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Monge-Loría M, Zhong W, Abrahamse NH, Hartter S, Garg N. Discovery of Peptidic Siderophore Degradation by Screening Natural Product Profiles in Marine-Derived Bacterial Mono- and Cocultures. Biochemistry 2025; 64:634-654. [PMID: 39807563 PMCID: PMC11800396 DOI: 10.1021/acs.biochem.4c00706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 12/12/2024] [Accepted: 12/31/2024] [Indexed: 01/16/2025]
Abstract
Coral reefs are hotspots of marine biodiversity, which results in the synthesis of a wide variety of compounds with unique molecular scaffolds, and bioactivities, rendering reefs an ecosystem of interest. The chemodiversity stems from the intricate relationships between inhabitants of the reef, as the chemistry produced partakes in intra- and interspecies communication, settlement, nutrient acquisition, and defense. However, the coral reefs are declining at an unprecedented rate due to climate change, pollution, and increased incidence of pathogenic diseases. Among pathogens, Vibrio spp. bacteria are key players resulting in high mortality. Thus, alternative strategies such as application of beneficial bacteria isolated from disease-resilient species are being explored to lower the burden of pathogenic species. Here, we apply coculturing of a coral-derived pathogenic species of Vibrio and beneficial bacteria and leverage recent advancements in untargeted metabolomics to discover engineerable beneficial traits. By chasing chemical change in coculture, we report Microbulbifer spp.-mediated degradation of amphibactins, produced by Vibrio spp. bacteria to sequester iron. Additional biochemical experiments revealed that the degradation occurs in the peptide backbone and requires the enzyme fraction of Microbulbifer. A reduction in iron affinity is expected due to the loss of one Fe(III) binding moiety. Therefore, we hypothesize that this degradation shapes community behaviors as it pertains to iron acquisition, a limiting nutrient in the marine environment, and survival. Furthermore, Vibrio sp. bacteria suppressed natural product synthesis by beneficial bacteria. Understanding biochemical mechanisms behind these interactions will enable engineering probiotic bacteria capable of lowering pathogenic burdens during heat waves and incidence of disease.
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Affiliation(s)
- Mónica Monge-Loría
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Weimao Zhong
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Nadine H. Abrahamse
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Stephen Hartter
- Georgia
Aquarium, 225 Baker St.
NW, Atlanta, Georgia 30313, United States
| | - Neha Garg
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332, United States
- Center
for Microbial Dynamics and Infection, Georgia
Institute of Technology, 315 Ferst Drive, Atlanta, Georgia 30332, United States
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Haeger G, Wirges J, Bongaerts J, Schörken U, Siegert P. Perspectives of aminoacylases in biocatalytic synthesis of N-acyl-amino acids surfactants. Appl Microbiol Biotechnol 2024; 108:495. [PMID: 39453420 PMCID: PMC11511702 DOI: 10.1007/s00253-024-13328-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 10/06/2024] [Accepted: 10/07/2024] [Indexed: 10/26/2024]
Abstract
Many industrial processes are performed using harmful chemicals. The current technical synthesis of N-acyl-amino acids relies on acyl chlorides, which are typically obtained from phosgene chemistry. A greener alternative is the application of whole cells or enzymes to carry out synthesis in an environmentally friendly manner. Aminoacylases belong to the hydrolase family and the resolution of racemic mixtures of N-acetyl-amino acids is a well-known industrial process. Several new enzymes accepting long-chain fatty acids as substrates were discovered in recent years. This article reviews the synthetic potential of aminoacylases to produce biobased N-acyl-amino acid surfactants. The focus lays on a survey of the different types of aminoacylases available for synthesis and their reaction products. The enzymes are categorized according to their protein family classification and their biochemical characteristics including substrate spectra, reaction optima and process stability, both in hydrolysis and under process conditions suitable for synthesis. Finally, the benefits and future challenges of enzymatic N-acyl-amino acid synthesis with aminoacylases will be discussed. KEY POINTS: • Enzymatic synthesis of N-acyl-amino acids, biobased surfactants by aminoacylases.
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Affiliation(s)
- Gerrit Haeger
- Novo Nordisk, Novo Nordisk Park 1, 2760, Måløv, Denmark
| | - Jessika Wirges
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Heinrich-Mussmannstr. 1, 52428, Jülich, Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Heinrich-Mussmannstr. 1, 52428, Jülich, Germany
| | - Ulrich Schörken
- Faculty of Applied Natural Sciences, TH Köln University of Applied Sciences - Leverkusen Campus, 51379, Leverkusen, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Heinrich-Mussmannstr. 1, 52428, Jülich, Germany.
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3
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Chen X, Zou H, Zhuo T, Rou W, Wu W, Fan X. Xanthomonas citri subsp. citri type III effector PthA4 directs the dynamical expression of a putative citrus carbohydrate-binding protein gene for canker formation. eLife 2024; 13:RP91684. [PMID: 39136681 PMCID: PMC11321762 DOI: 10.7554/elife.91684] [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] [Indexed: 08/15/2024] Open
Abstract
Xanthomonas citri subsp. citri (Xcc), the causal agent of citrus canker, elicits canker symptoms in citrus plants because of the transcriptional activator-like (TAL) effector PthA4, which activates the expression of the citrus susceptibility gene CsLOB1. This study reports the regulation of the putative carbohydrate-binding protein gene Cs9g12620 by PthA4-mediated induction of CsLOB1 during Xcc infection. We found that the transcription of Cs9g12620 was induced by infection with Xcc in a PthA4-dependent manner. Even though it specifically bound to a putative TAL effector-binding element in the Cs9g12620 promoter, PthA4 exerted a suppressive effect on the promoter activity. In contrast, CsLOB1 bound to the Cs9g12620 promoter to activate its expression. The silencing of CsLOB1 significantly reduced the level of expression of Cs9g12620, which demonstrated that Cs9g12620 was directly regulated by CsLOB1. Intriguingly, PhtA4 interacted with CsLOB1 and exerted feedback control that suppressed the induction of expression of Cs9g12620 by CsLOB1. Transient overexpression and gene silencing revealed that Cs9g12620 was required for the optimal development of canker symptoms. These results support the hypothesis that the expression of Cs9g12620 is dynamically directed by PthA4 for canker formation through the PthA4-mediated induction of CsLOB1.
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Affiliation(s)
- Xinyu Chen
- Plant Protection College, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Huasong Zou
- School of Life Sciences and Health, Huzhou CollegeHuzhouChina
| | - Tao Zhuo
- Plant Protection College, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Wei Rou
- Plant Protection College, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Wei Wu
- Plant Protection College, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiaojing Fan
- Plant Protection College, Fujian Agriculture and Forestry UniversityFuzhouChina
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4
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Kua GKB, Nguyen GKT, Li Z. Enzymatic Strategies for the Biosynthesis of N-Acyl Amino Acid Amides. Chembiochem 2024; 25:e202300672. [PMID: 38051126 DOI: 10.1002/cbic.202300672] [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: 09/29/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
Amide bond-containing biomolecules are functionally significant and useful compounds with diverse applications. For example, N-acyl amino acids (NAAAs) are an important class of lipoamino acid amides with extensive use in food, cosmetic and pharmaceutical industries. Their conventional chemical synthesis involves the use of toxic chlorinating agents for carboxylic acid activation. Enzyme-catalyzed biotransformation for the green synthesis of these amides is therefore highly desirable. Here, we review a range of enzymes suitable for the synthesis of NAAA amides and their strategies adopted in carboxylic acid activation. Generally, ATP-dependent enzymes for NAAA biosynthesis are acyl-adenylating enzymes that couple the hydrolysis of phosphoanhydride bond in ATP with the formation of an acyl-adenylate intermediate. In contrast, ATP-independent enzymes involve hydrolases such as lipases or aminoacylases, which rely on the transient activation of the carboxylic acid. This occurs either through an acyl-enzyme intermediate or by favorable interactions with surrounding residues to anchor the acyl donor in a suitable orientation for the incoming amine nucleophile. Recently, the development of an alternative pathway involving ester-amide interconversion has unraveled another possible strategy for amide formation through esterification-aminolysis cascade reactions, potentially expanding the substrate scope for enzymes to catalyze the synthesis of a diverse range of NAAA amides.
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Affiliation(s)
- Glen Kai Bin Kua
- Wilmar International Limited, 28 Biopolis Road, Singapore, 138568
| | | | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
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5
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Liu S, Silvano E, Li M, Mausz M, Rihtman B, Guillonneau R, Geiger O, Scanlan DJ, Chen Y. Aminolipids in bacterial membranes and the natural environment. THE ISME JOURNAL 2024; 18:wrae229. [PMID: 39520271 PMCID: PMC11631085 DOI: 10.1093/ismejo/wrae229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 10/01/2024] [Accepted: 11/07/2024] [Indexed: 11/16/2024]
Abstract
Our comprehension of membrane function has predominantly advanced through research on glycerophospholipids, also known as phosphoglycerides, which are glycerol phosphate-based lipids found across all three domains of life. However, in bacteria, a perplexing group of lipids distinct from glycerol phosphate-based ones also exists. These are amino acid-containing lipids that form an amide bond between an amino acid and a fatty acid. Subsequently, a second fatty acid becomes linked, often via the 3-hydroxy group on the first fatty acid. These amide-linked aminolipids have, as of now, been exclusively identified in bacteria. Several hydrophilic head groups have been discovered in these aminolipids including ornithine, glutamine, glycine, lysine, and more recently, a sulfur-containing non-proteinogenic amino acid cysteinolic acid. Here, we aim to review current advances in the genetics, biochemistry and function of these aminolipids as well as giving an ecological perspective. We provide evidence for their potential significance in the ecophysiology of all major microbiomes, i.e. gut, soil, and aquatic as well as highlighting their important roles in influencing biological interactions.
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Affiliation(s)
- Shengwei Liu
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Eleonora Silvano
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Mingyu Li
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Michaela Mausz
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Richard Guillonneau
- Faculty of Science and Technology, Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Otto Geiger
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Colonia Chamilpa, Cuernavaca, Morelos 62210, México
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Yin Chen
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
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6
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Beals DG, Puri AW. Linking methanotroph phenotypes to genotypes using a simple spatially resolved model ecosystem. THE ISME JOURNAL 2024; 18:wrae060. [PMID: 38622932 PMCID: PMC11072679 DOI: 10.1093/ismejo/wrae060] [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: 11/14/2023] [Revised: 02/20/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental context in laboratory settings. Laboratory-based model ecosystems offer a means to better account for environmental conditions compared with standard planktonic cultures and can help link genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs) within the methane-oxygen counter gradient typically found in the natural environment of these organisms. Culturing the methanotroph Methylomonas sp. strain LW13 in this system resulted in the formation of a distinct horizontal band at the intersection of the counter gradient, which we discovered was not due to increased numbers of bacteria at this location but instead to an increased amount of polysaccharides. We also discovered that different methanotrophic taxa form polysaccharide bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this band, we identified genes upregulated within the band and validated their involvement in growth and band formation within the model ecosystem using knockout strains. Notably, deletion of these genes did not negatively affect growth using standard planktonic culturing methods. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover bacterial phenotypes missing from standard laboratory conditions, and to link these phenotypes with their genetic determinants.
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Affiliation(s)
- Delaney G Beals
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, United States
| | - Aaron W Puri
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, United States
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Krishnamurthy HK, Pereira M, Bosco J, George J, Jayaraman V, Krishna K, Wang T, Bei K, Rajasekaran JJ. Gut commensals and their metabolites in health and disease. Front Microbiol 2023; 14:1244293. [PMID: 38029089 PMCID: PMC10666787 DOI: 10.3389/fmicb.2023.1244293] [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: 06/22/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose of review This review comprehensively discusses the role of the gut microbiome and its metabolites in health and disease and sheds light on the importance of a holistic approach in assessing the gut. Recent findings The gut microbiome consisting of the bacteriome, mycobiome, archaeome, and virome has a profound effect on human health. Gut dysbiosis which is characterized by perturbations in the microbial population not only results in gastrointestinal (GI) symptoms or conditions but can also give rise to extra-GI manifestations. Gut microorganisms also produce metabolites (short-chain fatty acids, trimethylamine, hydrogen sulfide, methane, and so on) that are important for several interkingdom microbial interactions and functions. They also participate in various host metabolic processes. An alteration in the microbial species can affect their respective metabolite concentrations which can have serious health implications. Effective assessment of the gut microbiome and its metabolites is crucial as it can provide insights into one's overall health. Summary Emerging evidence highlights the role of the gut microbiome and its metabolites in health and disease. As it is implicated in GI as well as extra-GI symptoms, the gut microbiome plays a crucial role in the overall well-being of the host. Effective assessment of the gut microbiome may provide insights into one's health status leading to more holistic care.
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Affiliation(s)
| | | | - Jophi Bosco
- Vibrant America LLC., San Carlos, CA, United States
| | | | | | | | - Tianhao Wang
- Vibrant Sciences LLC., San Carlos, CA, United States
| | - Kang Bei
- Vibrant Sciences LLC., San Carlos, CA, United States
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8
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Cho W, York AG, Wang R, Wyche TP, Piizzi G, Flavell RA, Crawford JM. N-Acyl Amides from Neisseria meningitidis and Their Role in Sphingosine Receptor Signaling. Chembiochem 2022; 23:e202200490. [PMID: 36112057 PMCID: PMC9762135 DOI: 10.1002/cbic.202200490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/15/2022] [Indexed: 02/03/2023]
Abstract
Neisseria meningitidis is a Gram-negative opportunistic pathogen that is responsible for causing human diseases with high mortality, such as septicemia and meningitis. The molecular mechanisms N. meningitidis employ to manipulate the immune system, translocate the mucosal and blood-brain barriers, and exert virulence are largely unknown. Human-associated bacteria encode a variety of bioactive small molecules with growing evidence for N-acyl amides as being important signaling molecules. However, only a small fraction of these metabolites has been identified from the human microbiota thus far. Here, we heterologously expressed an N-acyltransferase encoded in the obligate human pathogen N. meningitidis and identified 30 N-acyl amides with representative members serving as agonists of the G-protein coupled receptor (GPCR) S1PR4. During this process, we also characterized two mammalian N-acyl amides derived from the bovine medium. Both groups of metabolites suppress anti-inflammatory interleukin-10 signaling in human macrophage cell types, but they also suppress the pro-inflammatory interleukin-17A+ population in TH 17-differentiated CD4+ T cells.
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Affiliation(s)
- Wooyoung Cho
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
| | - Autumn G. York
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Rurun Wang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Thomas P. Wyche
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Grazia Piizzi
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Richard A. Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- correspondence,
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Darrington M, Leftwich PT, Holmes NA, Friend LA, Clarke NVE, Worsley SF, Margaritopolous JT, Hogenhout SA, Hutchings MI, Chapman T. Characterisation of the symbionts in the Mediterranean fruit fly gut. Microb Genom 2022; 8. [PMID: 35446250 PMCID: PMC9453069 DOI: 10.1099/mgen.0.000801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Symbioses between bacteria and their insect hosts can range from loose associations through to obligate interdependence. While fundamental evolutionary insights have been gained from the in-depth study of obligate mutualisms, there is increasing interest in the evolutionary potential of flexible symbiotic associations between hosts and their gut microbiomes. Understanding relationships between microbes and hosts also offers the potential for exploitation for insect control. Here, we investigate the gut microbiome of a global agricultural pest, the Mediterranean fruit fly (Ceratitis capitata). We used 16S rRNA profiling to compare the gut microbiomes of laboratory and wild strains raised on different diets and from flies collected from various natural plant hosts. The results showed that medfly guts harbour a simple microbiome that is primarily determined by the larval diet. However, regardless of the laboratory diet or natural plant host on which flies were raised, Klebsiella spp. dominated medfly microbiomes and were resistant to removal by antibiotic treatment. We sequenced the genome of the dominant putative Klebsiella spp. (‘Medkleb’) isolated from the gut of the Toliman wild-type strain. Genome-wide ANI analysis placed Medkleb within the K. oxytoca / michiganensis group. Species level taxonomy for Medkleb was resolved using a mutli-locus phylogenetic approach - and molecular, sequence and phenotypic analyses all supported its identity as K. michiganensis. Medkleb has a genome size (5825435 bp) which is 1.6 standard deviations smaller than the mean genome size of free-living Klebsiella spp. Medkleb also lacks some genes involved in environmental sensing. Moreover, the Medkleb genome contains at least two recently acquired unique genomic islands as well as genes that encode pectinolytic enzymes capable of degrading plant cell walls. This may be advantageous given that the medfly diet includes unripe fruits containing high proportions of pectin. The results suggest that the medfly harbours a commensal gut bacterium that may have developed a mutualistic association with its host and provide nutritional benefits.
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Affiliation(s)
- Mike Darrington
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Neil A Holmes
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Lucy A Friend
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Naomi V E Clarke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - John T Margaritopolous
- Department of Plant Protection, Institute of Industrial and Fodder Crops, Hellenic Agricultural Organization-DEMETER, Volos, Greece
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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Chakraborty P. Gene cluster from plant to microbes: Their role in genome architecture, organism's development, specialized metabolism and drug discovery. Biochimie 2021; 193:1-15. [PMID: 34890733 DOI: 10.1016/j.biochi.2021.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/01/2021] [Accepted: 12/04/2021] [Indexed: 02/07/2023]
Abstract
Plants and microbes fulfil our daily requirements through different high-value chemicals, e.g., nutraceuticals, pharmaceuticals, cosmetics, and through varieties of fruits, crops, vegetables, and many more. Utmost care would therefore be taken for growth, development and sustainability of these important crops and medicinal plants and microbes. Homeobox genes and HOX clusters and their recently characterized expanded family members, including newly discovered homeobox, WOX gene from medicinal herb, Panax ginseng, significantly contributes in the growth and development of these organisms. On the other hand, secondary metabolites produced through secondary metabolism of plants and microbes are used as organisms defense as well as drugs/drug-like molecules for humans. Both the developmental HOX cluster and the biosynthetic gene-cluster (BGC) for secondary metabolites are organised in organisms genome. Genome mining and genomewide analysis of these clusters will definitely identify and characterize many more important molecules from unexplored plants and microbes and underexplored human microbiota and the evolution studies of these clusters will indicate their source of origin. Although genomics revolution now continues at a pace, till date only few hundred plant genome sequences are available. However, next-generation sequencing (NGS) technology now in market and may be applied even for plants with recalcitrant genomes, eventually may discover genomic potential towards production of secondary metabolites of diverse plants and micro-organisms present in the environment and microbiota. Additionally, the development of tools for genome mining e.g., antiSMASH, plantiSMASH, and more and more computational approaches that predicts hundreds of secondary metabolite BGCs will be discussed.
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Affiliation(s)
- Prasanta Chakraborty
- Kalpana Chawla Center for Space and Nanoscience, Kolkata, Indian Institute of Chemical Biology (retd.), Kolkata, 700032, India.
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Genome analysis suggests the bacterial family Acetobacteraceae is a source of undiscovered specialized metabolites. Antonie van Leeuwenhoek 2021; 115:41-58. [PMID: 34761294 PMCID: PMC8776678 DOI: 10.1007/s10482-021-01676-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022]
Abstract
Acetobacteraceae is an economically important family of bacteria that is used for industrial fermentation in the food/feed sector and for the preparation of sorbose and bacterial cellulose. It comprises two major groups: acetous species (acetic acid bacteria) associated with flowers, fruits and insects, and acidophilic species, a phylogenetically basal and physiologically heterogeneous group inhabiting acid or hot springs, sludge, sewage and freshwater environments. Despite the biotechnological importance of the family Acetobacteraceae, the literature does not provide any information about its ability to produce specialized metabolites. We therefore constructed a phylogenomic tree based on concatenated protein sequences from 141 type strains of the family and predicted the presence of small-molecule biosynthetic gene clusters (BGCs) using the antiSMASH tool. This dual approach allowed us to associate certain biosynthetic pathways with particular taxonomic groups. We found that acidophilic and acetous species contain on average ~ 6.3 and ~ 3.4 BGCs per genome, respectively. All the Acetobacteraceae strains encoded proteins involved in hopanoid biosynthesis, with many also featuring genes encoding type-1 and type-3 polyketide and non-ribosomal peptide synthases, and enzymes for aryl polyene, lactone and ribosomal peptide biosynthesis. Our in silico analysis indicated that the family Acetobacteraceae is a potential source of many undiscovered bacterial metabolites and deserves more detailed experimental exploration.
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12
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Kallscheuer N, Jogler C. The bacterial phylum Planctomycetes as novel source for bioactive small molecules. Biotechnol Adv 2021; 53:107818. [PMID: 34537319 DOI: 10.1016/j.biotechadv.2021.107818] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Extensive knowledge and methodological expertise on the bacterial cell biology have been accumulated over the last decades and bacterial cells have now become an integral part of several (bio-)technological processes. While it appears reasonable to focus on a relatively small number of fast-growing and genetically easily manipulable model bacteria as biotechnological workhorses, the for the most part untapped diversity of bacteria needs to be explored when it comes to bioprospecting for natural product discovery. Members of the underexplored and evolutionarily deep-branching phylum Planctomycetes have only recently gained increased attention with respect to the production of small molecules with biomedical activities, e.g. as a natural source of novel antibiotics. Next-generation sequencing and metagenomics can provide access to the genomes of uncultivated bacteria from sparsely studied phyla, this, however, should be regarded as an addition rather than a substitute for classical strain isolation approaches. Ten years ago, a large sampling campaign was initiated to isolate planctomycetes from their varied natural habitats and protocols were developed to address complications during cultivation of representative species in the laboratory. The characterisation of approximately 90 novel strains by several research groups in the recent years opened a detailed in silico look into the coding potential of individual members of this phylum. Here, we review the current state of planctomycetal research, focusing on diversity, small molecule production and potential future applications. Although the field developed promising, the time frame of 10 years illustrates that the study of additional promising bacterial phyla as sources for novel small molecules needs to start rather today than tomorrow.
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Affiliation(s)
- Nicolai Kallscheuer
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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13
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Marian M, Fujikawa T, Shimizu M. Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114. Arch Microbiol 2021; 203:3373-3388. [PMID: 33880605 DOI: 10.1007/s00203-021-02327-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022]
Abstract
Mitsuaria sp. TWR114 is a biocontrol agent against tomato bacterial wilt (TBW). We aimed to gain genomic insights relevant to the biocontrol mechanisms and colonization ability of this strain. The draft genome size was found to be 5,632,523 bp, with a GC content of 69.5%, assembled into 1144 scaffolds. Genome annotation predicted a total of 4675 protein coding sequences (CDSs), 914 pseudogenes, 49 transfer RNAs, 3 noncoding RNAs, and 2 ribosomal RNAs. Genome analysis identified multiple CDSs associated with various pathways for the metabolism and transport of amino acids and carbohydrates, motility and chemotactic capacities, protection against stresses (oxidative, antibiotic, and phage), production of secondary metabolites, peptidases, quorum-quenching enzymes, and indole-3-acetic acid, as well as protein secretion systems and their related appendages. The genome resource will extend our understanding of the genomic features related to TWR114's biocontrol and colonization abilities and facilitate its development as a new biopesticide against TBW.
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Affiliation(s)
- Malek Marian
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.,College of Agriculture, Ibaraki University, Ami, Inashiki, Ibaraki, 300-0393, Japan
| | - Takashi Fujikawa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8605, Japan
| | - Masafumi Shimizu
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
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14
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Kallscheuer N, Jeske O, Sandargo B, Boedeker C, Wiegand S, Bartling P, Jogler M, Rohde M, Petersen J, Medema MH, Surup F, Jogler C. The planctomycete Stieleria maiorica Mal15 T employs stieleriacines to alter the species composition in marine biofilms. Commun Biol 2020; 3:303. [PMID: 32533057 PMCID: PMC7293339 DOI: 10.1038/s42003-020-0993-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/30/2020] [Indexed: 12/20/2022] Open
Abstract
Bacterial strains of the phylum Planctomycetes occur ubiquitously, but are often found on surfaces of aquatic phototrophs, e.g. alga. Despite slower growth, planctomycetes are not outcompeted by faster-growing bacteria in biofilms on such surfaces; however, strategies allowing them to compensate for slower growth have not yet been investigated. Here, we identified stieleriacines, a class of N-acylated tyrosines produced by the novel planctomycete Stieleria maiorica Mal15T, and analysed their effects on growth of the producing strain and bacterial species likely co-occurring with strain Mal15T. Stieleriacines reduced the lag phase of Mal15T and either stimulated or inhibited biofilm formation of two bacterial competitors, indicating that Mal15T employs stieleriacines to specifically alter microbial biofilm composition. The genetic organisation of the putative stieleriacine biosynthetic cluster in strain Mal15T points towards a functional link of stieleriacine biosynthesis to exopolysaccharide-associated protein sorting and biofilm formation.
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Affiliation(s)
| | - Olga Jeske
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.,Leibniz Institute DSMZ, Braunschweig, Germany
| | - Birthe Sandargo
- Helmholtz Centre for Infection Research, Braunschweig, Germany.,German Centre for Infection Research (DZIF), Braunschweig, Germany
| | | | - Sandra Wiegand
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.,Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Frank Surup
- Helmholtz Centre for Infection Research, Braunschweig, Germany. .,German Centre for Infection Research (DZIF), Braunschweig, Germany.
| | - Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands. .,Department of Microbial Interactions, Friedrich-Schiller University, Jena, Germany.
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15
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Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81-W87. [PMID: 31032519 PMCID: PMC6602434 DOI: 10.1093/nar/gkz310] [Citation(s) in RCA: 2077] [Impact Index Per Article: 346.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/02/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.
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Affiliation(s)
- Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Simon Shaw
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Katharina Steinke
- German Centre for Infection Research (DZIF), Interfaculty Institute of Microbiology and Infection Medicine, Auf der Morgenstelle 28, University of Tübingen, 72076 Tübingen, DE, Germany
| | - Rasmus Villebro
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Interfaculty Institute of Microbiology and Infection Medicine, Auf der Morgenstelle 28, University of Tübingen, 72076 Tübingen, DE, Germany
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and BioInformatics Research Center, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
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16
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Lee CM, Kim SY, Yoon SH, Kim JB, Yeo YS, Sim JS, Hahn BS, Kim DG. Characterization of a novel antibacterial N-acyl amino acid synthase from soil metagenome. J Biotechnol 2019; 294:19-25. [DOI: 10.1016/j.jbiotec.2019.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/19/2019] [Accepted: 01/22/2019] [Indexed: 11/30/2022]
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17
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Gao N, Xia M, Dai J, Yu D, An W, Li S, Liu S, He P, Zhang L, Wu Z, Bi X, Chen S, Haft DH, Qiu D. Both widespread PEP-CTERM proteins and exopolysaccharides are required for floc formation of Zoogloea resiniphila and other activated sludge bacteria. Environ Microbiol 2018; 20:1677-1692. [PMID: 29473278 DOI: 10.1111/1462-2920.14080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/12/2018] [Accepted: 02/19/2018] [Indexed: 12/28/2022]
Abstract
Bacterial floc formation plays a central role in the activated sludge (AS) process, which has been widely utilized for sewage and wastewater treatment. The formation of AS flocs has long been known to require exopolysaccharide biosynthesis. This study demonstrates an additional requirement for a PEP-CTERM protein in Zoogloea resiniphila, a dominant AS bacterium harboring a large exopolysaccharide biosynthesis gene cluster. Two members of a wide-spread family of high copy number-per-genome PEP-CTERM genes, transcriptionally regulated by the RpoN sigma factor and accessory PrsK-PrsR two-component system and at least one of these, pepA, must be expressed for Zoogloea to build the floc structures that allow gravitational sludge settling and recycling. Without PrsK or PrsR, Zoogloea cells were planktonic rather than flocculated and secreted exopolysaccharides were released into the growth broth in soluble form. Overexpression of PepA could circumvent the requirement of rpoN, prsK and prsR for the floc-forming phenotype by fixing the exopolysaccharides to bacterial cells. However, overexpression of PepA, which underwent post-translational modifications, could not rescue the long-rod morphology of the rpoN mutant. Consistently, PEP-CTERM genes and exopolysaccharide biosynthesis gene cluster are present in the genome of the floc-forming Nitrospira comammox and Mitsuaria strain as well as many other AS bacteria.
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Affiliation(s)
- Na Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dianzhen Yu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Weixing An
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shuyang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shuangyuan Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Penghui He
- College of Life Sciences, Hubei University, Wuhan 430070, China
| | - Liping Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhenbin Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xuezhi Bi
- Agency for Science, Technology and Research, Bioprocessing Technology Institute, Singapore 138668, Singapore
| | - Shouwen Chen
- College of Life Sciences, Hubei University, Wuhan 430070, China
| | - Daniel H Haft
- National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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18
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Bruns H, Herrmann J, Müller R, Wang H, Wagner Döbler I, Schulz S. Oxygenated N-Acyl Alanine Methyl Esters (NAMEs) from the Marine Bacterium Roseovarius tolerans EL-164. JOURNAL OF NATURAL PRODUCTS 2018; 81:131-139. [PMID: 29261310 DOI: 10.1021/acs.jnatprod.7b00757] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The marine bacterium Roseovarius tolerans EL-164 (Rhodobacteraceae) can produce unique N-acylalanine methyl esters (NAMEs) besides strucutrally related N-acylhomoserine lactones (AHLs), bacterial signaling compounds widespread in the Rhodobacteraceae. The structures of two unprecedented NAMEs carrying a rare terminally oxidized acyl chain are reported here. The compounds (Z)-N-16-hydroxyhexadec-9-enoyl-l-alanine methyl ester (Z9-16-OH-C16:1-NAME, 3) and (Z)-N-15-carboxypentadec-9-enoyl-l-alanine methyl ester (16COOH-C16:1-NAME, 4) were isolated, and the structures were determined by NMR and MS experiments. Both compounds were synthesized to prove assignments and to test their biological activity. Finally, non-natural, structurally related Z9-3-OH-C16:1-NAME (18) was synthesized to investigate the mass spectroscopy of structurally related NAMEs. Compound 3 showed moderate antibacterial activity against microorganisms such as Bacillus, Streptococcus, Micrococcus, or Mucor strains. In contrast to AHLs, quorum-sensing or quorum-quenching activity was not observed.
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Affiliation(s)
- Hilke Bruns
- Institute of Organic Chemistry, Technische Universität Braunschweig , Hagenring 30, 38106 Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarland University , Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarland University , Campus E8.1, 66123 Saarbrücken, Germany
| | - Hui Wang
- Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Irene Wagner Döbler
- Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig , Hagenring 30, 38106 Braunschweig, Germany
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19
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Anchoring of LPXTG-Like Proteins to the Gram-Positive Cell Wall Envelope. Curr Top Microbiol Immunol 2017; 404:159-175. [PMID: 27097813 DOI: 10.1007/82_2016_8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In Gram-positive bacteria, protein precursors with a signal peptide and a cell wall sorting signal (CWSS)-which begins with an LPXTG motif, followed by a hydrophobic domain and a tail of positively charged residues-are targeted to the cell envelope by a transpeptidase enzyme call sortase. Evolution and selective pressure gave rise to six classes of sortase, i.e., SrtA-F. Only class C sortases are capable of polymerizing substrates harboring the pilin motif and CWSS into protein polymers known as pili or fimbriae, whereas the others perform cell wall anchoring functions. Regardless of the products generated from these sortases, the basic principle of sortase-catalyzed transpeptidation is the same. It begins with the cleavage of the LPXTG motif, followed by the cross-linking of this cleaved product at the threonine residue to a nucleophile, i.e., an active amino group of the peptidoglycan stem peptide or the lysine residue of the pilin motif. This chapter will summarize the efforts to identify and characterize sortases and their associated pathways with emphasis on the cell wall anchoring function.
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20
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In silico analyses of conservational, functional and phylogenetic distribution of the LuxI and LuxR homologs in Gram-positive bacteria. Sci Rep 2017; 7:6969. [PMID: 28765541 PMCID: PMC5539150 DOI: 10.1038/s41598-017-07241-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 06/26/2017] [Indexed: 11/08/2022] Open
Abstract
LuxI and LuxR are key factors that drive quorum sensing (QS) in bacteria through secretion and perception of the signaling molecules e.g. N-Acyl homoserine lactones (AHLs). The role of these proteins is well established in Gram-negative bacteria for intercellular communication but remain under-explored in Gram-positive bacteria where QS peptides are majorly responsible for cell-to-cell communication. Therefore, in the present study, we explored conservation, potential function, topological arrangements and evolutionarily aspects of these proteins in Gram-positive bacteria. Putative LuxI/LuxR containing proteins were retrieved using the domain-based strategy from InterPro v62.0 meta-database. Conservational analyses via multiple sequence alignment and domain showed that these are well conserved in Gram-positive bacteria and possess relatedness with Gram-negative bacteria. Further, Gene ontology and ligand-based functional annotation explain their active involvement in signal transduction mechanism via QS signaling molecules. Moreover, Phylogenetic analyses (LuxI, LuxR, LuxI + LuxR and 16s rRNA) revealed horizontal gene transfer events with significant statistical support among Gram-positive and Gram-negative bacteria. This in-silico study offers a detailed overview of potential LuxI/LuxR distribution in Gram-positive bacteria (mainly Firmicutes and Actinobacteria) and their functional role in QS. It would further help in understanding the extent of interspecies communications between Gram-positive and Gram-negative bacteria through QS signaling molecules.
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21
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Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations. Mar Drugs 2017; 15:md15060165. [PMID: 28587290 PMCID: PMC5484115 DOI: 10.3390/md15060165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/22/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023] Open
Abstract
Genome mining has become an increasingly powerful, scalable, and economically accessible tool for the study of natural product biosynthesis and drug discovery. However, there remain important biological and practical problems that can complicate or obscure biosynthetic analysis in genomic and metagenomic sequencing projects. Here, we focus on limitations of available technology as well as computational and experimental strategies to overcome them. We review the unique challenges and approaches in the study of symbiotic and uncultured systems, as well as those associated with biosynthetic gene cluster (BGC) assembly and product prediction. Finally, to explore sequencing parameters that affect the recovery and contiguity of large and repetitive BGCs assembled de novo, we simulate Illumina and PacBio sequencing of the Salinispora tropica genome focusing on assembly of the salinilactam (slm) BGC.
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22
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Zhang X, Liu X, Liang Y, Xiao Y, Ma L, Guo X, Miao B, Liu H, Peng D, Huang W, Yin H. Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps. Front Microbiol 2017; 8:790. [PMID: 28529505 PMCID: PMC5418355 DOI: 10.3389/fmicb.2017.00790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 04/18/2017] [Indexed: 12/27/2022] Open
Abstract
The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Liyuan Ma
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Xue Guo
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
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23
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Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community. Sci Rep 2016; 6:27035. [PMID: 27271534 PMCID: PMC4897644 DOI: 10.1038/srep27035] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/04/2016] [Indexed: 12/02/2022] Open
Abstract
DNA derived from environmental samples is a rich source of novel bioactive molecules. The choice of the habitat to be sampled predefines the properties of the biomolecules to be discovered due to the physiological adaptation of the microbial community to the prevailing environmental conditions. We have constructed a metagenomic library in Escherichia coli DH10b with environmental DNA (eDNA) isolated from the microbial community of a slaughterhouse drain biofilm consisting mainly of species from the family Flavobacteriaceae. By functional screening of this library we have identified several lipases, proteases and two clones (SA343 and SA354) with biosurfactant and hemolytic activities. Sequence analysis of the respective eDNA fragments and subsequent structure homology modelling identified genes encoding putative N-acyl amino acid synthases with a unique two-domain organisation. The produced biosurfactants were identified by NMR spectroscopy as N-acyltyrosines with N-myristoyltyrosine as the predominant species. Critical micelle concentration and reduction of surface tension were similar to those of chemically synthesised N-myristoyltyrosine. Furthermore, we showed that the newly isolated N-acyltyrosines exhibit antibiotic activity against various bacteria. This is the first report describing the successful application of functional high-throughput screening assays for the identification of biosurfactant producing clones within a metagenomic library.
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24
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Ullrich SR, González C, Poehlein A, Tischler JS, Daniel R, Schlömann M, Holmes DS, Mühling M. Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum". Front Microbiol 2016; 7:797. [PMID: 27303384 PMCID: PMC4886054 DOI: 10.3389/fmicb.2016.00797] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/11/2016] [Indexed: 01/07/2023] Open
Abstract
Acid mine drainage (AMD), associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at pH below 4. Members of the recently proposed genus “Ferrovum” are the first acidophilic iron oxidizers to be described within the Betaproteobacteria. Although they have been detected as typical community members in AMD habitats worldwide, knowledge of their phylogenetic and metabolic diversity is scarce. Genomics approaches appear to be most promising in addressing this lacuna since isolation and cultivation of “Ferrovum” has proven to be extremely difficult and has so far only been successful for the designated type strain “Ferrovum myxofaciens” P3G. In this study, the genomes of two novel strains of “Ferrovum” (PN-J185 and Z-31) derived from water samples of a mine water treatment plant were sequenced. These genomes were compared with those of “Ferrovum” sp. JA12 that also originated from the mine water treatment plant, and of the type strain (P3G). Phylogenomic scrutiny suggests that the four strains represent three “Ferrovum” species that cluster in two groups (1 and 2). Comprehensive analysis of their predicted metabolic pathways revealed that these groups harbor characteristic metabolic profiles, notably with respect to motility, chemotaxis, nitrogen metabolism, biofilm formation and their potential strategies to cope with the acidic environment. For example, while the “F. myxofaciens” strains (group 1) appear to be motile and diazotrophic, the non-motile group 2 strains have the predicted potential to use a greater variety of fixed nitrogen sources. Furthermore, analysis of their genome synteny provides first insights into their genome evolution, suggesting that horizontal gene transfer and genome reduction in the group 2 strains by loss of genes encoding complete metabolic pathways or physiological features contributed to the observed diversification.
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Affiliation(s)
- Sophie R Ullrich
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres BelloSantiago, Chile; Bio-Computing and Applied Genetics Division, Fraunhofer Chile Research Foundation, Center for Systems BiotechnologySantiago, Chile
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Georg-August Universität Göttingen Göttingen, Germany
| | - Judith S Tischler
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Georg-August Universität Göttingen Göttingen, Germany
| | - Michael Schlömann
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Depto. de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello Santiago, Chile
| | - Martin Mühling
- Institute of Biological Sciences, TU Bergakademie Freiberg Freiberg, Germany
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25
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Luo J, Wei L, Hao T, Xue W, Mackey HR, Chen GH. Effect ofl-tyrosine on aerobic sludge granulation and its stability. RSC Adv 2015. [DOI: 10.1039/c5ra14596a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aerobic sludge granulation and its stability remain challenging in applications.
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Affiliation(s)
- Jinghai Luo
- Department of Civil and Environmental Engineering
- The Hong Kong University of Science and Technology
- China
| | - Li Wei
- Department of Civil and Environmental Engineering
- The Hong Kong University of Science and Technology
- China
| | - Tianwei Hao
- Department of Civil and Environmental Engineering
- The Hong Kong University of Science and Technology
- China
| | - Weiqi Xue
- Department of Civil and Environmental Engineering
- The Hong Kong University of Science and Technology
- China
| | - Hamish R. Mackey
- College of Science and Engineering
- Hamad Bin Khalifa University
- Education City
- Doha
- Qatar
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering
- The Hong Kong University of Science and Technology
- China
- SYSU-HKUST Research Centre for Innovative Environmental Technology
- Sun Yat-sen University
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26
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Aruni AW, Robles A, Fletcher HM. VimA mediates multiple functions that control virulence in Porphyromonas gingivalis. Mol Oral Microbiol 2012; 28:167-80. [PMID: 23279905 DOI: 10.1111/omi.12017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2012] [Indexed: 12/31/2022]
Abstract
Porphyromonas gingivalis, a black-pigmented, gram-negative anaerobe, is an important etiological agent of periodontal disease. Its ability to survive in the periodontal pocket and orchestrate the microbial/host activities that can lead to disease suggest that P. gingivalis possesses a complex regulatory network involving transcriptional and post-transcriptional mechanisms. The vimA (virulence modulating) gene is part of the 6.15-kb bcp-recA-vimA-vimE-vimF-aroG locus and plays a role in oxidative stress resistance. In addition to the glycosylation and anchorage of several surface proteins including the gingipains, VimA can also modulate sialylation, acetyl coenzyme A transfer, lipid A and its associated proteins and may be involved in protein sorting and transport. In this review, we examine the multifunctional role of VimA and discuss its possible involvement in a major regulatory network important for survival and virulence regulation in P. gingivalis. It is postulated that the multifunction of VimA is modulated via a post-translational mechanism involving acetylation.
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Affiliation(s)
- A W Aruni
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
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27
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He R, Wakimoto T, Egami Y, Kenmoku H, Ito T, Asakawa Y, Abe I. Heterologously expressed β-hydroxyl fatty acids from a metagenomic library of a marine sponge. Bioorg Med Chem Lett 2012; 22:7322-5. [DOI: 10.1016/j.bmcl.2012.10.082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 10/16/2012] [Accepted: 10/17/2012] [Indexed: 10/27/2022]
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28
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Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. J Bacteriol 2011; 194:36-48. [PMID: 22037399 DOI: 10.1128/jb.06026-11] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multiple new prokaryotic C-terminal protein-sorting signals were found that reprise the tripartite architecture shared by LPXTG and PEP-CTERM: motif, TM helix, basic cluster. Defining hidden Markov models were constructed for all. PGF-CTERM occurs in 29 archaeal species, some of which have more than 50 proteins that share the domain. PGF-CTERM proteins include the major cell surface protein in Halobacterium, a glycoprotein with a partially characterized diphytanylglyceryl phosphate linkage near its C terminus. Comparative genomics identifies a distant exosortase homolog, designated archaeosortase A (ArtA), as the likely protein-processing enzyme for PGF-CTERM. Proteomics suggests that the PGF-CTERM region is removed. Additional systems include VPXXXP-CTERM/archeaosortase B in two of the same archaea and PEF-CTERM/archaeosortase C in four others. Bacterial exosortases often fall into subfamilies that partner with very different cohorts of extracellular polymeric substance biosynthesis proteins; several species have multiple systems. Variant systems include the VPDSG-CTERM/exosortase C system unique to certain members of the phylum Verrucomicrobia, VPLPA-CTERM/exosortase D in several alpha- and deltaproteobacterial species, and a dedicated (single-target) VPEID-CTERM/exosortase E system in alphaproteobacteria. Exosortase-related families XrtF in the class Flavobacteria and XrtG in Gram-positive bacteria mark distinctive conserved gene neighborhoods. A picture emerges of an ancient and now well-differentiated superfamily of deeply membrane-embedded protein-processing enzymes. Their target proteins are destined to transit cellular membranes during their biosynthesis, during which most undergo additional posttranslational modifications such as glycosylation.
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