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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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2
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Zahari NIN, Engku Abd Rahman ENS, Irekeola AA, Ahmed N, Rabaan AA, Alotaibi J, Alqahtani SA, Halawi MY, Alamri IA, Almogbel MS, Alfaraj AH, Ibrahim FA, Almaghaslah M, Alissa M, Yean CY. A Review of the Resistance Mechanisms for β-Lactams, Macrolides and Fluoroquinolones among Streptococcus pneumoniae. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1927. [PMID: 38003976 PMCID: PMC10672801 DOI: 10.3390/medicina59111927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/22/2023] [Accepted: 10/29/2023] [Indexed: 11/26/2023]
Abstract
Streptococcus pneumoniae (S. pneumoniae) is a bacterial species often associated with the occurrence of community-acquired pneumonia (CAP). CAP refers to a specific kind of pneumonia that occurs in individuals who acquire the infection outside of a healthcare setting. It represents the leading cause of both death and morbidity on a global scale. Moreover, the declaration of S. pneumoniae as one of the 12 leading pathogens was made by the World Health Organization (WHO) in 2017. Antibiotics like β-lactams, macrolides, and fluoroquinolones are the primary classes of antimicrobial medicines used for the treatment of S. pneumoniae infections. Nevertheless, the efficacy of these antibiotics is diminishing as a result of the establishment of resistance in S. pneumoniae against these antimicrobial agents. In 2019, the WHO declared that antibiotic resistance was among the top 10 hazards to worldwide health. It is believed that penicillin-binding protein genetic alteration causes β-lactam antibiotic resistance. Ribosomal target site alterations and active efflux pumps cause macrolide resistance. Numerous factors, including the accumulation of mutations, enhanced efflux mechanisms, and plasmid gene acquisition, cause fluoroquinolone resistance. Furthermore, despite the advancements in pneumococcal vaccinations and artificial intelligence (AI), it is not feasible for individuals to rely on them indefinitely. The ongoing development of AI for combating antimicrobial resistance necessitates more research and development efforts. A few strategies can be performed to curb this resistance issue, including providing educational initiatives and guidelines, conducting surveillance, and establishing new antibiotics targeting another part of the bacteria. Hence, understanding the resistance mechanism of S. pneumoniae may aid researchers in developing a more efficacious antibiotic in future endeavors.
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Affiliation(s)
- Nurul Izzaty Najwa Zahari
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Malaysia (E.N.S.E.A.R.)
| | - Engku Nur Syafirah Engku Abd Rahman
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Malaysia (E.N.S.E.A.R.)
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Malaysia (E.N.S.E.A.R.)
- Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, Offa PMB 4412, Nigeria
| | - Naveed Ahmed
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Malaysia (E.N.S.E.A.R.)
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Jawaher Alotaibi
- Infectious Diseases Unit, Department of Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | | | - Mohammed Y. Halawi
- Cytogenetics Department, Dammam Regional Laboratory and Blood Bank, Dammam 31411, Saudi Arabia
| | - Ibrahim Ateeq Alamri
- Blood Bank Department, Dammam Regional Laboratory and Blood Bank, Dammam 31411, Saudi Arabia
| | - Mohammed S. Almogbel
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 4030, Saudi Arabia
| | - Amal H. Alfaraj
- Pediatric Department, Abqaiq General Hospital, First Eastern Health Cluster, Abqaiq 33261, Saudi Arabia
| | - Fatimah Al Ibrahim
- Infectious Disease Division, Department of Internal Medicine, Dammam Medical Complex, Dammam 32245, Saudi Arabia
| | - Manar Almaghaslah
- Infectious Disease Division, Department of Internal Medicine, Dammam Medical Complex, Dammam 32245, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Malaysia (E.N.S.E.A.R.)
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Malaysia
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Leonhardt SA, Purdy MD, Grover JR, Yang Z, Poulos S, McIntire WE, Tatham EA, Erramilli SK, Nosol K, Lai KK, Ding S, Lu M, Uchil PD, Finzi A, Rein A, Kossiakoff AA, Mothes W, Yeager M. Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry. Nat Commun 2023; 14:4368. [PMID: 37474505 PMCID: PMC10359404 DOI: 10.1038/s41467-023-39262-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/06/2023] [Indexed: 07/22/2023] Open
Abstract
The host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). Here, we determine cryoEM maps of full-length human SERINC3 and an ICL4 deletion construct, which reveal that hSERINC3 is comprised of two α-helical bundles connected by a ~ 40-residue, highly tilted, "crossmember" helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes induce flipping of phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. Furthermore, SERINC3, SERINC5 and the scramblase TMEM16F expose PS on the surface of HIV-1 and reduce infectivity, with similar results in MLV. SERINC effects in HIV-1 and MLV are counteracted by Nef and GlycoGag, respectively. Our results demonstrate that SERINCs are membrane transporters that flip lipids, resulting in a loss of membrane asymmetry that is strongly correlated with changes in Env conformation and loss of infectivity.
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Grants
- P01 AI150471 NIAID NIH HHS
- P41 GM103311 NIGMS NIH HHS
- G20 RR031199 NCRR NIH HHS
- R01 GM117372 NIGMS NIH HHS
- U54 AI170856 NIAID NIH HHS
- S10 OD018149 NIH HHS
- U24 GM129539 NIGMS NIH HHS
- S10 RR025067 NCRR NIH HHS
- This work was supported by the National Institutes of Health (NIH) grants P50 AI15046 and U54 AI170856-01 (M.Y., W.M. and A.K.K.), R01 AI154092 (M.Y.), R01 GM117372 (A.A.K.) and P01 AI150471 (W.M.)., by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research, and in part by the NIH Intramural AIDS Targeted Antiviral Program. S.D. and A.F. were supported by the CIHR grant 352417 and a Canada Research Chair. Some molecular graphics and analyses were performed with the University of California, San Francisco Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by the National Institute of General Medical Sciences Grant P41 GM103311).
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Affiliation(s)
- Susan A Leonhardt
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael D Purdy
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Molecular Electron Microscopy Core, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ziwei Yang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Sandra Poulos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - William E McIntire
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Elizabeth A Tatham
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Kamil Nosol
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 535, Frederick, MD, 21702, USA
| | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC, Canada
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, TX, USA
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Alan Rein
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 535, Frederick, MD, 21702, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA.
| | - Mark Yeager
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA.
- Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Medicine, Division of Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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Soni V, Rosenn EH, Venkataraman R. Insights into the central role of N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU) in peptidoglycan metabolism and its potential as a therapeutic target. Biochem J 2023; 480:1147-1164. [PMID: 37498748 DOI: 10.1042/bcj20230173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Several decades after the discovery of the first antibiotic (penicillin) microbes have evolved novel mechanisms of resistance; endangering not only our abilities to combat future bacterial pandemics but many other clinical challenges such as acquired infections during surgeries. Antimicrobial resistance (AMR) is attributed to the mismanagement and overuse of these medications and is complicated by a slower rate of the discovery of novel drugs and targets. Bacterial peptidoglycan (PG), a three-dimensional mesh of glycan units, is the foundation of the cell wall that protects bacteria against environmental insults. A significant percentage of drugs target PG, however, these have been rendered ineffective due to growing drug resistance. Identifying novel druggable targets is, therefore, imperative. Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) is one of the key building blocks in PG production, biosynthesized by the bifunctional enzyme N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU). UDP-GlcNAc metabolism has been studied in many organisms, but it holds some distinctive features in bacteria, especially regarding the bacterial GlmU enzyme. In this review, we provide an overview of different steps in PG biogenesis, discuss the biochemistry of GlmU, and summarize the characteristic structural elements of bacterial GlmU vital to its catalytic function. Finally, we will discuss various studies on the development of GlmU inhibitors and their significance in aiding future drug discoveries.
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Affiliation(s)
- Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Eric H Rosenn
- Tel Aviv University School of Medicine, Tel Aviv 6997801, Israel
| | - Ramya Venkataraman
- Laboratory of Innate Immunity, National Institute of Immunology, New Delhi 110067, India
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5
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Yue J, Huang R, Lan Z, Xiao B, Luo Z. Abnormal glycosylation in glioma: related changes in biology, biomarkers and targeted therapy. Biomark Res 2023; 11:54. [PMID: 37231524 DOI: 10.1186/s40364-023-00491-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Glioma is a rapidly growing and aggressive primary malignant tumor of the central nervous system that can diffusely invade the brain tissue around, and the prognosis of patients is not significantly improved by traditional treatments. One of the most general posttranslational modifications of proteins is glycosylation, and the abnormal distribution of this modification in gliomas may shed light on how it affects biological behaviors of glioma cells, including proliferation, migration, and invasion, which may be produced by regulating protein function, cell-matrix and cell‒cell interactions, and affecting receptor downstream pathways. In this paper, from the perspective of regulating protein glycosylation changes and abnormal expression of glycosylation-related proteins (such as glycosyltransferases in gliomas), we summarize how glycosylation may play a crucial role in the discovery of novel biomarkers and new targeted treatment options for gliomas. Overall, the mechanistic basis of abnormal glycosylation affecting glioma progression remains to be more widely and deeply explored, which not only helps to inspire researchers to further explore related diagnostic and prognostic markers but also provides ideas for discovering effective treatment strategies and improving glioma patient survival and prognosis.
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Affiliation(s)
- Juan Yue
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya road of Kaifu district, 410008, Changsha, Hunan, China
| | - Roujie Huang
- Department of Obstetrics and Gynecology, Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Shuaifuyuan No. 1, Dongcheng District, 100730, Beijing, China
| | - Zehao Lan
- Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya road of Kaifu district, 410008, Changsha, Hunan, China
- Clinical Research Center for Epileptic disease of Hunan Province, Central South University, 410008, Changsha, Hunan, P.R. China
| | - Zhaohui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya road of Kaifu district, 410008, Changsha, Hunan, China.
- Clinical Research Center for Epileptic disease of Hunan Province, Central South University, 410008, Changsha, Hunan, P.R. China.
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6
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Malarney KP, Chang PV. Chemoproteomic Approaches for Unraveling Prokaryotic Biology. Isr J Chem 2023; 63:e202200076. [PMID: 37842282 PMCID: PMC10575470 DOI: 10.1002/ijch.202200076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 03/07/2023]
Abstract
Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and human health. Many of the functions that bacteria perform are mediated by proteins and enzymes, which catalyze metabolic transformations of small molecules and modifications of proteins. To better understand these biological processes, chemical proteomic approaches, including activity-based protein profiling, have been developed to interrogate protein function and enzymatic activity in physiologically relevant contexts. Here, chemoproteomic strategies and technological advances for studying bacterial physiology, pathogenesis, and metabolism are discussed. The development of chemoproteomic approaches for characterizing protein function and enzymatic activity within bacteria remains an active area of research, and continued innovations are expected to provide breakthroughs in understanding bacterial biology.
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Affiliation(s)
- Kien P Malarney
- Department of Microbiology, Cornell University, Ithaca, NY 14853 (USA)
| | - Pamela V Chang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853 (USA)
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7
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Kumar S, Mollo A, Rubino FA, Kahne D, Ruiz N. Chloride Ions Are Required for Thermosipho africanus MurJ Function. mBio 2023; 14:e0008923. [PMID: 36752629 PMCID: PMC9973255 DOI: 10.1128/mbio.00089-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 02/09/2023] Open
Abstract
Most bacteria have a peptidoglycan cell wall that determines their cell shape and helps them resist osmotic lysis. Peptidoglycan synthesis depends on the translocation of the lipid-linked precursor lipid II across the cytoplasmic membrane by the MurJ flippase. Structure-function analyses of MurJ from Thermosipho africanus (MurJTa) and Escherichia coli (MurJEc) have revealed that MurJ adopts multiple conformations and utilizes an alternating-access mechanism to flip lipid II. MurJEc activity relies on membrane potential, but the specific counterion has not been identified. Crystal structures of MurJTa revealed a chloride ion bound to the N-lobe of the flippase and a sodium ion in its C-lobe, but the role of these ions in transport is unknown. Here, we investigated the effect of various ions on the function of MurJTa and MurJEc in vivo. We found that chloride, and not sodium, ions are necessary for MurJTa function, but neither ion is required for MurJEc function. We also showed that murJTa alleles encoding changes at the crystallographically identified sodium-binding site still complement the loss of native murJEc, although they decreased protein stability and/or function. Based on our data and previous work, we propose that chloride ions are necessary for the conformational change that resets MurJTa after lipid II translocation and suggest that MurJ orthologs may function similarly but differ in their requirements for counterions. IMPORTANCE The biosynthetic pathway of the peptidoglycan cell wall is one of the most favorable targets for antibiotic development. Lipid II, the lipid-linked PG precursor, is made in the inner leaflet of the cytoplasmic membrane and then transported by the MurJ flippase so that it can be used to build the peptidoglycan cell wall. MurJ functions using an alternating-access mechanism thought to depend on a yet-to-be-identified counterion. This study fills a gap in our understanding of MurJ's energy-coupling mechanism by showing that chloride ions are required for MurJ in some, but not all, organisms. Based on our data and prior studies, we propose that, while the general transport mechanism of MurJ may be conserved, its specific mechanistic details may differ across bacteria, as is common in transporters. These findings are important to understand MurJ function and its development as an antibiotic target.
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Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Aurelio Mollo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Frederick A. Rubino
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
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8
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Giacometti SI, MacRae MR, Dancel-Manning K, Bhabha G, Ekiert DC. Lipid Transport Across Bacterial Membranes. Annu Rev Cell Dev Biol 2022; 38:125-153. [PMID: 35850151 DOI: 10.1146/annurev-cellbio-120420-022914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The movement of lipids within and between membranes in bacteria is essential for building and maintaining the bacterial cell envelope. Moving lipids to their final destination is often energetically unfavorable and does not readily occur spontaneously. Bacteria have evolved several protein-mediated transport systems that bind specific lipid substrates and catalyze the transport of lipids across membranes and from one membrane to another. Specific protein flippases act in translocating lipids across the plasma membrane, overcoming the obstacle of moving relatively large and chemically diverse lipids between leaflets of the bilayer. Active transporters found in double-membraned bacteria have evolved sophisticated mechanisms to traffic lipids between the two membranes, including assembling to form large, multiprotein complexes that resemble bridges, shuttles, and tunnels, shielding lipids from the hydrophilic environment of the periplasm during transport. In this review, we explore our current understanding of the mechanisms thought to drive bacterial lipid transport.
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Affiliation(s)
- Sabrina I Giacometti
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Mark R MacRae
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Kristen Dancel-Manning
- Office of Science and Research, New York University School of Medicine, New York, NY, USA;
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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9
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Antimicrobial Activity of Rhenium Di- and Tricarbonyl Diimine Complexes: Insights on Membrane-Bound S. aureus Protein Binding. Pharmaceuticals (Basel) 2022; 15:ph15091107. [PMID: 36145328 PMCID: PMC9501577 DOI: 10.3390/ph15091107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance is one of the major human health threats, with significant impacts on the global economy. Antibiotics are becoming increasingly ineffective as drug-resistance spreads, imposing an urgent need for new and innovative antimicrobial agents. Metal complexes are an untapped source of antimicrobial potential. Rhenium complexes, amongst others, are particularly attractive due to their low in vivo toxicity and high antimicrobial activity, but little is known about their targets and mechanism of action. In this study, a series of rhenium di- and tricarbonyl diimine complexes were prepared and evaluated for their antimicrobial potential against eight different microorganisms comprising Gram-negative and -positive bacteria. Our data showed that none of the Re dicarbonyl or neutral tricarbonyl species have either bactericidal or bacteriostatic potential. In order to identify possible targets of the molecules, and thus possibly understand the observed differences in the antimicrobial efficacy of the molecules, we computationally evaluated the binding affinity of active and inactive complexes against structurally characterized membrane-bound S. aureus proteins. The computational analysis indicates two possible major targets for this class of compounds, namely lipoteichoic acids flippase (LtaA) and lipoprotein signal peptidase II (LspA). Our results, consistent with the published in vitro studies, will be useful for the future design of rhenium tricarbonyl diimine-based antibiotics.
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Walter JD, Remm S, Seeger MA. Fatty acid transporter MFSD2A is a multifunctional gatekeeper in brain and placenta. Nat Struct Mol Biol 2022; 29:504-506. [PMID: 35710837 PMCID: PMC7615496 DOI: 10.1038/s41594-022-00788-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
MFSD2A mediates uptake of the essential fatty acid DHA across the blood–brain barrier. Separately, via interactions with syncytin-2, MFSD2A contributes to the formation of the mother–fetus placental boundary. Cryo-EM analysis of a human MFSD2A–syncytin-2 complex provides new insights into how MFSD2A performs these dual roles.
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Affiliation(s)
- Justin D Walter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
| | - Sille Remm
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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11
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Kohga H, Mori T, Tanaka Y, Yoshikaie K, Taniguchi K, Fujimoto K, Fritz L, Schneider T, Tsukazaki T. Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms. Structure 2022; 30:1088-1097.e3. [PMID: 35660157 DOI: 10.1016/j.str.2022.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/15/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Abstract
The bacterial peptidoglycan enclosing the cytoplasmic membrane is a fundamental cellular architecture. The integral membrane protein MurJ plays an essential role in flipping the cell wall building block Lipid II across the cytoplasmic membrane for peptidoglycan biosynthesis. Previously reported crystal structures of MurJ have elucidated its V-shaped inward- or outward-facing forms with an internal cavity for substrate binding. MurJ transports Lipid II using its cavity through conformational transitions between these two forms. Here, we report two crystal structures of inward-facing forms from Arsenophonus endosymbiont MurJ and an unprecedented crystal structure of Escherichia coli MurJ in a "squeezed" form, which lacks a cavity to accommodate the substrate, mainly because of the increased proximity of transmembrane helices 2 and 8. Subsequent molecular dynamics simulations supported the hypothesis that the squeezed form is an intermediate conformation. This study fills a gap in our understanding of the Lipid II flipping mechanism.
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Affiliation(s)
- Hidetaka Kohga
- Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshiki Tanaka
- Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | | | | | - Kei Fujimoto
- Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Lisa Fritz
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Tomoya Tsukazaki
- Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
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12
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Kumar S, Mollo A, Kahne D, Ruiz N. The Bacterial Cell Wall: From Lipid II Flipping to Polymerization. Chem Rev 2022; 122:8884-8910. [PMID: 35274942 PMCID: PMC9098691 DOI: 10.1021/acs.chemrev.1c00773] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The peptidoglycan (PG) cell wall is an extra-cytoplasmic glycopeptide polymeric structure that protects bacteria from osmotic lysis and determines cellular shape. Since the cell wall surrounds the cytoplasmic membrane, bacteria must add new material to the PG matrix during cell elongation and division. The lipid-linked precursor for PG biogenesis, Lipid II, is synthesized in the inner leaflet of the cytoplasmic membrane and is subsequently translocated across the bilayer so that the PG building block can be polymerized and cross-linked by complex multiprotein machines. This review focuses on major discoveries that have significantly changed our understanding of PG biogenesis in the past decade. In particular, we highlight progress made toward understanding the translocation of Lipid II across the cytoplasmic membrane by the MurJ flippase, as well as the recent discovery of a novel class of PG polymerases, the SEDS (shape, elongation, division, and sporulation) glycosyltransferases RodA and FtsW. Since PG biogenesis is an effective target of antibiotics, these recent developments may lead to the discovery of much-needed new classes of antibiotics to fight bacterial resistance.
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Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aurelio Mollo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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13
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Gottstein J, Zaschke-Kriesche J, Unsleber S, Voitsekhovskaia I, Kulik A, Behrmann LV, Overbeck N, Stühler K, Stegmann E, Smits SHJ. New insights into the resistance mechanism for the BceAB-type transporter SaNsrFP. Sci Rep 2022; 12:4232. [PMID: 35273305 PMCID: PMC8913810 DOI: 10.1038/s41598-022-08095-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
Treatment of bacterial infections is one of the major challenges of our time due to the evolved resistance mechanisms of pathogens against antibiotics. To circumvent this problem, it is necessary to understand the mode of action of the drug and the mechanism of resistance of the pathogen. One of the most potent antibiotic targets is peptidoglycan (PGN) biosynthesis, as this is an exclusively occurring and critical feature of bacteria. Lipid II is an essential PGN precursor synthesized in the cytosol and flipped into the outer leaflet of the membrane prior to its incorporation into nascent PGN. Antimicrobial peptides (AMPs), such as nisin and colistin, targeting PGN synthesis are considered promising weapons against multidrug-resistant bacteria. However, human pathogenic bacteria that were also resistant to these compounds evolved by the expression of an ATP-binding cassette transporter of the bacitracin efflux (BceAB) type localized in the membrane. In the human pathogen Streptococcus agalactiae, the BceAB transporter SaNsrFP is known to confer resistance to the antimicrobial peptide nisin. The exact mechanism of action for SaNsrFP is poorly understood. For a detailed characterization of the resistance mechanism, we heterologously expressed SaNsrFP in Lactococcus lactis. We demonstrated that SaNsrFP conferred resistance not only to nisin but also to a structurally diverse group of antimicrobial PGN-targeting compounds such as ramoplanin, lysobactin, or bacitracin/(Zn)-bacitracin. Growth experiments revealed that SaNsrFP-producing cells exhibited normal behavior when treated with nisin and/or bacitracin, in contrast to the nonproducing cells, for which growth was significantly reduced. We further detected the accumulation of PGN precursors in the cytoplasm after treating the cells with bacitracin. This did not appear when SaNsrFP was produced. Whole-cell proteomic protein experiments verified that the presence of SaNsrFP in L. lactis resulted in higher production of several proteins associated with cell wall modification. These included, for example, the N-acetylmuramic acid-6-phosphate etherase MurQ and UDP-glucose 4-epimerase. Analysis of components of the cell wall of SaNsrFP-producing cells implied that the transporter is involved in cell wall modification. Since we used an ATP-deficient mutant of the transporter as a comparison, we can show that SaNsrFP and its inactive mutant do not show the same phenotype, albeit expressed at similar levels, which demonstrates the ATP dependency of the mediated resistance processes. Taken together, our data agree to a target protection mechanism and imply a direct involvement of SaNsrFP in resistance by shielding the membrane-localized target of these antimicrobial peptides, resulting in modification of the cell wall.
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Affiliation(s)
- Julia Gottstein
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Julia Zaschke-Kriesche
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Sandra Unsleber
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Irina Voitsekhovskaia
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Lara V Behrmann
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Nina Overbeck
- Molecular Proteomics Laboratory, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicin, Eberhard Karls University, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
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14
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del Alamo D, Sala D, Mchaourab HS, Meiler J. Sampling alternative conformational states of transporters and receptors with AlphaFold2. eLife 2022; 11:75751. [PMID: 35238773 PMCID: PMC9023059 DOI: 10.7554/elife.75751] [Citation(s) in RCA: 139] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
Equilibrium fluctuations and triggered conformational changes often underlie the functional cycles of membrane proteins. For example, transporters mediate the passage of molecules across cell membranes by alternating between inward- and outward-facing states, while receptors undergo intracellular structural rearrangements that initiate signaling cascades. Although the conformational plasticity of these proteins has historically posed a challenge for traditional de novo protein structure prediction pipelines, the recent success of AlphaFold2 (AF2) in CASP14 culminated in the modeling of a transporter in multiple conformations to high accuracy. Given that AF2 was designed to predict static structures of proteins, it remains unclear if this result represents an underexplored capability to accurately predict multiple conformations and/or structural heterogeneity. Here, we present an approach to drive AF2 to sample alternative conformations of topologically diverse transporters and G-protein-coupled receptors that are absent from the AF2 training set. Whereas models of most proteins generated using the default AF2 pipeline are conformationally homogeneous and nearly identical to one another, reducing the depth of the input multiple sequence alignments by stochastic subsampling led to the generation of accurate models in multiple conformations. In our benchmark, these conformations spanned the range between two experimental structures of interest, with models at the extremes of these conformational distributions observed to be among the most accurate (average template modeling score of 0.94). These results suggest a straightforward approach to identifying native-like alternative states, while also highlighting the need for the next generation of deep learning algorithms to be designed to predict ensembles of biophysically relevant states.
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Affiliation(s)
- Diego del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt UniversityNashvilleUnited States
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
| | - Davide Sala
- Institute for Drug Discovery, Leipzig UniversityLeipzigGermany
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt UniversityNashvilleUnited States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
- Institute for Drug Discovery, Leipzig UniversityLeipzigGermany
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15
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Abstract
Biosynthesis of many important polysaccharides (including peptidoglycan, lipopolysaccharide, and N-linked glycans) necessitates the transport of lipid-linked oligosaccharides (LLO) across membranes from their cytosolic site of synthesis to their sites of utilization. Much of our current understanding of LLO transport comes from genetic, biochemical, and structural studies of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) superfamily protein MurJ, which flips the peptidoglycan precursor lipid II. MurJ plays a pivotal role in bacterial cell wall synthesis and is an emerging antibiotic target. Here, we review the mechanism of LLO flipping by MurJ, including the structural basis for lipid II flipping and ion coupling. We then discuss inhibition of MurJ by antibacterials, including humimycins and the phage M lysis protein, as well as how studies on MurJ could provide insight into other flippases, both within and beyond the MOP superfamily. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Alvin C Y Kuk
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA; .,Current affiliation: Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Aili Hao
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA;
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA;
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16
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Sande C, Whitfield C. Capsules and Extracellular Polysaccharides in Escherichia coli and Salmonella. EcoSal Plus 2021; 9:eESP00332020. [PMID: 34910576 PMCID: PMC11163842 DOI: 10.1128/ecosalplus.esp-0033-2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 10/26/2021] [Indexed: 12/16/2022]
Abstract
Escherichia coli and Salmonella isolates produce a range of different polysaccharide structures that play important roles in their biology. E. coli isolates often possess capsular polysaccharides (K antigens), which form a surface structural layer. These possess a wide range of repeat-unit structures. In contrast, only one capsular polymer (Vi antigen) is found in Salmonella, and it is confined to typhoidal serovars. In both genera, capsules are vital virulence determinants and are associated with the avoidance of host immune defenses. Some isolates of these species also produce a largely secreted exopolysaccharide called colanic acid as part of their complex Rcs-regulated phenotypes, but the precise function of this polysaccharide in microbial cell biology is not fully understood. E. coli isolates produce two additional secreted polysaccharides, bacterial cellulose and poly-N-acetylglucosamine, which play important roles in biofilm formation. Cellulose is also produced by Salmonella isolates, but the genes for poly-N-acetylglucosamine synthesis appear to have been lost during its evolution toward enhanced virulence. Here, we discuss the structures, functions, relationships, and sophisticated assembly mechanisms for these important biopolymers.
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Affiliation(s)
- Caitlin Sande
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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17
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Wu D, Saleem M, He T, He G. The Mechanism of Metal Homeostasis in Plants: A New View on the Synergistic Regulation Pathway of Membrane Proteins, Lipids and Metal Ions. MEMBRANES 2021; 11:membranes11120984. [PMID: 34940485 PMCID: PMC8706360 DOI: 10.3390/membranes11120984] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/04/2021] [Accepted: 12/11/2021] [Indexed: 12/15/2022]
Abstract
Heavy metal stress (HMS) is one of the most destructive abiotic stresses which seriously affects the growth and development of plants. Recent studies have shown significant progress in understanding the molecular mechanisms underlying plant tolerance to HMS. In general, three core signals are involved in plants' responses to HMS; these are mitogen-activated protein kinase (MAPK), calcium, and hormonal (abscisic acid) signals. In addition to these signal components, other regulatory factors, such as microRNAs and membrane proteins, also play an important role in regulating HMS responses in plants. Membrane proteins interact with the highly complex and heterogeneous lipids in the plant cell environment. The function of membrane proteins is affected by the interactions between lipids and lipid-membrane proteins. Our review findings also indicate the possibility of membrane protein-lipid-metal ion interactions in regulating metal homeostasis in plant cells. In this review, we investigated the role of membrane proteins with specific substrate recognition in regulating cell metal homeostasis. The understanding of the possible interaction networks and upstream and downstream pathways is developed. In addition, possible interactions between membrane proteins, metal ions, and lipids are discussed to provide new ideas for studying metal homeostasis in plant cells.
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Affiliation(s)
- Danxia Wu
- College of Agricultural, Guizhou University, Guiyang 550025, China;
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
| | - Tengbing He
- College of Agricultural, Guizhou University, Guiyang 550025, China;
- Institute of New Rural Development, West Campus, Guizhou University, Guiyang 550025, China
- Correspondence: (T.H.); (G.H.)
| | - Guandi He
- College of Agricultural, Guizhou University, Guiyang 550025, China;
- Correspondence: (T.H.); (G.H.)
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18
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High-Throughput Mutagenesis and Cross-Complementation Experiments Reveal Substrate Preference and Critical Residues of the Capsule Transporters in Streptococcus pneumoniae. mBio 2021; 12:e0261521. [PMID: 34724815 PMCID: PMC8561386 DOI: 10.1128/mbio.02615-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MOP (Multidrug/Oligosaccharidyl-lipid/Polysaccharide) family transporters are found in almost all life forms. They are responsible for transporting lipid-linked precursors across the cell membrane to support the synthesis of various glycoconjugates. While significant progress has been made in elucidating their transport mechanism, how these transporters select their substrates remains unclear. Here, we systematically tested the MOP transporters in the Streptococcus pneumoniae capsule pathway for their ability to translocate noncognate capsule precursors. Sequence similarity cannot predict whether these transporters are interchangeable. We showed that subtle changes in the central aqueous cavity of the transporter are sufficient to accommodate a different cargo. These changes can occur naturally, suggesting a potential mechanism of expanding substrate selectivity. A directed evolution experiment was performed to identify gain-of-function variants that translocate a noncognate cargo. Coupled with a high-throughput mutagenesis and sequencing (Mut-seq) experiment, residues that are functionally important for the capsule transporter were revealed. Lastly, we showed that the expression of a flippase that can transport unfinished precursors resulted in an increased susceptibility to bacitracin and mild cell shape defects, which may be a driving force to maintain transporter specificity. IMPORTANCE All licensed pneumococcal vaccines target the capsular polysaccharide (CPS). This layer is highly variable and is important for virulence in many bacterial pathogens. Most of the CPSs are produced by the Wzx/Wzy mechanism. In this pathway, CPS repeating units are synthesized in the cytoplasm, which must be flipped across the cytoplasmic membrane before polymerization. This step is mediated by the widely conserved MOP (Multidrug/Oligosaccharidyl-lipid/Polysaccharide) family transporters. Here, we systematically evaluated the interchangeability of these transporters and identified the residues important for substrate specificity and function. Understanding how CPS is synthesized will inform glycoengineering, vaccine development, and antimicrobial discovery.
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19
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Abidi W, Torres-Sánchez L, Siroy A, Krasteva PV. Weaving of bacterial cellulose by the Bcs secretion systems. FEMS Microbiol Rev 2021; 46:6388354. [PMID: 34634120 PMCID: PMC8892547 DOI: 10.1093/femsre/fuab051] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022] Open
Abstract
Cellulose is the most abundant biological compound on Earth and while it is the predominant building constituent of plants, it is also a key extracellular matrix component in many diverse bacterial species. While bacterial cellulose was first described in the 19th century, it was not until this last decade that a string of structural works provided insights into how the cellulose synthase BcsA, assisted by its inner-membrane partner BcsB, senses c-di-GMP to simultaneously polymerize its substrate and extrude the nascent polysaccharide across the inner bacterial membrane. It is now established that bacterial cellulose can be produced by several distinct types of cellulose secretion systems and that in addition to BcsAB, they can feature multiple accessory subunits, often indispensable for polysaccharide production. Importantly, the last years mark significant progress in our understanding not only of cellulose polymerization per se but also of the bigger picture of bacterial signaling, secretion system assembly, biofilm formation and host tissue colonization, as well as of structural and functional parallels of this dominant biosynthetic process between the bacterial and eukaryotic domains of life. Here, we review current mechanistic knowledge on bacterial cellulose secretion with focus on the structure, assembly and cooperativity of Bcs secretion system components.
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Affiliation(s)
- Wiem Abidi
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.,École doctorale 'Innovation thérapeutique: du fundamental à l'appliqué' (ITFA), Université Paris-Saclay, 92296, Chatenay-Malabry, France
| | - Lucía Torres-Sánchez
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.,École doctorale 'Innovation thérapeutique: du fundamental à l'appliqué' (ITFA), Université Paris-Saclay, 92296, Chatenay-Malabry, France
| | - Axel Siroy
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
| | - Petya Violinova Krasteva
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
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20
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Abstract
Most bacteria are surrounded by a peptidoglycan cell wall that defines their shape and protects them from osmotic lysis. The expansion and division of this structure therefore plays an integral role in bacterial growth and division. Additionally, the biogenesis of the peptidoglycan layer is the target of many of our most effective antibiotics. Thus, a better understanding of how the cell wall is built will enable the development of new therapies to combat the rise of drug-resistant bacterial infections. This review covers recent advances in defining the mechanisms involved in assembling the peptidoglycan layer with an emphasis on discoveries related to the function and regulation of the cell elongation and division machineries in the model organisms Escherichia coli and Bacillus subtilis. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Patricia D A Rohs
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Current affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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21
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Phospholipid translocation captured in a bifunctional membrane protein MprF. Nat Commun 2021; 12:2927. [PMID: 34006869 PMCID: PMC8131360 DOI: 10.1038/s41467-021-23248-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/16/2021] [Indexed: 01/07/2023] Open
Abstract
As a large family of membrane proteins crucial for bacterial physiology and virulence, the Multiple Peptide Resistance Factors (MprFs) utilize two separate domains to synthesize and translocate aminoacyl phospholipids to the outer leaflets of bacterial membranes. The function of MprFs enables Staphylococcus aureus and other pathogenic bacteria to acquire resistance to daptomycin and cationic antimicrobial peptides. Here we present cryo-electron microscopy structures of MprF homodimer from Rhizobium tropici (RtMprF) at two different states in complex with lysyl-phosphatidylglycerol (LysPG). RtMprF contains a membrane-embedded lipid-flippase domain with two deep cavities opening toward the inner and outer leaflets of the membrane respectively. Intriguingly, a hook-shaped LysPG molecule is trapped inside the inner cavity with its head group bent toward the outer cavity which hosts a second phospholipid-binding site. Moreover, RtMprF exhibits multiple conformational states with the synthase domain adopting distinct positions relative to the flippase domain. Our results provide a detailed framework for understanding the mechanisms of MprF-mediated modification and translocation of phospholipids.
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22
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Claxton DP, Jagessar KL, Mchaourab HS. Principles of Alternating Access in Multidrug and Toxin Extrusion (MATE) Transporters. J Mol Biol 2021; 433:166959. [PMID: 33774036 DOI: 10.1016/j.jmb.2021.166959] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
The multidrug and toxin extrusion (MATE) transporters catalyze active efflux of a broad range of chemically- and structurally-diverse compounds including antimicrobials and chemotherapeutics, thus contributing to multidrug resistance in pathogenic bacteria and cancers. Multiple methodological approaches have been taken to investigate the structural basis of energy transduction and substrate translocation in MATE transporters. Crystal structures representing members from all three MATE subfamilies have been interpreted within the context of an alternating access mechanism that postulates occupation of distinct structural intermediates in a conformational cycle powered by electrochemical ion gradients. Here we review the structural biology of MATE transporters, integrating the crystallographic models with biophysical and computational studies to define the molecular determinants that shape the transport energy landscape. This holistic analysis highlights both shared and disparate structural and functional features within the MATE family, which underpin an emerging theme of mechanistic diversity within the framework of a conserved structural scaffold.
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Affiliation(s)
- Derek P Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 747 Light Hall, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Kevin L Jagessar
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 747 Light Hall, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 747 Light Hall, 2215 Garland Avenue, Nashville, TN 37232, USA.
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23
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Fisher JF, Mobashery S. β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium. Chem Rev 2021; 121:3412-3463. [PMID: 33373523 PMCID: PMC8653850 DOI: 10.1021/acs.chemrev.0c01010] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
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24
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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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25
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Conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na + in ion-coupled drug efflux. J Biol Chem 2021; 296:100262. [PMID: 33837745 PMCID: PMC7949106 DOI: 10.1016/j.jbc.2021.100262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
In both prokaryotes and eukaryotes, multidrug and toxic-compound extrusion (MATE) transporters catalyze the efflux of a broad range of cytotoxic compounds, including human-made antibiotics and anticancer drugs. MATEs are secondary-active antiporters, i.e., their drug-efflux activity is coupled to, and powered by, the uptake of ions down a preexisting transmembrane electrochemical gradient. Key aspects of this mechanism, however, remain to be delineated, such as its ion specificity and stoichiometry. We previously revealed the existence of a Na+-binding site in a MATE transporter from Pyroccocus furiosus (PfMATE) and hypothesized that this site might be broadly conserved among prokaryotic MATEs. Here, we evaluate this hypothesis by analyzing VcmN and ClbM, which along with PfMATE are the only three prokaryotic MATEs whose molecular structures have been determined at atomic resolution, i.e. better than 3 Å. Reinterpretation of existing crystallographic data and molecular dynamics simulations indeed reveal an occupied Na+-binding site in the N-terminal lobe of both structures, analogous to that identified in PfMATE. We likewise find this site to be strongly selective against K+, suggesting it is mechanistically significant. Consistent with these computational results, DEER spectroscopy measurements for multiple doubly-spin-labeled VcmN constructs demonstrate Na+-dependent changes in protein conformation. The existence of this binding site in three MATE orthologs implicates Na+ in the ion-coupled drug-efflux mechanisms of this class of transporters. These results also imply that observations of H+-dependent activity likely stem either from a site elsewhere in the structure, or from H+ displacing Na+ under certain laboratory conditions, as has been noted for other Na+-driven transport systems.
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Garde S, Chodisetti PK, Reddy M. Peptidoglycan: Structure, Synthesis, and Regulation. EcoSal Plus 2021; 9:eESP-0010-2020. [PMID: 33470191 PMCID: PMC11168573 DOI: 10.1128/ecosalplus.esp-0010-2020] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Indexed: 02/06/2023]
Abstract
Peptidoglycan is a defining feature of the bacterial cell wall. Initially identified as a target of the revolutionary beta-lactam antibiotics, peptidoglycan has become a subject of much interest for its biology, its potential for the discovery of novel antibiotic targets, and its role in infection. Peptidoglycan is a large polymer that forms a mesh-like scaffold around the bacterial cytoplasmic membrane. Peptidoglycan synthesis is vital at several stages of the bacterial cell cycle: for expansion of the scaffold during cell elongation and for formation of a septum during cell division. It is a complex multifactorial process that includes formation of monomeric precursors in the cytoplasm, their transport to the periplasm, and polymerization to form a functional peptidoglycan sacculus. These processes require spatio-temporal regulation for successful assembly of a robust sacculus to protect the cell from turgor and determine cell shape. A century of research has uncovered the fundamentals of peptidoglycan biology, and recent studies employing advanced technologies have shed new light on the molecular interactions that govern peptidoglycan synthesis. Here, we describe the peptidoglycan structure, synthesis, and regulation in rod-shaped bacteria, particularly Escherichia coli, with a few examples from Salmonella and other diverse organisms. We focus on the pathway of peptidoglycan sacculus elongation, with special emphasis on discoveries of the past decade that have shaped our understanding of peptidoglycan biology.
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Affiliation(s)
- Shambhavi Garde
- These authors contributed equally
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
| | - Pavan Kumar Chodisetti
- These authors contributed equally
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
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Su T, Nakamoto R, Chun YY, Chua WZ, Chen JH, Zik JJ, Sham LT. Decoding capsule synthesis in Streptococcus pneumoniae. FEMS Microbiol Rev 2020; 45:6041728. [PMID: 33338218 DOI: 10.1093/femsre/fuaa067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pneumoniae synthesizes more than one hundred types of capsular polysaccharides (CPS). While the diversity of the enzymes and transporters involved is enormous, it is not limitless. In this review, we summarized the recent progress on elucidating the structure-function relationships of CPS, the mechanisms by which they are synthesized, how their synthesis is regulated, the host immune response against them, and the development of novel pneumococcal vaccines. Based on the genetic and structural information available, we generated provisional models of the CPS repeating units that remain unsolved. In addition, to facilitate cross-species comparisons and assignment of glycosyltransferases, we illustrated the biosynthetic pathways of the known CPS in a standardized format. Studying the intricate steps of pneumococcal CPS assembly promises to provide novel insights for drug and vaccine development as well as improve our understanding of related pathways in other species.
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Affiliation(s)
- Tong Su
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Rei Nakamoto
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Ye Yu Chun
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Wan Zhen Chua
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Jia Hui Chen
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Justin J Zik
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
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28
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Okella H, Georrge JJ, Ochwo S, Ndekezi C, Koffi KT, Aber J, Ajayi CO, Fofana FG, Ikiriza H, Mtewa AG, Nkamwesiga J, Bassogog CBB, Kato CD, Ogwang PE. New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs. Front Bioeng Biotechnol 2020; 8:604041. [PMID: 33344436 PMCID: PMC7744477 DOI: 10.3389/fbioe.2020.604041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/09/2020] [Indexed: 12/04/2022] Open
Abstract
Antimicrobial resistance remains a great threat to global health. In response to the World Health Organizations’ global call for action, nature has been explored for novel and safe antimicrobial candidates. To date, fish have gained recognition as potential source of safe, broad spectrum and effective antimicrobial therapeutics. The use of computational methods to design antimicrobial candidates of industrial application has however, been lagging behind. To fill the gap and contribute to the current fish-derived antimicrobial peptide repertoire, this study used Support Vector Machines algorithm to fish out fish-antimicrobial peptide-motif candidates encrypted in 127 peptides submitted at the Antimicrobial Peptide Database (APD3), steered by their physico-chemical characteristics (i.e., positive net charge, hydrophobicity, stability, molecular weight and sequence length). The best two novel antimicrobial peptide-motifs (A15_B, A15_E) with the lowest instability index (−28.25, −22.49, respectively) and highest isoelectric point (pI) index (10.48 for each) were selected for further analysis. Their 3D structures were predicted using I-TASSER and PEP-FOLD servers while ProSA, PROCHECK, and ANOLEA were used to validate them. The models predicted by I-TASSER were found to be better than those predicted by PEP-FOLD upon validation. Two I-TASSER models with the lowest c-score of −0.10 and −0.30 for A15_B and A15_E peptide-motifs, respectively, were selected for docking against known bacterial-antimicrobial target-proteins retrieved from protein databank (PDB). Carbapenam-3-carboxylate synthase (PDB ID; 4oj8) yielded the lowest docking energy (−8.80 and −7.80 Kcal/mol) against motif A15_B and A15_E, respectively, using AutoDock VINA. Further, in addition to Carbapenam-3-carboxylate synthase, these peptides (A15_B and A15_E) were found to as well bind to membrane protein (PDB ID: 1by3) and Carbapenem synthetase (PDB: 1q15) when ClusPro and HPEPDOCK tools were used. The membrane protein yielded docking energy scores (DES): −290.094, −270.751; coefficient weight (CW): −763.6, 763.3 for A15_B and A15_E) whereas, Carbapenem synthetase (PDB: 1q15) had a DES of −236.802, −262.75 and a CW of −819.7, −829.7 for peptides A15_B and A15_E, respectively. Motif A15_B of amino acid positions 2–19 in Pleurocidin exhibited the strongest in silico antimicrobial potentials. This segment could be a good biological candidate of great application in pharmaceutical industries as an antimicrobial drug candidate.
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Affiliation(s)
- Hedmon Okella
- Pharm-Biotechnology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
| | - John J Georrge
- Department of Bioinformatics, Christ College, Rajkot, India
| | - Sylvester Ochwo
- College of Veterinary Medicine, Animal Resources and Bio-Security, Makerere University, Kampala, Uganda
| | - Christian Ndekezi
- College of Veterinary Medicine, Animal Resources and Bio-Security, Makerere University, Kampala, Uganda
| | - Kevin Tindo Koffi
- Biotechnology Engineering Department, V. V. P College of Engineering, Rajkot, India
| | - Jacqueline Aber
- Pharm-Biotechnology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Clement Olusoji Ajayi
- Pharm-Biotechnology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Fatoumata Gnine Fofana
- Department of Bioinformatics, African Center of Excellence in Bioinformatics, University of Science, Technique and Technology, Bamako, Mali
| | - Hilda Ikiriza
- Pharm-Biotechnology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Andrew G Mtewa
- Pharm-Biotechnology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda.,Chemistry Section, Malawi Institute of Technology, Malawi University of Science and Technology, Thyolo, Malawi
| | - Joseph Nkamwesiga
- College of Veterinary Medicine, Animal Resources and Bio-Security, Makerere University, Kampala, Uganda.,International Livestock Research Institute, Kampala, Uganda
| | | | - Charles Drago Kato
- College of Veterinary Medicine, Animal Resources and Bio-Security, Makerere University, Kampala, Uganda
| | - Patrick Engeu Ogwang
- Pharm-Biotechnology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
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29
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Baker BR, Ives CM, Bray A, Caffrey M, Cochrane SA. Undecaprenol kinase: Function, mechanism and substrate specificity of a potential antibiotic target. Eur J Med Chem 2020; 210:113062. [PMID: 33310291 DOI: 10.1016/j.ejmech.2020.113062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
The bifunctional undecaprenol kinase/phosphatase (UdpK) is a small, prokaryotic, integral membrane kinase, homologous with Escherichia coli diacylglycerol kinase and expressed by the dgkA gene. In Gram-positive bacteria, UdpK is involved in the homeostasis of the bacterial undecaprenoid pool, where it converts undecaprenol to undecaprenyl phosphate (C55P) and also catalyses the reverse process. C55P is the universal lipid carrier and critical to numerous glycopolymer and glycoprotein biosynthetic pathways in bacteria. DgkA gene expression has been linked to facilitating bacterial growth and survival in response to environmental stressors, as well being implicated as a resistance mechanism to the topical antibiotic bacitracin, by providing an additional route to C55P. Therefore, identification of UdpK inhibitors could lead to novel antibiotic treatments. A combination of homology modelling and mutagenesis experiments on UdpK have been used to identify residues that may be involved in kinase/phosphatase activity. In this review, we will summarise recent work on the mechanism and substrate specificity of UdpK.
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Affiliation(s)
- Brad R Baker
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Callum M Ives
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland; Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Ashley Bray
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland.
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK.
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30
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Batt SM, Burke CE, Moorey AR, Besra GS. Antibiotics and resistance: the two-sided coin of the mycobacterial cell wall. Cell Surf 2020; 6:100044. [PMID: 32995684 PMCID: PMC7502851 DOI: 10.1016/j.tcsw.2020.100044] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium tuberculosis, the bacterium responsible for tuberculosis, is the global leading cause of mortality from an infectious agent. Part of this success relies on the unique cell wall, which consists of a thick waxy coat with tightly packed layers of complexed sugars, lipids and peptides. This coat provides a protective hydrophobic barrier to antibiotics and the host's defences, while enabling the bacterium to spread efficiently through sputum to infect and survive within the macrophages of new hosts. However, part of this success comes at a cost, with many of the current first- and second-line drugs targeting the enzymes involved in cell wall biosynthesis. The flip side of this coin is that resistance to these drugs develops either in the target enzymes or the activation pathways of the drugs, paving the way for new resistant clinical strains. This review provides a synopsis of the structure and synthesis of the cell wall and the major current drugs and targets, along with any mechanisms of resistance.
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Affiliation(s)
- Sarah M. Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher E. Burke
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alice R. Moorey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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31
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Brown AR, Gordon RA, Hyland SN, Siegrist MS, Grimes CL. Chemical Biology Tools for Examining the Bacterial Cell Wall. Cell Chem Biol 2020; 27:1052-1062. [PMID: 32822617 DOI: 10.1016/j.chembiol.2020.07.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/06/2020] [Accepted: 07/29/2020] [Indexed: 01/22/2023]
Abstract
Bacteria surround themselves with cell walls to maintain cell rigidity and protect against environmental insults. Here we review chemical and biochemical techniques employed to study bacterial cell wall biogenesis. Recent advances including the ability to isolate critical intermediates, metabolic approaches for probe incorporation, and isotopic labeling techniques have provided critical insight into the biochemistry of cell walls. Fundamental manuscripts that have used these techniques to discover cell wall-interacting proteins, flippases, and cell wall stoichiometry are discussed in detail. The review highlights that these powerful methods and techniques have exciting potential to identify and characterize new targets for antibiotic development.
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Affiliation(s)
- Ashley R Brown
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Rebecca A Gordon
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst 01003-9298, USA
| | - Stephen N Hyland
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003-9298, USA; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst 01003-9298, USA
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA; Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA.
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32
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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: 123] [Impact Index Per Article: 30.8] [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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33
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Caffalette CA, Kuklewicz J, Spellmon N, Zimmer J. Biosynthesis and Export of Bacterial Glycolipids. Annu Rev Biochem 2020; 89:741-768. [DOI: 10.1146/annurev-biochem-011520-104707] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Complex carbohydrates are essential for many biological processes, from protein quality control to cell recognition, energy storage, and cell wall formation. Many of these processes are performed in topologically extracellular compartments or on the cell surface; hence, diverse secretion systems evolved to transport the hydrophilic molecules to their sites of action. Polyprenyl lipids serve as ubiquitous anchors and facilitators of these transport processes. Here, we summarize and compare bacterial biosynthesis pathways relying on the recognition and transport of lipid-linked complex carbohydrates. In particular, we compare transporters implicated in O antigen and capsular polysaccharide biosyntheses with those facilitating teichoic acid and N-linked glycan transport. Further, we discuss recent insights into the generation, recognition, and recycling of polyprenyl lipids.
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Affiliation(s)
- Christopher A. Caffalette
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Jeremi Kuklewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Nicholas Spellmon
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Jochen Zimmer
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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34
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Whitfield C, Williams DM, Kelly SD. Lipopolysaccharide O-antigens-bacterial glycans made to measure. J Biol Chem 2020; 295:10593-10609. [PMID: 32424042 DOI: 10.1074/jbc.rev120.009402] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/17/2020] [Indexed: 01/05/2023] Open
Abstract
Lipopolysaccharides are critical components of bacterial outer membranes. The more conserved lipid A part of the lipopolysaccharide molecule is a major element in the permeability barrier imposed by the outer membrane and offers a pathogen-associated molecular pattern recognized by innate immune systems. In contrast, the long-chain O-antigen polysaccharide (O-PS) shows remarkable structural diversity and fulfills a range of functions, depending on bacterial lifestyles. O-PS production is vital for the success of clinically important Gram-negative pathogens. The biological properties and functions of O-PSs are mostly independent of specific structures, but the size distribution of O-PS chains is particularly important in many contexts. Despite the vast O-PS chemical diversity, most are produced in bacterial cells by two assembly strategies, and the different mechanisms employed in these pathways to regulate chain-length distribution are emerging. Here, we review our current understanding of the mechanisms involved in regulating O-PS chain-length distribution and discuss their impact on microbial cell biology.
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Affiliation(s)
- Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Danielle M Williams
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Steven D Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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35
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Mann E, Kimber MS, Whitfield C. Bioinformatics analysis of diversity in bacterial glycan chain-termination chemistry and organization of carbohydrate-binding modules linked to ABC transporters. Glycobiology 2020; 29:822-838. [PMID: 31504498 DOI: 10.1093/glycob/cwz066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 12/22/2022] Open
Abstract
The structures of bacterial cell surface glycans are remarkably diverse. In spite of this diversity, the general strategies used for their assembly are limited. In one of the major processes, found in both Gram-positive and Gram-negative bacteria, the glycan is polymerized in the cytoplasm on a polyprenol lipid carrier and exported from the cytoplasm by an ATP-binding cassette (ABC) transporter. The ABC transporter actively participates in determining the chain length of the glycan substrate, which impacts functional properties of the glycoconjugate products. A subset of these systems employs an additional elaborate glycan capping strategy that dictates the size distribution of the products. The hallmarks of prototypical capped glycan systems are a chain-terminating enzyme possessing a coiled-coil molecular ruler and an ABC transporter possessing a carbohydrate-binding module, which recognizes the glycan cap. To date, detailed investigations are limited to a small number of prototypes, and here, we used our current understanding of these processes for a bioinformatics census of other examples in available genome sequences. This study not only revealed additional instances of existing terminators but also predicted new chemistries as well as systems that diverge from the established prototypes. These analyses enable some new functional hypotheses and offer a roadmap for future research.
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Affiliation(s)
- Evan Mann
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd. East, Guelph, Ontario N1G 2W1, Canada
| | - Matthew S Kimber
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd. East, Guelph, Ontario N1G 2W1, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd. East, Guelph, Ontario N1G 2W1, Canada
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36
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Rubino FA, Mollo A, Kumar S, Butler EK, Ruiz N, Walker S, Kahne DE. Detection of Transport Intermediates in the Peptidoglycan Flippase MurJ Identifies Residues Essential for Conformational Cycling. J Am Chem Soc 2020; 142:5482-5486. [PMID: 32129990 DOI: 10.1021/jacs.9b12185] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacterial cell wall synthesis is an essential process in bacteria and one of the best targets for antibiotics. A critical step on this pathway is the export of the lipid-linked cell wall monomer, Lipid II, by its transporter MurJ. The mechanism by which MurJ mediates the transbilayer movement of Lipid II is not understood because intermediate states of this process have not been observed. Here we demonstrate a method to capture and detect interactions between MurJ and its substrate Lipid II by photo-cross-linking and subsequent biotin-tagging. We show that this method can be used to covalently capture intermediate transport states of Lipid II on MurJ in living cells. Using this strategy we probed several lethal arginine mutants and found that they retain appreciable substrate-binding ability despite being defective in Lipid II transport. We propose that Lipid II binding to these residues during transport induces a conformational change in MurJ required to proceed through the Lipid II transport cycle. The methods described to detect intermediate transport states of MurJ will be useful for characterizing mechanisms of inhibitors.
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Affiliation(s)
- Frederick A Rubino
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Aurelio Mollo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Sujeet Kumar
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210, United States
| | - Emily K Butler
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210, United States
| | - Natividad Ruiz
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210, United States
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniel E Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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Bolla JR, Corey RA, Sahin C, Gault J, Hummer A, Hopper JTS, Lane DP, Drew D, Allison TM, Stansfeld PJ, Robinson CV, Landreh M. A Mass‐Spectrometry‐Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jani Reddy Bolla
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Robin A. Corey
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
- Department of BiologyUniversity of Copenhagen Copenhagen N 2200 Denmark
| | - Joseph Gault
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Alissa Hummer
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
| | - Jonathan T. S. Hopper
- OMass Therapeutics The Oxford Science Park, The Schrödinger Building Kidlington OX4 4GE UK
| | - David P. Lane
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
| | - David Drew
- Department of Biochemistry and BiophysicsStockholm University 10691 Stockholm Sweden
| | - Timothy M. Allison
- Biomolecular Interaction Centre and School of Physical and Chemical SciencesUniversity of Canterbury Christchurch 8140 New Zealand
| | - Phillip J. Stansfeld
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
- School of Life Sciences & Department of ChemistryUniversity of Warwick Coventry CV4 7AL UK
| | - Carol V. Robinson
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
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Rismondo J, Haddad TFM, Shen Y, Loessner MJ, Gründling A. GtcA is required for LTA glycosylation in Listeria monocytogenes serovar 1/2a and Bacillus subtilis. ACTA ACUST UNITED AC 2020; 6:100038. [PMID: 32743150 PMCID: PMC7389260 DOI: 10.1016/j.tcsw.2020.100038] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/16/2020] [Accepted: 02/11/2020] [Indexed: 11/26/2022]
Abstract
The cell wall polymers wall teichoic acid (WTA) and lipoteichoic acid (LTA) are often modified with glycosyl and D-alanine residues. Recent studies have shown that a three-component glycosylation system is used for the modification of LTA in several Gram-positive bacteria including Bacillus subtilis and Listeria monocytogenes. In the L. monocytogenes 1/2a strain 10403S, the cytoplasmic glycosyltransferase GtlA is thought to use UDP-galactose to produce the C55-P-galactose lipid intermediate, which is transported across the membrane by an unknown flippase. Next, the galactose residue is transferred onto the LTA backbone on the outside of the cell by the glycosyltransferase GtlB. Here we show that GtcA is necessary for the glycosylation of LTA in L. monocytogenes 10403S and B. subtilis 168 and we hypothesize that these proteins act as C55-P-sugar flippases. With this we revealed that GtcA is involved in the glycosylation of both teichoic acid polymers in L. monocytogenes 10403S, namely WTA with N-acetylglucosamine and LTA with galactose residues. These findings indicate that the L. monocytogenes GtcA protein can act on different C55-P-sugar intermediates. Further characterization of GtcA in L. monocytogenes led to the identification of residues essential for its overall function as well as residues, which predominately impact WTA or LTA glycosylation.
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Affiliation(s)
- Jeanine Rismondo
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Talal F M Haddad
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Yang Shen
- Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Angelika Gründling
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
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39
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Sequence and structural determinants of ligand-dependent alternating access of a MATE transporter. Proc Natl Acad Sci U S A 2020; 117:4732-4740. [PMID: 32075917 DOI: 10.1073/pnas.1917139117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multidrug and toxic compound extrusion (MATE) transporters are ubiquitous ion-coupled antiporters that extrude structurally and chemically dissimilar cytotoxic compounds and have been implicated in conferring multidrug resistance. Here, we integrate double electron-electron resonance (DEER) with functional assays and site-directed mutagenesis of conserved residues to illuminate principles of ligand-dependent alternating access of PfMATE, a proton-coupled MATE from the hyperthermophilic archaeon Pyrococcus furiosus Pairs of spin labels monitoring the two sides of the transporter reconstituted into nanodiscs reveal large-amplitude movement of helices that alter the orientation of a putative substrate binding cavity. We found that acidic pH favors formation of an inward-facing (IF) conformation, whereas elevated pH (>7) and the substrate rhodamine 6G stabilizes an outward-facing (OF) conformation. The lipid-dependent PfMATE isomerization between OF and IF conformation is driven by protonation of a previously unidentified intracellular glutamate residue that is critical for drug resistance. Our results can be framed in a mechanistic model of transport that addresses central aspects of ligand coupling and alternating access.
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40
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Analysis of the Topology and Active-Site Residues of WbbF, a Putative O-Polysaccharide Synthase from Salmonella enterica Serovar Borreze. J Bacteriol 2020; 202:JB.00625-19. [PMID: 31792013 DOI: 10.1128/jb.00625-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023] Open
Abstract
Bacterial lipopolysaccharides are major components and contributors to the integrity of Gram-negative outer membranes. The more conserved lipid A-core part of this complex glycolipid is synthesized separately from the hypervariable O-antigenic polysaccharide (OPS) part, and they are joined in the periplasm prior to translocation to the outer membrane. Three different biosynthesis strategies are recognized for OPS biosynthesis, and one, the synthase-dependent pathway, is currently confined to a single example: the O:54 antigen from Salmonella enterica serovar Borreze. Synthases are complex enzymes that have the capacity to both polymerize and export bacterial polysaccharides. Although synthases like cellulose synthase are widespread, they typically polymerize a glycan without employing a lipid-linked intermediate, unlike the O:54 synthase (WbbF), which produces an undecaprenol diphosphate-linked product. This raises questions about the overall similarity between WbbF and conventional synthases. In this study, we examine the topology of WbbF, revealing four membrane-spanning helices, compared to the eight in cellulose synthase. Molecular modeling of the glycosyltransferase domain of WbbF indicates a similar architecture, and site-directed mutagenesis confirmed that residues important for catalysis and processivity in cellulose synthase are conserved in WbbF and required for its activity. These findings indicate that the glycosyltransferase mechanism of WbbF and classic synthases are likely conserved despite the use of a lipid acceptor for chain extension by WbbF.IMPORTANCE Glycosyltransferases play a critical role in the synthesis of a wide variety of bacterial polysaccharides. These include O-antigenic polysaccharides, which form the distal component of lipopolysaccharides and provide a protective barrier important for survival and host-pathogen interactions. Synthases are a subset of glycosyltransferases capable of coupled synthesis and export of glycans. Currently, the O:54 antigen of Salmonella enterica serovar Borreze involves the only example of an O-polysaccharide synthase, and its generation of a lipid-linked product differentiates it from classical synthases. Here, we explore features conserved in the O:54 enzyme and classical synthases to shed light on the structure and function of the unusual O:54 enzyme.
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41
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Bolla JR, Corey RA, Sahin C, Gault J, Hummer A, Hopper JTS, Lane DP, Drew D, Allison TM, Stansfeld PJ, Robinson CV, Landreh M. A Mass-Spectrometry-Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins. Angew Chem Int Ed Engl 2020; 59:3523-3528. [PMID: 31886601 PMCID: PMC7065234 DOI: 10.1002/anie.201914411] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/29/2019] [Indexed: 01/21/2023]
Abstract
Membrane proteins engage in a variety of contacts with their surrounding lipids, but distinguishing between specifically bound lipids, and non‐specific, annular interactions is a challenging problem. Applying native mass spectrometry to three membrane protein complexes with different lipid‐binding properties, we explore the ability of detergents to compete with lipids bound in different environments. We show that lipids in annular positions on the presenilin homologue protease are subject to constant exchange with detergent. By contrast, detergent‐resistant lipids bound at the dimer interface in the leucine transporter show decreased koff rates in molecular dynamics simulations. Turning to the lipid flippase MurJ, we find that addition of the natural substrate lipid‐II results in the formation of a 1:1 protein–lipid complex, where the lipid cannot be displaced by detergent from the highly protected active site. In summary, we distinguish annular from non‐annular lipids based on their exchange rates in solution.
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Affiliation(s)
- Jani Reddy Bolla
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Solna, Sweden.,Department of Biology, University of Copenhagen, Copenhagen N, 2200, Denmark
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Alissa Hummer
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jonathan T S Hopper
- OMass Therapeutics, The Oxford Science Park, The Schrödinger Building, Kidlington, OX4 4GE, UK
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Solna, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Solna, Sweden
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Booth S, Lewis RJ. Structural basis for the coordination of cell division with the synthesis of the bacterial cell envelope. Protein Sci 2019; 28:2042-2054. [PMID: 31495975 PMCID: PMC6863701 DOI: 10.1002/pro.3722] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 01/02/2023]
Abstract
Bacteria are surrounded by a complex cell envelope made up of one or two membranes supplemented with a layer of peptidoglycan (PG). The envelope is responsible for the protection of bacteria against lysis in their oft-unpredictable environments and it contributes to cell integrity, morphology, signaling, nutrient/small-molecule transport, and, in the case of pathogenic bacteria, host-pathogen interactions and virulence. The cell envelope requires considerable remodeling during cell division in order to produce genetically identical progeny. Several proteinaceous machines are responsible for the homeostasis of the cell envelope and their activities must be kept coordinated in order to ensure the remodeling of the envelope is temporally and spatially regulated correctly during multiple cycles of cell division and growth. This review aims to highlight the complexity of the components of the cell envelope, but focusses specifically on the molecular apparatuses involved in the synthesis of the PG wall, and the degree of cross talk necessary between the cell division and the cell wall remodeling machineries to coordinate PG remodeling during division. The current understanding of many of the proteins discussed here has relied on structural studies, and this review concentrates particularly on this structural work.
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Affiliation(s)
- Simon Booth
- Institute for Cell and Molecular Biosciences, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Richard J. Lewis
- Institute for Cell and Molecular Biosciences, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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43
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Holland IB. Rise and rise of the ABC transporter families. Res Microbiol 2019; 170:304-320. [PMID: 31442613 DOI: 10.1016/j.resmic.2019.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/30/2019] [Accepted: 08/13/2019] [Indexed: 01/15/2023]
Abstract
This review will inevitably be influenced by my personal experience and personal view of the progression of this amazing family of proteins. This has generated a huge literature in over nearly five decades, some ideas have bloomed and faded while others have persisted, other contributions simply become redundant, overtaken by better techniques. At the outset, the pioneers had no idea of the magnitude of the topic they were working on, then a very rough idea of the significance emerged and, progressively, the picture becomes sharper and finally extraordinary. I have tried to produce at least an outline of that progression. My apologies for the also inevitable omissions, especially relating to the mass of biochemical and spectroscopy and genetical studies. I decided to prioritise structural biology because structures when successful are definitive and of course provide a 'visual' image. However, I tried to limit the structural aspects to the proteins that reflected the main advances.
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Affiliation(s)
- I Barry Holland
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Sud, Orsay, France.
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44
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Zubcevic L, Lee SY. The role of π-helices in TRP channel gating. Curr Opin Struct Biol 2019; 58:314-323. [PMID: 31378426 DOI: 10.1016/j.sbi.2019.06.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/21/2022]
Abstract
Transient Receptor Potential (TRP) channels are a large superfamily of polymodal ion channels, which perform important roles in numerous physiological processes. The architecture of their transmembrane (TM) domains closely resembles that of voltage-gated potassium channels (KV). However, recent cryoEM and crystallographic studies of TRP channels have identified π-helices in functionally important regions, and it is increasingly recognized that they utilize a distinct mechanism of gating that relies on α-to-π secondary structure transitions. Here we review our current understanding of the role of π-helices in TRP channel function and their broader impact on different classes of ion channels.
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Affiliation(s)
- Lejla Zubcevic
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.
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