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Sevillano E, Lafuente I, Peña N, Cintas LM, Muñoz-Atienza E, Hernández PE, Borrero J. Evaluation of Safety and Probiotic Traits from a Comprehensive Genome-Based In Silico Analysis of Ligilactobacillus salivarius P1CEA3, Isolated from Pigs and Producer of Nisin S. Foods 2023; 13:107. [PMID: 38201135 PMCID: PMC10778751 DOI: 10.3390/foods13010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Ligilactobacillus salivarius is an important member of the porcine gastrointestinal tract (GIT). Some L. salivarius strains are considered to have a beneficial effect on the host by exerting different probiotic properties, including the production of antimicrobial peptides which help maintain a healthy gut microbiota. L. salivarius P1CEA3, a porcine isolated strain, was first selected and identified by its antimicrobial activity against a broad range of pathogenic bacteria due to the production of the novel bacteriocin nisin S. The assembled L. salivarius P1CEA3 genome includes a circular chromosome, a megaplasmid (pMP1CEA3) encoding the nisin S gene cluster, and two small plasmids. A comprehensive genome-based in silico analysis of the L. salivarius P1CEA3 genome reveals the presence of genes related to probiotic features such as bacteriocin synthesis, regulation and production, adhesion and aggregation, the production of lactic acid, amino acids metabolism, vitamin biosynthesis, and tolerance to temperature, acid, bile salts and osmotic and oxidative stress. Furthermore, the strain is absent of risk-related genes for acquired antibiotic resistance traits, virulence factors, toxic metabolites and detrimental metabolic or enzymatic activities. Resistance to common antibiotics and gelatinase and hemolytic activities have been discarded by in vitro experiments. This study identifies several probiotic and safety traits of L. salivarius P1CEA3 and suggests its potential as a promising probiotic in swine production.
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Affiliation(s)
| | | | | | | | | | | | - Juan Borrero
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Spain; (E.S.); (I.L.); (N.P.); (L.M.C.); (E.M.-A.); (P.E.H.)
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2
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Wu F, Xie X, Du T, Jiang X, Miao W, Wang T. Lactococcus lactis, a bacterium with probiotic functions and pathogenicity. World J Microbiol Biotechnol 2023; 39:325. [PMID: 37776350 DOI: 10.1007/s11274-023-03771-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/16/2023] [Indexed: 10/02/2023]
Abstract
Lactococcus lactis (L. lactis) is the primary organism for lactic acid bacteria (LAB) and is a globally recognized safe microorganism for the regulation of the intestinal micro-ecological balance of animals and improving the immune performance of the host. L. lactis is known to play a commercially important role in feed fortification, milk fermentation, and vaccine production, but pathogenic L. lactis has been isolated from many clinical cases in recent years, such as the brain of silver carp with Lactococcosis, the liver and spleen of diseased waterfowl, milk samples and padding materials with cow mastitis, and blood and urine from human patients with endocarditis. In dairy farming, where L. lactis has been used as a probiotic in the past, however, some studies have found that L. lactis can cause mastitis in cows, but the lack of understanding of the pathogenesis of mastitis in cows caused by L. lactis has become a new problem. The main objective of this review is to analyze the increasingly serious clinical mastitis caused by L. lactis and combined with the wide application of L. lactis as probiotics, to comprehensively discuss the characteristics and diversity of L. lactis.
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Affiliation(s)
- Fan Wu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xinmei Xie
- Elanco (Shanghai)Animal Health Co, Ltd, No.1, Field Middle Road, Wusi Farm, Fengxian District, Shanghai, China
| | - Tao Du
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaodan Jiang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wei Miao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Tiancheng Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
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3
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Bank NC, Singh V, Grubb B, McCourt B, Burberry A, Roberts KD, Rodriguez-Palacios A. The basis of antigenic operon fragmentation in Bacteroidota and commensalism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543472. [PMID: 37398285 PMCID: PMC10312583 DOI: 10.1101/2023.06.02.543472] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The causes for variability of pro-inflammatory surface antigens that affect gut commensal/opportunistic dualism within the phylum Bacteroidota remain unclear (1, 2). Using the classical lipopolysaccharide/O-antigen 'rfb operon' in Enterobacteriaceae as a surface antigen model (5-gene-cluster rfbABCDX), and a recent rfbA-typing strategy for strain classification (3), we characterized the architecture/conservancy of the entire rfb operon in Bacteroidota. Analyzing complete genomes, we discovered that most Bacteroidota have the rfb operon fragmented into non-random gene-singlets and/or doublets/triplets, termed 'minioperons'. To reflect global operon integrity, duplication, and fragmentation principles, we propose a five-category (infra/supernumerary) cataloguing system and a Global Operon Profiling System for bacteria. Mechanistically, genomic sequence analyses revealed that operon fragmentation is driven by intra-operon insertions of predominantly Bacteroides-DNA (thetaiotaomicron/fragilis) and likely natural selection in specific micro-niches. Bacteroides-insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain why Bacteroidota have fewer KEGG-pathways despite large genomes (4). DNA insertions overrepresenting DNA-exchange-avid species, impact functional metagenomics by inflating gene-based pathway inference and overestimating 'extra-species' abundance. Using bacteria from inflammatory gut-wall cavernous micro-tracts (CavFT) in Crohn's Disease (5), we illustrate that bacteria with supernumerary-fragmented operons cannot produce O-antigen, and that commensal/CavFT Bacteroidota stimulate macrophages with lower potency than Enterobacteriaceae, and do not induce peritonitis in mice. The impact of 'foreign-DNA' insertions on pro-inflammatory operons, metagenomics, and commensalism offers potential for novel diagnostics and therapeutics.
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Affiliation(s)
- Nicholas C Bank
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Vaidhvi Singh
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Brandon Grubb
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Blake McCourt
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Aaron Burberry
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kyle D Roberts
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, USA
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, USA
- University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
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4
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Davray D, Bawane H, Kulkarni R. Non-redundant nature of Lactiplantibacillus plantarum plasmidome revealed by comparative genomic analysis of 105 strains. Food Microbiol 2023; 109:104153. [DOI: 10.1016/j.fm.2022.104153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
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Wang Z, Zeng Y, Cheng K, Cai Z, Zhou J. The quorum sensing system of Novosphingobium sp. ERN07 regulates aggregate formation that promotes cyanobacterial growth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158354. [PMID: 36041622 DOI: 10.1016/j.scitotenv.2022.158354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/03/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Microbial aggregates play key roles in cyanobacterial blooms. Being a bacterial communication mechanism, quorum sensing (QS) synchronizes gene expression in a density-dependent manner and regulates bacterial physiological behavior. However, the regulatory role of QS in the formation of cyanobacteria-associated bacterial aggregates remains poorly understood. Here, we present insight into the role of QS in regulating bacterial aggregate formation in a representative bacterial strain, Novosphingobium sp. ERN07, which was isolated from Microcystis blooms in Lake Taihu. A biosensor assay showed that ERN07 exhibits significant AHL-producing capacity. Biochemical and microscopic analysis revealed that this strain possesses the ability to form aggregated communities. Gene knockout experiments indicated that the AHL-mediated QS system positively regulates bacterial aggregation. The aggregated communities possess the ability to enhance the production of extracellular polymeric substances (EPS), alter EPS composition ratios, and affect biofilm formation. The addition of aggregated substances also has a significant growth-promoting effect on M. aeruginosa. Transcriptomic analysis revealed that the aggregated substances positively regulate photosynthetic efficiency and energy metabolism of M. aeruginosa. These findings show that QS can mediate the aggregation phenotype and associated substrate spectrum composition, contributing to a better understanding of microalgal-bacterial interactions and mechanisms of Microcystis bloom maintenance in the natural environment.
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Affiliation(s)
- Zhaoyi Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Yanhua Zeng
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou 570228, Hainan Province, PR China
| | - Keke Cheng
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Zhonghua Cai
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Jin Zhou
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China.
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Nagarajan D, Chen CY, Ariyadasa TU, Lee DJ, Chang JS. Macroalgal biomass as a potential resource for lactic acid fermentation. CHEMOSPHERE 2022; 309:136694. [PMID: 36206920 DOI: 10.1016/j.chemosphere.2022.136694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Lactic acid is an essential platform chemical with various applications in the chemicals, food, pharmaceutical, and cosmetic industries. Currently, the demand for lactic acid is driven by the role of lactic acid as the starting material for the production of bioplastic polylactide. Microbial fermentation for lactic acid production is favored due to the production of enantiomerically pure lactic acid required for polylactide synthesis, as opposed to the racemic mixture obtained via chemical synthesis. The utilization of first-generation feedstock for commercial lactic acid production is challenged by feedstock costs and sustainability issues. Macroalgae are photosynthetic benthic aquatic plants that contribute tremendously towards carbon capture with subsequent carbon-rich biomass production. Macroalgae are commercially cultivated to extract hydrocolloids, and recent studies have focused on applying biomass as a fermentation feedstock. This review provides comprehensive information on the design and development of sustainable and cost-effective, algae-based lactic acid production. The central carbon regulation in lactic acid bacteria and the metabolism of seaweed-derived sugars are described. An exhaustive compilation of lactic acid fermentation of macroalgae hydrolysates revealed that lactic acid bacteria can effectively ferment the mixture of sugars present in the hydrolysate with comparable yields. The environmental impacts and economic prospects of macroalgal lactic acid are analyzed. Valorization of the vast amounts of spent macroalgal biomass residue post hydrocolloid extraction in a biorefinery is a viable strategy for cost-effective lactic acid production.
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Affiliation(s)
- Dillirani Nagarajan
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan.
| | - Chun-Yen Chen
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Research Center for Circular Economy, National Cheng Kung University, Tainan, Taiwan
| | - Thilini U Ariyadasa
- Department of Chemical and Process Engineering, Faculty of Engineering, University of Moratuwa, Moratuwa, 10400, Sri Lanka
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung, 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, 407, Taiwan; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, 32003, Taiwan.
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7
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Hu TG, Zhu WL, Yu YS, Zou B, Xu YJ, Xiao GS, Wu JJ. The variation on structure and immunomodulatory activity of polysaccharide during the longan pulp fermentation. Int J Biol Macromol 2022; 222:599-609. [PMID: 36170929 DOI: 10.1016/j.ijbiomac.2022.09.195] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/19/2022]
Abstract
In the current study, the effects of fermentation manners on the structure and immunomodulatory activity of polysaccharide in longan wine or vinegar were investigated. Compared to longan polysaccharide (CP1), polysaccharide in longan wine (CP2) or vinegar (CP3 and CP4) had smaller molecular weights, and was consisted of more mannose, arabinose, rhamnose, galactose and less glucose. After purification, the major fraction (P1-P4) was obtained from CP1-CP4, respectively. The structures and immunoregulatory activities of P1-P4 were characterized. Fermentation and purification were favorable to increase the immunoregulatory activities of P2-P4, which were contributed to their different structural features. The structure-activity relationship analysis indicated that molecular weight, mannose, rhamnose, glucuronic acid, glucose and arabinose were significantly associated with the cytokines secretion. Compared with other polysaccharides, P3 displayed better immunomodulatory activity due to its lower molecular weight, lower contents of rhamnose and glucose, and higher levels of mannose and arabinose by activating MAPK and PI3K/Akt signaling pathways.
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Affiliation(s)
- Teng-Gen Hu
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture/Guangdong Key Laboratory of Agricultural Products Processing, China; Huagongliya (Foshan) Technology Industry Co., Ltd, China
| | - Wei-Lin Zhu
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture/Guangdong Key Laboratory of Agricultural Products Processing, China
| | - Yuan-Shan Yu
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture/Guangdong Key Laboratory of Agricultural Products Processing, China; Huagongliya (Foshan) Technology Industry Co., Ltd, China.
| | - Bo Zou
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture/Guangdong Key Laboratory of Agricultural Products Processing, China; Huagongliya (Foshan) Technology Industry Co., Ltd, China
| | - Yu-Juan Xu
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture/Guangdong Key Laboratory of Agricultural Products Processing, China
| | | | - Ji-Jun Wu
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture/Guangdong Key Laboratory of Agricultural Products Processing, China.
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8
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Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways. Microorganisms 2022; 10:microorganisms10081637. [PMID: 36014054 PMCID: PMC9415760 DOI: 10.3390/microorganisms10081637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.
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Forcone K, Coutinho FH, Cavalcanti GS, Silveira CB. Prophage Genomics and Ecology in the Family Rhodobacteraceae. Microorganisms 2021; 9:microorganisms9061115. [PMID: 34064105 PMCID: PMC8224337 DOI: 10.3390/microorganisms9061115] [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] [Received: 04/10/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.
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Affiliation(s)
- Kathryn Forcone
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Felipe H. Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, Aptdo. 18, Ctra. Alicante-Valencia, s/n, 03550 San Juan de Alicante, Spain;
| | - Giselle S. Cavalcanti
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Cynthia B. Silveira
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
- Correspondence:
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Ranjan M, Khokhani D, Nayaka S, Srivastava S, Keyser ZP, Ranjan A. Genomic diversity and organization of complex polysaccharide biosynthesis clusters in the genus Dickeya. PLoS One 2021; 16:e0245727. [PMID: 33571209 PMCID: PMC7877592 DOI: 10.1371/journal.pone.0245727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 01/07/2021] [Indexed: 11/18/2022] Open
Abstract
The pectinolytic genus Dickeya (formerly Erwinia chrysanthemi) comprises numerous pathogenic species which cause diseases in various crops and ornamental plants across the globe. Their pathogenicity is governed by complex multi-factorial processes of adaptive virulence gene regulation. Extracellular polysaccharides and lipopolysaccharides present on bacterial envelope surface play a significant role in the virulence of phytopathogenic bacteria. However, very little is known about the genomic location, diversity, and organization of the polysaccharide and lipopolysaccharide biosynthetic gene clusters in Dickeya. In the present study, we report the diversity and structural organization of the group 4 capsule (G4C)/O-antigen capsule, putative O-antigen lipopolysaccharide, enterobacterial common antigen, and core lipopolysaccharide biosynthesis clusters from 54 Dickeya strains. The presence of these clusters suggests that Dickeya has both capsule and lipopolysaccharide carrying O-antigen to their external surface. These gene clusters are key regulatory components in the composition and structure of the outer surface of Dickeya. The O-antigen capsule/group 4 capsule (G4C) coding region shows a variation in gene content and organization. Based on nucleotide sequence homology in these Dickeya strains, two distinct groups, G4C group I and G4C group II, exist. However, comparatively less variation is observed in the putative O-antigen lipopolysaccharide cluster in Dickeya spp. except for in Dickeya zeae. Also, enterobacterial common antigen and core lipopolysaccharide biosynthesis clusters are present mostly as conserved genomic regions. The variation in the O-antigen capsule and putative O-antigen lipopolysaccharide coding region in relation to their phylogeny suggests a role of multiple horizontal gene transfer (HGT) events. These multiple HGT processes might have been manifested into the current heterogeneity of O-antigen capsules and O-antigen lipopolysaccharides in Dickeya strains during its evolution.
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Affiliation(s)
- Manish Ranjan
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, Uttar Pradesh, India
| | - Devanshi Khokhani
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Plant Pathology, University of Minnesota—Twin Cities, St. Paul, Minnesota, United States of America
| | - Sanjeeva Nayaka
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, Uttar Pradesh, India
| | - Suchi Srivastava
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, Uttar Pradesh, India
| | - Zachary P. Keyser
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ashish Ranjan
- Department of Plant Pathology, University of Minnesota—Twin Cities, St. Paul, Minnesota, United States of America
- Department of Plant Sciences (SLS), University of Hyderabad, Hyderabad, India
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11
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Wu X, Zhou H, Li L, Wang E, Zhou X, Gu Y, Wu X, Shen L, Zeng W. Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability. Microorganisms 2020; 8:microorganisms8050716. [PMID: 32408484 PMCID: PMC7284689 DOI: 10.3390/microorganisms8050716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 11/26/2022] Open
Abstract
Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Han Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Enhui Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Xiangyu Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Yichao Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Xiaoyan Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
- Correspondence: ; Tel.: +86-0731-88877472
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12
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Pereira SB, Santos M, Leite JP, Flores C, Eisfeld C, Büttel Z, Mota R, Rossi F, De Philippis R, Gales L, Morais‐Cabral JH, Tamagnini P. The role of the tyrosine kinase Wzc (Sll0923) and the phosphatase Wzb (Slr0328) in the production of extracellular polymeric substances (EPS) by Synechocystis PCC 6803. Microbiologyopen 2019; 8:e00753. [PMID: 30675753 PMCID: PMC6562117 DOI: 10.1002/mbo3.753] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/10/2022] Open
Abstract
Many cyanobacteria produce extracellular polymeric substances (EPS) mainly composed of heteropolysaccharides with unique characteristics that make them suitable for biotechnological applications. However, manipulation/optimization of EPS biosynthesis/characteristics is hindered by a poor understanding of the production pathways and the differences between bacterial species. In this work, genes putatively related to different pathways of cyanobacterial EPS polymerization, assembly, and export were targeted for deletion or truncation in the unicellular Synechocystis sp. PCC 6803. No evident phenotypic changes were observed for some mutants in genes occurring in multiple copies in Synechocystis genome, namely ∆wzy (∆sll0737), ∆wzx (∆sll5049), ∆kpsM (∆slr2107), and ∆kpsM∆wzy (∆slr2107∆sll0737), strongly suggesting functional redundancy. In contrast, Δwzc (Δsll0923) and Δwzb (Δslr0328) influenced both the amount and composition of the EPS, establishing that Wzc participates in the production of capsular (CPS) and released (RPS) polysaccharides, and Wzb affects RPS production. The structure of Wzb was solved (2.28 Å), revealing structural differences relative to other phosphatases involved in EPS production and suggesting a different substrate recognition mechanism. In addition, Wzc showed the ATPase and autokinase activities typical of bacterial tyrosine kinases. Most importantly, Wzb was able to dephosphorylate Wzc in vitro, suggesting that tyrosine phosphorylation/dephosphorylation plays a role in cyanobacterial EPS production.
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Affiliation(s)
- Sara B. Pereira
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Marina Santos
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - José P. Leite
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - Carlos Flores
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - Carina Eisfeld
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Present address:
Department of Water ManagementDelft University of TechnologyDelftThe Netherlands
| | - Zsófia Büttel
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Present address:
Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Rita Mota
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Federico Rossi
- Department of Agrifood Production and Environmental SciencesUniversity of FlorenceFlorenceItaly
| | - Roberto De Philippis
- Department of Agrifood Production and Environmental SciencesUniversity of FlorenceFlorenceItaly
| | - Luís Gales
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - João H. Morais‐Cabral
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Paula Tamagnini
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Faculdade de Ciências, Departamento de BiologiaUniversidade do PortoPortoPortugal
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Siciliano RA, Pannella G, Lippolis R, Ricciardi A, Mazzeo MF, Zotta T. Impact of aerobic and respirative life-style on Lactobacillus casei N87 proteome. Int J Food Microbiol 2019; 298:51-62. [PMID: 30925356 DOI: 10.1016/j.ijfoodmicro.2019.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 01/10/2019] [Accepted: 03/10/2019] [Indexed: 12/27/2022]
Abstract
Lactic acid bacteria (LAB) are used as starter, adjunct and/or probiotic cultures in fermented foods. Several species are recognized as oxygen-tolerant anaerobes, and aerobic and respiratory cultivations may provide them with physiological and technological benefits. In this light, mechanisms involved in the adaptation to aerobic and respiratory (supplementation with heme and menaquinone) growth conditions of the O2-tolerant strain Lactobacillus casei N87 were investigated by proteomics. In fact, in this bacterial strain, respiration induced an increase in biomass yield and robustness to oxidative, long-term starvation and freeze-drying stresses, while high concentrations of dissolved O2 (dO2 60%) negatively affected its growth and cell survival. Proteomic results well paralleled with physiological and metabolic features and clearly showed that aerobic life-style led to a higher abundance of several proteins involved in carbohydrate metabolism and stress response mechanisms and, concurrently, impaired the biosynthesis of proteins involved in nucleic acid formation and translation processes, thus providing evidence at molecular level of the significant damage to L.casei N87 fitness. On the contrary, the activation of respiratory pathways due to heme and menaquinone supplementation, led to a decreased amount of chaperones and other stress related proteins. These findings confirmed that respiration reduced oxidative stress condition, allowing to positively modulate the central carbohydrate and energy metabolism and improve growth and stress tolerance features. Results of this study could be potentially functional to develop competitive adjunct and probiotic cultures effectively focused on the improvement of quality of fermented foods and the promotion of human health.
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Affiliation(s)
- Rosa Anna Siciliano
- Institute of Food Sciences, National Research Council (CNR-ISA), Avellino, Italy
| | - Gianfranco Pannella
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Rosa Lippolis
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), Bari, Italy
| | - Annamaria Ricciardi
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | | | - Teresa Zotta
- Institute of Food Sciences, National Research Council (CNR-ISA), Avellino, Italy
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14
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Wels M, Siezen R, van Hijum S, Kelly WJ, Bachmann H. Comparative Genome Analysis of Lactococcus lactis Indicates Niche Adaptation and Resolves Genotype/Phenotype Disparity. Front Microbiol 2019; 10:4. [PMID: 30766512 PMCID: PMC6365430 DOI: 10.3389/fmicb.2019.00004] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/07/2019] [Indexed: 01/21/2023] Open
Abstract
Lactococcus lactis is one of the most important micro-organisms in the dairy industry for the fermentation of cheese and buttermilk. Besides the conversion of lactose to lactate it is responsible for product properties such as flavor and texture, which are determined by volatile metabolites, proteolytic activity and exopolysaccharide production. While the species Lactococcus lactis consists of the two subspecies lactis and cremoris their taxonomic position is confused by a group of strains that, despite of a cremoris genotype, display a lactis phenotype. Here we compared and analyzed the (draft) genomes of 43 L. lactis strains, of which 19 are of dairy and 24 are of non-dairy origin. Machine-learning algorithms facilitated the identification of orthologous groups of protein sequences (OGs) that are predictors for either the taxonomic position or the source of isolation. This allowed the unambiguous categorization of the genotype/phenotype disparity of ssp. lactis and ssp. cremoris strains. A detailed analysis of phenotypic properties including plasmid-encoded genes indicates evolutionary changes during niche adaptations. The results are consistent with the hypothesis that dairy isolates evolved from plant isolates. The analysis further suggests that genomes of cremoris phenotype strains are so eroded that they are restricted to a dairy environment. Overall the genome comparison of a diverse set of strains allowed the identification of niche and subspecies specific genes. This explains evolutionary relationships and will aid the identification and selection of industrial starter cultures.
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Affiliation(s)
- Michiel Wels
- NIZO Food Research B.V., Ede, Netherlands.,TI Food and Nutrition, Wageningen, Netherlands
| | - Roland Siezen
- TI Food and Nutrition, Wageningen, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Microbial Bioinformatics, Ede, Netherlands
| | - Sacha van Hijum
- NIZO Food Research B.V., Ede, Netherlands.,TI Food and Nutrition, Wageningen, Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Herwig Bachmann
- NIZO Food Research B.V., Ede, Netherlands.,TI Food and Nutrition, Wageningen, Netherlands.,Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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15
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Škraban J, Cleenwerck I, Vandamme P, Fanedl L, Trček J. Genome sequences and description of novel exopolysaccharides producing species Komagataeibacter pomaceti sp. nov. and reclassification of Komagataeibacter kombuchae (Dutta and Gachhui 2007) Yamada et al., 2013 as a later heterotypic synonym of Komagataeibacter hansenii (Gosselé et al. 1983) Yamada et al., 2013. Syst Appl Microbiol 2018; 41:581-592. [PMID: 30177404 DOI: 10.1016/j.syapm.2018.08.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 11/30/2022]
Abstract
Strains T5K1 and AV446 isolated from apple cider vinegars during a submerged vinegar production in two separate vinegar facilities showed 94% 16S rRNA gene similarity to its closest neighbors Komagataeibacter maltaceti LMG 1529T and Gluconacetobacter entanii LTH 4560T. Further phylogenetic and phenotypic characterizations indicated that the isolates belonged to a novel species of the Komagataeibacter genus. Comparison based on 16S-23S rRNA gene ITS sequences and concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, grouped both strains to a single phylogenetic cluster well separated from the other species of the Komagataeibacter genus. Average nucleotide identity of T5K1 and AV446 draft genome sequences compared to other Komagataeibacter type strains was below 94% and at the same time, in-silico DNA-DNA hybridization was below 70%. Both strains on the other hand showed approximately 98% (average nucleotide identity) and 87% (in silico DNA-DNA hybridization) similarity to each other. Strains T5K1 and AV446 can be differentiated from other Komagataeibacter type strains based on their ability to produce 2-keto-d-gluconic acid and at the same time inability to produce 5-keto-d-gluconic acid. Furthermore, strains of the new species do not grow on Asai medium supplemented with d-glucose or d-mannitol. The growth is also absent (T5K1) or weak (AV446) on Hoyer-Frateur medium supplemented with afore mentioned sugars. Both strains produce cellulose. In addition, draft genome analysis revealed that strains T5K1 and AV446 possess genes involved in the synthesis of acetan-like extracellular heteropolysaccharide. We propose the name Komagataeibacter pomaceti sp. nov. for the new species with LMG 30150T [=CCM 8723T=ZIM B1029T] as the type strain. Data collected in this study and in a previous study also revealed that Komagataeibacter kombuchae is a later heterotypic synonym of Komagataeibacter hansenii.
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Affiliation(s)
- Jure Škraban
- University of Maribor, Faculty of Natural Sciences and Mathematics, Department of Biology, Maribor, Slovenia
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Faculty of Sciences, Ghent, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Faculty of Sciences, Ghent, Belgium
| | - Lijana Fanedl
- University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Janja Trček
- University of Maribor, Faculty of Natural Sciences and Mathematics, Department of Biology, Maribor, Slovenia; University of Maribor, Faculty of Chemistry and Chemical Engineering, Maribor, Slovenia.
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16
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Comparative genomic and metabolic analysis of three Lactobacillus paracasei cheese isolates reveals considerable genomic differences in strains from the same niche. BMC Genomics 2018; 19:205. [PMID: 29554864 PMCID: PMC5859408 DOI: 10.1186/s12864-018-4586-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/08/2018] [Indexed: 11/10/2022] Open
Abstract
Background Strains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals. Their adaptation to various niches is correlated to intra-species diversity at the genomic and metabolic level. In this study, we compared the genome sequences of three L. paracasei strains isolated from mature Cheddar cheeses, two of which (DPC4206 and DPC4536) shared the same genomic fingerprint by PFGE, but demonstrated varying metabolic capabilities. Results Genome sizes varied from 2.9 Mbp for DPC2071, to 3.09 Mbp for DPC4206 and 3.08 Mpb for DPC4536. The presence of plasmids was a distinguishing feature between the strains with strain DPC2071 possessing an unusually high number of plasmids (up to 11), while DPC4206 had one plasmid and DPC4536 harboured no plasmids. Each of the strains possessed specific genes not present in the other two analysed strains. The three strains differed in their abundance of sugar-converting genes, and in the types of sugars that could be used as energy sources. Genes involved in the metabolism of sugars not usually connected with the dairy niche, such as myo-inositol and pullulan were also detected, but strains did not utilise these sugars. The genetic content of the three strains differed in regard to specific genes for arginine and sulfur-containing amino acid metabolism and genes contributing to resistance to heavy metal ions. In addition, variability in the presence of phage remnants and phage protection systems was evident. Conclusions The findings presented in this study confirm a considerable level of heterogeneity of Lactobacillus paracasei strains, even between strains isolated from the same niche.
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Abstract
Glycosylation is a universal strategy to posttranslationally modify proteins. The recently discovered arginine rhamnosylation activates the polyproline-specific bacterial translation elongation factor EF-P. EF-P is rhamnosylated on arginine 32 by the glycosyltransferase EarP. However, the enzymatic mechanism remains elusive. In the present study, we solved the crystal structure of EarP from Pseudomonas putida. The enzyme is composed of two opposing domains with Rossmann folds, thus constituting a B pattern-type glycosyltransferase (GT-B). While dTDP-β-l-rhamnose is located within a highly conserved pocket of the C-domain, EarP recognizes the KOW-like N-domain of EF-P. Based on our data, we propose a structural model for arginine glycosylation by EarP. As EarP is essential for pathogenicity in P. aeruginosa, our study provides the basis for targeted inhibitor design. The structural and biochemical characterization of the EF-P-specific rhamnosyltransferase EarP not only provides the first molecular insights into arginine glycosylation but also lays the basis for targeted-inhibitor design against Pseudomonas aeruginosa infection.
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18
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Zeidan AA, Poulsen VK, Janzen T, Buldo P, Derkx PMF, Øregaard G, Neves AR. Polysaccharide production by lactic acid bacteria: from genes to industrial applications. FEMS Microbiol Rev 2017; 41:S168-S200. [DOI: 10.1093/femsre/fux017] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/29/2017] [Indexed: 01/14/2023] Open
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19
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Li S, Wang H, Ma J, Gu G, Chen Z, Guo Z. One-pot four-enzyme synthesis of thymidinediphosphate-l-rhamnose. Chem Commun (Camb) 2016; 52:13995-13998. [DOI: 10.1039/c6cc08366h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A concise and effective one-pot four-enzyme synthesis of dTDP-Rha, the substrate of rhamnosyltransferases, is described.
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Affiliation(s)
- Siqiang Li
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology
- Shandong University
- Jinan 250100
- China
| | - Hong Wang
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology
- Shandong University
- Jinan 250100
- China
| | - Juncai Ma
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology
- Shandong University
- Jinan 250100
- China
| | - Guofeng Gu
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology
- Shandong University
- Jinan 250100
- China
| | - Zonggang Chen
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology
- Shandong University
- Jinan 250100
- China
| | - Zhongwu Guo
- Department of Chemistry
- University of Florida
- Gainesville
- USA
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20
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Ellegaard KM, Tamarit D, Javelind E, Olofsson TC, Andersson SGE, Vásquez A. Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut. BMC Genomics 2015; 16:284. [PMID: 25880915 PMCID: PMC4449606 DOI: 10.1186/s12864-015-1476-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 03/23/2015] [Indexed: 01/09/2023] Open
Abstract
Background In the honeybee Apis mellifera, the bacterial gut community is consistently colonized by eight distinct phylotypes of bacteria. Managed bee colonies are of considerable economic interest and it is therefore important to elucidate the diversity and role of this microbiota in the honeybee. In this study, we have sequenced the genomes of eleven strains of lactobacilli and bifidobacteria isolated from the honey crop of the honeybee A. mellifera. Results Single gene phylogenies confirmed that the isolated strains represent the diversity of lactobacilli and bifidobacteria in the gut, as previously identified by 16S rRNA gene sequencing. Core genome phylogenies of the lactobacilli and bifidobacteria further indicated extensive divergence between strains classified as the same phylotype. Phylotype-specific protein families included unique surface proteins. Within phylotypes, we found a remarkably high level of gene content diversity. Carbohydrate metabolism and transport functions contributed up to 45% of the accessory genes, with some genomes having a higher content of genes encoding phosphotransferase systems for the uptake of carbohydrates than any previously sequenced genome. These genes were often located in highly variable genomic segments that also contained genes for enzymes involved in the degradation and modification of sugar residues. Strain-specific gene clusters for the biosynthesis of exopolysaccharides were identified in two phylotypes. The dynamics of these segments contrasted with low recombination frequencies and conserved gene order structures for the core genes. Hits for CRISPR spacers were almost exclusively found within phylotypes, suggesting that the phylotypes are associated with distinct phage populations. Conclusions The honeybee gut microbiota has been described as consisting of a modest number of phylotypes; however, the genomes sequenced in the current study demonstrated a very high level of gene content diversity within all three described phylotypes of lactobacilli and bifidobacteria, particularly in terms of metabolic functions and surface structures, where many features were strain-specific. Together, these results indicate niche differentiation within phylotypes, suggesting that the honeybee gut microbiota is more complex than previously thought. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1476-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kirsten M Ellegaard
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Daniel Tamarit
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Emelie Javelind
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Tobias C Olofsson
- Department of Laboratory Medicine, Medical Microbiology, Lund University, Medicon Village, Scheelevägen 2, SE-223 62, Lund, Sweden.
| | - Siv G E Andersson
- Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Husargatan 3, SE-751 24, Uppsala, Sweden.
| | - Alejandra Vásquez
- Department of Laboratory Medicine, Medical Microbiology, Lund University, Medicon Village, Scheelevägen 2, SE-223 62, Lund, Sweden.
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Casey A, Fox EM, Schmitz-Esser S, Coffey A, McAuliffe O, Jordan K. Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility. Front Microbiol 2014; 5:68. [PMID: 24616718 PMCID: PMC3937556 DOI: 10.3389/fmicb.2014.00068] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/07/2014] [Indexed: 12/02/2022] Open
Abstract
Listeria monocytogenes is a virulent food-borne pathogen most often associated with the consumption of “ready-to-eat” foods. The organism is a common contaminant of food processing plants where it may persist for extended periods of time. A commonly used approach for the control of Listeria monocytogenes in the processing environment is the application of biocides such as quaternary ammonium compounds. In this study, the transcriptomic response of a persistent strain of L. monocytogenes (strain 6179) on exposure to a sub-lethal concentration of the quaternary ammonium compound benzethonium chloride (BZT) was assessed. Using RNA-Seq, gene expression levels were quantified by sequencing the transcriptome of L. monocytogenes 6179 in the presence (4 ppm) and absence of BZT, and mapping each data set to the sequenced genome of strain 6179. Hundreds of differentially expressed genes were identified, and subsequent analysis suggested that many biological processes such as peptidoglycan biosynthesis, bacterial chemotaxis and motility, and carbohydrate uptake, were involved in the response of L. monocyotogenes to the presence of BZT. The information generated in this study further contributes to our understanding of the response of bacteria to environmental stress. In addition, this study demonstrates the importance of using the bacterium's own genome as a reference when analysing RNA-Seq data.
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Affiliation(s)
- Aidan Casey
- Teagasc Food Research Centre Fermoy, Ireland
| | - Edward M Fox
- CSIRO Animal Food and Health Sciences Werribee, VIC, Australia
| | - Stephan Schmitz-Esser
- Department of Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, University of Veterinary Medicine Vienna, Austria
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology Cork, Ireland
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From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria. Biotechnol Adv 2013; 31:764-88. [DOI: 10.1016/j.biotechadv.2013.03.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 03/28/2013] [Accepted: 03/31/2013] [Indexed: 11/21/2022]
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Mak TN, Schmid M, Brzuszkiewicz E, Zeng G, Meyer R, Sfanos KS, Brinkmann V, Meyer TF, Brüggemann H. Comparative genomics reveals distinct host-interacting traits of three major human-associated propionibacteria. BMC Genomics 2013; 14:640. [PMID: 24053623 PMCID: PMC3848858 DOI: 10.1186/1471-2164-14-640] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/17/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Propionibacteria are part of the human microbiota. Many studies have addressed the predominant colonizer of sebaceous follicles of the skin, Propionibacterium acnes, and investigated its association with the skin disorder acne vulgaris, and lately with prostate cancer. Much less is known about two other propionibacterial species frequently found on human tissue sites, Propionibacterium granulosum and Propionibacterium avidum. Here we analyzed two and three genomes of P. granulosum and P. avidum, respectively, and compared them to two genomes of P. acnes; we further highlight differences among the three cutaneous species with proteomic and microscopy approaches. RESULTS Electron and atomic force microscopy revealed an exopolysaccharide (EPS)-like structure surrounding P. avidum cells, that is absent in P. acnes and P. granulosum. In contrast, P. granulosum possesses pili-like appendices, which was confirmed by surface proteome analysis. The corresponding genes were identified; they are clustered with genes encoding sortases. Both, P. granulosum and P. avidum lack surface or secreted proteins for predicted host-interacting factors of P. acnes, including several CAMP factors, sialidases, dermatan-sulphate adhesins, hyaluronidase and a SH3 domain-containing lipoprotein; accordingly, only P. acnes exhibits neuraminidase and hyaluronidase activities. These functions are encoded on previously unrecognized island-like regions in the genome of P. acnes. CONCLUSIONS Despite their omnipresence on human skin little is known about the role of cutaneous propionibacteria. All three species are associated with a variety of diseases, including postoperative and device-related abscesses and infections. We showed that the three organisms have evolved distinct features to interact with their human host. Whereas P. avidum and P. granulosum produce an EPS-like surface structure and pili-like appendices, respectively, P. acnes possesses a number of unique surface-exposed proteins with host-interacting properties. The different surface properties of the three cutaneous propionibacteria are likely to determine their colonizing ability and pathogenic potential on the skin and at non-skin sites.
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Affiliation(s)
- Tim N Mak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
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Hamon E, Horvatovich P, Bisch M, Bringel F, Marchioni E, Aoudé-Werner D, Ennahar S. Investigation of Biomarkers of Bile Tolerance in Lactobacillus casei Using Comparative Proteomics. J Proteome Res 2011; 11:109-18. [DOI: 10.1021/pr200828t] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Erwann Hamon
- Equipe de Chimie Analytique des Molécules Bio-Actives, IPHC-DSA, Université de Strasbourg, CNRS, 67400, Illkirch-Graffenstaden, France
- Aérial, Parc d’Innovation, 67400 Illkirch-Graffenstaden, France
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Centre for Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Magali Bisch
- Equipe de Chimie Analytique des Molécules Bio-Actives, IPHC-DSA, Université de Strasbourg, CNRS, 67400, Illkirch-Graffenstaden, France
| | - Françoise Bringel
- Laboratoire de Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, CNRS, 67083 Strasbourg, France
| | - Eric Marchioni
- Equipe de Chimie Analytique des Molécules Bio-Actives, IPHC-DSA, Université de Strasbourg, CNRS, 67400, Illkirch-Graffenstaden, France
| | | | - Saïd Ennahar
- Equipe de Chimie Analytique des Molécules Bio-Actives, IPHC-DSA, Université de Strasbourg, CNRS, 67400, Illkirch-Graffenstaden, France
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Loss of IrpT Function in Lactococcus lactis subsp. lactis N8 Results in Increased Nisin Resistance. Curr Microbiol 2010; 61:329-34. [DOI: 10.1007/s00284-010-9615-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 02/12/2010] [Indexed: 10/19/2022]
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Ávila M, Jaquet M, Moine D, Requena T, Peláez C, Arigoni F, Jankovic I. Physiological and biochemical characterization of the two α-l-rhamnosidases of Lactobacillus plantarum NCC245. Microbiology (Reading) 2009; 155:2739-2749. [DOI: 10.1099/mic.0.027789-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This work is believed to be the first report on the physiological and biochemical characterization of α-l-rhamnosidases in lactic acid bacteria. A total of 216 strains representing 37 species and eight genera of food-grade bacteria were screened for α-l-rhamnosidase activity. The majority of positive bacteria (25 out of 35) were Lactobacillus plantarum strains, and activity of the L. plantarum strain NCC245 was examined in more detail. The analysis of α-l-rhamnosidase activity under different growth conditions revealed dual regulation of the enzyme activity, involving carbon catabolite repression and induction: the enzyme activity was downregulated by glucose and upregulated by l-rhamnose. The expression of the two α-l-rhamnosidase genes rhaB1 and rhaB2 and two predicted permease genes rhaP1 and rhaP2, identified in a probable operon rhaP2B2P1B1, was repressed by glucose and induced by l-rhamnose, showing regulation at the transcriptional level. The two α-l-rhamnosidase genes were overexpressed and purified from Escherichia coli. RhaB1 activity was maximal at 50 °C and at neutral pH and RhaB2 maximal activity was detected at 60 °C and at pH 5, with high residual activity at 70 °C. Both enzymes showed a preference for the α-1,6 linkage of l-rhamnose to β-d-glucose, hesperidin and rutin being their best substrates, but, surprisingly, no activity was detected towards the α-1,2 linkage in naringin under the tested conditions. In conclusion, we identified and characterized the strain L. plantarum NCC245 and its two α-l-rhamnosidase enzymes, which might be applied for improvement of bioavailability of health-beneficial polyphenols, such as hesperidin, in humans.
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Affiliation(s)
- Marta Ávila
- Departamento de Ciencia y Tecnología de Productos Lácteos, Instituto del Frío (CSIC), José Antonio Novais 10, Madrid 28040, Spain
| | - Muriel Jaquet
- Nestlé Research Center, Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland
| | - Deborah Moine
- Nestlé Research Center, Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland
| | - Teresa Requena
- Departamento de Ciencia y Tecnología de Productos Lácteos, Instituto del Frío (CSIC), José Antonio Novais 10, Madrid 28040, Spain
| | - Carmen Peláez
- Departamento de Ciencia y Tecnología de Productos Lácteos, Instituto del Frío (CSIC), José Antonio Novais 10, Madrid 28040, Spain
| | - Fabrizio Arigoni
- Nestlé Research Center, Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland
| | - Ivana Jankovic
- Nestlé Research Center, Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland
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27
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Qu H, Xin Y, Dong X, Ma Y. An rmlA gene encoding d-glucose-1-phosphate thymidylyltransferase is essential for mycobacterial growth. FEMS Microbiol Lett 2007; 275:237-43. [PMID: 17784859 DOI: 10.1111/j.1574-6968.2007.00890.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The rhamnose-GlcNAc disaccharide is a critical linker which connects arabinogalactan to peptidoglycan via a phosphodiester linkage. The biosynthesis of dTDP-rhamnose is catalysed by four enzymes, and the first reaction is catalysed by an rmlA gene encoding d-glucose-1-phosphate thymidylyltransferase (RmlA). We generated a Mycobacterium smegmatis mc(2)155 mutant lacking the rmlA gene via a homologous recombination method. We tested the requirement for the rmlA gene and the effect of a lack of RmlA on bacterial cell morphology. The results demonstrate that the rmlA gene is essential for mycobacterial growth and that lack of RmlA activity has profound negative effects on bacterial cell morphology. RmlA is thus a potential target for the development of new antituberculosis drugs.
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Affiliation(s)
- Hong Qu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, China
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28
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Nierop Groot M, Kleerebezem M. Mutational analysis of the Lactococcus lactis NIZO B40 exopolysaccharide (EPS) gene cluster: EPS biosynthesis correlates with unphosphorylated EpsB. J Appl Microbiol 2007; 103:2645-56. [DOI: 10.1111/j.1365-2672.2007.03516.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Knoshaug EP, Ahlgren JA, Trempy JE. Exopolysaccharide expression in Lactococcus lactis subsp. cremoris Ropy352: evidence for novel gene organization. Appl Environ Microbiol 2006; 73:897-905. [PMID: 17122391 PMCID: PMC1800743 DOI: 10.1128/aem.01945-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis subsp. cremoris Ropy352 produces two distinct heteropolysaccharides, phenotypically described as ropy and mucoid, when cultured in nonfat milk. One exopolysaccharide precipitated with 50% ethanol as a series of elongated threads and was composed of glucose and galactose in a molar ratio of 3:2. The second exopolysaccharide precipitated with 75% ethanol as a fine flocculant and consisted of galactose, glucose, and mannose with a molar ratio of 67:21:12. A mutant strain, L. lactis subsp. cremoris EK240, lacking the ropy phenotype did not produce the exopolysaccharide that precipitated with 50% ethanol; however, it produced the exopolysaccharide that precipitated with 75% ethanol, indicating that the former exopolysaccharide is essential for the ropy phenotype. Cultures of L. lactis subsp. cremoris Ropy352 in 10% nonfat milk reached a viscosity of 25 Pa-s after 24 h, while those of the nonropy L. lactis subsp. cremoris EK240 mutant did not change. A mutation abolishing ropy exopolysaccharide expression mapped to a region on a plasmid containing two open reading frames, epsM and epsN, encoding novel glycosyltransferases bordered by ISS1 elements oriented in the same direction. Sequencing of this plasmid revealed two other regions involved in exopolysaccharide expression, an operon located between partial IS981 and IS982 elements, and an independent gene, epsU. Two and possibly three of these regions are involved in L. lactis subsp. cremoris Ropy352 exopolysaccharide expression and are arranged in a novel fashion different from that of typical lactococcal exopolysaccharide loci, and this provides genetic evidence for exopolysaccharide gene reorganization and evolution in Lactococcus.
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Affiliation(s)
- Eric P Knoshaug
- Department of Microbiology, Nash Hall 220, Oregon State University, Corvallis, OR 97331-3804, USA
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Zhou XX, Li WF, Ma GX, Pan YJ. The nisin-controlled gene expression system: Construction, application and improvements. Biotechnol Adv 2006; 24:285-95. [PMID: 16380225 DOI: 10.1016/j.biotechadv.2005.11.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 10/26/2005] [Accepted: 11/03/2005] [Indexed: 10/25/2022]
Abstract
Lactic acid bacteria are widely used in industrial fermentation. The potential use of these bacteria as homologous and heterologous protein expression hosts has been investigated extensively. The NIsin-Controlled gene Expression system (the NICE system) is an efficient and promising gene expression system based on the autoregulation mechanism of nisin biosynthesis in the Lactococcus lactis. In the NICE system, the membrane-located histidine kinase NisK senses the inducing signal nisin and autophosphorylates, then transfers phosphorous group to intracellular response regulator protein NisR which activates nisA promoter to express the downstream gene(s). The NICE system allows regulated overproduction of a variety of interest proteins by several Gram-positive bacteria, especially L. lactis. The essential elements for system construction, its application for expression of some biotechnologically important proteins and further improvements of this system are discussed.
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Affiliation(s)
- Xu Xia Zhou
- Department of Chemistry, Zhejiang University, the Laboratory of Natural and BioChemistry, Hangzhou, 310027, China
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31
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Deeraksa A, Moonmangmee S, Toyama H, Yamada M, Adachi O, Matsushita K. Characterization and spontaneous mutation of a novel gene, polE, involved in pellicle formation in Acetobacter tropicalis SKU1100. Microbiology (Reading) 2005; 151:4111-4120. [PMID: 16339956 DOI: 10.1099/mic.0.28350-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acetobacter tropicalis SKU1100 produces a pellicle polysaccharide, consisting of galactose, glucose and rhamnose, which attaches to the cell surface. This strain forms two types of colony on agar plates: a rough-surfaced colony (R strain) and a mucoid smooth-surfaced colony (S strain). The R strain forms a pellicle, allowing it to float on the medium surface in static culture, while the S strain does not. The pellicle is an assemblage of cells which are tightly associated with capsular polysaccharides (CPS) on the cell surface. In this study, a gene required for pellicle formation by the R strain was investigated by transposon mutagenesis using Tn10. The resulting mutant, designated Pel−, has a smooth-surfaced colony and a defect in pellicle formation, as for the S strain. The mutant produced polysaccharide which was instead secreted into the culture medium as extracellular polysaccharide (EPS). An ORF was identified at the Tn10 insertion site, designated polE, upstream of which polABCD genes were also found. The deduced amino acid sequences of polABCD showed a high level of homology to those of rfbBACD which are involved in dTDP-rhamnose synthesis, whereas polE had a relatively low level of homology to glycosyltransferase. In this study a polB (rfbA) disruptant was also prepared, which lacked both CPS and EPS production. A plasmid harbouring the polE or polB genes could restore pellicle formation in the Pel− mutant and S strains, and in the ΔpolB mutant, respectively. Thus both polE and polB are evidently involved in pellicle formation, most likely by anchoring polysaccharide to the cell surface and through the production of dTDP-rhamnose, respectively. The Pel− and ΔpolB mutants were unable to grow in static culture and became more sensitive to acetic acid due to the loss of pellicle formation. Additionally, this study identified the mutation sites of several S strains which were spontaneously isolated from the original culture and found them to be concentrated in a sequence of 7 C residues in the coding sequence of polE, with the deletion or addition of a single C nucleotide.
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Affiliation(s)
- Arpaporn Deeraksa
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Somporn Moonmangmee
- Department of Biotechnology, Thailand Institute of Scientific and Technological Research, Khlong Luang, Pathumthani 12120, Thailand
| | - Hirohide Toyama
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Mamoru Yamada
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Osao Adachi
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Kazunobu Matsushita
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan
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Silva E, Marques AR, Fialho AM, Granja AT, Sá-Correia I. Proteins encoded by Sphingomonas elodea ATCC 31461 rmlA and ugpG genes, involved in gellan gum biosynthesis, exhibit both dTDP- and UDP-glucose pyrophosphorylase activities. Appl Environ Microbiol 2005; 71:4703-12. [PMID: 16085866 PMCID: PMC1183319 DOI: 10.1128/aem.71.8.4703-4712.2005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The commercial gelling agent gellan is a heteropolysaccharide produced by Sphingomonas elodea ATCC 31461. In this work, we carried out the biochemical characterization of the enzyme encoded by the first gene (rmlA) of the rml 4-gene cluster present in the 18-gene cluster required for gellan biosynthesis (gel cluster). Based on sequence homology, the putative rml operon is presumably involved in the biosynthesis of dTDP-rhamnose, the sugar necessary for the incorporation of rhamnose in the gellan repeating unit. Heterologous RmlA was purified as a fused His6-RmlA protein from extracts prepared from Escherichia coli IPTG (isopropyl-beta-D-thiogalactopyranoside)-induced cells, and the protein was proven to exhibit dTDP-glucose pyrophosphorylase (Km of 12.0 microM for dTDP-glucose) and UDP-glucose pyrophosphorylase (Km of 229.0 microM for UDP-glucose) activities in vitro. The N-terminal region of RmlA exhibits the motif G-X-G-T-R-X2-P-X-T, which is highly conserved among bacterial XDP-sugar pyrophosphorylases. The motif E-E-K-P, with the conserved lysine residue (K163) predicted to be essential for glucose-1-phosphate binding, was observed. The S. elodea ATCC 31461 UgpG protein, encoded by the ugpG gene which maps outside the gel cluster, was previously identified as the UDP-glucose pyrophosphorylase involved in the formation of UDP-glucose, also required for gellan synthesis. In this study, we demonstrate that UgpG also exhibits dTDP-glucose pyrophosphorylase activity in vitro and compare the kinetic parameters of the two proteins for both substrates. DNA sequencing of ugpG gene-adjacent regions and sequence similarity studies suggest that this gene maps with others involved in the formation of sugar nucleotides presumably required for the biosynthesis of another cell polysaccharide(s).
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Affiliation(s)
- Elisabete Silva
- Biological Sciences Research Group, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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Mierau I, Kleerebezem M. 10 years of the nisin-controlled gene expression system (NICE) in Lactococcus lactis. Appl Microbiol Biotechnol 2005; 68:705-17. [PMID: 16088349 DOI: 10.1007/s00253-005-0107-6] [Citation(s) in RCA: 375] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Revised: 07/13/2005] [Accepted: 07/17/2005] [Indexed: 10/25/2022]
Abstract
Lactococcus lactis is a Gram-positive lactic acid bacterium that, in addition to its traditional use in food fermentations, is increasingly used in modern biotechnological applications. In the last 25 years great progress has been made in the development of genetic engineering tools and the molecular characterization of this species. A new versatile and tightly controlled gene expression system, based on the auto-regulation mechanism of the bacteriocin nisin, was developed 10 years ago-the NIsin Controlled gene Expression system, called NICE. This system has become one of the most successful and widely used tools for regulated gene expression in Gram-positive bacteria. The review describes, after a brief introduction of the host bacterium L. lactis, the fundaments, components and function of the NICE system. Furthermore, an extensive overview is provided of the different applications in lactococci and other Gram-positive bacteria: (1) over-expression of homologous and heterologous genes for functional studies and to obtain large quantities of specific gene products, (2) metabolic engineering, (3) expression of prokaryotic and eukaryotic membrane proteins, (4) protein secretion and anchoring in the cell envelope, (5) expression of genes with toxic products and analysis of essential genes and (6) large-scale applications. Finally, an overview is given of growth and induction conditions for lab-scale and industrial-scale applications.
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Affiliation(s)
- Igor Mierau
- NIZO food research, P.O. Box 20, 6710, Ede, The Netherlands.
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Construction of a rhamnose mutation in Bacillus anthracis affects adherence to macrophages but not virulence in guinea pigs. Microb Pathog 2005; 38:1-12. [DOI: 10.1016/j.micpath.2004.10.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Revised: 10/01/2004] [Accepted: 10/05/2004] [Indexed: 11/17/2022]
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Kleerebezem M. Quorum sensing control of lantibiotic production; nisin and subtilin autoregulate their own biosynthesis. Peptides 2004; 25:1405-14. [PMID: 15374644 DOI: 10.1016/j.peptides.2003.10.021] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2003] [Accepted: 10/15/2003] [Indexed: 10/26/2022]
Abstract
Lantibiotics are produced by a variety of Gram-positive bacteria. The production of these peptides appears to be regulated at the transcriptional level in a cell-density-dependent manner in various bacteria. This phenomenon has been studied in detail for the production of nisin by Lactococcus lactis, and the production of the structurally similar subtilin by Bacillus subtilis. In this paper, the molecular mechanism underlying regulation of nisin and subtilin production is reviewed. This quorum sensing, autoregulatory module includes the lantibiotics themselves as peptide pheromones, the signal transduction by the corresponding two-component regulatory systems, and the lantibiotic-responsive promoter elements in the biosynthesis gene clusters. Finally, the exploitation of these regulatory characteristics for the development of highly effective controlled gene expression systems in Gram-positive bacteria is discussed.
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Affiliation(s)
- Michiel Kleerebezem
- NIZO Food Research, Wageningen Centre for Food Sciences, Kernhemseweg 2, PO Box 20, 6710 BA Ede, The Netherlands.
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