1
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Wang Z, Li T, Huang X, Xu R, Zhao Y, Wei J, Pi W, Yao S, Lu J, Zhang X, Lei H, Wang P. Chiral helix amplification and enhanced bioadhesion of two-component low molecular weight hydrogels regulated by OH to eradicate MRSA biofilms. MATERIALS HORIZONS 2025; 12:575-586. [PMID: 39499027 DOI: 10.1039/d4mh01213e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2024]
Abstract
The supramolecular chemistry of small chiral molecules has attracted widespread attention owing to their similarity to natural assembly codes. Two-component low-molecular-weight (LMW) hydrogels are crucial as they form helical structures via chirality transfer, enabling diverse functions. Herein, we report a pair of two-component chiral LMW hydrogels based on the small molecular drugs baicalin (BA), scutellarin (SCU) and berberine (BBR). The two hydrogels exhibited different helicities and abilities to adhere to methicillin-resistant staphylococcus aureus (MRSA) biofilms. The BA or SCU can each laterally interact with BBR in a tail-to-tail configuration, forming a stable hydrophobic structure, while hydrophilic glucuronide groups are exposed to a water solution to form a hydrogel. However, the tiny variant steric hindrance of the terminal OH moiety of SCU affects π-π stacking in the layered assembly, resulting in SCU-BBR having much stronger chirality deviation and supramolecular chirality amplification than BA-BBR. Thereafter, the OH group in SCU-BBR forms more intermolecular hydrogen bonds with MRSA biofilms, enhancing stronger adhesion and better scavenging effects than BA-BBR. This work provides a unique chiral supramolecular assembly pattern, expands the antibacterial application prospect of a two-component LMW hydrogel accompanying chirality amplification, and provides a new perspective and strategy for biofilm removal.
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Affiliation(s)
- Zhijia Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Tong Li
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Xuemei Huang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Ran Xu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Yihang Zhao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Jichang Wei
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Wenmin Pi
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Shuchang Yao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Jihui Lu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Xiang Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Haimin Lei
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Penglong Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, China.
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2
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Agarwal H, Gurnani B, Pippal B, Jain N. Capturing the micro-communities: Insights into biogenesis and architecture of bacterial biofilms. BBA ADVANCES 2024; 7:100133. [PMID: 39839441 PMCID: PMC11750278 DOI: 10.1016/j.bbadva.2024.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2025] Open
Abstract
Biofilm is an assemblage of microorganisms embedded within the extracellular matrix that provides mechanical stability, nutrient absorption, antimicrobial resistance, cell-cell interactions, and defence against host immune system. Various biomolecules such as lipids, carbohydrates, protein polymers (amyloid), and eDNA are present in the matrix playing significant role in determining the distinctive properties of biofilm. The formation of biofilms contributes to resistance against antimicrobial therapy in most of the human infections and exacerbates existing diseases. Therefore, this field requires several state-of-the-art techniques to fully understand the 3-D organization of biofilms, their cell behaviour and responses to pharmaceutical treatments. Here, we explore the assembly and regulation of biofilm biogenesis in the context of matrix components and highlight the significance of high-resolution imaging and analysing techniques for monitoring complex biofilm architecture. Our review also emphasizes the novelty and advancements in techniques to visualise biofilm structure and composition, providing valuable insights to understand biofilm-related infections.
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Affiliation(s)
- Harshita Agarwal
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 65, Nagaur Road, Karwar, Rajasthan 342037, India
| | - Bharat Gurnani
- Centre of Excellence-AyurTech, Indian Institute of Technology Jodhpur, NH 65, Nagaur Road, Karwar, Rajasthan 342037, India
| | - Bhumika Pippal
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 65, Nagaur Road, Karwar, Rajasthan 342037, India
| | - Neha Jain
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 65, Nagaur Road, Karwar, Rajasthan 342037, India
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3
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Han S, Kim S, Sedlacek CJ, Farooq A, Song C, Lee S, Liu S, Brüggemann N, Rohe L, Kwon M, Rhee SK, Jung MY. Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea. mBio 2024; 15:e0216924. [PMID: 39360821 PMCID: PMC11559005 DOI: 10.1128/mbio.02169-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 09/03/2024] [Indexed: 10/05/2024] Open
Abstract
Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems. IMPORTANCE Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.
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Affiliation(s)
- Saem Han
- Interdisciplinary Graduate Program in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
| | - Seongwook Kim
- Interdisciplinary Graduate Program in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
| | - Christopher J. Sedlacek
- Division of Microbial Ecology, Centre for Microbiology and Environmental System Science, University of Vienna, Vienna, Austria
- Department of Biology, University of Southern Indiana, Evansville, Indiana, USA
| | - Adeel Farooq
- Department of Biology Education, Jeju National University, Jeju, South Korea
| | - Chihong Song
- Core Research Facility, Pusan National University, Yangsan, South Korea
| | - Sujin Lee
- Core Research Facility, Pusan National University, Yangsan, South Korea
| | - Shurong Liu
- School of Agriculture, Sun Yat-Sen University, Shenzhen, China
| | - Nicolas Brüggemann
- Agrosphäre (IBG-3), Institut für Bio- und Geowissenschaften (IBG), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Lena Rohe
- Thünen Institute of Climate-Smart Agriculture, Braunschweig, Germany
| | - Miye Kwon
- Biodiversity Research Institute, Jeju Technopark, Jeju, South Korea
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro,Seowon-Gu, Cheongju, South Korea
| | - Man-Young Jung
- Interdisciplinary Graduate Program in Advance Convergence Technology and Science, Jeju National University, Jeju, South Korea
- Department of Biology Education, Jeju National University, Jeju, South Korea
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4
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Ruijgrok G, Wu DY, Overkleeft HS, Codée JDC. Synthesis and application of bacterial exopolysaccharides. Curr Opin Chem Biol 2024; 78:102418. [PMID: 38134611 DOI: 10.1016/j.cbpa.2023.102418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/02/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023]
Abstract
Exopolysaccharides are produced and excreted by bacteria in the generation of biofilms to provide a protective environment. These polysaccharides are generally generated as heterogeneous polymers of varying length, featuring diverse substitution patterns. To obtain well-defined fragments of these polysaccharides, organic synthesis often is the method of choice, as it allows for full control over chain length and the installation of a pre-determined substitution pattern. This review presents several recent syntheses of exopolysaccharide fragments of Pseudomonas aeruginosa and Staphylococcus aureus and illustrates how these have been used to study biosynthesis enzymes and generate synthetic glycoconjugate vaccines.
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Affiliation(s)
- Gijs Ruijgrok
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333, CC Leiden, the Netherlands
| | - Dung-Yeh Wu
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333, CC Leiden, the Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333, CC Leiden, the Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333, CC Leiden, the Netherlands.
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5
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Eddenden A, Dooda MK, Morrison ZA, Subramanian AS, Howell PL, Troutman JM, Nitz M. Metabolic Usage and Glycan Destinations of GlcNAz in E. coli. ACS Chem Biol 2024; 19:69-80. [PMID: 38146215 PMCID: PMC11138243 DOI: 10.1021/acschembio.3c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Bacteria use a diverse range of carbohydrates to generate a profusion of glycans, with amino sugars, such as N-acetylglucosamine (GlcNAc), being prevalent in the cell wall and in many exopolysaccharides. The primary substrate for GlcNAc-containing glycans, UDP-GlcNAc, is the product of the bacterial hexosamine pathway and a key target for bacterial metabolic glycan engineering. Using the strategy of expressing NahK, to circumvent the hexosamine pathway, it is possible to directly feed the analogue of GlcNAc, N-azidoacetylglucosamine (GlcNAz), for metabolic labeling in Escherichia coli. The cytosolic production of UDP-GlcNAz was confirmed by using fluorescence-assisted polyacrylamide gel electrophoresis. The key question of where GlcNAz is incorporated was interrogated by analyzing potential sites including peptidoglycan (PGN), the biofilm-related exopolysaccharide poly-β-1,6-N-acetylglucosamine (PNAG), lipopolysaccharide (LPS), and the enterobacterial common antigen (ECA). The highest levels of incorporation were observed in PGN with lower levels in PNAG and no observable incorporation in LPS or ECA. The promiscuity of the PNAG synthase (PgaCD) toward UDP-GlcNAz in vitro and the lack of undecaprenyl-pyrophosphoryl-GlcNAz intermediates generated in vivo confirmed the incorporation preferences. The results of this work will guide the future development of carbohydrate-based probes and metabolic engineering strategies.
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Affiliation(s)
- Alexander Eddenden
- Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada
| | - Manoj K. Dooda
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223-0001, United States
| | - Zachary A. Morrison
- Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada
| | - Adithya Shankara Subramanian
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 0A4, Canada
| | - P. Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 0A4, Canada
| | - Jerry M. Troutman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223-0001, United States
| | - Mark Nitz
- Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada
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6
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Moran CL, Debowski A, Vrielink A, Stubbs K, Sarkar-Tyson M. N-acetyl-β-hexosaminidase activity is important for chitooligosaccharide metabolism and biofilm formation in Burkholderia pseudomallei. Environ Microbiol 2024; 26:e16571. [PMID: 38178319 DOI: 10.1111/1462-2920.16571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Burkholderia pseudomallei is a saprophytic Gram-negative bacillus that can cause the disease melioidosis. Although B. pseudomallei is a recognised member of terrestrial soil microbiomes, little is known about its contribution to the saprophytic degradation of polysaccharides within its niche. For example, while chitin is predicted to be abundant within terrestrial soils the chitinolytic capacity of B. pseudomallei is yet to be defined. This study identifies and characterises a putative glycoside hydrolase, bpsl0500, which is expressed by B. pseudomallei K96243. Recombinant BPSL0500 was found to exhibit activity against substrate analogues and GlcNAc disaccharides relevant to chitinolytic N-acetyl-β-d-hexosaminidases. In B. pseudomallei, bpsl0500 was found to be essential for both N-acetyl-β-d-hexosaminidase activity and chitooligosaccharide metabolism. Furthermore, bpsl0500 was also observed to significantly affect biofilm deposition. These observations led to the identification of BPSL0500 activity against model disaccharide linkages that are present in biofilm exopolysaccharides, a feature that has not yet been described for chitinolytic enzymes. The results in this study indicate that chitinolytic N-acetyl-β-d-hexosaminidases like bpsl0500 may facilitate biofilm disruption as well as chitin assimilation, providing dual functionality for saprophytic bacteria such as B. pseudomallei within the competitive soil microbiome.
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Affiliation(s)
- Clare L Moran
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Aleksandra Debowski
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
| | - Keith Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, University of Western Australia, Crawley, Australia
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
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7
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Giovannini M, Petroni G, Castelli M. Novel evolutionary insights on the interactions of the Holosporales (Alphaproteobacteria) with eukaryotic hosts from comparative genomics. Environ Microbiol 2024; 26:e16562. [PMID: 38173299 DOI: 10.1111/1462-2920.16562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Holosporales are an alphaproteobacterial order engaging in obligate and complex associations with eukaryotes, in particular protists. The functional and evolutionary features of those interactions are still largely undisclosed. Here, we sequenced the genomes of two members of the species Bealeia paramacronuclearis (Holosporales, Holosporaceae) intracellularly associated with the ciliate protist Paramecium, which resulted in high correspondence. Consistent with the short-branched early-divergent phylogenetic position, Bealeia presents a larger functional repertoire than other Holosporaceae, comparable to those of other Holosporales families, particularly for energy metabolism and motility. Our analyses indicate that different Holosporales likely experienced at least partly autonomous genome reduction and adaptation to host interactions, for example regarding dependence on host biotin driven by multiple independent horizontal acquisitions of transporters. Among Alphaproteobacteria, this is reminiscent of the convergently evolved Rickettsiales, which however appear more diverse, possibly due to a probably more ancient origin. We identified in Bealeia and other Holosporales the plasmid-encoded putative genetic determinants of R-bodies, which may be involved in a killer trait towards symbiont-free hosts. While it is not clear whether these genes are ancestral or recently horizontally acquired, an intriguing and peculiar role of R-bodies is suggested in the evolution of the interactions of multiple Holosporales with their hosts.
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Affiliation(s)
| | | | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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8
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Wang S, Zhao Y, Breslawec AP, Liang T, Deng Z, Kuperman LL, Yu Q. Strategy to combat biofilms: a focus on biofilm dispersal enzymes. NPJ Biofilms Microbiomes 2023; 9:63. [PMID: 37679355 PMCID: PMC10485009 DOI: 10.1038/s41522-023-00427-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/15/2023] [Indexed: 09/09/2023] Open
Abstract
Bacterial biofilms, which consist of three-dimensional extracellular polymeric substance (EPS), not only function as signaling networks, provide nutritional support, and facilitate surface adhesion, but also serve as a protective shield for the residing bacterial inhabitants against external stress, such as antibiotics, antimicrobials, and host immune responses. Biofilm-associated infections account for 65-80% of all human microbial infections that lead to serious mortality and morbidity. Tremendous effort has been spent to address the problem by developing biofilm-dispersing agents to discharge colonized microbial cells to a more vulnerable planktonic state. Here, we discuss the recent progress of enzymatic eradicating strategies against medical biofilms, with a focus on dispersal mechanisms. Particularly, we review three enzyme classes that have been extensively investigated, namely glycoside hydrolases, proteases, and deoxyribonucleases.
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Affiliation(s)
- Shaochi Wang
- Otorhinolaryngology Hospital, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Yanteng Zhao
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Alexandra P Breslawec
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20740, USA
| | - Tingting Liang
- Key Laboratory of Natural Medicine and Immune-Engineering of Henan Province, Henan University Jinming Campus, 475004, Kaifeng, Henan, China
| | - Zhifen Deng
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Laura L Kuperman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20740, USA.
- Mirimus Inc., 760 Parkside Avenue, Brooklyn, NY, 11226, USA.
| | - Qiuning Yu
- Otorhinolaryngology Hospital, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
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9
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Eddenden A, Dooda MK, Morrison ZA, Subramanian AS, Howell PL, Troutman JM, Nitz M. The Metabolic Usage and Glycan Destinations of GlcNAz in E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553294. [PMID: 37645909 PMCID: PMC10462111 DOI: 10.1101/2023.08.17.553294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Bacteria use a diverse range of carbohydrates to generate a profusion of glycans, with amino sugars such as N-acetylglucosamine (GlcNAc) being prevalent in the cell wall and in many exopolysaccharides. The primary substrate for GlcNAc-containing glycans, UDP-GlcNAc, is the product of the bacterial hexosamine pathway, and a key target for bacterial metabolic glycan engineering. Using the strategy of expressing NahK, to circumvent the hexosamine pathway, it is possible to directly feed the analogue of GlcNAc, N-azidoacetylglucosamine (GlcNAz), for metabolic labelling in E. coli. The cytosolic production of UDP-GlcNAz was confirmed using fluorescence assisted polyacrylamide gel electrophoresis. The key question of where GlcNAz is incorporated, was interrogated by analyzing potential sites including: peptidoglycan (PGN), the biofilm-related exopolysaccharide poly-β-1,6-N-acetylglucosamine (PNAG), lipopolysaccharide (LPS) and the enterobacterial common antigen (ECA). The highest levels of incorporation were observed in PGN with lower levels in PNAG and no observable incorporation in LPS or ECA. The promiscuity of the PNAG synthase (PgaCD) towards UDP-GlcNAz in vitro and lack of undecaprenyl-pyrophosphoryl-GlcNAz intermediates generated in vivo confirmed the incorporation preferences. The results of this work will guide the future development of carbohydrate-based probes and metabolic engineering strategies.
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Affiliation(s)
- Alexander Eddenden
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Manoj K Dooda
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, United States
| | - Zachary A Morrison
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Adithya Shankara Subramanian
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jerry M Troutman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, United States
| | - Mark Nitz
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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10
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Liu L, Xia Y, Li Y, Zhou Y, Su X, Yan X, Wang Y, Liu W, Cheng H, Wang Y, Yang Q. Inhibition of chitin deacetylases to attenuate plant fungal diseases. Nat Commun 2023; 14:3857. [PMID: 37385996 PMCID: PMC10310857 DOI: 10.1038/s41467-023-39562-7] [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] [Received: 11/18/2022] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
Phytopathogenic fungi secrete chitin deacetylase (CDA) to escape the host's immunological defense during infection. Here, we showed that the deacetylation activity of CDA toward chitin is essential for fungal virulence. Five crystal structures of two representative and phylogenetically distant phytopathogenic fungal CDAs, VdPDA1 from Verticillium dahliae and Pst_13661 from Puccinia striiformis f. sp. tritici, were obtained in ligand-free and inhibitor-bound forms. These structures suggested that both CDAs have an identical substrate-binding pocket and an Asp-His-His triad for coordinating a transition metal ion. Based on the structural identities, four compounds with a benzohydroxamic acid (BHA) moiety were obtained as phytopathogenic fungal CDA inhibitors. BHA exhibited high effectiveness in attenuating fungal diseases in wheat, soybean, and cotton. Our findings revealed that phytopathogenic fungal CDAs share common structural features, and provided BHA as a lead compound for the design of CDA inhibitors aimed at attenuating crop fungal diseases.
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Affiliation(s)
- Lin Liu
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518000, Shenzhen, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Yeqiang Xia
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, 210095, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yingchen Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Yong Zhou
- School of Software, Dalian University of Technology, 116024, Dalian, China
| | - Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaojing Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, 210095, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China.
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, 210095, Nanjing, China.
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Qing Yang
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518000, Shenzhen, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
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11
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Öztürk FY, Darcan C, Kariptaş E. The Determination, Monitoring, Molecular Mechanisms and Formation of Biofilm in E. coli. Braz J Microbiol 2023; 54:259-277. [PMID: 36577889 PMCID: PMC9943865 DOI: 10.1007/s42770-022-00895-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
Biofilms are cell assemblies embedded in an exopolysaccharide matrix formed by microorganisms of a single or many different species. This matrix in which they are embedded protects the bacteria from external influences and antimicrobial effects. The biofilm structure that microorganisms form to protect themselves from harsh environmental conditions and survive is found in nature in many different environments. These environments where biofilm formation occurs have in common that they are in contact with fluids. The gene expression of bacteria in complex biofilm differs from that of bacteria in the planktonic state. The differences in biofilm cell expression are one of the effects of community life. Means of quorum sensing, bacteria can act in coordination with each other. At the same time, while biofilm formation provides many benefits to bacteria, it has positive and negative effects in many different areas. Depending on where they occur, biofilms can cause serious health problems, contamination risks, corrosion, and heat and efficiency losses. However, they can also be used in water treatment plants, bioremediation, and energy production with microbial fuel cells. In this review, the basic steps of biofilm formation and biofilm regulation in the model organism Escherichia coli were discussed. Finally, the methods by which biofilm formation can be detected and monitored were briefly discussed.
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Affiliation(s)
- Fırat Yavuz Öztürk
- Department of Molecular Biology and Genetic, Faculty of Arts and Science, Bilecik Seyh Edebali University, Bilecik, Turkey.
| | - Cihan Darcan
- Department of Molecular Biology and Genetic, Faculty of Arts and Science, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Ergin Kariptaş
- Department of Medical Microbiology, Faculty of Medicine, Samsun University, Samsun, Turkey
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12
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Lai SJ, Tu IF, Tseng TS, Tsai YH, Wu SH. The deficiency of poly-β-1,6-N-acetyl-glucosamine deacetylase trigger A. baumannii to convert to biofilm-independent colistin-tolerant cells. Sci Rep 2023; 13:2800. [PMID: 36797306 PMCID: PMC9935895 DOI: 10.1038/s41598-023-30065-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen that can be resistant to antibiotics by rapidly modulating its anti-drug mechanisms. The multidrug-resistant A. baumannii has been considered one of the most threatening pathogens to our society. Biofilm formation and persistent cells within the biofilm matrix are recognized as intractable problems, especially in hospital-acquired infections. Poly-β-1,6-N-acetyl-glucosamine (PNAG) is one of the important building blocks in A. baumannii's biofilm. Here, we discover a protein phosphoryl-regulation on PNAG deacetylase, AbPgaB1, in which residue Ser411 was phosphorylated. The phosphoryl-regulation on AbPgaB1 modulates the product turnover rate in which deacetylated PNAG is produced and reflected in biofilm production. We further uncovered the PgaB deficient A. baumannii strain shows the lowest level of biofilm production but has a high minimal inhibition concentration to antibiotic colistin and tetracycline. Based on bactericidal post-antibiotic effects and time-dependent killing assays with antibacterial drugs, we claim that the PgaB-deficient A. baumannii converts to colistin-tolerant cells. This study utilizes a biofilm-independent colistin-tolerant model of A. baumannii to further investigate its characteristics and mechanisms to better understand clinical outcomes.
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Affiliation(s)
- Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan. .,Research Center for Cancer Biology, China Medical University, Taichung, 404333, Taiwan.
| | - I-Fan Tu
- grid.28665.3f0000 0001 2287 1366Institute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Tien-Sheng Tseng
- grid.260542.70000 0004 0532 3749Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Hsuan Tsai
- grid.510951.90000 0004 7775 6738Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, 518132 China
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan. .,Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan.
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13
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Dueholm MKD, Besteman M, Zeuner EJ, Riisgaard-Jensen M, Nielsen ME, Vestergaard SZ, Heidelbach S, Bekker NS, Nielsen PH. Genetic potential for exopolysaccharide synthesis in activated sludge bacteria uncovered by genome-resolved metagenomics. WATER RESEARCH 2023; 229:119485. [PMID: 36538841 DOI: 10.1016/j.watres.2022.119485] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
A good floc formation of activated sludge (AS) is crucial for solid-liquid separation and production of clean effluent during wastewater treatment. Floc formation is partly controlled by self-produced extracellular polymeric substances (EPS) such as exopolysaccharides, proteins, and nucleic acids. Little is known about the composition, structure, and function of EPS in AS and which bacteria produce them. To address this knowledge gap for the exopolysaccharides, we took advantage of 1083 high-quality metagenome-assembled genomes (MAGs) obtained from 23 Danish wastewater treatment plants. We investigated the genomic potential for exopolysaccharide biosynthesis in bacterial species typical in AS systems based on genome mining and gene synteny analyses. Putative gene clusters associated with the biosynthesis of alginate, cellulose, curdlan, diutan, hyaluronic acids, Pel, poly-β-1,6-N-acetyl-d-glucosamine (PNAG), Psl, S88 capsular polysaccharide, salecan, succinoglycan, and xanthan were identified and linked to individual MAGs, providing a comprehensive overview of the genome-resolved potential for these exopolysaccharides in AS bacteria. The approach and results provide a starting point for a more comprehensive understanding of EPS composition in wastewater treatment systems, which may facilitate a more refined regulation of the activated sludge process for improved stability.
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Affiliation(s)
- Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Maaike Besteman
- Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Emil Juel Zeuner
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marie Riisgaard-Jensen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Eneberg Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sofie Zacho Vestergaard
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Søren Heidelbach
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Nicolai Sundgaard Bekker
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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14
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Dell'Anno F, Joaquim van Zyl L, Trindade M, Buschi E, Cannavacciuolo A, Pepi M, Sansone C, Brunet C, Ianora A, de Pascale D, Golyshin PN, Dell'Anno A, Rastelli E. Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120772. [PMID: 36455775 DOI: 10.1016/j.envpol.2022.120772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.
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Affiliation(s)
- Filippo Dell'Anno
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Leonardo Joaquim van Zyl
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa.
| | - Marla Trindade
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa.
| | - Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Antonio Cannavacciuolo
- Department of Integrative Marine Ecology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Milva Pepi
- Department of Integrative Marine Ecology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Clementina Sansone
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Christophe Brunet
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Gwynedd LL57 2UW, UK.
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
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15
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The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing. PLoS Pathog 2022; 18:e1010750. [PMID: 35930610 PMCID: PMC9384988 DOI: 10.1371/journal.ppat.1010750] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/17/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022] Open
Abstract
The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB. Exopolysaccharides are an important component of the extracellular matrix of bacterial and fungal biofilms and provide protection against the host immune response and antibiotics. In Gram-negative bacteria, these polymers are synthesized in the inner membrane and translocated across the periplasm before being secreted across the outer membrane. The periplasm presents both a challenge as an additional environment to cross and an opportunity to chemically alter the polymer prior to secretion to render it more effective. This study focuses on a periplasmic alpha-helical repeat domain whose wide-spread homologues are involved in the export of many chemically distinct exopolysaccharides. We found that in E. coli this superhelical TPR domain acts as a scaffold that can bind the polymer PNAG and alter the enzymatic activity of PgaB, thus providing a means to affect the deacetylation level and chain length of the secreted polymer. Scaffold proteins are known as binding hubs within cellular pathways that often have a central regulatory function and facilitate evolution due to their repetitive modular building blocks. Our study sheds light on the principles of polysaccharide modification and export, which we hope will promote the development of applications against bacterial infections.
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16
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Anderson AC, Burnett AJN, Constable S, Hiscock L, Maly KE, Weadge JT. A Mechanistic Basis for Phosphoethanolamine Modification of the Cellulose Biofilm Matrix in Escherichia coli. Biochemistry 2021; 60:3659-3669. [PMID: 34762795 DOI: 10.1021/acs.biochem.1c00605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biofilms are communities of self-enmeshed bacteria in a matrix of exopolysaccharides. The widely distributed human pathogen and commensal Escherichia coli produces a biofilm matrix composed of phosphoethanolamine (pEtN)-modified cellulose and amyloid protein fibers, termed curli. The addition of pEtN to the cellulose exopolysaccharide is accomplished by the action of the pEtN transferase, BcsG, and is essential for the overall integrity of the biofilm. Here, using the synthetic co-substrates p-nitrophenyl phosphoethanolamine and β-d-cellopentaose, we demonstrate using an in vitro pEtN transferase assay that full activity of the pEtN transferase domain of BcsG from E. coli (EcBcsGΔN) requires Zn2+ binding, a catalytic nucleophile/acid-base arrangement (Ser278/Cys243/His396), disulfide bond formation, and other newly uncovered essential residues. We further confirm that EcBcsGΔN catalysis proceeds by a ping-pong bisubstrate-biproduct reaction mechanism and displays inefficient kinetic behavior (kcat/KM = 1.81 × 10-4 ± 2.81 × 10-5 M-1 s-1), which is typical of exopolysaccharide-modifying enzymes in bacteria. Thus, the results presented, especially with respect to donor binding (as reflected by KM), have importantly broadened our understanding of the substrate profile and catalytic mechanism of this class of enzymes, which may aid in the development of inhibitors targeting BcsG or other characterized members of the pEtN transferase family, including the intrinsic and mobile colistin resistance factors.
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17
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Tenea GN, Hurtado P. Next-Generation Sequencing for Whole-Genome Characterization of Weissella cibaria UTNGt21O Strain Originated From Wild Solanum quitoense Lam. Fruits: An Atlas of Metabolites With Biotechnological Significance. Front Microbiol 2021; 12:675002. [PMID: 34163450 PMCID: PMC8215347 DOI: 10.3389/fmicb.2021.675002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
The whole genome of Weissella cibaria strain UTNGt21O isolated from wild fruits of Solanum quitoense (naranjilla) shrub was sequenced and annotated. The similarity proportions based on the genus level, as a result of the best hits for the entire contig, were 54.84% with Weissella, 6.45% with Leuconostoc, 3.23% with Lactococcus, and 35.48% no match. The closest genome was W. cibaria SP7 (GCF_004521965.1) with 86.21% average nucleotide identity (ANI) and 3.2% alignment coverage. The genome contains 1,867 protein-coding genes, among which 1,620 were assigned with the EggNOG database. On the basis of the results, 438 proteins were classified with unknown function from which 247 new hypothetical proteins have no match in the nucleotide Basic Local Alignment Search Tool (BLASTN) database. It also contains 78 tRNAs, six copies of 5S rRNA, one copy of 16S rRNA, one copy of 23S rRNA, and one copy of tmRNA. The W. cibaria UTNGt21O strain harbors several genes responsible for carbohydrate metabolism, cellular process, general stress responses, cofactors, and vitamins, conferring probiotic features. A pangenome analysis indicated the presence of various strain-specific genes encoded for proteins responsible for the defense mechanisms as well as gene encoded for enzymes with biotechnological value, such as penicillin acylase and folates; thus, W. cibaria exhibited high genetic diversity. The genome characterization indicated the presence of a putative CRISPR-Cas array and five prophage regions and the absence of acquired antibiotic resistance genes, virulence, and pathogenic factors; thus, UTNGt21O might be considered a safe strain. Besides, the interaction between the peptide extracts from UTNGt21O and Staphylococcus aureus results in cell death caused by the target cell integrity loss and the release of aromatic molecules from the cytoplasm. The results indicated that W. cibaria UTNGt21O can be considered a beneficial strain to be further exploited for developing novel antimicrobials and probiotic products with improved technological characteristics.
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Affiliation(s)
- Gabriela N Tenea
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Technical University of the North, Ibarra, Ecuador
| | - Pamela Hurtado
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Technical University of the North, Ibarra, Ecuador
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18
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Kashiwabara D, Kondo K, Usami R, Kan D, Kawamura I, Kawasaki Y, Sato M, Nittami T, Suzuki I, Katahira M, Takeda M. Structural determination of the sheath-forming polysaccharide of Sphaerotilus montanus using thiopeptidoglycan lyase which recognizes the 1,4 linkage between α-d-GalN and β-d-GlcA. Int J Biol Macromol 2021; 183:992-1001. [PMID: 33964269 DOI: 10.1016/j.ijbiomac.2021.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 04/01/2021] [Accepted: 05/01/2021] [Indexed: 11/30/2022]
Abstract
Sphaerotilus natans is a filamentous sheath-forming bacterium commonly found in activated sludge. Its sheath is assembled from a thiolic glycoconjugate called thiopeptidoglycan. S. montanus ATCC-BAA-2725 is a sheath-forming member of stream biofilms, and its sheath is morphologically similar to that of S. natans. However, it exhibits heat susceptibility, which distinguishes it from the S. natans sheath. In this study, chemical composition and solid-state NMR analyses suggest that the S. montanus sheath is free of cysteine, indicating that disulfide linkage is not mandatory for sheath formation. The S. montanus sheath was successfully solubilized by N-acetylation, allowing solution-state NMR analysis to determine the sugar sequence. The sheath was susceptible to thiopeptidoglycan lyase prepared from the thiopeptidoglycan-assimilating bacterium, Paenibacillus koleovorans. The reducing ends of the enzymatic digests were labeled with 4-aminobenzoic acid ethyl ester, followed by HPLC. Two derivatives were detected, and their structures were determined. We found that the sheath has no peptides and is assembled as follows: [→4)-β-d-GlcA-(1→4)-β-d-Glc-(1→3)-β-d-GalNAc-(1→4)-α-d-GalNAc-(1→4)-α-d-GalN-(1→]n (β-d-Glc and α-d-GalNAc are stoichiometrically and substoichiometrically 3-O-acetylated, respectively). Thiopeptidoglycan lyase was thus confirmed to cleave the 1,4 linkage between α-d-GalN and β-d-GlcA, regardless of the peptide moiety. Furthermore, vital fluorescent staining of the sheath demonstrated that elongation takes place at the tips, as with the S. natans sheath.
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Affiliation(s)
- Daisuke Kashiwabara
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Keiko Kondo
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Ryoji Usami
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Daisuke Kan
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Izuru Kawamura
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Yuta Kawasaki
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Michio Sato
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama, Kawasaki 214-8571, Japan
| | - Tadashi Nittami
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Ichiro Suzuki
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan; Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Minoru Takeda
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan.
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19
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Jennings LK, Dreifus JE, Reichhardt C, Storek KM, Secor PR, Wozniak DJ, Hisert KB, Parsek MR. Pseudomonas aeruginosa aggregates in cystic fibrosis sputum produce exopolysaccharides that likely impede current therapies. Cell Rep 2021; 34:108782. [PMID: 33626358 PMCID: PMC7958924 DOI: 10.1016/j.celrep.2021.108782] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/18/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022] Open
Abstract
In cystic fibrosis (CF) airways, Pseudomonas aeruginosa forms cellular aggregates called biofilms that are thought to contribute to chronic infection. To form aggregates, P. aeruginosa can use different mechanisms, each with its own pathogenic implications. However, how they form in vivo is controversial and unclear. One mechanism involves a bacterially produced extracellular matrix that holds the aggregates together. Pel and Psl exopolysaccharides are structural and protective components of this matrix. We develop an immunohistochemical method to visualize Pel and Psl in CF sputum. We demonstrate that both exopolysaccharides are expressed in the CF airways and that the morphology of aggregates is consistent with an exopolysaccharide-dependent aggregation mechanism. We reason that the cationic exopolysaccharide Pel may interact with some of the abundant anionic host polymers in sputum. We show that Pel binds extracellular DNA (eDNA) and that this interaction likely impacts current therapies by increasing antimicrobial tolerance and protecting eDNA from digestion.
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Affiliation(s)
- Laura K Jennings
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Julia E Dreifus
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Courtney Reichhardt
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Kelly M Storek
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Patrick R Secor
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Daniel J Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Katherine B Hisert
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
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20
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Warkentin R, Kwan DH. Resources and Methods for Engineering "Designer" Glycan-Binding Proteins. Molecules 2021; 26:E380. [PMID: 33450899 PMCID: PMC7828330 DOI: 10.3390/molecules26020380] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/04/2021] [Accepted: 01/10/2021] [Indexed: 12/11/2022] Open
Abstract
This review provides information on available methods for engineering glycan-binding proteins (GBP). Glycans are involved in a variety of physiological functions and are found in all domains of life and viruses. Due to their wide range of functions, GBPs have been developed with diagnostic, therapeutic, and biotechnological applications. The development of GBPs has traditionally been hindered by a lack of available glycan targets and sensitive and selective protein scaffolds; however, recent advances in glycobiology have largely overcome these challenges. Here we provide information on how to approach the design of novel "designer" GBPs, starting from the protein scaffold to the mutagenesis methods, selection, and characterization of the GBPs.
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Affiliation(s)
- Ruben Warkentin
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada;
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - David H. Kwan
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada;
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada
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21
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Gening ML, Pier GB, Nifantiev NE. Broadly protective semi-synthetic glycoconjugate vaccine against pathogens capable of producing poly-β-(1→6)-N-acetyl-d-glucosamine exopolysaccharide. DRUG DISCOVERY TODAY. TECHNOLOGIES 2020; 35-36:13-21. [PMID: 33388124 DOI: 10.1016/j.ddtec.2020.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 11/15/2022]
Abstract
Poly-β-(1→6)-N-acetylglucosamine (PNAG) was first discovered as a major component of biofilms formed by Staphylococcus aureus and some other staphylococci but later this exopolysaccharide was also found to be produced by pathogens of various nature. This common antigen is considered as a promising target for construction of a broadly protective vaccine. Extensive studies of PNAG, its de-N-acetylated derivative (dPNAG, containing around 15% of residual N-acetates) and their conjugates with Tetanus Toxoid (TT) revealed the crucial role of de-N-acetylated glucosamine units for the induction of protective immunity. Conjugates of synthetic penta- (5GlcNH2) and nona-β-(1→6)-d-glucosamines (9GlcNH2) were tested in vitro and in different animal models and proved to be effective in passive and active protection against different microbial pathogens. Presently conjugate 5GlcNH2-TT is being produced under GMP conditions and undergoes safety and effectiveness evaluation in humans and economically important animals. Current review summarizes all stages of this long-termed study.
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Affiliation(s)
- Marina L Gening
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia
| | - Gerald B Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA 02115, USA.
| | - Nikolay E Nifantiev
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia.
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22
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Falasconi I, Fontana A, Patrone V, Rebecchi A, Duserm Garrido G, Principato L, Callegari ML, Spigno G, Morelli L. Genome-Assisted Characterization of Lactobacillus fermentum, Weissella cibaria, and Weissella confusa Strains Isolated from Sorghum as Starters for Sourdough Fermentation. Microorganisms 2020; 8:E1388. [PMID: 32927810 PMCID: PMC7565839 DOI: 10.3390/microorganisms8091388] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 12/13/2022] Open
Abstract
Sourdough fermentation of bakery products is a well-established and widespread technique to confer an added value to the resulting food. In recent decades, gluten-free raw materials have gained more attention due to the diffusion of food disorders such as coeliac disease, but, at the same time, they present difficult manipulation and scarce technological properties because of the absence of gluten. For this reason, the present work was aimed at selecting starter cultures for sourdough application that are isolated from fermentation of sorghum flour. Three isolates of Lactobacillus fermentum, Weissella cibaria, and Weissella confusa were selected for the following properties: exopolysaccharide synthesis, acidification, CO2 production, and amylase activity. The investigated phenotypic characteristics were confirmed by genomic analyses, which also highlighted other potentially beneficial features for use in bakery products employment. These strains, together with bakery yeast, were used for bread preparation using sorghum and wheat flour and after 24 h of fermentation the resulting dough was analyzed to assess the improvement of its characteristics. The presence of lactic acid bacteria (LAB) had a great impact on the final dough, and the best preparation, from a rheological point of view, resulted in one made of sorghum and wheat flour with added LAB and bakery yeast, whose resulting characteristics were similar to all wheat flour doughs. The results of this study suggest a potential application of the selected starters in sorghum composite bread and should be validated with data from large-scale pilot tests conducted in industrial bakeries.
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Affiliation(s)
- Irene Falasconi
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Alessandra Fontana
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Vania Patrone
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Annalisa Rebecchi
- Biotechnological Research Centre, Università Cattolica del Sacro Cuore, 26100 Cremona, Italy; (A.R.); (M.L.C.)
| | - Guillermo Duserm Garrido
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Laura Principato
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Maria Luisa Callegari
- Biotechnological Research Centre, Università Cattolica del Sacro Cuore, 26100 Cremona, Italy; (A.R.); (M.L.C.)
| | - Giorgia Spigno
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
| | - Lorenzo Morelli
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (I.F.); (A.F.); (G.D.G.); (L.P.); (G.S.); (L.M.)
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23
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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: 161] [Impact Index Per Article: 32.2] [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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24
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Eddenden A, Kitova EN, Klassen JS, Nitz M. An Inactive Dispersin B Probe for Monitoring PNAG Production in Biofilm Formation. ACS Chem Biol 2020; 15:1204-1211. [PMID: 31917539 DOI: 10.1021/acschembio.9b00907] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial exopolysaccharide poly-β-1,6-N-acetylglucosamine is a major extracellular matrix component in biofilms of both Gram-positive and Gram-negative organisms. We have leveraged the specificity of the biofilm-dispersing glycoside hydrolase Dispersin B (DspB) to generate a probe (Dispersin B PNAG probe, DiPP) for monitoring PNAG production and localization during biofilm formation. Mutation of the active site of Dispersin B gave DiPP, which was an effective probe despite its low affinity for PNAG oligosaccharides (KD ∼ 1-10 mM). Imaging of PNAG-dependent and -independent biofilms stained with a fluorescent-protein fusion of DiPP (GFP-DiPP) demonstrated the specificity of the probe for the structure of PNAG on both single-cell and biofilm levels, indicating a high local concentration of PNAG at the bacterial cell surface. Through quantitative bacterial cell binding assays and confocal microscopy analysis using GFP-DiPP, discrete areas of local high concentrations of PNAG were detected on the surface of early log phase cells. These distinct areas were seen to grow, slough from cells, and accumulate in interbacterial regions over the course of several cell divisions, showing the development of a PNAG-dependent biofilm. A potential helical distribution of staining was also noted, suggesting some degree of organization of PNAG production at the cell surface prior to cell aggregation. Together, these experiments shed light on the early stages of PNAG-dependent biofilm formation and demonstrate the value of a low-affinity-high-specificity probe for monitoring the production of bacterial exopolysaccharides.
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Affiliation(s)
- Alexander Eddenden
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario, Canada M5S 3H6
| | - Elena N. Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr. Edmonton, Alberta, Canada T6G 2G2
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr. Edmonton, Alberta, Canada T6G 2G2
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario, Canada M5S 3H6
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25
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Acheson JF, Derewenda ZS, Zimmer J. Architecture of the Cellulose Synthase Outer Membrane Channel and Its Association with the Periplasmic TPR Domain. Structure 2019; 27:1855-1861.e3. [PMID: 31604608 PMCID: PMC6939607 DOI: 10.1016/j.str.2019.09.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/12/2019] [Accepted: 09/16/2019] [Indexed: 02/06/2023]
Abstract
Extracellular bacterial cellulose contributes to biofilm stability and to the integrity of the bacterial cell envelope. In Gram-negative bacteria, cellulose is synthesized and secreted by a multi-component cellulose synthase complex. The BcsA subunit synthesizes cellulose and also transports the polymer across the inner membrane. Translocation across the outer membrane occurs through the BcsC porin, which extends into the periplasm via 19 tetra-tricopeptide repeats (TPR). We present the crystal structure of a truncated BcsC, encompassing the last TPR repeat and the complete outer membrane channel domain, revealing a 16-stranded, β barrel pore architecture. The pore is blocked by an extracellular gating loop, while the extended C terminus inserts deeply into the channel and positions a conserved Trp residue near its extracellular exit. The channel is lined with hydrophilic and aromatic residues suggesting a mechanism for facilitated cellulose diffusion based on aromatic stacking and hydrogen bonding.
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Affiliation(s)
- Justin F Acheson
- University of Virginia, School of Medicine, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22903, USA
| | - Zygmunt S Derewenda
- University of Virginia, School of Medicine, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22903, USA
| | - Jochen Zimmer
- University of Virginia, School of Medicine, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22903, USA.
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26
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Forman A, Pfoh R, Eddenden A, Howell PL, Nitz M. Synthesis of defined mono-de-N-acetylated β-(1→6)-N-acetyl-d-glucosamine oligosaccharides to characterize PgaB hydrolase activity. Org Biomol Chem 2019; 17:9456-9466. [PMID: 31642455 DOI: 10.1039/c9ob02079a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many clinically-relevant biofilm-forming bacterial strains produce partially de-N-acetylated poly-β-(1→6)-N-acetyl-d-glucosamine (dPNAG) as an exopolysaccharide. In Gram-negative bacteria, the periplasmic protein PgaB is responsible for partial de-N-acetylation of PNAG prior to its export to the extracellular space. In addition to de-N-acetylase activity found in the N-terminal domain, PgaB contains a C-terminal hydrolase domain that can disrupt dPNAG-dependent biofilms and hydrolyzes dPNAG but not fully acetylated PNAG. The role of this C-terminal domain in biofilm formation has yet to be determined in vivo. Further characterization of the enzyme's hydrolase activity has been hampered by a lack of specific dPNAG oligosaccharides. Here, we report the synthesis of a defined mono de-N-acetylated dPNAG penta- and hepta-saccharide. Using mass spectrometry analysis and a fluorescence-based thin-layer chromatography (TLC) assay, we found that our defined dPNAG oligosaccharides are hydrolase substrates. In addition to the expected cleavage site, two residues to the reducing side of the de-N-acetylated residue, minor cleavage products on the non-reducing side of the de-N-acetylation site were observed. These findings provide quantitative data to support how PNAG is processed in Gram-negative bacteria.
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Affiliation(s)
- Adam Forman
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6.
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27
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Oxidative stress under low oxygen conditions triggers hyperflagellation and motility in the Antarctic bacterium Pseudomonas extremaustralis. Extremophiles 2019; 23:587-597. [PMID: 31250111 DOI: 10.1007/s00792-019-01110-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Reactive oxygen species and nitrogen species (ROS and RNS), produced in a wide range of physiological process even under low oxygen availability, are among the main stressors found in the environment. Strategies developed to combat them constitute key features in bacterial adaptability and survival. Pseudomonas extremaustralis is a metabolic versatile and stress resistant Antarctic bacterium, able to grow under different oxygen conditions. The present work explores the effect of oxidative stress under low oxygen conditions in P. extremaustralis, by combining RNA deep sequencing analysis and physiological studies. Cells grown under microaerobiosis exhibited more oxidative damage in macromolecules and lower survival rates than under aerobiosis. RNA-seq analysis showed an up-regulation of genes related with oxidative stress response, flagella, chemotaxis and biofilm formation while chaperones and cytochromes were down-regulated. Microaerobic cultures exposed to H2O2 also displayed a hyper-flagellated phenotype coupled with a high motility behavior. Moreover, cells that were subjected to oxidative stress presented increased biofilm formation. Altogether, our results suggest that a higher motile behavior and augmented capacity to form biofilm structures could work in addition to well-known antioxidant enzymes and non-enzymatic ROS scavenging mechanisms to cope with oxidative stress at low oxygen tensions.
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28
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Computational Thermodynamic Analysis of the Interaction between Coagulants and Monosaccharides as a Tool to Quantify the Fouling Potential Reduction in the Biofilm Membrane Bioreactor. WATER 2019. [DOI: 10.3390/w11061275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The membrane bioreactor (MBR) and the biofilm membrane bioreactor (BF-MBR) are among key solutions to water scarcity; however, membrane fouling is the major bottleneck for any expansion of these technologies. Prepolymerized aluminum coagulants tend to exhibit the greatest extent of fouling alleviation, with the reduction of soluble microbial products (SMPs) being among the governing mechanisms, which, nevertheless, has been poorly understood. This current study demonstrates that the investigation of the chemical coordination of monosaccharides, which are the major foulants in MBR and BF-MBR, to the main hydrolysis species of the prepolymerized aluminum coagulant, is among the key approaches to the comprehension of the fouling mitigation mechanisms in BF-MBR. Quantum chemical and thermodynamic calculations, together with the multivariate chemometric analysis, allowed the team to determine the principal mechanisms of the SMPs removal, understand the thermodynamic patterns of fouling mitigation, develop the model for the prediction of the fouling mitigation based on the thermodynamic stability of the inorganic-organic complexes, and classify these complexes into thermodynamically stable and less stable species. The results of the study are practically significant for the development of plant surveillance and automated process control with regard to MBR and BF-MBR systems.
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29
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Liu L, Zhou Y, Qu M, Qiu Y, Guo X, Zhang Y, Liu T, Yang J, Yang Q. Structural and biochemical insights into the catalytic mechanisms of two insect chitin deacetylases of the carbohydrate esterase 4 family. J Biol Chem 2019; 294:5774-5783. [PMID: 30755482 PMCID: PMC6463723 DOI: 10.1074/jbc.ra119.007597] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/08/2019] [Indexed: 12/15/2022] Open
Abstract
Insect chitin deacetylases (CDAs) catalyze the removal of acetyl groups from chitin and modify this polymer during its synthesis and reorganization. CDAs are essential for insect survival and therefore represent promising targets for insecticide development. However, the structural and biochemical characteristics of insect CDAs have remained elusive. Here, we report the crystal structures of two insect CDAs from the silk moth Bombyx mori: BmCDA1, which may function in cuticle modification, and BmCDA8, which may act in modifying peritrophic membranes in the midgut. Both enzymes belong to the carbohydrate esterase 4 (CE4) family. Comparing their overall structures at 1.98–2.4 Å resolution with those from well-studied microbial CDAs, we found that two unique loop regions in BmCDA1 and BmCDA8 contribute to the distinct architecture of their substrate-binding clefts. These comparisons revealed that both BmCDA1 and BmCDA8 possess a much longer and wider substrate-binding cleft with a very open active site in the center than the microbial CDAs, including VcCDA from Vibrio cholerae and ArCE4A from Arthrobacter species AW19M34-1. Biochemical analyses indicated that BmCDA8 is an active enzyme that requires its substrates to occupy subsites 0, +1, and +2 for catalysis. In contrast, BmCDA1 also required accessory proteins for catalysis. To the best of our knowledge, our work is the first to unveil the structural and biochemical features of insect proteins belonging to the CE4 family.
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Affiliation(s)
- Lin Liu
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Yong Zhou
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Mingbo Qu
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Yu Qiu
- Department of Protein Engineering, Biologics Research, Sanofi, Bridgewater, New Jersey 08807
| | - Xingming Guo
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Yuebin Zhang
- the Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116024, China
| | - Tian Liu
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Jun Yang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China
| | - Qing Yang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China; the State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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30
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Micoli F, Costantino P, Adamo R. Potential targets for next generation antimicrobial glycoconjugate vaccines. FEMS Microbiol Rev 2018; 42:388-423. [PMID: 29547971 PMCID: PMC5995208 DOI: 10.1093/femsre/fuy011] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/13/2018] [Indexed: 12/21/2022] Open
Abstract
Cell surface carbohydrates have been proven optimal targets for vaccine development. Conjugation of polysaccharides to a carrier protein triggers a T-cell-dependent immune response to the glycan moiety. Licensed glycoconjugate vaccines are produced by chemical conjugation of capsular polysaccharides to prevent meningitis caused by meningococcus, pneumococcus and Haemophilus influenzae type b. However, other classes of carbohydrates (O-antigens, exopolysaccharides, wall/teichoic acids) represent attractive targets for developing vaccines. Recent analysis from WHO/CHO underpins alarming concern toward antibiotic-resistant bacteria, such as the so called ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) and additional pathogens such as Clostridium difficile and Group A Streptococcus. Fungal infections are also becoming increasingly invasive for immunocompromised patients or hospitalized individuals. Other emergencies could derive from bacteria which spread during environmental calamities (Vibrio cholerae) or with potential as bioterrorism weapons (Burkholderia pseudomallei and mallei, Francisella tularensis). Vaccination could aid reducing the use of broad-spectrum antibiotics and provide protection by herd immunity also to individuals who are not vaccinated. This review analyzes structural and functional differences of the polysaccharides exposed on the surface of emerging pathogenic bacteria, combined with medical need and technological feasibility of corresponding glycoconjugate vaccines.
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Affiliation(s)
- Francesca Micoli
- GSK Vaccines Institute for Global Health (GVGH), Via Fiorentina 1, 53100 Siena
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31
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Low KE, Howell PL. Gram-negative synthase-dependent exopolysaccharide biosynthetic machines. Curr Opin Struct Biol 2018; 53:32-44. [DOI: 10.1016/j.sbi.2018.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/03/2018] [Accepted: 05/07/2018] [Indexed: 11/16/2022]
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32
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Little DJ, Pfoh R, Le Mauff F, Bamford NC, Notte C, Baker P, Guragain M, Robinson H, Pier GB, Nitz M, Deora R, Sheppard DC, Howell PL. PgaB orthologues contain a glycoside hydrolase domain that cleaves deacetylated poly-β(1,6)-N-acetylglucosamine and can disrupt bacterial biofilms. PLoS Pathog 2018; 14:e1006998. [PMID: 29684093 PMCID: PMC5933820 DOI: 10.1371/journal.ppat.1006998] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 05/03/2018] [Accepted: 03/29/2018] [Indexed: 11/24/2022] Open
Abstract
Poly-β(1,6)-N-acetyl-D-glucosamine (PNAG) is a major biofilm component of many pathogenic bacteria. The production, modification, and export of PNAG in Escherichia coli and Bordetella species require the protein products encoded by the pgaABCD operon. PgaB is a two-domain periplasmic protein that contains an N-terminal deacetylase domain and a C-terminal PNAG binding domain that is critical for export. However, the exact function of the PgaB C-terminal domain remains unclear. Herein, we show that the C-terminal domains of Bordetella bronchiseptica PgaB (PgaBBb) and E. coli PgaB (PgaBEc) function as glycoside hydrolases. These enzymes hydrolyze purified deacetylated PNAG (dPNAG) from Staphylococcus aureus, disrupt PNAG-dependent biofilms formed by Bordetella pertussis, Staphylococcus carnosus, Staphylococcus epidermidis, and E. coli, and potentiate bacterial killing by gentamicin. Furthermore, we found that PgaBBb was only able to hydrolyze PNAG produced in situ by the E. coli PgaCD synthase complex when an active deacetylase domain was present. Mass spectrometry analysis of the PgaB-hydrolyzed dPNAG substrate showed a GlcN-GlcNAc-GlcNAc motif at the new reducing end of detected fragments. Our 1.76 Å structure of the C-terminal domain of PgaBBb reveals a central cavity within an elongated surface groove that appears ideally suited to recognize the GlcN-GlcNAc-GlcNAc motif. The structure, in conjunction with molecular modeling and site directed mutagenesis led to the identification of the dPNAG binding subsites and D474 as the probable catalytic acid. This work expands the role of PgaB within the PNAG biosynthesis machinery, defines a new glycoside hydrolase family GH153, and identifies PgaB as a possible therapeutic agent for treating PNAG-dependent biofilm infections. From plaque on teeth to infections in the lungs of cystic fibrosis patients, biofilms are a serious health concern and difficult to eradicate. One of the key building blocks involved in biofilm formation are polymeric sugar compounds that are secreted by the bacteria. Our work focuses on the biopolymer poly-β(1,6)-N-acetyl-D-glucosamine (PNAG), which is produced by numerous pathogenic organisms. Deacetylation of PNAG by the N-terminal domain of PgaB is a critical step in polymer maturation and is required for the formation of robust biofilms. Herein, we show that the C-terminal domain of PgaB is a glycoside hydrolase active on partially deacetylated PNAG, and that the enzyme disrupts PNAG-dependent biofilms and potentiates killing by antibiotics. Only deacetylated PNAG could be cleaved, suggesting that PgaB deacetylates and hydrolyses the polymer in sequential order. Analyzing the chemical structure of the cleaved dPNAG fragments revealed a distinct motif of sugar units. Structural and functional studies identify key amino acids positioned in an elongated polymer-binding groove that potentially recognize the sugar motif during cleavage. Our study provides further insight into the mechanism of periplasmic PNAG modification, and suggests PgaB could be utilized as a therapeutic agent to eliminate biofilms.
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Affiliation(s)
- Dustin J Little
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Roland Pfoh
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - François Le Mauff
- Departments of Medicine and of Microbiology and Immunology, McGill University, Montréal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Natalie C Bamford
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Christina Notte
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Perrin Baker
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Manita Guragain
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, United States of America.,Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, OH, United States of America
| | - Howard Robinson
- Photon Sciences Division, Brookhaven National Laboratory, Upton, NY, United States of America
| | - Gerald B Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Mark Nitz
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Rajendar Deora
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, United States of America.,Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, OH, United States of America
| | - Donald C Sheppard
- Departments of Medicine and of Microbiology and Immunology, McGill University, Montréal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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Soliman C, Walduck AK, Yuriev E, Richards JS, Cywes-Bentley C, Pier GB, Ramsland PA. Structural basis for antibody targeting of the broadly expressed microbial polysaccharide poly- N-acetylglucosamine. J Biol Chem 2018; 293:5079-5089. [PMID: 29449370 DOI: 10.1074/jbc.ra117.001170] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/08/2018] [Indexed: 01/19/2023] Open
Abstract
In response to the widespread emergence of antibiotic-resistant microbes, new therapeutic agents are required for many human pathogens. A non-mammalian polysaccharide, poly-N-acetyl-d-glucosamine (PNAG), is produced by bacteria, fungi, and protozoan parasites. Antibodies that bind to PNAG and its deacetylated form (dPNAG) exhibit promising in vitro and in vivo activities against many microbes. A human IgG1 mAb (F598) that binds both PNAG and dPNAG has opsonic and protective activities against multiple microbial pathogens and is undergoing preclinical and clinical assessments as a broad-spectrum antimicrobial therapy. Here, to understand how F598 targets PNAG, we determined crystal structures of the unliganded F598 antigen-binding fragment (Fab) and its complexes with N-acetyl-d-glucosamine (GlcNAc) and a PNAG oligosaccharide. We found that F598 recognizes PNAG through a large groove-shaped binding site that traverses the entire light- and heavy-chain interface and accommodates at least five GlcNAc residues. The Fab-GlcNAc complex revealed a deep binding pocket in which the monosaccharide and a core GlcNAc of the oligosaccharide were almost identically positioned, suggesting an anchored binding mechanism of PNAG by F598. The Fab used in our structural analyses retained binding to PNAG on the surface of an antibiotic-resistant, biofilm-forming strain of Staphylococcus aureus Additionally, a model of intact F598 binding to two pentasaccharide epitopes indicates that the Fab arms can span at least 40 GlcNAc residues on an extended PNAG chain. Our findings unravel the structural basis for F598 binding to PNAG on microbial surfaces and biofilms.
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Affiliation(s)
- Caroline Soliman
- From the School of Science, Royal Melbourne Institute of Technology (RMIT) University, Bundoora, Victoria 3083, Australia
| | - Anna K Walduck
- From the School of Science, Royal Melbourne Institute of Technology (RMIT) University, Bundoora, Victoria 3083, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Jack S Richards
- Disease Elimination Program, Burnet Institute, Melbourne, Victoria 3004, Australia.,Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria 3052, Australia.,Department of Medicine, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Infectious Diseases, Central Clinical School, Alfred Hospital, Melbourne, Victoria 3004, Australia
| | - Colette Cywes-Bentley
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts 02115
| | - Gerald B Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts 02115
| | - Paul A Ramsland
- From the School of Science, Royal Melbourne Institute of Technology (RMIT) University, Bundoora, Victoria 3083, Australia, .,Disease Elimination Program, Burnet Institute, Melbourne, Victoria 3004, Australia.,Department of Immunology, Central Clinical School, Monash University, Victoria 3004, Melbourne, Australia, and.,Department of Surgery Austin Health, University of Melbourne, Heidelberg, Victoria 3084
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Bradshaw WJ, Kirby JM, Roberts AK, Shone CC, Acharya KR. The molecular structure of the glycoside hydrolase domain of Cwp19 from Clostridium difficile. FEBS J 2017; 284:4343-4357. [PMID: 29083543 PMCID: PMC5765458 DOI: 10.1111/febs.14310] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/03/2017] [Accepted: 10/25/2017] [Indexed: 12/15/2022]
Abstract
Clostridium difficile is a burden to healthcare systems around the world, causing tens of thousands of deaths annually. The S‐layer of the bacterium, a layer of protein found of the surface of cells, has received a significant amount of attention over the past two decades as a potential target to combat the growing threat presented by C. difficile infections. The S‐layer contains a wide range of proteins, each of which possesses three cell wall‐binding domains, while many also possess a “functional” region. Here, we present the high resolution structure of the functional region of one such protein, Cwp19 along with preliminary functional characterisation of the predicted glycoside hydrolase. Cwp19 has a TIM barrel fold and appears to possess a high degree of substrate selectivity. The protein also exhibits peptidoglycan hydrolase activity, an order of magnitude slower than that of lysozyme and is the first member of glycoside hydrolase‐like family 10 to be characterised. This research goes some way to understanding the role of Cwp19 in the S‐layer of C. difficile. Database Structural data are available in the PDB under the accession numbers 5OQ2 and 5OQ3.
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Affiliation(s)
- William J Bradshaw
- Department of Biology and Biochemistry, University of Bath, UK.,Public Health England, Salisbury, UK
| | | | | | | | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, UK
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Parthiban C, Varudharasu D, Shanmugam M, Gopal P, Ragunath C, Thomas L, Nitz M, Ramasubbu N. Structural and functional analysis of de-N-acetylase PgaB from periodontopathogen Aggregatibacter actinomycetemcomitans. Mol Oral Microbiol 2017; 32:324-340. [PMID: 27706922 PMCID: PMC11471279 DOI: 10.1111/omi.12175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2016] [Indexed: 10/15/2024]
Abstract
The oral pathogen Aggregatibacter actinomycetemcomitans uses pga gene locus for the production of an exopolysaccharide made up of a linear homopolymer of β-1,6-N-acetyl-d-glucosamine (PGA). An enzyme encoded by the pgaB of the pga operon in A. actinomycetemcomitans is a de-N-acetylase, which is used to alter the PGA. The full length enzyme (AaPgaB) and the N-terminal catalytic domain (residues 25-290, AaPgaBN) from A. actinomycetemcomitans were cloned, expressed and purified. The enzymatic activities of the AaPgaB enzymes were determined using 7-acetoxycoumarin-3-carboxylic acid as the substrate. The AaPgaB enzymes displayed significantly lower de-N-acetylase activity compared with the activity of the deacetylase PdaA from Bacillus subtilis, a member of the CE4 family of enzymes. To delineate the differences in the activity and the active site architecture, the structure of AaPgaBN was determined. The AaPgaBN structure has two metal ions in the active site instead of one found in other CE4 enzymes. Based on the crystal structure comparisons among the various CE4 enzymes, two residues, Q51 and R271, were identified in AaPgaB, which could potentially affect the enzyme activity. Of the two mutants generated, Q51E and R271K, the variant Q51E showed enhanced activity compared with AaPgaB, validating the requirement that an activating aspartate residue in the active site is essential for higher activity. In summary, our study provides the first structural evidence for a di-nuclear metal site at the active site of a member of the CE4 family of enzymes, evidence that AaPgaBN is catalytically active and that mutant Q51E exhibits higher de-N-acetylase activity.
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Affiliation(s)
- C Parthiban
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - D Varudharasu
- Selvam Structure Based Drug Design Laboratory, Selvam College of Technology, Namakkal, Tamilnadu, India
| | - M Shanmugam
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - P Gopal
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - C Ragunath
- Scientific Chemical Technologies, Malden, MA, USA
| | - L Thomas
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - M Nitz
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - N Ramasubbu
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
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36
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Shanmugam M, Oyeniyi AO, Parthiban C, Gujjarlapudi SK, Pier GB, Ramasubbu N. Role of de-N-acetylase PgaB from Aggregatibacter actinomycetemcomitans in exopolysaccharide export in biofilm mode of growth. Mol Oral Microbiol 2017; 32:500-510. [PMID: 28548373 DOI: 10.1111/omi.12188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2017] [Indexed: 11/29/2022]
Abstract
Aggregatibacter actinomycetemcomitans, a Gram-negative bacterium, is the causative agent of localized aggressive periodontitis. Attachment to a biotic surface is a critical first step in the A. actinomycetemcomitans infection process for which exopolysaccharides have been shown to be essential. In addition, the pga operon, containing genes encoding for biosynthetic proteins for poly-N-acetyl glucosamine (PNAG), plays a key role in A. actinomycetemcomitans virulence, as a mutant strain lacking the pga operon induces significantly less bone resorption. Among the genes in the pga operon, pgaB codes for a de-N-acetylase that is responsible for the deacetylation of the PNAG exopolysaccharide. Here we report the role of PgaB in regulation of virulence genes using a markerless, scarless deletion mutant targeting the coding region of the N-terminal catalytic domain of PgaB. The results demonstrate that the N-terminal, catalytic domain of PgaB is crucial for exopolysaccharide export.
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Affiliation(s)
- M Shanmugam
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - A O Oyeniyi
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - C Parthiban
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - S K Gujjarlapudi
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - G B Pier
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N Ramasubbu
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
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Skurnik D, Cywes-Bentley C, Pier GB. The exceptionally broad-based potential of active and passive vaccination targeting the conserved microbial surface polysaccharide PNAG. Expert Rev Vaccines 2016; 15:1041-53. [PMID: 26918288 PMCID: PMC4985264 DOI: 10.1586/14760584.2016.1159135] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/24/2016] [Indexed: 11/08/2022]
Abstract
A challenging component of vaccine development is the large serologic diversity of protective antigens. Remarkably, there is a conserved surface/capsular polysaccharide, one of the most effective vaccine targets, expressed by a large number of bacterial, fungal and eukaryotic pathogens: poly-N-acetyl glucosamine (PNAG). Natural antibodies to PNAG are poorly effective at mediating in vitro microbial killing or in vivo protection. Removing most of the acetate substituents to produce a deacetylated glycoform, or using synthetic oligosaccharides of poly-β-1-6-linked glucosamine conjugated to carrier proteins, results in vaccines that elicit high levels of broad-based immunity. A fully human monoclonal antibody is highly active in laboratory and preclinical studies and has been successfully tested in a phase-I setting. Both the synthetic oligosaccharide conjugate vaccine and MAb will be further tested in humans starting in 2016; but, even if effective against only a fraction of the PNAG-producing pathogens, a major advance in vaccine-preventable diseases will occur.
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Affiliation(s)
- David Skurnik
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Ave., Boston, MA 02115, Phone: 617-525-2269; FAX: 617-525-2510
| | - Colette Cywes-Bentley
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Ave., Boston, MA 02115, Phone: 617-525-2269; FAX: 617-525-2510
| | - Gerald B. Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Ave., Boston, MA 02115, Phone: 617-525-2269; FAX: 617-525-2510
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38
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Kang Y, Gohlke U, Engström O, Hamark C, Scheidt T, Kunstmann S, Heinemann U, Widmalm G, Santer M, Barbirz S. Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions. J Am Chem Soc 2016; 138:9109-18. [DOI: 10.1021/jacs.6b00240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yu Kang
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ulrich Gohlke
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Olof Engström
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Christoffer Hamark
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Tom Scheidt
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Sonja Kunstmann
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Institut
für Chemie und Biochemie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Mark Santer
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Stefanie Barbirz
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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39
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Wang Y, Andole Pannuri A, Ni D, Zhou H, Cao X, Lu X, Romeo T, Huang Y. Structural Basis for Translocation of a Biofilm-supporting Exopolysaccharide across the Bacterial Outer Membrane. J Biol Chem 2016; 291:10046-57. [PMID: 26957546 DOI: 10.1074/jbc.m115.711762] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 12/14/2022] Open
Abstract
The partially de-N-acetylated poly-β-1,6-N-acetyl-d-glucosamine (dPNAG) polymer serves as an intercellular biofilm adhesin that plays an essential role for the development and maintenance of integrity of biofilms of diverse bacterial species. Translocation of dPNAG across the bacterial outer membrane is mediated by a tetratricopeptide repeat-containing outer membrane protein, PgaA. To understand the molecular basis of dPNAG translocation, we determined the crystal structure of the C-terminal transmembrane domain of PgaA (residues 513-807). The structure reveals that PgaA forms a 16-strand transmembrane β-barrel, closed by four loops on the extracellular surface. Half of the interior surface of the barrel that lies parallel to the translocation pathway is electronegative, suggesting that the corresponding negatively charged residues may assist the secretion of the positively charged dPNAG polymer. In vivo complementation assays in a pgaA deletion bacterial strain showed that a cluster of negatively charged residues proximal to the periplasm is necessary for biofilm formation. Biochemical analyses further revealed that the tetratricopeptide repeat domain of PgaA binds directly to the N-deacetylase PgaB and is critical for biofilm formation. Our studies support a model in which the positively charged PgaB-bound dPNAG polymer is delivered to PgaA through the PgaA-PgaB interaction and is further targeted to the β-barrel lumen of PgaA potentially via a charge complementarity mechanism, thus priming the translocation of dPNAG across the bacterial outer membrane.
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Affiliation(s)
- Yan Wang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Archana Andole Pannuri
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611-0700
| | - Dongchun Ni
- Department of Cardiovascular Diseases, Tianjin Xiqing Hospital, Tianjin 300380, China
| | - Haizhen Zhou
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiou Cao
- School of Life Sciences, Peking University, Beijing 100871, China, and
| | - Xiaomei Lu
- Dongguan Institute of Pediatrics, the Eighth People's Hospital of Dongguan, Dongguan 523325, Guangdong Province, China
| | - Tony Romeo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611-0700,
| | - Yihua Huang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China,
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40
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Baker P, Whitfield GB, Hill PJ, Little DJ, Pestrak MJ, Robinson H, Wozniak DJ, Howell PL. Characterization of the Pseudomonas aeruginosa Glycoside Hydrolase PslG Reveals That Its Levels Are Critical for Psl Polysaccharide Biosynthesis and Biofilm Formation. J Biol Chem 2015; 290:28374-28387. [PMID: 26424791 DOI: 10.1074/jbc.m115.674929] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Indexed: 01/04/2023] Open
Abstract
A key component of colonization, biofilm formation, and protection of the opportunistic human pathogen Pseudomonas aeruginosa is the biosynthesis of the exopolysaccharide Psl. Composed of a pentameric repeating unit of mannose, glucose, and rhamnose, the biosynthesis of Psl is proposed to occur via a Wzx/Wzy-dependent mechanism. Previous genetic studies have shown that the putative glycoside hydrolase PslG is essential for Psl biosynthesis. To understand the function of this protein, the apo-structure of the periplasmic domain of PslG (PslG(31-442)) and its complex with mannose were determined to 2.0 and 1.9 Å resolution, respectively. Despite a domain architecture and positioning of catalytic residues similar to those of other family 39 glycoside hydrolases, PslG(31-442) exhibits a unique 32-Å-long active site groove that is distinct from other structurally characterized family members. PslG formed a complex with two mannose monosaccharides in this groove, consistent with binding data obtained from intrinsic tryptophan fluorescence. PslG was able to catalyze the hydrolysis of surface-associated Psl, and this activity was abolished in a E165Q/E276Q double catalytic variant. Surprisingly, P. aeruginosa variants with these chromosomal mutations as well as a pslG deletion mutant were still capable of forming Psl biofilms. However, overexpression of PslG in a pslG deletion background impaired biofilm formation and resulted in less surface-associated Psl, suggesting that regulation of this enzyme is important during polysaccharide biosynthesis.
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Affiliation(s)
- Perrin Baker
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Gregory B Whitfield
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Preston J Hill
- Division of Infectious Disease, Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio 43210
| | - Dustin J Little
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Matthew J Pestrak
- Division of Infectious Disease, Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio 43210
| | - Howard Robinson
- Photon Sciences Division, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - Daniel J Wozniak
- Division of Infectious Disease, Center for Microbial Interface Biology, Ohio State University, Columbus, Ohio 43210.
| | - P Lynne Howell
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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41
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Bamford NC, Snarr BD, Gravelat FN, Little DJ, Lee MJ, Zacharias CA, Chabot JC, Geller AM, Baptista SD, Baker P, Robinson H, Howell PL, Sheppard DC. Sph3 Is a Glycoside Hydrolase Required for the Biosynthesis of Galactosaminogalactan in Aspergillus fumigatus. J Biol Chem 2015; 290:27438-50. [PMID: 26342082 DOI: 10.1074/jbc.m115.679050] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 11/06/2022] Open
Abstract
Aspergillus fumigatus is the most virulent species within the Aspergillus genus and causes invasive infections with high mortality rates. The exopolysaccharide galactosaminogalactan (GAG) contributes to the virulence of A. fumigatus. A co-regulated five-gene cluster has been identified and proposed to encode the proteins required for GAG biosynthesis. One of these genes, sph3, is predicted to encode a protein belonging to the spherulin 4 family, a protein family with no known function. Construction of an sph3-deficient mutant demonstrated that the gene is necessary for GAG production. To determine the role of Sph3 in GAG biosynthesis, we determined the structure of Aspergillus clavatus Sph3 to 1.25 Å. The structure revealed a (β/α)8 fold, with similarities to glycoside hydrolase families 18, 27, and 84. Recombinant Sph3 displayed hydrolytic activity against both purified and cell wall-associated GAG. Structural and sequence alignments identified three conserved acidic residues, Asp-166, Glu-167, and Glu-222, that are located within the putative active site groove. In vitro and in vivo mutagenesis analysis demonstrated that all three residues are important for activity. Variants of Asp-166 yielded the greatest decrease in activity suggesting a role in catalysis. This work shows that Sph3 is a glycoside hydrolase essential for GAG production and defines a new glycoside hydrolase family, GH135.
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Affiliation(s)
- Natalie C Bamford
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Brendan D Snarr
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Fabrice N Gravelat
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Dustin J Little
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Mark J Lee
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Caitlin A Zacharias
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Josée C Chabot
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Alexander M Geller
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Stefanie D Baptista
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Perrin Baker
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Howard Robinson
- the Photon Sciences Division, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - P Lynne Howell
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada,
| | - Donald C Sheppard
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
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42
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Little DJ, Milek S, Bamford NC, Ganguly T, DiFrancesco BR, Nitz M, Deora R, Howell PL. The protein BpsB is a poly-β-1,6-N-acetyl-D-glucosamine deacetylase required for biofilm formation in Bordetella bronchiseptica. J Biol Chem 2015. [PMID: 26203190 DOI: 10.1074/jbc.m115.672469] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Bordetella pertussis and Bordetella bronchiseptica are the causative agents of whooping cough in humans and a variety of respiratory diseases in animals, respectively. Bordetella species produce an exopolysaccharide, known as the Bordetella polysaccharide (Bps), which is encoded by the bpsABCD operon. Bps is required for Bordetella biofilm formation, colonization of the respiratory tract, and confers protection from complement-mediated killing. In this report, we have investigated the role of BpsB in the biosynthesis of Bps and biofilm formation by B. bronchiseptica. BpsB is a two-domain protein that localizes to the periplasm and outer membrane. BpsB displays metal- and length-dependent deacetylation on poly-β-1,6-N-acetyl-d-glucosamine (PNAG) oligomers, supporting previous immunogenic data that suggests Bps is a PNAG polymer. BpsB can use a variety of divalent metal cations for deacetylase activity and showed highest activity in the presence of Ni(2+) and Co(2+). The structure of the BpsB deacetylase domain is similar to the PNAG deacetylases PgaB and IcaB and contains the same circularly permuted family four carbohydrate esterase motifs. Unlike PgaB from Escherichia coli, BpsB is not required for polymer export and has unique structural differences that allow the N-terminal deacetylase domain to be active when purified in isolation from the C-terminal domain. Our enzymatic characterizations highlight the importance of conserved active site residues in PNAG deacetylation and demonstrate that the C-terminal domain is required for maximal deacetylation of longer PNAG oligomers. Furthermore, we show that BpsB is critical for the formation and complex architecture of B. bronchiseptica biofilms.
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Affiliation(s)
- Dustin J Little
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sonja Milek
- the Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, and
| | - Natalie C Bamford
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tridib Ganguly
- the Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, and
| | | | - Mark Nitz
- the Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Rajendar Deora
- the Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, and
| | - P Lynne Howell
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada,
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Ariyakumaran R, Pokrovskaya V, Little DJ, Howell PL, Nitz M. Direct Staudinger-Phosphonite Reaction Provides Methylphosphonamidates as Inhibitors of CE4 De-N-acetylases. Chembiochem 2015; 16:1350-6. [PMID: 25864869 DOI: 10.1002/cbic.201500091] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Indexed: 11/09/2022]
Abstract
De-N-acetylases of β-(1→6)-D-N-acetylglucosamine polymers (PNAG) and β-(1→4)-D-N-acetylglucosamine residues in peptidoglycan are attractive targets for antimicrobial agents. PNAG de-N-acetylases are necessary for biofilm formation in numerous pathogenic bacteria. Peptidoglycan de-N-acetylation facilitates bacterial evasion of innate immune defenses. To target these enzymes, transition-state analogue inhibitors containing a methylphosphonamidate have been synthesized through a direct Staudinger-phosphonite reaction. The inhibitors were tested on purified PgaB, a PNAG de-N-acetylase from Escherichia coli, and PgdA, a peptidoglycan de-N-acetylase from Streptococcus pneumonia. Herein, we describe the most potent inhibitor of peptidoglycan de-N-acetylases reported to date (Ki =80 μM). The minimal inhibition of PgaB observed provides insight into key structural and functional differences in these enzymes that will need to be considered during the development of future inhibitors.
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Affiliation(s)
- Rishikesh Ariyakumaran
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6 (Canada)
| | - Varvara Pokrovskaya
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6 (Canada)
| | - Dustin J Little
- Program in Molecular Structure and Function, The Hospital for Sick Children and Department of Biochemistry, University of Toronto, 555 University Avenue, Toronto, Ontario M5G 1X8 (Canada)
| | - P Lynne Howell
- Program in Molecular Structure and Function, The Hospital for Sick Children and Department of Biochemistry, University of Toronto, 555 University Avenue, Toronto, Ontario M5G 1X8 (Canada)
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6 (Canada).
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Whitfield GB, Marmont LS, Howell PL. Enzymatic modifications of exopolysaccharides enhance bacterial persistence. Front Microbiol 2015; 6:471. [PMID: 26029200 PMCID: PMC4432689 DOI: 10.3389/fmicb.2015.00471] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/29/2015] [Indexed: 12/25/2022] Open
Abstract
Biofilms are surface-attached communities of bacterial cells embedded in a self-produced matrix that are found ubiquitously in nature. The biofilm matrix is composed of various extracellular polymeric substances, which confer advantages to the encapsulated bacteria by protecting them from eradication. The matrix composition varies between species and is dependent on the environmental niche that the bacteria inhabit. Exopolysaccharides (EPS) play a variety of important roles in biofilm formation in numerous bacterial species. The ability of bacteria to thrive in a broad range of environmental settings is reflected in part by the structural diversity of the EPS produced both within individual bacterial strains as well as by different species. This variability is achieved through polymerization of distinct sugar moieties into homo- or hetero-polymers, as well as post-polymerization modification of the polysaccharide. Specific enzymes that are unique to the production of each polymer can transfer or remove non-carbohydrate moieties, or in other cases, epimerize the sugar units. These modifications alter the physicochemical properties of the polymer, which in turn can affect bacterial pathogenicity, virulence, and environmental adaptability. Herein, we review the diversity of modifications that the EPS alginate, the Pel polysaccharide, Vibrio polysaccharide, cepacian, glycosaminoglycans, and poly-N-acetyl-glucosamine undergo during biosynthesis. These are EPS produced by human pathogenic bacteria for which studies have begun to unravel the effect modifications have on their physicochemical and biological properties. The biological advantages these polymer modifications confer to the bacteria that produce them will be discussed. The expanding list of identified modifications will allow future efforts to focus on linking these modifications to specific biosynthetic genes and biofilm phenotypes.
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Affiliation(s)
- Gregory B Whitfield
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children Toronto, ON, Canada ; Department of Biochemistry, Faculty of Medicine, University of Toronto Toronto, ON, Canada
| | - Lindsey S Marmont
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children Toronto, ON, Canada ; Department of Biochemistry, Faculty of Medicine, University of Toronto Toronto, ON, Canada
| | - P Lynne Howell
- Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children Toronto, ON, Canada ; Department of Biochemistry, Faculty of Medicine, University of Toronto Toronto, ON, Canada
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Little DJ, Bamford NC, Pokrovskaya V, Robinson H, Nitz M, Howell PL. Structural basis for the De-N-acetylation of Poly-β-1,6-N-acetyl-D-glucosamine in Gram-positive bacteria. J Biol Chem 2014; 289:35907-17. [PMID: 25359777 DOI: 10.1074/jbc.m114.611400] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Exopolysaccharides are required for the development and integrity of biofilms produced by a wide variety of bacteria. In staphylococci, partial de-N-acetylation of the exopolysaccharide poly-β-1,6-N-acetyl-d-glucosamine (PNAG) by the extracellular protein IcaB is required for biofilm formation. To understand the molecular basis for PNAG de-N-acetylation, the structure of IcaB from Ammonifex degensii (IcaBAd) has been determined to 1.7 Å resolution. The structure of IcaBAd reveals a (β/α)7 barrel common to the family four carbohydrate esterases (CE4s) with the canonical motifs circularly permuted. The metal dependence of IcaBAd is similar to most CE4s showing the maximum rates of de-N-acetylation with Ni(2+), Co(2+), and Zn(2+). From docking studies with β-1,6-GlcNAc oligomers and structural comparison to PgaB from Escherichia coli, the Gram-negative homologue of IcaB, we identify Arg-45, Tyr-67, and Trp-180 as key residues for PNAG binding during catalysis. The absence of these residues in PgaB provides a rationale for the requirement of a C-terminal domain for efficient deacetylation of PNAG in Gram-negative species. Mutational analysis of conserved active site residues suggests that IcaB uses an altered catalytic mechanism in comparison to other characterized CE4 members. Furthermore, we identified a conserved surface-exposed hydrophobic loop found only in Gram-positive homologues of IcaB. Our data suggest that this loop is required for membrane association and likely anchors IcaB to the membrane during polysaccharide biosynthesis. The work presented herein will help guide the design of IcaB inhibitors to combat biofilm formation by staphylococci.
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Affiliation(s)
- Dustin J Little
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Natalie C Bamford
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Varvara Pokrovskaya
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada, and
| | - Howard Robinson
- Photon Sciences Division, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - Mark Nitz
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada, and
| | - P Lynne Howell
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada,
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Periplasmic de-acylase helps bacteria don their biofilm coat. Proc Natl Acad Sci U S A 2014; 111:10904-5. [PMID: 25006258 DOI: 10.1073/pnas.1410789111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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