1
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Mach N. The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases. Vet Q 2024; 44:1-18. [PMID: 38606662 PMCID: PMC11018052 DOI: 10.1080/01652176.2024.2340003] [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: 05/23/2023] [Accepted: 03/31/2024] [Indexed: 04/13/2024] Open
Abstract
Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.
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Affiliation(s)
- Núria Mach
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
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2
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Dhanabalan K, Cheng Y, Thach T, Subramanian R. Many locks to one key: N-acetylneuraminic acid binding to proteins. IUCRJ 2024; 11:664-674. [PMID: 38965900 PMCID: PMC11364026 DOI: 10.1107/s2052252524005360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
Sialic acids play crucial roles in cell surface glycans of both eukaryotic and prokaryotic organisms, mediating various biological processes, including cell-cell interactions, development, immune response, oncogenesis and host-pathogen interactions. This review focuses on the β-anomeric form of N-acetylneuraminic acid (Neu5Ac), particularly its binding affinity towards various proteins, as elucidated by solved protein structures. Specifically, we delve into the binding mechanisms of Neu5Ac to proteins involved in sequestering and transporting Neu5Ac in Gram-negative bacteria, with implications for drug design targeting these proteins as antimicrobial agents. Unlike the initial assumptions, structural analyses revealed significant variability in the Neu5Ac binding pockets among proteins, indicating diverse evolutionary origins and binding modes. By comparing these findings with existing structures from other systems, we can effectively highlight the intricate relationship between protein structure and Neu5Ac recognition, emphasizing the need for tailored drug design strategies to inhibit Neu5Ac-binding proteins across bacterial species.
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Affiliation(s)
| | - YiYang Cheng
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Trung Thach
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47907USA
| | - Ramaswamy Subramanian
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47907USA
- Weldon School of Biomedical EngineeringPurdue UniversityWest LafayetteIN47907USA
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3
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Andrews KR, Besser TE, Stalder T, Top EM, Baker KN, Fagnan MW, New DD, Schneider GM, Gal A, Andrews-Dickert R, Hunter SS, Beckmen KB, Christensen L, Justice-Allen A, Konetchy D, Lehman CP, Manlove K, Miyasaki H, Nordeen T, Roug A, Cassirer EF. Comparative genomic analysis identifies potential adaptive variation in Mycoplasma ovipneumoniae. Microb Genom 2024; 10:001279. [PMID: 39213169 PMCID: PMC11364169 DOI: 10.1099/mgen.0.001279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/16/2024] [Indexed: 09/04/2024] Open
Abstract
Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes for 99 samples from 6 countries (Australia, Bosnia and Herzegovina, Brazil, China, France and USA) and 4 host species (domestic sheep, domestic goats, bighorn sheep and caribou). Core genome sequences of M. ovipneumoniae assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4 %) of accessory genes (i.e. genes found only in a subset of assemblies) compared to core genes (i.e. genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three M. ovipneumoniae genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall, our results suggest that adaptation of M. ovipneumoniae has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species.
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Affiliation(s)
- Kimberly R. Andrews
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Thomas E. Besser
- Department of Veterinary Microbiology and Pathology, Washington State University College of Veterinary Medicine, Pullman, WA, USA
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Eva M. Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Katherine N. Baker
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Matthew W. Fagnan
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Daniel D. New
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - G. Maria Schneider
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Alexandra Gal
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Rebecca Andrews-Dickert
- Department of Physiology and Pharmacology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX, USA
| | - Samuel S. Hunter
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | | | - Lauren Christensen
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow ID, USA
| | | | - Denise Konetchy
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow ID, USA
| | | | - Kezia Manlove
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT, USA
| | | | - Todd Nordeen
- Nebraska Game and Parks Commission, Alliance, NE, USA
| | - Annette Roug
- Utah Division of Wildlife Resources, Salt Lake City, UT, USA
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4
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Flores JA, Antonio JM, Suntornsaratoon P, Meadows V, Bandyopadhyay S, Han J, Singh R, Balasubramanian I, Upadhyay R, Liu Y, Bonder EM, Kiela P, Su X, Ferraris R, Gao N. The arginine and nitric oxide metabolic pathway regulate the gut colonization and expansion of Ruminococcous gnavus. J Biol Chem 2024; 300:107614. [PMID: 39089585 DOI: 10.1016/j.jbc.2024.107614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 08/04/2024] Open
Abstract
Ruminococcus gnavus is a mucolytic commensal bacterium whose increased gut colonization has been associated with chronic inflammatory and metabolic diseases in humans. Whether R. gnavus metabolites can modulate host intestinal physiology remains largely understudied. We performed untargeted metabolomic and bulk RNA-seq analyses using R. gnavus monocolonization in germ-free mice. Based on transcriptome-metabolome correlations, we tested the impact of specific arginine metabolites on intestinal epithelial production of nitric oxide (NO) and examined the effect of NO on the growth of various strains of R. gnavus in vitro and in nitric oxide synthase 2 (Nos2)-deficient mice. R. gnavus produces specific arginine, tryptophan, and tyrosine metabolites, some of which are regulated by the environmental richness of sialic acid and mucin. R. gnavus colonization promotes expression of amino acid transporters and enzymes involved in metabolic flux of arginine and associated metabolites into NO. R. gnavus induced elevated levels of NOS2, while Nos2 ablation resulted in R. gnavus expansion in vivo. The growth of various R. gnavus strains can be inhibited by NO. Specific R. gnavus metabolites modulate intestinal epithelial cell NOS2 abundance and reduce epithelial barrier function at higher concentrations. Intestinal colonization and interaction with R. gnavus are partially regulated by an arginine-NO metabolic pathway, whereby a balanced control by the gut epithelium may restrain R. gnavus growth in healthy individuals. Disruption in this arginine metabolic regulation will contribute to the expansion and blooming of R. gnavus.
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Affiliation(s)
- Juan A Flores
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | - Jayson M Antonio
- Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Panan Suntornsaratoon
- Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Vik Meadows
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA; Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | | | - Jiangmeng Han
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA; Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Rajbir Singh
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | | | - Ravij Upadhyay
- Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Yue Liu
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | - Pawel Kiela
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children's Research Center, Department of Pediatrics, University of Arizona, Tucson, Arizona, USA
| | - Xiaoyang Su
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | - Ronaldo Ferraris
- Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA.
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA; Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA.
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5
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Li S, Chen M, Wang Z, Abudourexiti W, Zhang L, Ding C, Ding L, Gong J. Ant may well destroy a whole dam: glycans of colonic mucus barrier disintegrated by gut bacteria. Microbiol Res 2024; 281:127599. [PMID: 38219635 DOI: 10.1016/j.micres.2023.127599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
The colonic mucus layer plays a critical role in maintaining the integrity of the colonic mucosal barrier, serving as the primary defense against colonic microorganisms. Predominantly composed of mucin 2 (MUC2), a glycosylation-rich protein, the mucus layer forms a gel-like coating that covers the colonic epithelium surface. This layer provides a habitat for intestinal microorganisms, which can utilize mucin glycans present in the mucus layer as a sustainable source of nutrients. Additionally, metabolites produced by the microbiota during the metabolism of mucus glycans have a profound impact on host health. Under normal conditions, the production and consumption of mucus maintain a dynamic balance. However, several studies have demonstrated that certain factors, such as dietary fiber deficiency, can enhance the metabolism of mucus glycans by gut bacteria, thereby disturbing this balance and weakening the mucus barrier function of the mucus layer. To better understand the occurrence and development of colon-related diseases, it is crucial to investigate the complex metabolic patterns of mucus glycosylation by intestinal microorganisms. Our objective was to comprehensively review these patterns in order to clarify the effects of mucus layer glycan metabolism by intestinal microorganisms on the host.
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Affiliation(s)
- Song Li
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Mingfei Chen
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Zhongyuan Wang
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Waresi Abudourexiti
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Liang Zhang
- Department of Gastrointestinal Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, Jiangsu, China
| | - Chao Ding
- Department of General Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China.
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Jianfeng Gong
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China.
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6
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Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early-life colonization by a pioneering gut commensal. Cell Host Microbe 2024; 32:181-190.e9. [PMID: 38228143 PMCID: PMC10922750 DOI: 10.1016/j.chom.2023.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/14/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The early microbial colonization of the gastrointestinal tract can have long-term impacts on development and health. Keystone species, including Bacteroides spp., are prominent in early life and play crucial roles in maintaining the structure of the intestinal ecosystem. However, the process by which a resilient community is curated during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa in early life and regulates a commensal colonization program. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. NanH is required for vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and microbiota mediated through host-derived glycans to promote stable colonization.
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Affiliation(s)
- Ekaterina Buzun
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristija Sejane
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Renee E Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Luke R Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiaqi Zhao
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dominic M McGrosso
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA; Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA 92093, USA; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada.
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7
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Kijner S, Ennis D, Shmorak S, Florentin A, Yassour M. CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei. Nat Commun 2024; 15:105. [PMID: 38167825 PMCID: PMC10761964 DOI: 10.1038/s41467-023-44437-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
The infant gut microbiome is impacted by early-life feeding, as human milk oligosaccharides (HMOs) found in breastmilk cannot be digested by infants and serve as nutrients for their gut bacteria. While the vast majority of HMO-utilization research has focused on Bifidobacterium species, recent studies have suggested additional HMO-utilizers, mostly Bacteroides, yet their utilization mechanism is poorly characterized. Here, we investigate Bacteroides dorei isolates from breastfed-infants and identify that polysaccharide utilization locus (PUL) 33 enables B. dorei to utilize sialylated HMOs. We perform transcriptional profiling and identity upregulated genes when growing on sialylated HMOs. Using CRISPR-Cas12 to knock-out four PUL33 genes, combined with complementation assays, we identify GH33 as the critical gene in PUL33 for sialylated HMO-utilization. This demonstration of an HMO-utilization system by Bacteroides species isolated from infants opens the way to further characterization of additional such systems, to better understand HMO-utilization in the infant gut.
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Affiliation(s)
- Sivan Kijner
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dena Ennis
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shimrit Shmorak
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Florentin
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Kuvin Center for the Study of Infectious and Tropical Diseases, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Moran Yassour
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
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8
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Kiely LJ, Busca K, Lane JA, van Sinderen D, Hickey RM. Molecular strategies for the utilisation of human milk oligosaccharides by infant gut-associated bacteria. FEMS Microbiol Rev 2023; 47:fuad056. [PMID: 37793834 PMCID: PMC10629584 DOI: 10.1093/femsre/fuad056] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023] Open
Abstract
A number of bacterial species are found in high abundance in the faeces of healthy breast-fed infants, an occurrence that is understood to be, at least in part, due to the ability of these bacteria to metabolize human milk oligosaccharides (HMOs). HMOs are the third most abundant component of human milk after lactose and lipids, and represent complex sugars which possess unique structural diversity and are resistant to infant gastrointestinal digestion. Thus, these sugars reach the infant distal intestine intact, thereby serving as a fermentable substrate for specific intestinal microbes, including Firmicutes, Proteobacteria, and especially infant-associated Bifidobacterium spp. which help to shape the infant gut microbiome. Bacteria utilising HMOs are equipped with genes associated with their degradation and a number of carbohydrate-active enzymes known as glycoside hydrolase enzymes have been identified in the infant gut, which supports this hypothesis. The resulting degraded HMOs can also be used as growth substrates for other infant gut bacteria present in a microbe-microbe interaction known as 'cross-feeding'. This review describes the current knowledge on HMO metabolism by particular infant gut-associated bacteria, many of which are currently used as commercial probiotics, including the distinct strategies employed by individual species for HMO utilisation.
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Affiliation(s)
- Leonie Jane Kiely
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61C996, Ireland
- Health and Happiness Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co. Cork P61K202, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland
| | - Kizkitza Busca
- Health and Happiness Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co. Cork P61K202, Ireland
| | - Jonathan A Lane
- Health and Happiness Group, H&H Research, National Food Innovation Hub, Teagasc Moorepark, Fermoy, Co. Cork P61K202, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
- School of Microbiology, University College Cork, Cork T12 YN60, Ireland
| | - Rita M Hickey
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61C996, Ireland
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
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9
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Jaramillo-Rodríguez JB, Vega-Alvarado L, Rodríguez-Torres LM, Huerta-Miranda GA, Hernández-Eligio A, Juarez K. Global transcriptional analysis of Geobacter sulfurreducens gsu1771 mutant biofilm grown on two different support structures. PLoS One 2023; 18:e0293359. [PMID: 37878651 PMCID: PMC10599522 DOI: 10.1371/journal.pone.0293359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023] Open
Abstract
Electroactive biofilms formation by the metal-reducing bacterium Geobacter sulfurreducens is a step crucial for bioelectricity generation and bioremediation. The transcriptional regulator GSU1771 controls the expression of essential genes involved in electron transfer and biofilm formation in G. sulfurreducens, with GSU1771-deficient producing thicker and more electroactive biofilms. Here, RNA-seq analyses were conducted to compare the global gene expression patterns of wild-type and Δgsu1771 mutant biofilms grown on non-conductive (glass) and conductive (graphite electrode) materials. The Δgsu1771 biofilm grown on the glass surface exhibited 467 differentially expressed (DE) genes (167 upregulated and 300 downregulated) versus the wild-type biofilm. In contrast, the Δgsu1771 biofilm grown on the graphite electrode exhibited 119 DE genes (79 upregulated and 40 downregulated) versus the wild-type biofilm. Among these DE genes, 67 were also differentially expressed in the Δgsu1771 biofilm grown on glass (56 with the same regulation and 11 exhibiting counter-regulation). Among the upregulated genes in the Δgsu1771 biofilms, we identified potential target genes involved in exopolysaccharide synthesis (gsu1961-63, gsu1959, gsu1972-73, gsu1976-77). RT-qPCR analyses were then conducted to confirm the differential expression of a selection of genes of interest. DNA-protein binding assays demonstrated the direct binding of the GSU1771 regulator to the promoter region of pgcA, pulF, relA, and gsu3356. Furthermore, heme-staining and western blotting revealed an increase in c-type cytochromes including OmcS and OmcZ in Δgsu1771 biofilms. Collectively, our findings demonstrated that GSU1771 is a global regulator that controls extracellular electron transfer and exopolysaccharide synthesis in G. sulfurreducens, which is crucial for electroconductive biofilm development.
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Affiliation(s)
- Juan B. Jaramillo-Rodríguez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Luis M. Rodríguez-Torres
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Guillermo A. Huerta-Miranda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alberto Hernández-Eligio
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Investigador por México, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Katy Juarez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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10
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Li Y, Fan Y, Ma X, Wang Y, Liu J. Metagenomic survey reveals global distribution and evolution of microbial sialic acid catabolism. Front Microbiol 2023; 14:1267152. [PMID: 37840734 PMCID: PMC10570557 DOI: 10.3389/fmicb.2023.1267152] [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: 07/26/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Sialic acids comprise a varied group of nine-carbon amino sugars found mostly in humans and other higher metazoans, playing major roles in cell interactions with external environments as well as other cells. Microbial sialic acid catabolism (SAC) has long been considered a virulence determinant, and appears to be mainly the purview of pathogenic and commensal bacterial species associated with eukaryotic hosts. Here, we used 2,521 (pre-)assembled metagenomes to evaluate the distribution of SAC in microbial communities from diverse ecosystems and human body parts. Our results demonstrated that microorganisms possessing SAC globally existed in non-host associated environments, although much less frequently than in mammal hosts. We also showed that the ecological significance and taxonomic diversity of microbial SAC have so far been largely underestimated. Phylogenetic analysis revealed a strong signal of horizontal gene transfer among distinct taxa and habitats, and also suggested a specific ecological pressure and a relatively independent evolution history in environmental communities. Our study expanded the known diversity of microbial SAC, and has provided the backbone for further studies on its ecological roles and potential pathogenesis.
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Affiliation(s)
- Yisong Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Yeshun Fan
- School of Public Health, Qingdao University, Qingdao, China
| | - Xiaofang Ma
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | - Ying Wang
- School of Public Health, Qingdao University, Qingdao, China
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
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11
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Buzun E, Hsu CY, Sejane K, Oles RE, Ayala AV, Loomis LR, Zhao J, Rossitto LA, McGrosso D, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early life colonization by a pioneering gut commensal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552477. [PMID: 37609270 PMCID: PMC10441351 DOI: 10.1101/2023.08.08.552477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The early microbial colonization of the gastrointestinal tract can lead to long-term impacts in development and overall human health. Keystone species, including Bacteroides spp ., play a crucial role in maintaining the structure, diversity, and function of the intestinal ecosystem. However, the process by which a defined and resilient community is curated and maintained during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa and regulates the commensal colonization program during the first weeks of life. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. After examining the dynamics between pioneer gut Bacteroides species in the murine gut, we discovered that NanH enables vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, we demonstrate that NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and the microbiota mediated through host-derived glycans to promote stable intestinal colonization.
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12
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Kim J, Kim BS. Bacterial Sialic Acid Catabolism at the Host–Microbe Interface. J Microbiol 2023; 61:369-377. [PMID: 36972004 DOI: 10.1007/s12275-023-00035-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023]
Abstract
Sialic acids consist of nine-carbon keto sugars that are commonly found at the terminal end of mucins. This positional feature of sialic acids contributes to host cell interactions but is also exploited by some pathogenic bacteria in evasion of host immune system. Moreover, many commensals and pathogens use sialic acids as an alternative energy source to survive within the mucus-covered host environments, such as the intestine, vagina, and oral cavity. Among the various biological events mediated by sialic acids, this review will focus on the processes necessary for the catabolic utilization of sialic acid in bacteria. First of all, transportation of sialic acid should be preceded before its catabolism. There are four types of transporters that are used for sialic acid uptake; the major facilitator superfamily (MFS), the tripartite ATP-independent periplasmic C4-dicarboxilate (TRAP) multicomponent transport system, the ATP binding cassette (ABC) transporter, and the sodium solute symporter (SSS). After being moved by these transporters, sialic acid is degraded into an intermediate of glycolysis through the well-conserved catabolic pathway. The genes encoding the catabolic enzymes and transporters are clustered into an operon(s), and their expression is tightly controlled by specific transcriptional regulators. In addition to these mechanisms, we will cover some researches about sialic acid utilization by oral pathogens.
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Affiliation(s)
- Jaeeun Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Byoung Sik Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, 03760, Republic of Korea.
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13
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McDonald ND, Rosenberger JR, Almagro-Moreno S, Boyd EF. The Role of Nutrients and Nutritional Signals in the Pathogenesis of Vibrio cholerae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:195-211. [PMID: 36792877 DOI: 10.1007/978-3-031-22997-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Vibrio cholerae, the agent of cholera, is a natural inhabitant of aquatic environments. Over the past decades, the importance of specific nutrients and micronutrients in the environmental survival, host colonization, and pathogenesis of this species has become increasingly clear. For instance, V. cholerae has evolved ingenious mechanisms that allow the bacterium to colonize and establish a niche in the intestine of human hosts, where it competes with commensals (gut microbiota) and other pathogenic bacteria for available nutrients. Here, we discuss the carbon and energy sources utilized by V. cholerae and what is known about the role of nutrition in V. cholerae colonization. We examine how nutritional signals affect virulence gene regulation and how interactions with intestinal commensal species can affect intestinal colonization.
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Affiliation(s)
- N D McDonald
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - J R Rosenberger
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - S Almagro-Moreno
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA.,National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA
| | - E Fidelma Boyd
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.
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14
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Balasubramanian D, López-Pérez M, Almagro-Moreno S. Cholera Dynamics and the Emergence of Pandemic Vibrio cholerae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:127-147. [PMID: 36792874 DOI: 10.1007/978-3-031-22997-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Cholera is a severe diarrheal disease caused by the aquatic bacterium Vibrio cholerae. Interestingly, to date, only one major clade has emerged to cause pandemic disease in humans: the clade that encompasses the strains from the O1 and O139 serogroups. In this chapter, we provide a comprehensive perspective on the virulence factors and mobile genetic elements (MGEs) associated with the emergence of pandemic V. cholerae strains and highlight novel findings such as specific genomic background or interactions between MGEs that explain their confined distribution. Finally, we discuss pandemic cholera dynamics contextualizing them within the evolution of the bacterium.
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Affiliation(s)
- Deepak Balasubramanian
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA
| | - Mario López-Pérez
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA.
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15
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Bell A, Severi E, Owen CD, Latousakis D, Juge N. Biochemical and structural basis of sialic acid utilization by gut microbes. J Biol Chem 2023; 299:102989. [PMID: 36758803 PMCID: PMC10017367 DOI: 10.1016/j.jbc.2023.102989] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
The human gastrointestinal (GI) tract harbors diverse microbial communities collectively known as the gut microbiota that exert a profound impact on human health and disease. The repartition and availability of sialic acid derivatives in the gut have a significant impact on the modulation of gut microbes and host susceptibility to infection and inflammation. Although N-acetylneuraminic acid (Neu5Ac) is the main form of sialic acids in humans, the sialic acid family regroups more than 50 structurally and chemically distinct modified derivatives. In the GI tract, sialic acids are found in the terminal location of mucin glycan chains constituting the mucus layer and also come from human milk oligosaccharides in the infant gut or from meat-based foods in adults. The repartition of sialic acid in the GI tract influences the gut microbiota composition and pathogen colonization. In this review, we provide an update on the mechanisms underpinning sialic acid utilization by gut microbes, focusing on sialidases, transporters, and metabolic enzymes.
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Affiliation(s)
- Andrew Bell
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich, United Kingdom
| | - Emmanuele Severi
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - C David Owen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Dimitrios Latousakis
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich, United Kingdom
| | - Nathalie Juge
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich, United Kingdom.
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16
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Lin L, Lai Z, Yang H, Zhang J, Qi W, Xie F, Mao S. Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications. THE ISME JOURNAL 2023; 17:172-184. [PMID: 36261508 PMCID: PMC9750977 DOI: 10.1038/s41396-022-01333-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Although the importance of bile acid (BA)-related microbial strains and enzymes is increasingly recognized for monogastric animals, a lack of knowledge about BA metabolism in dairy cows limits functional applications aimed at the targeted modulation of microbe-host interactions for animal production and health. In the present study, 108 content samples from six intestinal regions of dairy cows were used for shotgun metagenomic sequencing. Overall, 372 high-quality metagenome-assembled genomes (MAGs) were involved in BA deconjugation, oxidation, and dehydroxylation pathways. Furthermore, the BA-metabolizing microbiome predominately occurred in the large intestine, resulting in the accumulation of secondary unconjugated BAs. Comparative genomic analysis revealed that the bile salt hydrolase (BSH)-carrying microbial populations managed with the selective environment of the dairy cow intestine by adopting numerous host mucin glycan-degrading abilities. A sequence similarity network analysis classified 439 BSH homologs into 12 clusters and identified different clusters with diverse evolution, taxonomy, signal peptides, and ecological niches. Our omics data further revealed that the strains of Firmicutes bacterium CAG-110 processed the increased abundance of BSHs from Cluster 1, coinciding with the changes in the colon cholic acid concentration after grain introduction, and were intricately related to intestinal inflammation. This study is the first to use a genome-centric approach and whole intestine-targeted metabolomics to reveal microbial BA metabolism and its diet-induced functional implications in dairy cows. These findings provide insight into the manipulation of intestinal microorganisms for improving host health.
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Affiliation(s)
- Limei Lin
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zheng Lai
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Huisheng Yang
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiyou Zhang
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weibiao Qi
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Fei Xie
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China. .,Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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17
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Eneva R, Engibarov S, Gocheva Y, Mitova S, Arsov A, Petrov K, Abrashev R, Lazarkevich I, Petrova P. Safe Sialidase Production by the Saprophyte Oerskovia paurometabola: Gene Sequence and Enzyme Purification. Molecules 2022; 27:molecules27248922. [PMID: 36558051 PMCID: PMC9782813 DOI: 10.3390/molecules27248922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/01/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Sialidase preparations are applied in structural and functional studies on sialoglycans, in the production of sialylated therapeutic proteins and synthetic substrates for use in biochemical research, etc. They are obtained mainly from pathogenic microorganisms; therefore, the demand for apathogenic producers of sialidase is of exceptional importance for the safe production of this enzyme. Here, we report for the first time the presence of a sialidase gene and enzyme in the saprophytic actinomycete Oerskovia paurometabola strain O129. An electrophoretically pure, glycosylated enzyme with a molecular weight of 70 kDa was obtained after a two-step chromatographic procedure using DEAE cellulose and Q-sepharose. The biochemical characterization showed that the enzyme is extracellular, inductive, and able to cleave α(2→3,6,8) linked sialic acids with preference for α(2→3) bonds. The enzyme production was strongly induced by glycomacropeptide (GMP) from milk whey, as well as by sialic acid. Investigation of the deduced amino acid sequence revealed that the protein molecule has the typical six-bladed β-propeller structure and contains all features of bacterial sialidases, i.e., an YRIP motif, five Asp-boxes, and the conserved amino acids in the active site. The presence of an unusual signal peptide of 40 amino acids was predicted. The sialidase-producing O. paurometabola O129 showed high and constant enzyme production. Together with its saprophytic nature, this makes it a reliable producer with high potential for industrial application.
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Affiliation(s)
- Rumyana Eneva
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Correspondence:
| | - Stephan Engibarov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Yana Gocheva
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Simona Mitova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Alexander Arsov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Kaloyan Petrov
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Radoslav Abrashev
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Irina Lazarkevich
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Penka Petrova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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18
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Proteome Profile Changes Induced by Heterologous Overexpression of Mycobacterium tuberculosis-Derived Antigens PstS-1 (Rv0934) and Ag85B (Rv1886c) in Mycobacterium microti. Biomolecules 2022; 12:biom12121836. [PMID: 36551264 PMCID: PMC9775975 DOI: 10.3390/biom12121836] [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: 09/14/2022] [Revised: 11/01/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022] Open
Abstract
The development of new tuberculosis vaccines remains a global priority, and recombinant vaccines are a frequently investigated option. These vaccines follow a molecular strategy that may enhance protective efficacy. However, their functional differences, particularly with respect to glycosylation, remain unknown. Recent studies have shown that glycosylation plays a key role in the host-pathogen interactions during immune recognition. The aim of this study was to determine the differences in the glycosylation profiles of two recombinant strains of Mycobacterium microti, overexpressing Ag85B (Rv1886c) and PstS-1 (Rv0934) antigens of M. tuberculosis. For each strain, the glycosylation profile was determined by Western blotting with lectins. The results showed the presence of mannosylated proteins and evidence of linked sialic acid proteins. Interestingly, different proteome and glycoproteome profiles were observed between the two recombinant strains and the wild-type strain. We have shown here that the construction of the recombinant strains of M. microti has altered the proteome and glycosylation profiles of these strains, leading us to ask what impact these changes might have on the immune response.
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19
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Bozzola T, Johnsson RE, Nilsson UJ, Ellervik U. Sialic Acid 4-N-Piperazine and Piperidine Derivatives Bind with High Affinity to the P. mirabilis Sialic Acid Sodium Solute Symporter. ChemMedChem 2022; 17:e202200351. [PMID: 36121381 PMCID: PMC10092485 DOI: 10.1002/cmdc.202200351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/16/2022] [Indexed: 01/14/2023]
Abstract
In search for novel antibacterial compounds, bacterial sialic acid uptake inhibition represents a promising strategy. Sialic acid plays a critical role for growth and colonisation of several pathogenic bacteria, and its uptake inhibition in bacteria was recently demonstrated to be a viable strategy by targeting the SiaT sodium solute symporters from Proteus mirabilis and Staphylococcus aureus. Here we report the design, synthesis and evaluation of potential sialic acid uptake inhibitors bearing 4-N-piperidine and piperazine moieties. The 4-N-derivatives were obtained via 4-N-functionalization with piperidine and piperazine nucleophiles in an efficient direct substitution of the 4-O-acetate of Neu5Ac. Evaluation for binding to bacterial transport proteins with nanoDSF and ITC revealed compounds possessing nanomolar affinity for the P. mirabilis SiaT symporter. Computational analyses indicate the engagement of a previously untargeted portion of the binding site.
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Affiliation(s)
- Tiago Bozzola
- Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | | | - Ulf J Nilsson
- Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Ulf Ellervik
- Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden
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20
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Association of Midgut Bacteria and Their Metabolic Pathways with Zika Infection and Insecticide Resistance in Colombian Aedes aegypti Populations. Viruses 2022; 14:v14102197. [PMID: 36298752 PMCID: PMC9609292 DOI: 10.3390/v14102197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
INTRODUCTION Aedes aegypti is the vector of several arboviruses such as dengue, Zika, and chikungunya. In 2015-16, Zika virus (ZIKV) had an outbreak in South America associated with prenatal microcephaly and Guillain-Barré syndrome. This mosquito's viral transmission is influenced by microbiota abundance and diversity and its interactions with the vector. The conditions of cocirculation of these three arboviruses, failure in vector control due to insecticide resistance, limitations in dengue management during the COVID-19 pandemic, and lack of effective treatment or vaccines make it necessary to identify changes in mosquito midgut bacterial composition and predict its functions through the infection. Its study is fundamental because it generates knowledge for surveillance of transmission and the risk of outbreaks of these diseases at the local level. METHODS Midgut bacterial compositions of females of Colombian Ae. aegypti populations were analyzed using DADA2 Pipeline, and their functions were predicted with PICRUSt2 analysis. These analyses were done under the condition of natural ZIKV infection and resistance to lambda-cyhalothrin, alone and in combination. One-step RT-PCR determined the percentage of ZIKV-infected females. We also measured the susceptibility to the pyrethroid lambda-cyhalothrin and evaluated the presence of the V1016I mutation in the sodium channel gene. RESULTS We found high ZIKV infection rates in Ae. aegypti females from Colombian rural municipalities with deficient water supply, such as Honda with 63.6%. In the face of natural infection with an arbovirus such as Zika, the diversity between an infective and non-infective form was significantly different. Bacteria associated with a state of infection with ZIKV and lambda-cyhalothrin resistance were detected, such as the genus Bacteroides, which was related to functions of pathogenicity, antimicrobial resistance, and bioremediation of insecticides. We hypothesize that it is a vehicle for virus entry, as it is in human intestinal infections. On the other hand, Bello, the only mosquito population classified as susceptible to lambda-cyhalothrin, was associated with bacteria related to mucin degradation functions in the intestine, belonging to the Lachnospiraceae family, with the genus Dorea being increased in ZIKV-infected females. The Serratia genus presented significantly decreased functions related to phenazine production, potentially associated with infection control, and control mechanism functions for host defense and quorum sensing. Additionally, Pseudomonas was the genus principally associated with functions of the degradation of insecticides related to tryptophan metabolism, ABC transporters with a two-component system, efflux pumps, and alginate synthesis. CONCLUSIONS Microbiota composition may be modulated by ZIKV infection and insecticide resistance in Ae. aegypti Colombian populations. The condition of resistance to lambda-cyhalothrin could be inducing a phenome of dysbiosis in field Ae. aegypti affecting the transmission of arboviruses.
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21
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Yokoi T, Nishiyama K, Kushida Y, Uribayashi K, Kunihara T, Fujimoto R, Yamamoto Y, Ito M, Miki T, Haneda T, Mukai T, Okada N. O-acetylesterase activity of Bifidobacterium bifidum sialidase facilities the liberation of sialic acid and encourages the proliferation of sialic acid scavenging Bifidobacterium breve. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:637-645. [PMID: 35581157 DOI: 10.1111/1758-2229.13083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Bifidobacterium bifidum possesses two extracellular sialidases (SiaBb1 and SiaBb2) that release free sialic acid from mucin sialoglycans, which can be utilized via cross-feeding by Bifidobacterium breve that, otherwise, is prevented from utilizing this nutrient source. Modification of sialic acids with O-acetyl esters is known to protect mucin glycans from degradation by bacterial sialidases. Compared to SiaBb2, SiaBb1 has an additional O-acetylesterase (Est) domain. We aimed to elucidate the role of the SiaBb1 Est domain from B. bifidum in sialic acid cross-feeding within Bifidobacterium. Pre-treatment of mucin secreted from bovine submaxillary glands (BSM) using His6 -tagged-Est and -SiaBb2 released a higher amount of sialic acid compared to the pre-treatment by His6 -SiaBb2. Growth of B. breve increased with an increase in nanE expression when supplemented with both His6 -Est- and His6 -SiaBb2-treated BSM. These results indicate that the esterase activity of the SiaBb1 Est domain enhances the efficiency of SiaBb2 to cleave sialic acid from mucin. This free sialic acid can be utilized by coexisting sialic acid scavenging B. breve via cross-feeding. Here, we provide the molecular mechanism underlying the unique sialoglycan degradation property of B. bifidum which is mediated by the complementary activities of SiaBb1 and SiaBb2 in the context of sialic acid cross-feeding.
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Affiliation(s)
- Tatsunari Yokoi
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Keita Nishiyama
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yuka Kushida
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Kazuya Uribayashi
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Takahiro Kunihara
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Rika Fujimoto
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yuji Yamamoto
- Laboratory of Biomolecular Science, School of Veterinary Medicine and Animal Sciences, Kitasato University, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Masahiro Ito
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Tsuyoshi Miki
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Takeshi Haneda
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Takao Mukai
- Laboratory of Biomolecular Science, School of Veterinary Medicine and Animal Sciences, Kitasato University, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Nobuhiko Okada
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
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22
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Bozzola T, Scalise M, Larsson CU, Newton-Vesty MC, Rovegno C, Mitra A, Cramer J, Wahlgren WY, Radhakrishnan Santhakumari P, Johnsson RE, Schwardt O, Ernst B, Friemann R, Dobson RCJ, Indiveri C, Schelin J, Nilsson UJ, Ellervik U. Sialic Acid Derivatives Inhibit SiaT Transporters and Delay Bacterial Growth. ACS Chem Biol 2022; 17:1890-1900. [PMID: 35675124 PMCID: PMC9295122 DOI: 10.1021/acschembio.2c00321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Antibiotic resistance
is a major worldwide concern, and new drugs
with mechanistically novel modes of action are urgently needed. Here,
we report the structure-based drug design, synthesis, and evaluation
in vitro and in cellular systems of sialic acid derivatives able to
inhibit the bacterial sialic acid symporter SiaT. We designed and
synthesized 21 sialic acid derivatives and screened their affinity
for SiaT by a thermal shift assay and elucidated the inhibitory mechanism
through binding thermodynamics, computational methods, and inhibitory
kinetic studies. The most potent compounds, which have a 180-fold
higher affinity compared to the natural substrate, were tested in
bacterial growth assays and indicate bacterial growth delay in methicillin-resistant Staphylococcus aureus. This study represents the
first example and a promising lead in developing sialic acid uptake
inhibitors as novel antibacterial agents.
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Affiliation(s)
- Tiago Bozzola
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,Molecular Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036 Arcavacata di Rende, Italy
| | - Christer U Larsson
- Division of Applied Microbiology, Department of Chemistry, Lund University, 22100 Lund, Sweden
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, 8140 Christchurch, New Zealand
| | - Caterina Rovegno
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ankita Mitra
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Jonathan Cramer
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University of Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Gothenburg, Sweden
| | - Partha Radhakrishnan Santhakumari
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka 560065, India.,Manipal Academy of Higher Education, Tiger Circle Road, Manipal, Karnataka 576104, India
| | | | - Oliver Schwardt
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Beat Ernst
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, 41345 Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, 8140 Christchurch, New Zealand.,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036 Arcavacata di Rende, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology (IBIOM), National Research Council-CNR, Via Amendola 122/O, 70126 Bari, Italy
| | - Jenny Schelin
- Division of Applied Microbiology, Department of Chemistry, Lund University, 22100 Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ellervik
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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23
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Tomás-Martínez S, Chen LM, Neu TR, Weissbrodt DG, van Loosdrecht MCM, Lin Y. Catabolism of sialic acids in an environmental microbial community. FEMS Microbiol Ecol 2022; 98:6571932. [PMID: 35446356 DOI: 10.1093/femsec/fiac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 11/14/2022] Open
Abstract
Sialic acids are a family of nine-carbon negatively charged carbohydrates. In animals, they are abundant on mucosa surfaces as terminal carbohydrates of mucin glycoproteins. Some commensal and pathogenic bacteria are able to release, take up, and catabolize sialic acids. Recently, sialic acids have been discovered to be widespread among most microorganisms. Although the catabolism of sialic acids has been intensively investigated in the field of host-microbe interactions, very limited information is available on microbial degradation of sialic acids produced by environmental microorganisms. In this study, the catabolic pathways of sialic acids within an microbial community dominated by 'Candidatus Accumulibacter' was evaluated. Protein alignment tools were used to detect the presence of the different proteins involved in the utilization of sialic acids in the flanking populations detected by 16S rRNA gene amplicon sequencing. The results showed the ability of Clostridium to release sialic acids from the glycan chains by the action of a sialidase. Clostridium and Chryseobacterium can take up free sialic acids and utilize them as nutrient. Interestingly, these results display similarities with the catabolism of sialic acids by the gut microbiota. This study points at the importance of sialic acids in environmental communities in the absence of eukaryotic hosts.
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Affiliation(s)
- Sergio Tomás-Martínez
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Le Min Chen
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Thomas R Neu
- Microbiology of Interfaces, Department River Ecology, Helmholtz Centre of Environmental Research - UFZ, Brueckstrasse 3A, 39114, Magdeburg, Germany
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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24
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Irons EE, Cortes Gomez E, Andersen VL, Lau JTY. Bacterial colonization and TH17 immunity are shaped by intestinal sialylation in neonatal mice. Glycobiology 2022; 32:414-428. [PMID: 35157771 PMCID: PMC9022908 DOI: 10.1093/glycob/cwac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/10/2022] [Accepted: 01/30/2022] [Indexed: 11/14/2022] Open
Abstract
Interactions between the neonate host and its gut microbiome are central to the development of a healthy immune system. However, the mechanisms by which animals alter early colonization of microbiota for their benefit remain unclear. Here, we investigated the role of early-life expression of the α2,6-sialyltransferase ST6GAL1 in microbiome phylogeny and mucosal immunity. Fecal, upper respiratory, and oral microbiomes of pups expressing or lacking St6gal1 were analyzed by 16S rRNA sequencing. At weaning, the fecal microbiome of St6gal1-KO mice had reduced Clostridiodes, Coprobacillus, and Adlercreutzia, but increased Helicobacter and Bilophila. Pooled fecal microbiomes from syngeneic donors were transferred to antibiotic-treated wild-type mice, before analysis of recipient mucosal immune responses by flow cytometry, RT-qPCR, microscopy, and ELISA. Transfer of St6gal1-KO microbiome induced a mucosal Th17 response, with expression of T-bet and IL-17, and IL-22-dependent gut lengthening. Early life intestinal sialylation was characterized by RT-qPCR, immunoblot, microscopy, and sialyltransferase enzyme assays in genetic mouse models at rest or with glucocorticoid receptor modulators. St6gal1 expression was greatest in the duodenum, where it was mediated by the P1 promoter and efficiently inhibited by dexamethasone. Our data show that the inability to produce α2,6-sialyl ligands contributes to microbiome-dependent Th17 inflammation, highlighting a pathway by which the intestinal glycosylation regulates mucosal immunity.
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Affiliation(s)
- Eric E Irons
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, United States
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, United States
| | - Valerie L Andersen
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, United States
| | - Joseph T Y Lau
- Corresponding author: Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, USA.
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25
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Abstract
Sialic acids are present in humans and other metazoans, playing essential roles in physiological and pathological processes. Commensal and pathogenic bacteria have evolved the capacity to utilize sialic acids as nutrient and energy sources. However, in some actinobacteria, sialic acid catabolism (SAC) is associated with free-living populations. To unravel the distribution and evolutionary history of SAC in the phylum Actinobacteria, we analyzed the presence and diversity of the putative SAC gene cluster (nan) in 7,180 high-quality, nonredundant actinobacterial genomes that covered 1,969 species. The results showed that ∼13% of actinobacterial species had the potential to utilize sialic acids, with 45 species capable of anhydro-SAC, all except two of them through the canonical pathway. These species belonged to 20 orders and 81 genera, with ∼36% of them from four genera, Actinomyces, Bifidobacterium, Corynebacterium, and Streptomyces. Moreover, ∼40% of the nan-positive species are free living. Phylogenetic analysis of the key nan genes, nanA, nanK, and nanE, revealed a strong signal of horizontal gene transfer (HGT), accompanied with vertical inheritance and gene loss. This evolutionary pattern led to high diversity and differential distribution of nan among actinobacterial taxa and might cause the cluster to spread to some free-living species while losing in some host-associated species. The evolution of SAC in actinobacteria probably represents the evolution of certain kinds of noncore bacterial functions for environmental adaptation and lifestyle switch, in which HGT plays a dominant role. IMPORTANCE Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored. Here, by examining all actinobacterial genomes available, we demonstrate that putative SAC is present in a small proportion of actinobacterial species, of which, however, ∼40% are free-living species. We also reveal remarkable difference in the distribution of SAC among actinobacterial taxa and high diversity of the putative SAC gene clusters. HGT plays a significant role in the evolution of SAC, accompanied with vertical inheritance and gene loss. Our results provide a comprehensive and systematic picture of the distribution and evolutionary history of SAC in actinobacteria, expanding the current knowledge on bacterial adaptation and diversification.
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26
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Oinam L, Minoshima F, Tateno H. Glycan profiling of the gut microbiota by Glycan-seq. ISME COMMUNICATIONS 2022; 2:1. [PMID: 37938656 PMCID: PMC9723764 DOI: 10.1038/s43705-021-00084-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/09/2021] [Accepted: 12/16/2021] [Indexed: 05/07/2023]
Abstract
Bacterial glycans modulate the cross talk between the gut microbiota and its host. However, little is known about these glycans because of the lack of appropriate technology to study them. In this study, we applied Glycan-seq technology for glycan profiling of the intact gut microbiota of mice. The evaluation of cultured gram-positive (Deinococcus radiodurans) and gram-negative (Escherichia coli) bacteria showed significantly distinct glycan profiles between these bacteria, which were selected and further analyzed by flow cytometry. The results of flow cytometry agreed well with those obtained by Glycan-seq, indicating that Glycan-seq can be used for bacterial glycan profiling. We thus applied Glycan-seq for comparative glycan profiling of pups and adult mice gut microbiotas. The glycans of the pups and adult microbiotas had significantly distinct glycan profiles, which reflect the different bacterial compositions of pups and adult gut microbiotas based on 16S rRNA gene sequencing.α2-6Sia-binders bound specifically to the pups microbiota. Lectin pull-down followed by 16S rRNA gene sequencing of the pups microbiota identified Lactobacillaceae as the most abundant bacterial family with glycans reacting with α2-6Sia-binders. The Glycan-seq system can reveal the glycan profile of the intact bacterial gut microbiota.
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Affiliation(s)
- Lalhaba Oinam
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Fumi Minoshima
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
- AMED-Prime, AMED, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
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27
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Indraratna AD, Everest-Dass A, Skropeta D, Sanderson-Smith M. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6519265. [PMID: 35104861 PMCID: PMC9075583 DOI: 10.1093/femsre/fuac001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/29/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
Host carbohydrates, or glycans, have been implicated in the pathogenesis of many bacterial infections. Group A Streptococcus (GAS) is a Gram-positive bacterium that readily colonises the skin and oropharynx, and is a significant cause of mortality in humans. While the glycointeractions orchestrated by many other pathogens are increasingly well-described, the understanding of the role of human glycans in GAS disease remains incomplete. Although basic investigation into the mechanisms of GAS disease is ongoing, several glycointeractions have been identified and are examined herein. The majority of research in this context has focussed on bacterial adherence, however, glycointeractions have also been implicated in carbohydrate metabolism; evasion of host immunity; biofilm adaptations; and toxin-mediated haemolysis. The involvement of human glycans in these diverse avenues of pathogenesis highlights the clinical value of understanding glycointeractions in combatting GAS disease.
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Affiliation(s)
- Anuk D Indraratna
- Illawarra Health and Medical Research Institute, Northfields Ave, Keiraville New South Wales 2522, Australia
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong, Northfields Avenue, Keiraville, New South Wales, 2522, Australia
| | - Arun Everest-Dass
- Institute for Glycomics, Griffith University, Gold Coast Campus, Parklands Drive, Southport, Queensland, 4215, Australia
| | - Danielle Skropeta
- Illawarra Health and Medical Research Institute, Northfields Ave, Keiraville New South Wales 2522, Australia
- School of Chemistry and Molecular Bioscience, Molecular Horizons, University of Wollongong, Northfields Avenue, Keiraville, New South Wales, 2522, Australia
| | - Martina Sanderson-Smith
- Corresponding author: Illawarra Health and Medical Research Institute, Bld 32, University of Wollongong, Northfields Avenue, Keiraville, New South Wales, 2522, Australia. Tel: +61 2 42981935; E-mail:
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28
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Lin X, Yao H, Guo J, Huang Y, Wang W, Yin B, Li X, Wang T, Li C, Xu X, Zhou G, Voglmeir J, Liu L. Protein Glycosylation and Gut Microbiota Utilization Can Limit the in vitro and in vivo Metabolic Cellular Incorporation of Neu5Gc. Mol Nutr Food Res 2021; 66:e2100615. [PMID: 34921741 DOI: 10.1002/mnfr.202100615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/01/2021] [Indexed: 11/06/2022]
Abstract
SCOPE Red meat intake was reported to be correlated with chronic diseases. A potential causal factor is N-glycolylneuraminic acid (Neu5Gc) which metabolically incorporates into diverse glycoconjugates in humans. This study aims to investigate the impact of exposure to Neu5Gc-rich red meat on healthy cytidine-5'-monophospho-N-acetylneuraminic acid hydroxylase (Cmah) knock-out mice and the underlying mechanisms. METHODS AND RESULTS CMAH-/- mice were fed Neu5Gc-rich diet for short-term (4 months) and long-term (10 months). Health status and levels of inflammatory cytokines were assessed. Caco-2 cells were used to investigate the intestinal absorption of Neu5Gc-containing glycoprotein, and in vitro fermentation was used to investigate the Neu5Gc utilization by gut microbiota. Neu5Gc-rich diets showed neither measurable abnormality in physio-biochemical and inflammatory indexes nor observable alterations of liver tissue in mice. Glycosylation of lactoferrin limited its intestinal epithelial absorption, and the absorption of Neu5Gc attached onto glycoprotein was thus limited. Neu5Gc was also simultaneously utilized by microorganisms under simulated gut conditions. CONCLUSION The results indicated that the long-term intake of Neu5Gc-rich red meat had no adverse effect on the health of CMAH-/- mice, which may be related to the limited absorption of Neu5Gc regulated by protein glycosylation, and the metabolism of Neu5Gc by gut microorganisms. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xisha Lin
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Hongliang Yao
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.,Food Science Department, Jinling Institute of Technology, Nanjing, China
| | - Jingyu Guo
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yingying Huang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Wenjiao Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Binru Yin
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiang'an Li
- Haidu College, Qingdao Agricultural University, Qingdao, China
| | - Ting Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Chunbao Li
- Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xinglian Xu
- Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Guanghong Zhou
- Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.,Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.,Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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29
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Berkhout MD, Plugge CM, Belzer C. How microbial glycosyl hydrolase activity in the gut mucosa initiates microbial cross-feeding. Glycobiology 2021; 32:182-200. [PMID: 34939101 PMCID: PMC8966484 DOI: 10.1093/glycob/cwab105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 11/12/2022] Open
Abstract
The intestinal epithelium is protected from direct contact with gut microbes by a mucus layer. This mucus layer consists of secreted mucin glycoproteins. The outer mucus layer in the large intestine forms a niche that attracts specific gut microbiota members of which several gut commensals can degrade mucin. Mucin glycan degradation is a complex process that requires a broad range of glycan degrading enzymes, as mucin glycans are intricate and diverse molecules. Consequently, it is hypothesised that microbial mucin breakdown requires concerted action of various enzymes in a network of multiple resident microbes at the gut mucosa. This review investigates the evolutionary relationships of microbial CAZymes that are potentially involved in mucin glycan degradation and focuses on the role that microbial enzymes play in the degradation of gut mucin glycans in microbial cross-feeding and syntrophic interactions.
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Affiliation(s)
- Maryse D Berkhout
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
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30
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López-Pérez M, Jayakumar JM, Grant TA, Zaragoza-Solas A, Cabello-Yeves PJ, Almagro-Moreno S. Ecological diversification reveals routes of pathogen emergence in endemic Vibrio vulnificus populations. Proc Natl Acad Sci U S A 2021; 118:e2103470118. [PMID: 34593634 PMCID: PMC8501797 DOI: 10.1073/pnas.2103470118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Pathogen emergence is a complex phenomenon that, despite its public health relevance, remains poorly understood. Vibrio vulnificus, an emergent human pathogen, can cause a deadly septicaemia with over 50% mortality rate. To date, the ecological drivers that lead to the emergence of clinical strains and the unique genetic traits that allow these clones to colonize the human host remain mostly unknown. We recently surveyed a large estuary in eastern Florida, where outbreaks of the disease frequently occur, and found endemic populations of the bacterium. We established two sampling sites and observed strong correlations between location and pathogenic potential. One site is significantly enriched with strains that belong to one phylogenomic cluster (C1) in which the majority of clinical strains belong. Interestingly, strains isolated from this site exhibit phenotypic traits associated with clinical outcomes, whereas strains from the second site belong to a cluster that rarely causes disease in humans (C2). Analyses of C1 genomes indicate unique genetic markers in the form of clinical-associated alleles with a potential role in virulence. Finally, metagenomic and physicochemical analyses of the sampling sites indicate that this marked cluster distribution and genetic traits are strongly associated with distinct biotic and abiotic factors (e.g., salinity, nutrients, or biodiversity), revealing how ecosystems generate selective pressures that facilitate the emergence of specific strains with pathogenic potential in a population. This knowledge can be applied to assess the risk of pathogen emergence from environmental sources and integrated toward the development of novel strategies for the prevention of future outbreaks.
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Affiliation(s)
- Mario López-Pérez
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
| | - Jane M Jayakumar
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
| | - Trudy-Ann Grant
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
| | - Asier Zaragoza-Solas
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
| | - Pedro J Cabello-Yeves
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816;
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
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31
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Belzer C. Nutritional strategies for mucosal health: the interplay between microbes and mucin glycans. Trends Microbiol 2021; 30:13-21. [PMID: 34217596 DOI: 10.1016/j.tim.2021.06.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Many aspects of the mechanisms underlying the symbiosis between humans and gut microbes remain unknown and encompass some of the most intriguing questions in microbiome research. An important factor in this symbiosis is the interplay between microbes and human-produced glycans in mucin and breast milk. In this Opinion paper, I propose a synergy between the structural diversity of human mucin glycans and the enzymatic repertoire of the gut microbiome. The contribution of microbes to mucosal health is discussed, and the role of breast milk glycans in mucosal colonization by microbes is explained. The use of prebiotic mucin glycans in general, and specialized infant and medical nutrition in particular, should be considered as the field of interest to modulate the microbiota and improve mucosal health.
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Affiliation(s)
- Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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32
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Severi E, Rudden M, Bell A, Palmer T, Juge N, Thomas GH. Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals. Microb Genom 2021; 7. [PMID: 34184979 PMCID: PMC8461474 DOI: 10.1099/mgen.0.000614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Located at the tip of cell surface glycoconjugates, sialic acids are at the forefront of host-microbe interactions and, being easily liberated by sialidase enzymes, are used as metabolites by numerous bacteria, particularly by pathogens and commensals living on or near diverse mucosal surfaces. These bacteria rely on specific transporters for the acquisition of host-derived sialic acids. Here, we present the first comprehensive genomic and phylogenetic analysis of bacterial sialic acid transporters, leading to the identification of multiple new families and subfamilies. Our phylogenetic analysis suggests that sialic acid-specific transport has evolved independently at least eight times during the evolution of bacteria, from within four of the major families/superfamilies of bacterial transporters, and we propose a robust classification scheme to bring together a myriad of different nomenclatures that exist to date. The new transporters discovered occur in diverse bacteria, including Spirochaetes, Bacteroidetes, Planctomycetes and Verrucomicrobia, many of which are species that have not been previously recognized to have sialometabolic capacities. Two subfamilies of transporters stand out in being fused to the sialic acid mutarotase enzyme, NanM, and these transporter fusions are enriched in bacteria present in gut microbial communities. Our analysis supports the increasing experimental evidence that competition for host-derived sialic acid is a key phenotype for successful colonization of complex mucosal microbiomes, such that a strong evolutionary selection has occurred for the emergence of sialic acid specificity within existing transporter architectures.
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Affiliation(s)
- Emmanuele Severi
- Department of Biology, University of York, York, UK.,Microbes in Health and Disease, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Andrew Bell
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Tracy Palmer
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Nathalie Juge
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
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33
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Geier RR, Rehberger TG, Smith AH. Comparative Genomics of Clostridium perfringens Reveals Patterns of Host-Associated Phylogenetic Clades and Virulence Factors. Front Microbiol 2021; 12:649953. [PMID: 34177831 PMCID: PMC8220089 DOI: 10.3389/fmicb.2021.649953] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/30/2021] [Indexed: 11/23/2022] Open
Abstract
Clostridium perfringens is an opportunistic pathogenic bacterium that infects both animals and humans. Clostridium perfringens genomes encode a diverse array of toxins and virulence proteins, which continues to expand as more genomes are sequenced. In this study, the genomes of 44 C. perfringens strains isolated from intestinal sections of diseased cattle and from broiler chickens from diseased and healthy flocks were sequenced. These newly assembled genomes were compared to 141 publicly available C. perfringens genome assemblies, by aligning known toxin and virulence protein sequences in the assemblies using BLASTp. The genes for alpha toxin, collagenase, a sialidase (nanH), and alpha-clostripain were present in at least 99% of assemblies analyzed. In contrast, beta toxin, epsilon toxin, iota toxin, and binary enterotoxin of toxinotypes B, C, D, and E were present in less than 5% of assemblies analyzed. Additional sequence variants of beta2 toxin were detected, some of which were missing the leader or signal peptide sequences and therefore likely not secreted. Some pore-forming toxins involved in intestinal diseases were host-associated, the netB gene was only found in avian isolates, while netE, netF, and netG were only present in canine and equine isolates. Alveolysin was positively associated with canine and equine strains and only present in a single monophyletic clade. Strains from ruminant were not associated with known virulence factors and, except for the food poisoning associated clade, were present across the phylogenetic diversity identified to date for C. perfringens. Many C. perfringens strains associated with food poisoning lacked the genes for hyaluronidases and sialidases, important for attaching to and digesting complex carbohydrates found in animal tissues. Overall, the diversity of virulence factors in C. perfringens makes these species capable of causing disease in a wide variety of hosts and niches.
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Affiliation(s)
| | | | - Alexandra H. Smith
- Arm and Hammer Animal and Food Production, Church & Dwight Co., Inc., Waukesha, WI, United States
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34
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Moradali MF, Davey ME. Metabolic plasticity enables lifestyle transitions of Porphyromonas gingivalis. NPJ Biofilms Microbiomes 2021; 7:46. [PMID: 34031416 PMCID: PMC8144566 DOI: 10.1038/s41522-021-00217-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/28/2021] [Indexed: 02/04/2023] Open
Abstract
Our understanding of how the oral anaerobe Porphyromonas gingivalis can persist below the gum line, induce ecological changes, and promote polymicrobial infections remains limited. P. gingivalis has long been described as a highly proteolytic and asaccharolytic pathogen that utilizes protein substrates as the main source for energy production and proliferation. Here, we report that P. gingivalis displays a metabolic plasticity that enables the exploitation of non-proteinaceous substrates, specifically the monocarboxylates pyruvate and lactate, as well as human serum components, for colonization and biofilm formation. We show that anabolism of carbohydrates from pyruvate is powered by catabolism of amino acids. Concomitantly, the expression of fimbrial adhesion is upregulated, leading to the enhancement of biofilm formation, stimulation of multispecies biofilm development, and increase of colonization and invasion of the primary gingival epithelial cells by P. gingivalis. These studies provide the first glimpse into the metabolic plasticity of P. gingivalis and its adaptation to the nutritional condition of the host niche. Our findings support the model that in response to specific nutritional parameters, P. gingivalis has the potential to promote host colonization and development of a pathogenic community.
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Affiliation(s)
- M Fata Moradali
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA.
- Department of Oral Immunology and Infectious Diseases, University of Louisville, School of Dentistry, Room 355 B, Louisville, KY, USA.
| | - Mary E Davey
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
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35
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Albers M, Schröter L, Belousov S, Hartmann M, Grove M, Abeln M, Mühlenhoff M. The sialyl-O-acetylesterase NanS of Tannerella forsythia encompasses two catalytic modules with different regiospecificity for O7 and O9 of sialic acid. Glycobiology 2021; 31:1176-1191. [PMID: 33909048 DOI: 10.1093/glycob/cwab034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
The periodontal pathogen Tannerella forsythia utilizes host sialic acids as a nutrient source. To also make O-acetylated sialyl residues susceptible to the action of its sialidase and sialic acid up-take system, Tannerella produces NanS, an O-acetylesterase with two putative catalytic domains. Here, we analyzed NanS by homology modeling, predicted a catalytic serine-histidine-aspartate triad for each catalytic domain and performed individual domain inactivation by single alanine exchanges of the triad nucleophiles S32 and S311. Subsequent functional analyses revealed that both domains possess sialyl-O-acetylesterase activity, but differ in their regioselectivity with respect to position O9 and O7 of sialic acid. The 7-O-acetylesterase activity inherent to the C-terminal domain of NanS is unique among sialyl-O-acetylesterases and fills the current gap in tools targeting 7-O-acetylation. Application of the O7-specific variant NanS-S32A allowed us to evidence the presence of cellular 7,9-di-O-acetylated sialoglycans by monitoring the gain in 9-O-acetylation upon selective removal of acetyl groups from O7. Moreover, we established de-7,9-O-acetylation by wild-type NanS as an easy and efficient method to validate the specific binding of three viral lectins commonly used for the recognition of (7),9-O-acetylated sialoglycans. Their binding critically depends on an acetyl group in O9, yet de-7,9-O-acetylation proved advantageous over de-9-O-acetylation as the additional removal of the 7-O-acetyl group eliminated ligand formation by 7,9-ester migration. Together, our data show that NanS gained dual functionality through recruitment of two esterase modules with complementary activities. This enables Tannerella to scavenge 7,9-di-O-acetylated sialyl residues and provides a novel, O7-specific tool for studying sialic acid O-acetylation.
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Affiliation(s)
- Malena Albers
- Institute of Clinical Biochemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Larissa Schröter
- Institute of Clinical Biochemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Sergej Belousov
- Institute of Clinical Biochemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Maike Hartmann
- Institute of Clinical Biochemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Grove
- Institute of Clinical Biochemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Abeln
- Institute of Clinical Biochemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Martina Mühlenhoff
- Institute of Clinical Biochemistry, Hannover Medical School, 30625 Hannover, Germany
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36
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Horne CR, Venugopal H, Panjikar S, Wood DM, Henrickson A, Brookes E, North RA, Murphy JM, Friemann R, Griffin MDW, Ramm G, Demeler B, Dobson RCJ. Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism. Nat Commun 2021; 12:1988. [PMID: 33790291 PMCID: PMC8012715 DOI: 10.1038/s41467-021-22253-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 03/03/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism. The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.
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Affiliation(s)
- Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Hariprasad Venugopal
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - David M Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Emre Brookes
- Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Michael D W Griffin
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Georg Ramm
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. .,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia.
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37
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Eneva R, Engibarov S, Abrashev R, Krumova E, Angelova M. Sialic acids, sialoconjugates and enzymes of their metabolism in fungi. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1879678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Rumyana Eneva
- Department of General Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Stephan Engibarov
- Department of General Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Radoslav Abrashev
- Department of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Ekaterina Krumova
- Department of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Angelova
- Department of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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38
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McDonald ND, Boyd EF. Structural and Biosynthetic Diversity of Nonulosonic Acids (NulOs) That Decorate Surface Structures in Bacteria. Trends Microbiol 2021; 29:142-157. [PMID: 32950378 PMCID: PMC7855311 DOI: 10.1016/j.tim.2020.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022]
Abstract
Nonulosonic acids (NulOs) are a diverse family of 9-carbon α-keto acid sugars that are involved in a wide range of functions across all branches of life. The family of NulOs includes the sialic acids as well as the prokaryote-specific NulOs. Select bacteria biosynthesize the sialic acid N-acetylneuraminic acid (Neu5Ac), and the ability to produce this sugar and its subsequent incorporation into cell-surface structures is implicated in a variety of bacteria-host interactions. Furthermore, scavenging of sialic acid from the environment for energy has been characterized across a diverse group of bacteria, mainly human commensals and pathogens. In addition to sialic acid, bacteria have the ability to biosynthesize prokaryote-specific NulOs, of which there are several known isomers characterized. These prokaryotic NulOs are similar in structure to Neu5Ac but little is known regarding their role in bacterial physiology. Here, we discuss the diversity in structure, the biosynthesis pathways, and the functions of bacteria-specific NulOs. These carbohydrates are phylogenetically widespread among bacteria, with numerous structurally unique modifications recognized. Despite the diversity in structure, the NulOs are involved in similar functions such as motility, biofilm formation, host colonization, and immune evasion.
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Affiliation(s)
- Nathan D McDonald
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - E Fidelma Boyd
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA.
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39
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Exploring the Impact of Ketodeoxynonulosonic Acid in Host-Pathogen Interactions Using Uptake and Surface Display by Nontypeable Haemophilus influenzae. mBio 2021; 12:mBio.03226-20. [PMID: 33468699 PMCID: PMC7845648 DOI: 10.1128/mbio.03226-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
All cells in vertebrates are coated with a dense array of glycans often capped with sugars called sialic acids. Sialic acids have many functions, including serving as a signal for recognition of “self” cells by the immune system, thereby guiding an appropriate immune response against foreign “nonself” and/or damaged cells. Surface expression of the common vertebrate sialic acid (Sia) N-acetylneuraminic acid (Neu5Ac) by commensal and pathogenic microbes appears structurally to represent “molecular mimicry” of host sialoglycans, facilitating multiple mechanisms of host immune evasion. In contrast, ketodeoxynonulosonic acid (Kdn) is a more ancestral Sia also present in prokaryotic glycoconjugates that are structurally quite distinct from vertebrate sialoglycans. We detected human antibodies against Kdn-terminated glycans, and sialoglycan microarray studies found these anti-Kdn antibodies to be directed against Kdn-sialoglycans structurally similar to those on human cell surface Neu5Ac-sialoglycans. Anti-Kdn-glycan antibodies appear during infancy in a pattern similar to those generated following incorporation of the nonhuman Sia N-glycolylneuraminic acid (Neu5Gc) onto the surface of nontypeable Haemophilus influenzae (NTHi), a human commensal and opportunistic pathogen. NTHi grown in the presence of free Kdn took up and incorporated the Sia into its lipooligosaccharide (LOS). Surface display of the Kdn within NTHi LOS blunted several virulence attributes of the pathogen, including Neu5Ac-mediated resistance to complement and whole blood killing, complement C3 deposition, IgM binding, and engagement of Siglec-9. Upper airway administration of Kdn reduced NTHi infection in human-like Cmah null (Neu5Gc-deficient) mice that express a Neu5Ac-rich sialome. We propose a mechanism for the induction of anti-Kdn antibodies in humans, suggesting that Kdn could be a natural and/or therapeutic “Trojan horse” that impairs colonization and virulence phenotypes of free Neu5Ac-assimilating human pathogens.
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40
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Coker JK, Moyne O, Rodionov DA, Zengler K. Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health. Gut Microbes 2021; 13:1-18. [PMID: 33615984 PMCID: PMC7899658 DOI: 10.1080/19490976.2020.1869502] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/20/2020] [Accepted: 12/15/2020] [Indexed: 02/08/2023] Open
Abstract
Gut microbiome composition depends heavily upon diet and has strong ties to human health. Dietary carbohydrates shape the gut microbiome by providing a potent nutrient source for particular microbes. This review explores how dietary carbohydrates in general, including individual monosaccharides and complex polysaccharides, influence the gut microbiome with subsequent effects on host health and disease. In particular, the effects of sialic acids, a prominent and influential class of monosaccharides, are discussed. Complex plant carbohydrates, such as dietary fiber, generally promote microbial production of compounds beneficial to the host while preventing degradation of host carbohydrates from colonic mucus. In contrast, simple and easily digestible sugars such as glucose are often associated with adverse effects on health and the microbiome. The monosaccharide class of sialic acids exerts a powerful but nuanced effect on gut microbiota. Sialic acid consumption (in monosaccharide form, or as part of human milk oligosaccharides or certain animal-based foods) drives the growth of organisms with sialic acid metabolism capabilities. Minor chemical modifications of Neu5Ac, the most common form of sialic acid, can alter these effects. All aspects of carbohydrate composition are therefore relevant to consider when designing dietary therapeutic strategies to alter the gut microbiome.
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Affiliation(s)
- Joanna K Coker
- Department of Pediatrics, University of California, San Diego, La Jolla, USA
| | - Oriane Moyne
- Department of Pediatrics, University of California, San Diego, La Jolla, USA
| | - Dmitry A. Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
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41
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Gangi Setty T, Sarkar A, Coombes D, Dobson RCJ, Subramanian R. Structure and Function of N-Acetylmannosamine Kinases from Pathogenic Bacteria. ACS OMEGA 2020; 5:30923-30936. [PMID: 33324800 PMCID: PMC7726757 DOI: 10.1021/acsomega.0c03699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Several pathogenic bacteria import and catabolize sialic acids as a source of carbon and nitrogen. Within the sialic acid catabolic pathway, the enzyme N-acetylmannosamine kinase (NanK) catalyzes the phosphorylation of N-acetylmannosamine to N-acetylmannosamine-6-phosphate. This kinase belongs to the ROK superfamily of enzymes, which generally contain a conserved zinc-finger (ZnF) motif that is important for their structure and function. Previous structural studies have shown that the ZnF motif is absent in NanK of Fusobacterium nucleatum (Fn-NanK), a Gram-negative bacterium that causes the gum disease gingivitis. However, the effect in loss of the ZnF motif on the kinase activity is unknown. Using kinetic and thermodynamic studies, we have studied the functional properties of Fn-NanK to its substrates ManNAc and ATP, compared its activity with other ZnF motif-containing NanK enzymes from closely related Gram-negative pathogenic bacteria Haemophilus influenzae (Hi-NanK), Pasteurella multocida (Pm-NanK), and Vibrio cholerae (Vc-NanK). Our studies show a 10-fold decrease in substrate binding affinity between Fn-NanK (apparent KM ≈ 700 μM) and ZnF motif-containing NanKs (apparent KM ≈ 60 μM). To understand the structural features that combat the loss of the ZnF motif in Fn-NanK, we solved the crystal structures of functionally homologous ZnF motif-containing NanKs from P. multocida and H. influenzae. Here, we report Pm-NanK:unliganded, Pm-NanK:AMPPNP, Pm-NanK:ManNAc, Hi-NanK:ManNAc, and Hi-NanK:ManNAc-6P:ADP crystal structures. Structural comparisons of Fn-NanK with Hi-NanK, Pm-NanK, and hMNK (human N-acetylmannosamine kinase domain of UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase, GNE) show that even though there is less sequence identity, they have high degree of structural similarity. Furthermore, our structural analyses highlight that the ZnF motif of Fn-NanK is substituted by a set of hydrophobic residues, which forms a hydrophobic cluster that helps the proper orientation of ManNac in the active site. In summary, ZnF-containing and ZnF-lacking NanK enzymes from different Gram-negative pathogenic bacteria are functionally very similar but differ in their metal requirement. Our structural studies unveil the structural modifications in Fn-NanK that compensate the loss of the ZnF motif in comparison to other NanK enzymes.
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Affiliation(s)
- Thanuja Gangi Setty
- Institute for Stem
Cell Science and Regenerative Medicine, GKVK Post, Bangalore, KA 560065, India
- The University of Trans-Disciplinary Health Sciences
& Technology (TDU), Bangalore, KA 560064, India
| | - Arunabha Sarkar
- National Centre for Biological Sciences − TIFR, Bangalore 560065, India
| | - David Coombes
- Biomolecular Interaction Centre and School
of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School
of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Bio21 Molecular Science and Biotechnology
Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ramaswamy Subramanian
- Institute for Stem
Cell Science and Regenerative Medicine, GKVK Post, Bangalore, KA 560065, India
- Department of Biological
Sciences and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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42
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Yang H, Lu L, Chen X. An overview and future prospects of sialic acids. Biotechnol Adv 2020; 46:107678. [PMID: 33285252 DOI: 10.1016/j.biotechadv.2020.107678] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/11/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022]
Abstract
Sialic acids (Sias) are negatively charged functional monosaccharides present in a wide variety of natural sources (plants, animals and microorganisms). Sias play an important role in many life processes, which are widely applied in the medical and food industries as intestinal antibacterials, antivirals, anti-oxidative agents, food ingredients, and detoxification agents. Most Sias are composed of N-acetylneuraminic acid (Neu5Ac, >99%), and Sia is its most commonly used name. In this article, we review Sias in terms of their structures, applications, determination methods, metabolism, and production strategies. In particular, we summarise and compare different production strategies, including extraction from natural sources, chemical synthesis, polymer decomposition, enzymatic synthesis, whole-cell catalysis, and de novo biosynthesis via microorganism fermentation. We also discuss research on their physiological functions and applications, barriers to efficient production, and strategies for overcoming these challenges. We focus on efficient de novo biosynthesis strategies for Neu5Ac via microbial fermentation using novel synthetic biology tools and methods that may be applied in future. This work provides a comprehensive overview of recent advances on Sias, and addresses future challenges regarding their functions, applications, and production.
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Affiliation(s)
- Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Liping Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; College of life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Xianzhong Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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43
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Multi-wavelength analytical ultracentrifugation as a tool to characterise protein-DNA interactions in solution. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:819-827. [PMID: 33219833 DOI: 10.1007/s00249-020-01481-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022]
Abstract
Understanding how proteins interact with DNA, and particularly the stoichiometry of a protein-DNA complex, is key information needed to elucidate the biological role of the interaction, e.g. transcriptional regulation. Here, we present an emerging analytical ultracentrifugation method that features multi-wavelength detection to characterise complex mixtures by deconvoluting the spectral signals of the interaction partners into separate sedimentation profiles. The spectral information obtained in this experiment provides direct access to the molar stoichiometry of the interacting system to complement traditional hydrodynamic information. We demonstrate this approach by characterising a multimeric assembly process between the transcriptional repressor of bacterial sialic acid metabolism, NanR and its DNA-binding sequence. The method introduced in this study can be extended to quantitatively analyse any complex interaction in solution, providing the interaction partners have different optical properties.
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44
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Manjunath L, Coombes D, Davies J, Dhurandhar M, Tiwari VR, Dobson RCJ, Sowdhamini R, Ramaswamy S, Bose S. Quaternary variations in the structural assembly of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella multocida. Proteins 2020; 89:81-93. [PMID: 32865821 DOI: 10.1002/prot.25996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/14/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]
Abstract
N-acetylglucosamine 6-phosphate deacetylase (NagA) catalyzes the conversion of N-acetylglucosamine-6-phosphate to glucosamine-6-phosphate in amino sugar catabolism. This conversion is an essential step in the catabolism of sialic acid in several pathogenic bacteria, including Pasteurella multocida, and thus NagA is identified as a potential drug target. Here, we report the unique structural features of NagA from P. multocida (PmNagA) resolved to 1.95 Å. PmNagA displays an altered quaternary architecture with unique interface interactions compared to its close homolog, the Escherichia coli NagA (EcNagA). We confirmed that the altered quaternary structure is not a crystallographic artifact using single particle electron cryo-microscopy. Analysis of the determined crystal structure reveals a set of hot-spot residues involved in novel interactions at the dimer-dimer interface. PmNagA binds to one Zn2+ ion in the active site and demonstrates kinetic parameters comparable to other bacterial homologs. Kinetic studies reveal that at high substrate concentrations (~10-fold the KM ), the tetrameric PmNagA displays hysteresis similar to its distant neighbor, the dimeric Staphylococcus aureus NagA (SaNagA). Our findings provide key information on structural and functional properties of NagA in P. multocida that could be utilized to design novel antibacterials.
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Affiliation(s)
- Lavanyaa Manjunath
- Institute for Stem Cell Science and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Tiger Circle, Manipal, Karnataka, India
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - James Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mugdha Dhurandhar
- National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India
| | - Vikas R Tiwari
- National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | - R Sowdhamini
- National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India
| | - S Ramaswamy
- Institute for Stem Cell Science and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka, India
- Department of Biological Sciences and Department of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Sucharita Bose
- Institute for Stem Cell Science and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka, India
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Bell A, Severi E, Lee M, Monaco S, Latousakis D, Angulo J, Thomas GH, Naismith JH, Juge N. Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria. J Biol Chem 2020; 295:13724-13736. [PMID: 32669363 PMCID: PMC7535918 DOI: 10.1074/jbc.ra120.014454] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The human gut symbiont Ruminococcus gnavus scavenges host-derived N-acetylneuraminic acid (Neu5Ac) from mucins by converting it to 2,7-anhydro-Neu5Ac. We previously showed that 2,7-anhydro-Neu5Ac is transported into R. gnavus ATCC 29149 before being converted back to Neu5Ac for further metabolic processing. However, the molecular mechanism leading to the conversion of 2,7-anhydro-Neu5Ac to Neu5Ac remained elusive. Using 1D and 2D NMR, we elucidated the multistep enzymatic mechanism of the oxidoreductase (RgNanOx) that leads to the reversible conversion of 2,7-anhydro-Neu5Ac to Neu5Ac through formation of a 4-keto-2-deoxy-2,3-dehydro-N-acetylneuraminic acid intermediate and NAD+ regeneration. The crystal structure of RgNanOx in complex with the NAD+ cofactor showed a protein dimer with a Rossman fold. Guided by the RgNanOx structure, we identified catalytic residues by site-directed mutagenesis. Bioinformatics analyses revealed the presence of RgNanOx homologues across Gram-negative and Gram-positive bacterial species and co-occurrence with sialic acid transporters. We showed by electrospray ionization spray MS that the Escherichia coli homologue YjhC displayed activity against 2,7-anhydro-Neu5Ac and that E. coli could catabolize 2,7-anhydro-Neu5Ac. Differential scanning fluorimetry analyses confirmed the binding of YjhC to the substrates 2,7-anhydro-Neu5Ac and Neu5Ac, as well as to co-factors NAD and NADH. Finally, using E. coli mutants and complementation growth assays, we demonstrated that 2,7-anhydro-Neu5Ac catabolism in E. coli depended on YjhC and on the predicted sialic acid transporter YjhB. These results revealed the molecular mechanisms of 2,7-anhydro-Neu5Ac catabolism across bacterial species and a novel sialic acid transport and catabolism pathway in E. coli.
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Affiliation(s)
- Andrew Bell
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Micah Lee
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Dimitrios Latousakis
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom; Departamento de Química Orgánica, Universidad de Sevilla, Sevilla, Spain; Instituto de Investigaciones Químicas (CSIC-US), Sevilla, Spain
| | - Gavin H Thomas
- Department of Biology, University of York, York, United Kingdom
| | - James H Naismith
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Nathalie Juge
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom.
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Josenhans C, Müthing J, Elling L, Bartfeld S, Schmidt H. How bacterial pathogens of the gastrointestinal tract use the mucosal glyco-code to harness mucus and microbiota: New ways to study an ancient bag of tricks. Int J Med Microbiol 2020; 310:151392. [DOI: 10.1016/j.ijmm.2020.151392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/28/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
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Sialylation and fucosylation modulate inflammasome-activating eIF2 Signaling and microbial translocation during HIV infection. Mucosal Immunol 2020; 13:753-766. [PMID: 32152415 PMCID: PMC7434596 DOI: 10.1038/s41385-020-0279-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 02/04/2023]
Abstract
An emerging paradigm suggests that gut glycosylation is a key force in maintaining the homeostatic relationship between the gut and its microbiota. Nevertheless, it is unclear how gut glycosylation contributes to the HIV-associated microbial translocation and inflammation that persist despite viral suppression and contribute to the development of several comorbidities. We examined terminal ileum, right colon, and sigmoid colon biopsies from HIV-infected virally-suppressed individuals and found that gut glycomic patterns are associated with distinct microbial compositions and differential levels of chronic inflammation and HIV persistence. In particular, high levels of the pro-inflammatory hypo-sialylated T-antigen glycans and low levels of the anti-inflammatory fucosylated glycans were associated with higher abundance of glycan-degrading microbial species (in particular, Bacteroides vulgatus), a less diverse microbiome, higher levels of inflammation, and higher levels of ileum-associated HIV DNA. These findings are linked to the activation of the inflammasome-mediating eIF2 signaling pathway. Our study thus provides the first proof-of-concept evidence that a previously unappreciated factor, gut glycosylation, is a force that may impact the vicious cycle between HIV infection, microbial translocation, and chronic inflammation.
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Bartling B, Rehfeld JS, Boßmann D, de Vries I, Fohrer J, Lammers F, Scheper T, Beutel S. Determination of the Structural Integrity and Stability of Polysialic Acid during Alkaline and Thermal Treatment. Molecules 2019; 25:E165. [PMID: 31906121 PMCID: PMC6982714 DOI: 10.3390/molecules25010165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 11/16/2022] Open
Abstract
Polysialic acid (polySia) is a linear homopolymer of varying chain lengths that exists mostly on the outer cell membrane surface of certain bacteria, such as Escherichia coli (E. coli) K1. PolySia, with an average degree of polymerization of 20 (polySia avDP20), possesses material properties that can be used for therapeutic applications to treat inflammatory neurodegenerative diseases. The fermentation of E. coli K1 enables the large-scale production of endogenous long-chain polySia (DP ≈ 130) (LC polySia), from which polySia avDP20 can be manufactured using thermal hydrolysis. To ensure adequate biopharmaceutical quality of the product, the removal of byproducts and contaminants, such as endotoxins, is essential. Recent studies have revealed that the long-term incubation in alkaline sodium hydroxide (NaOH) solutions reduces the endotoxin content down to 3 EU (endotoxin units) per mg, which is in the range of pharmaceutical applications. In this study, we analyzed interferences in the intramolecular structure of polySia caused by harsh NaOH treatment or thermal hydrolysis. Nuclear magnetic resonance (NMR) spectroscopy revealed that neither the incubation in an alkaline solution nor the thermal hydrolysis induced any chemical modification. In addition, HPLC analysis with a preceding 1,2-diamino-4,5-methylenedioxybenzene (DMB) derivatization demonstrated that the alkaline treatment did not induce any hydrolytic effects to reduce the maximum polymer length and that the controlled thermal hydrolysis reduced the maximum chain length effectively, while cost-effective incubation in alkaline solutions had no adverse effects on LC polySia. Therefore, both methods guarantee the production of high-purity, low-molecular-weight polySia without alterations in the structure, which is a prerequisite for the submission of a marketing authorization application as a medicinal product. However, a specific synthesis of low-molecular-weight polySia with defined chain lengths is only possible to a limited extent.
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Affiliation(s)
- Bastian Bartling
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (B.B.); (J.S.R.); (D.B.); (I.d.V.); (T.S.)
| | - Johanna S. Rehfeld
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (B.B.); (J.S.R.); (D.B.); (I.d.V.); (T.S.)
| | - Daniel Boßmann
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (B.B.); (J.S.R.); (D.B.); (I.d.V.); (T.S.)
| | - Ingo de Vries
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (B.B.); (J.S.R.); (D.B.); (I.d.V.); (T.S.)
| | - Jörg Fohrer
- Institute of Organic Chemistry, Leibniz University Hannover, 30167 Hannover, Germany;
| | - Frank Lammers
- Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65929 Frankfurt am Main, Germany;
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (B.B.); (J.S.R.); (D.B.); (I.d.V.); (T.S.)
| | - Sascha Beutel
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (B.B.); (J.S.R.); (D.B.); (I.d.V.); (T.S.)
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Horne CR, Kind L, Davies JS, Dobson RCJ. On the structure and function of Escherichia coli YjhC: An oxidoreductase involved in bacterial sialic acid metabolism. Proteins 2019; 88:654-668. [PMID: 31697432 DOI: 10.1002/prot.25846] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 10/11/2019] [Accepted: 11/03/2019] [Indexed: 11/06/2022]
Abstract
Human pathogenic and commensal bacteria have evolved the ability to scavenge host-derived sialic acids and subsequently degrade them as a source of nutrition. Expression of the Escherichia coli yjhBC operon is controlled by the repressor protein nanR, which regulates the core machinery responsible for the import and catabolic processing of sialic acid. The role of the yjhBC encoded proteins is not known-here, we demonstrate that the enzyme YjhC is an oxidoreductase/dehydrogenase involved in bacterial sialic acid degradation. First, we demonstrate in vivo using knockout experiments that YjhC is broadly involved in carbohydrate metabolism, including that of N-acetyl-d-glucosamine, N-acetyl-d-galactosamine and N-acetylneuraminic acid. Differential scanning fluorimetry demonstrates that YjhC binds N-acetylneuraminic acid and its lactone variant, along with NAD(H), which is consistent with its role as an oxidoreductase. Next, we solved the crystal structure of YjhC in complex with the NAD(H) cofactor to 1.35 Å resolution. The protein fold belongs to the Gfo/Idh/MocA protein family. The dimeric assembly observed in the crystal form is confirmed through solution studies. Ensemble refinement reveals a flexible loop region that may play a key role during catalysis, providing essential contacts to stabilize the substrate-a unique feature to YjhC among closely related structures. Guided by the structure, in silico docking experiments support the binding of sialic acid and several common derivatives in the binding pocket, which has an overall positive charge distribution. Taken together, our results verify the role of YjhC as a bona fide oxidoreductase/dehydrogenase and provide the first evidence to support its involvement in sialic acid metabolism.
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Affiliation(s)
- Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
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Desialylation by Edwardsiella tarda is the initial step in the regulation of its invasiveness. Biochem J 2019; 476:3183-3196. [DOI: 10.1042/bcj20190367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/03/2019] [Accepted: 10/14/2019] [Indexed: 01/15/2023]
Abstract
AbstractEdwardsiella tarda is a gram-negative bacterium causing significant economic losses to aquaculture. E. tarda possesses NanA sialidase which removes sialic acids from α2–3 sialo-glycoprotein of host cells. However, the relationship between NanA sialidase activity and E. tarda invasiveness remains poorly understood. Furthermore, the pathway of sialic acid metabolism in E. tarda remains to be elucidated. We studied sialidase activity in several E. tarda strains and found that the pathogenic strains exhibited higher sialidase activity and greater up-regulation of the NanA mRNA level than non-pathogenic strain. Pathogenic strains also showed higher rates of infection in GAKS cells, and the infection was drastically suppressed by sialidase inhibitor. Additionally, NanA gene overexpression significantly increased infection and treatment of E. tarda with free sialic acid enhanced the rate of infection in GAKS cells. Sialic acid treatment enhanced mRNA levels of two N-acetylneuraminate lyases and one N-acetylneuraminate cytidylyltransferase. E. tarda uses sialic acid as a carbon source for growth via N-acetylneuraminate lyases. The strains with high N-acetylneuraminate cytidylyltransferase level showed greater sialylation of the lipopolysaccharides and glycoproteins. Our study establishes the significance of desialylation by E. tarda sialidase in the regulation of its invasiveness.
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