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Li J, Cheng JH, Teng ZJ, Sun ZZ, He XY, Wang P, Shi M, Song XY, Chen XL, Zhang YZ, Tian X, Zhang XY. Taxonomic and Enzymatic Characterization of Flocculibacter collagenilyticus gen. nov., sp. nov., a Novel Gammaproteobacterium With High Collagenase Production. Front Microbiol 2021; 12:621161. [PMID: 33786038 PMCID: PMC8005334 DOI: 10.3389/fmicb.2021.621161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
Collagens from marine animals are an important component of marine organic nitrogen. Collagenase-producing bacteria and their collagenases play important roles in collagen degradation and organic nitrogen recycling in the ocean. However, only a few collagenase-producing marine bacteria have been so far discovered. Here, we reported the isolation and characterization of a collagenase-secreting bacterium, designated strain SM1988T, isolated from a green alga Codium fragile sample. Strain SM1988T is a Gram-negative, aerobic, oxidase-, and catalase-positive, unipolar flagellated, and rod-shaped bacterium capable of hydrolyzing casein, gelatin and collagens. Phylogenetic analysis revealed that strain SM1988T formed a distinct phylogenetic lineage along with known genera within the family Pseudoalteromonadaceae, with 16S rRNA gene sequence similarity being less than 93.3% to all known species in the family. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data, strain SM1988T was considered to represent a novel species in a novel genus in the family Pseudoalteromonadaceae, for which the name Flocculibacter collagenilyticus gen. nov., sp. nov. is proposed, with the type strain being SM1988T (= MCCC 1K04279T = KCTC 72761T). Strain SM1988T showed a high production of extracellular collagenases, which had high activity against both bovine collagen and codfish collagen. Biochemical tests combined with genome and secretome analyses indicated that the collagenases secreted by strain SM1988T are serine proteases from the MEROPS S8 family. These data suggest that strain SM1988T acts as an important player in marine collagen degradation and recycling and may have a promising potential in collagen resource utilization.
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Affiliation(s)
- Jian Li
- College of Life Science and Technology, Xinjiang University, Urumqi, China.,State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Zhong-Zhi Sun
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Yan He
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Peng Wang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xinmin Tian
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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Meena KK, Sorty AM, Bitla UM, Choudhary K, Gupta P, Pareek A, Singh DP, Prabha R, Sahu PK, Gupta VK, Singh HB, Krishanani KK, Minhas PS. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies. FRONTIERS IN PLANT SCIENCE 2017; 8:172. [PMID: 28232845 PMCID: PMC5299014 DOI: 10.3389/fpls.2017.00172] [Citation(s) in RCA: 250] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/27/2017] [Indexed: 05/19/2023]
Abstract
Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant-microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms.
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Affiliation(s)
- Kamlesh K. Meena
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Ajay M. Sorty
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Utkarsh M. Bitla
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Khushboo Choudhary
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Priyanka Gupta
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Dhananjaya P. Singh
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Ratna Prabha
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Pramod K. Sahu
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Vijai K. Gupta
- Molecular Glyco-Biotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland GalwayGalway, Ireland
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, School of Science, Tallinn University of TechnologyTallinn, Estonia
| | - Harikesh B. Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu UniversityVaranasi, India
| | - Kishor K. Krishanani
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Paramjit S. Minhas
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
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Wilmes B, Kock H, Glagla S, Albrecht D, Voigt B, Markert S, Gardebrecht A, Bode R, Danchin A, Feller G, Hecker M, Schweder T. Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125. Appl Environ Microbiol 2011; 77:1276-83. [PMID: 21183643 PMCID: PMC3067249 DOI: 10.1128/aem.01750-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/13/2010] [Indexed: 11/20/2022] Open
Abstract
The psychrophilic model bacterium Pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, of P. haloplanktis strain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacterium P. haloplanktis in its natural environments.
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Affiliation(s)
- Boris Wilmes
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Holger Kock
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Susanne Glagla
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Dirk Albrecht
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Birgit Voigt
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Stephanie Markert
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Antje Gardebrecht
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Rüdiger Bode
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Antoine Danchin
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Georges Feller
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Michael Hecker
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Thomas Schweder
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
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