved in such processes are encoded by a so called core-genome. However, beside identification of fundamental processes, genes specific for certain cyanobacterial features can be identified by a holistic genome analysis as well. We identified 559 genes that define the core-genome of 58 analyzed cyanobacteria, as well as three genes likely to be signature genes for thermophilic and 57 genes likely to be signature genes for heterocyst-forming cyanobacteria. To get insights into cyanobacterial systems for the interaction with the environment we also inspected the diversity of the outer membrane proteome with focus on β-barrel proteins. We observed that most of the transporting outer membrane β-barrel proteins are not globally conserved in the cyanobacterial phylum. In turn, the occurrence of β-barrel proteins shows high strain specificity. The core set of outer membrane proteins globally conserved in cyanobacteria comprises three proteins only, namely the outer membrane β-barrel assembly protein Omp85, the lipid A transfer protein LptD, and an OprB-type porin. Thus, we conclude that cyanobacteria have developed individual strategies for the interaction with the environment, while other intracellular processes like the regulation of the protein homeostasis are globally conserved.
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Affiliation(s)
- Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, Germany
| | - Mario Keller
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, Germany
| | - Mario Selymesi
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, Germany ; Cluster of Excellence Frankfurt, Goethe University Frankfurt am Main, Germany ; Center of Membrane Proteomics, Goethe University Frankfurt am Main, Germany ; Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt am Main, Germany
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Wiech EM, Cheng HP, Singh SM. Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. Protein Sci 2015; 24:319-27. [PMID: 25492513 PMCID: PMC4353358 DOI: 10.1002/pro.2616] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 12/12/2022]
Abstract
The Sinorhizobium meliloti periplasmic ExoR protein and the ExoS/ChvI two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. In the absence of crystal structures, understanding the molecular mechanism of interaction between ExoR and the ExoS sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. In this study, we present a theoretical structural model of the active form of ExoR protein, ExoRm , generated using computational methods. Our model suggests that ExoR possesses a super-helical fold comprising 12 α-helices forming six Sel1-like repeats, including two that were unidentified in previous studies. This fold is highly conducive to mediating protein-protein interactions and this is corroborated by the identification of putative protein binding sites on the surface of the ExoRm protein. Our studies reveal two novel insights: (a) an extended conformation of the third Sel1-like repeat that might be important for ExoR regulatory function and (b) a buried proteolytic site that implies a unique proteolytic mechanism. This study provides new and interesting insights into the structure of S. meliloti ExoR, lays the groundwork for elaborating the molecular mechanism of ExoRm cleavage, ExoRm -ExoS interactions, and studies of ExoR homologs in other bacterial host interactions.
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Affiliation(s)
- Eliza M Wiech
- Department of Biology, The Graduate Center of the City University of New YorkNew York, New York, 10016
- Department of Biology, Brooklyn College, The City University of New YorkBrooklyn, New York, 11210
| | - Hai-Ping Cheng
- Department of Biology, The Graduate Center of the City University of New YorkNew York, New York, 10016
- Biological Sciences Department, Lehman College, The City University of New YorkBronx, New York, 10468
| | - Shaneen M Singh
- Department of Biology, The Graduate Center of the City University of New YorkNew York, New York, 10016
- Department of Biology, Brooklyn College, The City University of New YorkBrooklyn, New York, 11210
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50
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Abstract
Cellulose is the most abundant biopolymer on Earth, and certain organisms from bacteria to plants and animals synthesize cellulose as an extracellular polymer for various biological functions. Humans have used cellulose for millennia as a material and an energy source, and the advent of a lignocellulosic fuel industry will elevate it to the primary carbon source for the burgeoning renewable energy sector. Despite the biological and societal importance of cellulose, the molecular mechanism by which it is synthesized is now only beginning to emerge. On the basis of recent advances in structural and molecular biology on bacterial cellulose synthases, we review emerging concepts of how the enzymes polymerize glucose molecules, how the nascent polymer is transported across the plasma membrane, and how bacterial cellulose biosynthesis is regulated during biofilm formation. Additionally, we review evolutionary commonalities and differences between cellulose synthases that modulate the nature of the cellulose product formed.
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Affiliation(s)
- Joshua T. McNamara
- Center for Membrane Biology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Jacob L.W. Morgan
- Center for Membrane Biology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
| | - Jochen Zimmer
- Center for Membrane Biology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908
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