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Hernández-Soto LM, Martínez-Abarca F, Ramírez-Saad H, López-Pérez M, Aguirre-Garrido JF. Genome analysis of haloalkaline isolates from the soda saline crater lake of Isabel Island; comparative genomics and potential metabolic analysis within the genus Halomonas. BMC Genomics 2023; 24:696. [PMID: 37986038 PMCID: PMC10662389 DOI: 10.1186/s12864-023-09800-9] [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: 06/23/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Isabel Island is a Mexican volcanic island primarily composed of basaltic stones. It features a maar known as Laguna Fragatas, which is classified as a meromictic thalassohaline lake. The constant deposition of guano in this maar results in increased levels of phosphorus, nitrogen, and carbon. The aim of this study was to utilize high-quality genomes from the genus Halomonas found in specialized databases as a reference for genome mining of moderately halophilic bacteria isolated from Laguna Fragatas. This research involved genomic comparisons employing phylogenetic, pangenomic, and metabolic-inference approaches. RESULTS The Halomonas genus exhibited a large open pangenome, but several genes associated with salt metabolism and homeostatic regulation (ectABC and betABC), nitrogen intake through nitrate and nitrite transporters (nasA, and narGI), and phosphorus uptake (pstABCS) were shared among the Halomonas isolates. CONCLUSIONS The isolated bacteria demonstrate consistent adaptation to high salt concentrations, and their nitrogen and phosphorus uptake mechanisms are highly optimized. This optimization is expected in an extremophile environment characterized by minimal disturbances or abrupt seasonal variations. The primary significance of this study lies in the dearth of genomic information available for this saline and low-disturbance environment. This makes it important for ecosystem conservation and enabling an exploration of its biotechnological potential. Additionally, the study presents the first two draft genomes of H. janggokensis.
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Affiliation(s)
- Luis Mario Hernández-Soto
- Doctorado en Ciencias Biológicas y de La Salud, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Francisco Martínez-Abarca
- Estructura, Dinámica y Función de Genomas de Rizobacterias, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - Hugo Ramírez-Saad
- Departamento Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de Mexico, México
| | - Marcos López-Pérez
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana-Lerma, Estado de México, Lerma, México
| | - José Félix Aguirre-Garrido
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana-Lerma, Estado de México, Lerma, México.
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Sukmarini L. Recent Advances in Discovery of Lead Structures from Microbial Natural Products: Genomics- and Metabolomics-Guided Acceleration. Molecules 2021; 26:molecules26092542. [PMID: 33925414 PMCID: PMC8123854 DOI: 10.3390/molecules26092542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 01/17/2023] Open
Abstract
Natural products (NPs) are evolutionarily optimized as drug-like molecules and remain the most consistently successful source of drugs and drug leads. They offer major opportunities for finding novel lead structures that are active against a broad spectrum of assay targets, particularly those from secondary metabolites of microbial origin. Due to traditional discovery approaches’ limitations relying on untargeted screening methods, there is a growing trend to employ unconventional secondary metabolomics techniques. Aided by the more in-depth understanding of different biosynthetic pathways and the technological advancement in analytical instrumentation, the development of new methodologies provides an alternative that can accelerate discoveries of new lead-structures of natural origin. This present mini-review briefly discusses selected examples regarding advancements in bioinformatics and genomics (focusing on genome mining and metagenomics approaches), as well as bioanalytics (mass-spectrometry) towards the microbial NPs-based drug discovery and development. The selected recent discoveries from 2015 to 2020 are featured herein.
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Affiliation(s)
- Linda Sukmarini
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Cibinong, Bogor 16911, West Java, Indonesia
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3
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Genome Mining as New Challenge in Natural Products Discovery. Mar Drugs 2020; 18:md18040199. [PMID: 32283638 PMCID: PMC7230286 DOI: 10.3390/md18040199] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/17/2022] Open
Abstract
Drug discovery is based on bioactivity screening of natural sources, traditionally represented by bacteria fungi and plants. Bioactive natural products and their secondary metabolites have represented the main source for new therapeutic agents, used as drug leads for new antibiotics and anticancer agents. After the discovery of the first biosynthetic genes in the last decades, the researchers had in their hands the tool to understand the biosynthetic logic and genetic basis leading to the production of these compounds. Furthermore, in the genomic era, in which the number of available genomes is increasing, genome mining joined to synthetic biology are offering a significant help in drug discovery. In the present review we discuss the importance of genome mining and synthetic biology approaches to identify new natural products, also underlining considering the possible advantages and disadvantages of this technique. Moreover, we debate the associated techniques that can be applied following to genome mining for validation of data. Finally, we review on the literature describing all novel natural drugs isolated from bacteria, fungi, and other living organisms, not only from the marine environment, by a genome-mining approach, focusing on the literature available in the last ten years.
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Bruns H, Crüsemann M, Letzel AC, Alanjary M, McInerney JO, Jensen PR, Schulz S, Moore BS, Ziemert N. Function-related replacement of bacterial siderophore pathways. ISME JOURNAL 2017; 12:320-329. [PMID: 28809850 PMCID: PMC5776446 DOI: 10.1038/ismej.2017.137] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/13/2017] [Accepted: 07/14/2017] [Indexed: 01/16/2023]
Abstract
Bacterial genomes are rife with orphan biosynthetic gene clusters (BGCs) associated with secondary metabolism of unrealized natural product molecules. Often up to a tenth of the genome is predicted to code for the biosynthesis of diverse metabolites with mostly unknown structures and functions. This phenomenal diversity of BGCs coupled with their high rates of horizontal transfer raise questions about whether they are really active and beneficial, whether they are neutral and confer no advantage, or whether they are carried in genomes because they are parasitic or addictive. We previously reported that Salinispora bacteria broadly use the desferrioxamine family of siderophores for iron acquisition. Herein we describe a new and unrelated group of peptidic siderophores called salinichelins from a restricted number of Salinispora strains in which the desferrioxamine biosynthesis genes have been lost. We have reconstructed the evolutionary history of these two different siderophore families and show that the acquisition and retention of the new salinichelin siderophores co-occurs with the loss of the more ancient desferrioxamine pathway. This identical event occurred at least three times independently during the evolution of the genus. We surmise that certain BGCs may be extraneous because of their functional redundancy and demonstrate that the relative evolutionary pace of natural pathway replacement shows high selective pressure against retention of functionally superfluous gene clusters.
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Affiliation(s)
- Hilke Bruns
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mohammad Alanjary
- German Center for Infection Biology (DZIF), Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - James O McInerney
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, Health and Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nadine Ziemert
- German Center for Infection Biology (DZIF), Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
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Molloy EM, Tietz JI, Blair PM, Mitchell DA. Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products. Bioorg Med Chem 2016; 24:6276-6290. [PMID: 27234886 PMCID: PMC5108699 DOI: 10.1016/j.bmc.2016.05.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/08/2016] [Accepted: 05/13/2016] [Indexed: 01/04/2023]
Abstract
The hygrolides, a family of 16-member-ring-containing plecomacrolides produced by Actinobacteria, exhibit numerous reported bioactivities. Using HR-MS/MS, nucleophilic 1,4-addition-based labeling, NMR, and bioinformatic analysis, we identified Streptomyces varsoviensis as a novel producer of JBIR-100, a fumarate-containing hygrolide, and elucidated the previously unknown stereochemistry of the natural product. We investigated the antimicrobial activity of JBIR-100, with preliminary insight into mode of action indicating that it perturbs the membrane of Bacillus subtilis. S. varsoviensis is known to produce compounds from multiple hygrolide sub-families, namely hygrobafilomycins (JBIR-100 and hygrobafilomycin) and bafilomycins (bafilomycin C1 and D). In light of this, we identified the biosynthetic gene cluster for JBIR-100, which, to our knowledge, represents the first reported for a hygrobafilomycin. Finally, we performed a bioinformatic analysis of the hygrolide family, describing clusters from known and predicted producers. Our results indicate that potential remains for the Actinobacteria to yield novel hygrolide congeners, perhaps with differing biological activities.
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Affiliation(s)
- Evelyn M Molloy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Patricia M Blair
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Walther E, Boldt S, Kage H, Lauterbach T, Martin K, Roth M, Hertweck C, Sauerbrei A, Schmidtke M, Nett M. Zincophorin - biosynthesis in Streptomyces griseus and antibiotic properties. GMS INFECTIOUS DISEASES 2016; 4:Doc08. [PMID: 30671322 PMCID: PMC6301713 DOI: 10.3205/id000026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Zincophorin is a polyketide antibiotic that possesses potent activity against Gram-positive bacteria, including human pathogens. While a number of total syntheses of this highly functionalized natural product were reported since its initial discovery, the genetic basis for the biosynthesis of zincophorin has remained unclear. In this study, the co-linearity inherent to polyketide pathways was used to identify the zincophorin biosynthesis gene cluster in the genome of the natural producer Streptomyces griseus HKI 0741. Interestingly, the same locus is fully conserved in the streptomycin-producing actinomycete S. griseus IFO 13350, suggesting that the latter bacterium is also capable of zincophorin biosynthesis. Biological profiling of zincophorin revealed a dose-dependent inhibition of the Gram-positive bacterium Streptococcus pneumoniae. The antibacterial effect, however, is accompanied by cytotoxicity. Antibiotic and cytotoxic activities were completely abolished upon esterification of the carboxylic acid group in zincophorin.
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Affiliation(s)
- Elisabeth Walther
- Jena University Hospital, Department of Virology and Antiviral Therapy, Jena, Germany
| | - Sabrina Boldt
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Hirokazu Kage
- Technical University Dortmund, Department of Biochemical and Chemical Engineering, Dortmund, Germany
| | - Tom Lauterbach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Karin Martin
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Andreas Sauerbrei
- Jena University Hospital, Department of Virology and Antiviral Therapy, Jena, Germany
| | - Michaela Schmidtke
- Jena University Hospital, Department of Virology and Antiviral Therapy, Jena, Germany
| | - Markus Nett
- Technical University Dortmund, Department of Biochemical and Chemical Engineering, Dortmund, Germany
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7
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Ziemert N, Alanjary M, Weber T. The evolution of genome mining in microbes - a review. Nat Prod Rep 2016; 33:988-1005. [PMID: 27272205 DOI: 10.1039/c6np00025h] [Citation(s) in RCA: 404] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.
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Affiliation(s)
- Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tuebingen, Germany.
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Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis. Appl Environ Microbiol 2016; 82:1945-1957. [PMID: 26773087 DOI: 10.1128/aem.03011-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/10/2016] [Indexed: 11/20/2022] Open
Abstract
Here, we report the complete genome sequence of the type strain of the myxobacterial genus Chondromyces, Chondromyces crocatus Cm c5. It presents one of the largest prokaryotic genomes featuring a single circular chromosome and no plasmids. Analysis revealed an enlarged set of tRNA genes, along with reduced pressure on preferred codon usage compared to that of other bacterial genomes. The large coding capacity and the plethora of encoded secondary metabolite biosynthetic gene clusters are in line with the capability of Cm c5 to produce an arsenal of antibacterial, antifungal, and cytotoxic compounds. Known pathways of the ajudazol, chondramide, chondrochloren, crocacin, crocapeptin, and thuggacin compound families are complemented by many more natural compound biosynthetic gene clusters in the chromosome. Whole-genome comparison of the fruiting-body-forming type strain (Cm c5, DSM 14714) to an accustomed laboratory strain which has lost this ability (nonfruiting phenotype, Cm c5 fr-) revealed genetic changes in three loci. In addition to the low synteny found with the closest sequenced representative of the same family, Sorangium cellulosum, extensive genetic information duplication and broad application of eukaryotic-type signal transduction systems are hallmarks of this 11.3-Mbp prokaryotic genome.
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9
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Kleigrewe K, Almaliti J, Tian IY, Kinnel RB, Korobeynikov A, Monroe EA, Duggan BM, Di Marzo V, Sherman DH, Dorrestein PC, Gerwick L, Gerwick WH. Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria. JOURNAL OF NATURAL PRODUCTS 2015; 78:1671-82. [PMID: 26149623 PMCID: PMC4681511 DOI: 10.1021/acs.jnatprod.5b00301] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
An innovative approach was developed for the discovery of new natural products by combining mass spectrometric metabolic profiling with genomic analysis and resulted in the discovery of the columbamides, a new class of di- and trichlorinated acyl amides with cannabinomimetic activity. Three species of cultured marine cyanobacteria, Moorea producens 3L, Moorea producens JHB, and Moorea bouillonii PNG, were subjected to genome sequencing and analysis for their recognizable biosynthetic pathways, and this information was then compared with their respective metabolomes as detected by MS profiling. By genome analysis, a presumed regulatory domain was identified upstream of several previously described biosynthetic gene clusters in two of these cyanobacteria, M. producens 3L and M. producens JHB. A similar regulatory domain was identified in the M. bouillonii PNG genome, and a corresponding downstream biosynthetic gene cluster was located and carefully analyzed. Subsequently, MS-based molecular networking identified a series of candidate products, and these were isolated and their structures rigorously established. On the basis of their distinctive acyl amide structure, the most prevalent metabolite was evaluated for cannabinomimetic properties and found to be moderate affinity ligands for CB1.
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Affiliation(s)
- Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
| | - Jehad Almaliti
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
| | - Isaac Yuheng Tian
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
- University of California Berkeley, USA
| | | | - Anton Korobeynikov
- Faculty of Mathematics and Mechanics, Saint Petersburg State University, Russia
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Russia
- Algorithmic Biology Laboratory, Saint Petersburg Academic University, Russia
| | - Emily A. Monroe
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
- Department of Biology, William Paterson University of New Jersey, USA
| | - Brendan M. Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, USA
| | - Vincenzo Di Marzo
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Italy
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, USA
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Kage H, Riva E, Parascandolo JS, Kreutzer MF, Tosin M, Nett M. Chemical chain termination resolves the timing of ketoreduction in a partially reducing iterative type I polyketide synthase. Org Biomol Chem 2015; 13:11414-7. [DOI: 10.1039/c5ob02009c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Feeding of Ralstonia solanacearum with synthetic probes unravels the programming of a partially reducing iterative type I polyketide synthase.
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Affiliation(s)
- Hirokazu Kage
- Leibniz Institute for Natural Product Research and Infection Biology
- Hans-Knöll-Institute
- D-07745 Jena
- Germany
| | - Elena Riva
- Department of Chemistry
- University of Warwick
- Coventry CV4 7AC
- UK
| | | | - Martin F. Kreutzer
- Leibniz Institute for Natural Product Research and Infection Biology
- Hans-Knöll-Institute
- D-07745 Jena
- Germany
| | - Manuela Tosin
- Department of Chemistry
- University of Warwick
- Coventry CV4 7AC
- UK
| | - Markus Nett
- Leibniz Institute for Natural Product Research and Infection Biology
- Hans-Knöll-Institute
- D-07745 Jena
- Germany
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