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Sundaramahalingam MA, Amrutha C, Rajeshbanu J, Thirukumaran K, Manibalan S, Ashokkumar M, Sivashanmugam P. In silico approach for enhancing innate lipid content of Yarrowia lipolytica, by blocking the acyl-CoA oxidase-1 enzyme, using various analogous compounds of lipids. J Biomol Struct Dyn 2023; 41:511-524. [PMID: 34825634 DOI: 10.1080/07391102.2021.2008498] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Yarrowia lipolytica is used as a model in this study to screen the potential candidates for inflating the innate lipid content of the cell. This study focuses on reducing the lipid degradation that occurs by the β-oxidation process and discursively increasing the innate lipid content. Acyl-CoA oxidase-1, the primary and initial enzyme involved in the lipid degradation pathway, was selected as a target and blocked using various lipid analogous compounds. The blocking study was carried out using molecular docking and dynamic studies using computation tools. The largest active site pocket located around the Phe-394 amino acid of the target protein is taken as a site for docking. The molecular docking was performed for the selected compounds (citric acid, Finsolv, lactic acid, oxalic acid, Tween-80 and Triton X-100) and the docking results were compared with the outcome of the standard molecule (octadecatrienoic acid). Citric acid, Finsolv, Tween-80 and Triton X-100 were found to be the potential candidates for blocking the target molecule in the static condition using docking studies, revealing a minimum binding energy requirement than the standard molecule. They were further taken for a dynamics study using GROMACS software. The RMSD, RMSF, number of hydrogen bond interactions and radius of gyration of the complex molecules were studied in a dynamic approach for 100 ns. Citric acid has been found to be the potential hit compound to block acyl-CoA oxidase-1 enzyme with its maximum hydrogen interaction and minimum fluctuations. It also revealed out the minimum total energy requirement for the complex formation.
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Affiliation(s)
- M A Sundaramahalingam
- Chemical and Biochemical Process Engineering Laboratory, Department of Chemical Engineering, National Institute of Technology Tiruchirappalli, Tamilnadu, India
| | - C Amrutha
- Chemical and Biochemical Process Engineering Laboratory, Department of Chemical Engineering, National Institute of Technology Tiruchirappalli, Tamilnadu, India
| | - J Rajeshbanu
- Department of Life Sciences, Central University of Tamil Nadu, Neelakudi, Thiruvarur, Tamilnadu, India
| | - K Thirukumaran
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India
| | - S Manibalan
- Department of Biotechnology, Kamaraj College of Engineering and Technology, Madurai, Tamilnadu, India
| | | | - P Sivashanmugam
- Chemical and Biochemical Process Engineering Laboratory, Department of Chemical Engineering, National Institute of Technology Tiruchirappalli, Tamilnadu, India
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Sukrama IDM, Pinatih KJP, Hendrayana MA, Rasyid B, Wedari NLPH. Escherichia coli Clonal Variability Based on Genetic Diversity Pattern with Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction Methods for Traveler’s Diarrhea Cases in Bali. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.8990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Bali is a favorite tourism destination in the world. As a major tourist destination, the incidence of illness that afflicts tourists greatly affects the image of tourism. Diarrhea is a health problem that is most often experienced and is a major obstacle for foreign tourists when traveling, especially to Bali. Escherichia coli (E. coli) bacteria cause diarrhea more often than viruses in some developing countries. Genetic differences can affect the characteristics of E. coli, especially in relation to the medical field.
AIM: We would like to assess the genetic diversity of the different pathogenic E. coli from various clinical isolates including those from traveler’s diarrhea in Bali, Indonesia.
MATERIALS AND METHODS: One of the molecular techniques used in this study is to use enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). The sample in this study was the feces of foreign tourists with traveler’s diarrhea in Bali. This study carried out research procedures in the form of Isolation of E. coli genome DNA from culture, amplification of E. coli 16S rRNA encoding genes, sequencing of E. coli 16S rRNA encoding genes, phylogenetic tree construction, and then analysis of E. coli genetic diversity with ERIC-PCR sequences.
RESULTS: The results showed that the ERIC-PCR method was more discriminatory than other methods to analyze the genetic diversity of E. coli from fecal samples of patients with traveler’s diarrhea. It was found that clonal variability based on the genetic similarity of all sample E. coli isolates varied from 0% to 100%.
CONCLUSIONS: This shows that the source of transmission and the strains of E. coli that cause it comes from diverse populations.
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Singh NK, Choudhary S. Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:58819-58836. [PMID: 33410029 DOI: 10.1007/s11356-020-11705-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Hydrocarbon is a primary source of energy in the current urbanized society. Considering the increasing demand, worldwide oil productions are declining due to maturity of oil fields and because of difficulty in discovering new oil fields to substitute the exploited ones. To meet current and future energy demands, further exploitation of oil resources is highly required. Microorganisms inhabiting in these areas exhibit highly diverse catabolic activities to degrade, transform, or accumulate various hydrocarbons. Enrichment of hydrocarbon-utilizing bacteria in oil basin is caused by continuous long duration and low molecular weight hydrocarbon microseepage which plays a very important role as an indicator for petroleum prospecting. The important microbial metabolic processes in most of the oil reservoir are sulfate reduction, fermentation, acetogenesis, methanogenesis, NO3- reduction, and Fe (III) and Mn (IV) reduction. The microorganisms residing in these sites have critical control on petroleum composition, recovery, and production methods. Physical characteristics of heavy oil are altered by microbial biotransformation and biosurfactant production. Considering oil to be one of the most vital energy resources, it is important to have a comprehensive understanding of petroleum microbiology. This manuscript reviews the recent research work referring to the diversity of bacteria in oil field and reservoir sites and their applications for enhancing oil transformation in the target reservoir and geomicrobial prospecting scope for petroleum exploration.
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Affiliation(s)
- Nishi Kumari Singh
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan, 304022, India
| | - Sangeeta Choudhary
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan, 304022, India.
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Sangannavar PA, Kumar JS, Subrahmanyam G, Kutala S. Genomics and omics tools to assess complex microbial communities in silkworms: A paradigm shift towards translational research. J Microbiol Methods 2021. [DOI: 10.1016/bs.mim.2021.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Jack CN, Petipas RH, Cheeke TE, Rowland JL, Friesen ML. Microbial Inoculants: Silver Bullet or Microbial Jurassic Park? Trends Microbiol 2020; 29:299-308. [PMID: 33309525 DOI: 10.1016/j.tim.2020.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023]
Abstract
The appeal of using microbial inoculants to mediate plant traits and productivity in managed ecosystems has increased over the past decade, because microbes represent an alternative to fertilizers, pesticides, and direct genetic modification of plants. Using microbes bypasses many societal and environmental concerns because microbial products are considered a more sustainable and benign technology. In our desire to harness the power of plant-microbial symbioses, are we ignoring the possibility of precipitating microbial invasions, potentially setting ourselves up for a microbial Jurassic Park? Here, we outline potential negative consequences of microbial invasions and describe a set of practices (Testing, Regulation, Engineering, and Eradication, TREE) based on the four stages of invasion to prevent microbial inoculants from becoming invasive. We aim to stimulate discussion about best practices to proactively prevent microbial invasions.
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Affiliation(s)
- Chandra N Jack
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA.
| | - Renee H Petipas
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Tanya E Cheeke
- Department of Biological Sciences, Washington State University, Richland, WA 99354, USA
| | - Jennifer L Rowland
- AAAS Science and Technology Policy Fellow hosted by United States Department of Agriculture- APHIS Plant Protection and Quarantine, Riverdale, MD 20737, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA; Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
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A meta-barcoding analysis of soil mycobiota of the upper Andean Colombian agro-environment. Sci Rep 2019; 9:10085. [PMID: 31300737 PMCID: PMC6625999 DOI: 10.1038/s41598-019-46485-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/17/2019] [Indexed: 11/23/2022] Open
Abstract
Colombia is a country for which one of the highest biodiversity rates is reported, and one of the first in the tropical areas where an effort was made to gather information on indigenous fungi. Nevertheless, mycological data are still scarce and discontinuous, above all on soil fungi. The present study wanted to contribute to unveil the large soil fungal biodiversity in the upper Andean Colombian agro-ecosystems. The studied area is located in the department of Boyacà, considered with a notable economical value, partly devoted to subsistence agriculture. More than 150 described species were revealed in this study, belonging to 5 phyla with Ascomycota representing the dominant taxon. Basidiomycota and Zygomycota are also well represented, dominated by species of the genus Sebacina and Mortierella respectively, mainly distributed in the semi-natural plots (woodland and grassland). Most of the species are reported as first records for Colombia. Some of them are particularly interesting for their conservation significance such as Geoglossum fallax, which is the dominant species in the unimproved grassland plot. The bootstrap-based clustering analysis showed a different distribution of the species in orchards and non-cultivated areas as a possible response of the fungal community to different use of soil in the agro-environment.
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Calderon D, Peña L, Suarez A, Villamil C, Ramirez-Rojas A, Anzola JM, García-Betancur JC, Cepeda ML, Uribe D, Del Portillo P, Mongui A. Recovery and functional validation of hidden soil enzymes in metagenomic libraries. Microbiologyopen 2019; 8:e00572. [PMID: 30851083 PMCID: PMC6460280 DOI: 10.1002/mbo3.572] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/01/2017] [Accepted: 11/09/2017] [Indexed: 11/10/2022] Open
Abstract
The vast microbial diversity on the planet represents an invaluable source for identifying novel activities with potential industrial and therapeutic application. In this regard, metagenomics has emerged as a group of strategies that have significantly facilitated the analysis of DNA from multiple environments and has expanded the limits of known microbial diversity. However, the functional characterization of enzymes, metabolites, and products encoded by diverse microbial genomes is limited by the inefficient heterologous expression of foreign genes. We have implemented a pipeline that combines NGS and Sanger sequencing as a way to identify fosmids within metagenomic libraries. This strategy facilitated the identification of putative proteins, subcloning of targeted genes and preliminary characterization of selected proteins. Overall, the in silico approach followed by the experimental validation allowed us to efficiently recover the activity of previously hidden enzymes derived from agricultural soil samples. Therefore, the methodology workflow described herein can be applied to recover activities encoded by environmental DNA from multiple sources.
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Affiliation(s)
- Dayana Calderon
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Luis Peña
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Friedrich-Schiller Universität, Jena, Germany
| | - Angélica Suarez
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Carolina Villamil
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Adan Ramirez-Rojas
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Juan M Anzola
- Computational Biology, Corporación CorpoGen, Bogotá, Colombia
| | | | - Martha L Cepeda
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Daniel Uribe
- Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Alvaro Mongui
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia.,Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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8
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New tuberculosis drug leads from naturally occurring compounds. Int J Infect Dis 2017; 56:212-220. [PMID: 28062229 DOI: 10.1016/j.ijid.2016.12.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis (TB) continues to be a significant cause of mortality and morbidity worldwide. An estimated 2 billion individuals are infected with Mycobacterium tuberculosis and annually there are approximately 10 million new cases of clinical TB and 1.5 million deaths. Currently available drugs and vaccines have had no significant impact on TB control. In addition, the emergence of drug resistant TB is considered a public health crisis, with some strains now resistant to all available drugs. Unfortunately, the growing burden of antibiotic resistance is coupled with decreased effort in the development of new antibiotics. Natural sources are attractive starting points in the search for anti-tubercular drugs because they are extremely rich in chemical diversity and have privileged antimicrobial activity. This review will discuss recent advances in the development of TB drug leads from natural products, with a particular focus on anti-mycobacterial compounds in late-stage preclinical and clinical development.
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Mourembou G, Yasir M, Azhar EI, Lagier JC, Bibi F, Jiman-Fatani AA, Helmy N, Robert C, Rathored J, Fournier PE, Raoult D, Million M. Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:766-76. [PMID: 26669711 DOI: 10.1089/omi.2015.0143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Microbial culturomics is a new field of omics sciences that examines the bacterial diversity of human gut coupled with a taxono-genomic strategy. Using microbial culturomics, we report here for the first time a novel Gram negative, catalase- and oxidase-negative, strict anaerobic bacilli named Beduini massiliensis gen. nov., sp nov. strain GM1 (= CSUR P1440 = DSM 100188), isolated from the stools of a female nomadic Bedouin from Saudi Arabia. With a length of 2,850,586 bp, the Beduini massiliensis genome exhibits a G + C content of 35.9%, and contains 2819 genes (2744 protein-coding and 75 RNA genes including 57 tRNA and 18 rRNA genes). It is composed of 6 scaffolds (composed of 6 contigs). A total of 1859 genes (67.75%) were assigned a putative function (by COGs or by NR blast). At least 1457 (53%) orthologous proteins were not shared with the closest phylogenetic species. 274 genes (10.0%) were identified as ORFans. These results show that microbial culturomics can dramatically improve the characterization of the human microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in health and disease. Microbial culturomics is an emerging frontier of omics systems sciences and integrative biology and thus, warrants further consideration as part of the postgenomics methodology toolbox.
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Affiliation(s)
- Gaël Mourembou
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France .,2 Regional Doctoral School of Central Africa , Franceville, Gabon
| | - Muhammad Yasir
- 3 Special Infectious Agents Unit, King Fahd Medical Research Center , King Abdulaziz University , Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- 3 Special Infectious Agents Unit, King Fahd Medical Research Center , King Abdulaziz University , Jeddah, Saudi Arabia .,4 Department of Medical Laboratory Technology, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Jean Christophe Lagier
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Fehmida Bibi
- 3 Special Infectious Agents Unit, King Fahd Medical Research Center , King Abdulaziz University , Jeddah, Saudi Arabia
| | - Asif Ahmad Jiman-Fatani
- 5 Department of Medical Microbiology and Parasitology, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Nayel Helmy
- 6 Department of Obstetrics and Gynaecology, Suliman Fageeh Hospital , Jeddah, Saudi Arabia
| | - Catherine Robert
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Jaishriram Rathored
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Pierre-Edouard Fournier
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France .,3 Special Infectious Agents Unit, King Fahd Medical Research Center , King Abdulaziz University , Jeddah, Saudi Arabia
| | - Matthieu Million
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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Bernabò N, Ordinelli A, Di Agostino R, Mattioli M, Barboni B. Network analyses of sperm-egg recognition and binding: ready to rethink fertility mechanisms? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 18:740-53. [PMID: 25454512 DOI: 10.1089/omi.2014.0128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The rapid growth of published literature makes biomedical text mining increasingly invaluable for unpacking implicit knowledge hidden in unstructured text. We employed biomedical text mining and biological networks analyses to research the process of sperm egg recognition and binding (SERB). We selected from the literature the molecules expressed either on spermatozoa or on oocytes thought to be involved in SERB and, using an automated literature search software (Agilent Literature Search), we realized a network, SERBN, characterized by a hierarchical scale free and a small world topology. We used an integrated approach, either based on selection of hubs or by a cluster analysis, to discern the key molecules of SERB. We found that in most cases some of them are not directly situated on spermatozoa and oocyte, but are dispersed in oviductal fluid or embedded in exosomes present in the perivitelline space. To confirm and validate our results, we performed further analyses using STRING and Reactome FI software. Our findings underscore that the fertility is not a property of gametes in isolation, but rather depends on the functional integrity of the entire reproductive system. These observations collectively underscore the importance of integrative biology in exploring biological systems and in rethinking of fertility mechanisms in the light of this innovative approach.
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Affiliation(s)
- Nicola Bernabò
- Faculty of Veterinary Medicine, University of Teramo , Teramo, Italy
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A Delphi Technology Foresight Study: Mapping Social Construction of Scientific Evidence on Metagenomics Tests for Water Safety. PLoS One 2015; 10:e0129706. [PMID: 26066837 PMCID: PMC4465892 DOI: 10.1371/journal.pone.0129706] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 05/12/2015] [Indexed: 11/19/2022] Open
Abstract
Access to clean water is a grand challenge in the 21st century. Water safety testing for pathogens currently depends on surrogate measures such as fecal indicator bacteria (e.g., E. coli). Metagenomics concerns high-throughput, culture-independent, unbiased shotgun sequencing of DNA from environmental samples that might transform water safety by detecting waterborne pathogens directly instead of their surrogates. Yet emerging innovations such as metagenomics are often fiercely contested. Innovations are subject to shaping/construction not only by technology but also social systems/values in which they are embedded, such as experts’ attitudes towards new scientific evidence. We conducted a classic three-round Delphi survey, comprised of 107 questions. A multidisciplinary expert panel (n = 24) representing the continuum of discovery scientists and policymakers evaluated the emergence of metagenomics tests. To the best of our knowledge, we report here the first Delphi foresight study of experts’ attitudes on (1) the top 10 priority evidentiary criteria for adoption of metagenomics tests for water safety, (2) the specific issues critical to governance of metagenomics innovation trajectory where there is consensus or dissensus among experts, (3) the anticipated time lapse from discovery to practice of metagenomics tests, and (4) the role and timing of public engagement in development of metagenomics tests. The ability of a test to distinguish between harmful and benign waterborne organisms, analytical/clinical sensitivity, and reproducibility were the top three evidentiary criteria for adoption of metagenomics. Experts agree that metagenomic testing will provide novel information but there is dissensus on whether metagenomics will replace the current water safety testing methods or impact the public health end points (e.g., reduction in boil water advisories). Interestingly, experts view the publics relevant in a “downstream capacity” for adoption of metagenomics rather than a co-productionist role at the “upstream” scientific design stage of metagenomics tests. In summary, these findings offer strategic foresight to govern metagenomics innovations symmetrically: by identifying areas where acceleration (e.g., consensus areas) and deceleration/reconsideration (e.g., dissensus areas) of the innovation trajectory might be warranted. Additionally, we show how scientific evidence is subject to potential social construction by experts’ value systems and the need for greater upstream public engagement on metagenomics innovations.
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Harvey AL, Edrada-Ebel R, Quinn RJ. The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 2015; 14:111-29. [PMID: 25614221 DOI: 10.1038/nrd4510] [Citation(s) in RCA: 1508] [Impact Index Per Article: 167.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.
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Affiliation(s)
- Alan L Harvey
- 1] Research and Innovation Support, Dublin City University, Dublin 9, Ireland. [2] Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
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Alcaide M, Stogios PJ, Lafraya Á, Tchigvintsev A, Flick R, Bargiela R, Chernikova TN, Reva ON, Hai T, Leggewie CC, Katzke N, La Cono V, Matesanz R, Jebbar M, Jaeger KE, Yakimov MM, Yakunin AF, Golyshin PN, Golyshina OV, Savchenko A, Ferrer M. Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats. Environ Microbiol 2014; 17:332-45. [PMID: 25330254 DOI: 10.1111/1462-2920.12660] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/01/2014] [Accepted: 10/02/2014] [Indexed: 12/22/2022]
Abstract
The present study provides a deeper view of protein functionality as a function of temperature, salt and pressure in deep-sea habitats. A set of eight different enzymes from five distinct deep-sea (3040-4908 m depth), moderately warm (14.0-16.5°C) biotopes, characterized by a wide range of salinities (39-348 practical salinity units), were investigated for this purpose. An enzyme from a 'superficial' marine hydrothermal habitat (65°C) was isolated and characterized for comparative purposes. We report here the first experimental evidence suggesting that in salt-saturated deep-sea habitats, the adaptation to high pressure is linked to high thermal resistance (P value = 0.0036). Salinity might therefore increase the temperature window for enzyme activity, and possibly microbial growth, in deep-sea habitats. As an example, Lake Medee, the largest hypersaline deep-sea anoxic lake of the Eastern Mediterranean Sea, where the water temperature is never higher than 16°C, was shown to contain halopiezophilic-like enzymes that are most active at 70°C and with denaturing temperatures of 71.4°C. The determination of the crystal structures of five proteins revealed unknown molecular mechanisms involved in protein adaptation to poly-extremes as well as distinct active site architectures and substrate preferences relative to other structurally characterized enzymes.
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Affiliation(s)
- María Alcaide
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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Vester JK, Glaring MA, Stougaard P. Improved cultivation and metagenomics as new tools for bioprospecting in cold environments. Extremophiles 2014; 19:17-29. [PMID: 25399309 PMCID: PMC4272415 DOI: 10.1007/s00792-014-0704-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/28/2014] [Indexed: 11/28/2022]
Abstract
Only a small minority of microorganisms from an environmental sample can be cultured in the laboratory leaving the enormous bioprospecting potential of the uncultured diversity unexplored. This resource can be accessed by improved cultivation methods in which the natural environment is brought into the laboratory or through metagenomic approaches where culture-independent DNA sequence information can be combined with functional screening. The coupling of these two approaches circumvents the need for pure, cultured isolates and can be used to generate targeted information on communities enriched for specific activities or properties. Bioprospecting in extreme environments is often associated with additional challenges such as low biomass, slow cell growth, complex sample matrices, restricted access, and problematic in situ analyses. In addition, the choice of vector system and expression host may be limited as few hosts are available for expression of genes with extremophilic properties. This review summarizes the methods developed for improved cultivation as well as the metagenomic approaches for bioprospecting with focus on the challenges faced by bioprospecting in cold environments.
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Affiliation(s)
- Jan Kjølhede Vester
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark,
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Bertrand S, Bohni N, Schnee S, Schumpp O, Gindro K, Wolfender JL. Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery. Biotechnol Adv 2014; 32:1180-204. [PMID: 24651031 DOI: 10.1016/j.biotechadv.2014.03.001] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 02/08/2023]
Abstract
Microorganisms have a long track record as important sources of novel bioactive natural products, particularly in the field of drug discovery. While microbes have been shown to biosynthesize a wide array of molecules, recent advances in genome sequencing have revealed that such organisms have the potential to yield even more structurally diverse secondary metabolites. Thus, many microbial gene clusters may be silent under standard laboratory growth conditions. In the last ten years, several methods have been developed to aid in the activation of these cryptic biosynthetic pathways. In addition to the techniques that demand prior knowledge of the genome sequences of the studied microorganisms, several genome sequence-independent tools have been developed. One of these approaches is microorganism co-culture, involving the cultivation of two or more microorganisms in the same confined environment. Microorganism co-culture is inspired by the natural microbe communities that are omnipresent in nature. Within these communities, microbes interact through signaling or defense molecules. Such compounds, produced dynamically, are of potential interest as new leads for drug discovery. Microorganism co-culture can be achieved in either solid or liquid media and has recently been used increasingly extensively to study natural interactions and discover new bioactive metabolites. Because of the complexity of microbial extracts, advanced analytical methods (e.g., mass spectrometry methods and metabolomics) are key for the successful detection and identification of co-culture-induced metabolites. This review focuses on co-culture studies that aim to increase the diversity of metabolites obtained from microbes. The various strategies are summarized with a special emphasis on the multiple methods of performing co-culture experiments. The analytical approaches for studying these interaction phenomena are discussed, and the chemical diversity and biological activity observed among the induced metabolites are described.
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Affiliation(s)
- Samuel Bertrand
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland; Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Nadine Bohni
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
| | - Sylvain Schnee
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Olivier Schumpp
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Katia Gindro
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland.
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Vauclare P, Madern D, Girard E, Gabel F, Zaccai G, Franzetti B. New insights into microbial adaptation to extreme saline environments. BIO WEB OF CONFERENCES 2014. [DOI: 10.1051/bioconf/20140202001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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