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Christi K, Hudson J, Egan S. Current approaches to genetic modification of marine bacteria and considerations for improved transformation efficiency. Microbiol Res 2024; 284:127729. [PMID: 38663232 DOI: 10.1016/j.micres.2024.127729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/25/2024] [Accepted: 04/15/2024] [Indexed: 05/26/2024]
Abstract
Marine bacteria play vital roles in symbiosis, biogeochemical cycles and produce novel bioactive compounds and enzymes of interest for the pharmaceutical, biofuel and biotechnology industries. At present, investigations into marine bacterial functions and their products are primarily based on phenotypic observations, -omic type approaches and heterologous gene expression. To advance our understanding of marine bacteria and harness their full potential for industry application, it is critical that we have the appropriate tools and resources to genetically manipulate them in situ. However, current genetic tools that are largely designed for model organisms such as E. coli, produce low transformation efficiencies or have no transfer ability in marine bacteria. To improve genetic manipulation applications for marine bacteria, we need to improve transformation methods such as conjugation and electroporation in addition to identifying more marine broad host range plasmids. In this review, we aim to outline the reported methods of transformation for marine bacteria and discuss the considerations for each approach in the context of improving efficiency. In addition, we further discuss marine plasmids and future research areas including CRISPR tools and their potential applications for marine bacteria.
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Affiliation(s)
- Katrina Christi
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia.
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2
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Yu Y, Wang P, Cao HY, Teng ZJ, Zhu Y, Wang M, McMinn A, Chen Y, Xiang H, Zhang YZ, Chen XL, Zhang YQ. Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea. THE ISME JOURNAL 2023; 17:537-548. [PMID: 36690779 PMCID: PMC10030869 DOI: 10.1038/s41396-023-01364-6] [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: 07/21/2022] [Revised: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 01/25/2023]
Abstract
D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However, little is known on D-Glu catabolism by marine microorganisms. Here, a novel catabolic pathway for D-Glu was identified using the marine bacterium Pseudoalteromonas sp. CF6-2 as the model. Two novel enzymes (DgcN, DgcA), together with a transcriptional regulator DgcR, are crucial for D-Glu catabolism in strain CF6-2. Genetic and biochemical data confirm that DgcN is a N-acetyltransferase which catalyzes the formation of N-acetyl-D-Glu from D-Glu. DgcA is a racemase that converts N-acetyl-D-Glu to N-acetyl-L-Glu, which is further hydrolyzed to L-Glu. DgcR positively regulates the transcription of dgcN and dgcA. Structural and biochemical analyses suggested that DgcN and its homologs, which use D-Glu as the acyl receptor, represent a new group of the general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) superfamily. DgcA and DgcN occur widely in marine bacteria (particularly Rhodobacterales) and halophilic archaea (Halobacteria) and are abundant in marine and hypersaline metagenome datasets. Thus, this study reveals a novel D-Glu catabolic pathway in ecologically important marine bacteria and halophilic archaea and helps better understand the catabolism and recycling of D-Glu in these ecosystems.
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Affiliation(s)
- Yang Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Peng Wang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hai-Yan Cao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yanping Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Yin Chen
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hua Xiang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Resources, the Institute of Microbiology CAS, Beijing, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yu-Qiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
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Diaminopimelic Acid Metabolism by Pseudomonadota in the Ocean. Microbiol Spectr 2022; 10:e0069122. [PMID: 36040174 PMCID: PMC9602339 DOI: 10.1128/spectrum.00691-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Diaminopimelic acid (DAP) is a unique component of the cell wall of Gram-negative bacteria. It is also an important component of organic matter and is widely utilized by microbes in the world's oceans. However, neither DAP concentrations nor marine DAP-utilizing microbes have been investigated. Here, DAP concentrations in seawater were measured and the diversity of marine DAP-utilizing bacteria and the mechanisms for their DAP metabolism were investigated. Free DAP concentrations in seawater, from surface to a 5,000 m depth, were found to be between 0.61 μM and 0.96 μM in the western Pacific Ocean. DAP-utilizing bacteria from 20 families in 4 phyla were recovered from the western Pacific seawater and 14 strains were further isolated, in which Pseudomonadota bacteria were dominant. Based on genomic and transcriptomic analyses combined with gene deletion and in vitro activity detection, DAP decarboxylase (LysA), which catalyzes the decarboxylation of DAP to form lysine, was found to be a key and specific enzyme involved in DAP metabolism in the isolated Pseudomonadota strains. Interrogation of the Tara Oceans database found that most LysA-like sequences (92%) are from Pseudomonadota, which are widely distributed in multiple habitats. This study provides an insight into DAP metabolism by marine bacteria in the ocean and contributes to our understanding of the mineralization and recycling of DAP by marine bacteria. IMPORTANCE DAP is a unique component of peptidoglycan in Gram-negative bacterial cell walls. Due to the large number of marine Gram-negative bacteria, DAP is an important component of marine organic matter. However, it remains unclear how DAP is metabolized by marine microbes. This study investigated marine DAP-utilizing bacteria by cultivation and bioinformational analysis and examined the mechanism of DAP metabolism used by marine bacteria. The results demonstrate that Pseudomonadota bacteria are likely to be an important DAP-utilizing group in the ocean and that DAP decarboxylase is a key enzyme involved in DAP metabolism. This study also sheds light on the mineralization and recycling of DAP driven by bacteria.
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Yu Y, Yang J, Teng ZJ, Zheng LY, Sheng Q, Li PY, Fu HH, Li CY, Chen Y, Zhang YZ, Ding JM, Chen XL. d-Alanine Metabolism via d-Ala Aminotransferase by a Marine Gammaproteobacterium, Pseudoalteromonas sp. Strain CF6-2. Appl Environ Microbiol 2022; 88:e0221921. [PMID: 34818098 PMCID: PMC8824272 DOI: 10.1128/aem.02219-21] [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: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/20/2022] Open
Abstract
As the most abundant d-amino acid (DAA) in the ocean, d-alanine (d-Ala) is a key component of peptidoglycan in the bacterial cell wall. However, the underlying mechanisms of bacterial metabolization of d-Ala through the microbial food web remain largely unknown. In this study, the metabolism of d-Ala by marine bacterium Pseudoalteromonas sp. strain CF6-2 was investigated. Based on genomic, transcriptional, and biochemical analyses combined with gene knockout, d-Ala aminotransferase was found to be indispensable for the catabolism of d-Ala in strain CF6-2. Investigation on other marine bacteria also showed that d-Ala aminotransferase gene is a reliable indicator for their ability to utilize d-Ala. Bioinformatic investigation revealed that d-Ala aminotransferase sequences are prevalent in genomes of marine bacteria and metagenomes, especially in seawater samples, and Gammaproteobacteria represents the predominant group containing d-Ala aminotransferase. Thus, Gammaproteobacteria is likely the dominant group to utilize d-Ala via d-Ala aminotransferase to drive the recycling and mineralization of d-Ala in the ocean. IMPORTANCE As the most abundant d-amino acid in the ocean, d-Ala is a component of the marine DON (dissolved organic nitrogen) pool. However, the underlying mechanism of bacterial metabolization of d-Ala to drive the recycling and mineralization of d-Ala in the ocean is still largely unknown. The results in this study showed that d-Ala aminotransferase is specific and indispensable for d-Ala catabolism in marine bacteria and that marine bacteria containing d-Ala aminotransferase genes are predominantly Gammaproteobacteria widely distributed in global oceans. This study reveals marine d-Ala-utilizing bacteria and the mechanism of their metabolization of d-Ala. The results shed light on the mechanisms of recycling and mineralization of d-Ala driven by bacteria in the ocean, which are helpful in understanding oceanic microbial-mediated nitrogen cycle.
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Affiliation(s)
- Yang Yu
- State Key Laboratory of Microbial Technology and Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jie Yang
- State Key Laboratory of Microbial Technology and Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Zhao-Jie Teng
- State Key Laboratory of Microbial Technology and Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Li-Yuan Zheng
- State Key Laboratory of Microbial Technology and Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi Sheng
- State Key Laboratory of Microbial Technology and Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology and Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Hui-Hui Fu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yin Chen
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology and Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jun-Mei Ding
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology and Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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Duan J, Guo W. The cold adaption profiles of Pseudoalteromonas shioyasakiensis D1497 from Yap trench to cope with cold. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00689. [PMID: 34987981 PMCID: PMC8711050 DOI: 10.1016/j.btre.2021.e00689] [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: 10/05/2021] [Revised: 11/01/2021] [Accepted: 11/11/2021] [Indexed: 01/08/2023]
Abstract
P. shioyasakiensis D1497converted more substrate into biomass at low temperature. P. shioyasakiensis D1497 prefered to use codons with A/T in the third position. The energy metabolism related genes were down regulated in cold environment. P. shioyasakiensis D1497 presented an energy saving metabolism strategy to cope with cold.
Genome sequencing of Pseudoalteromonas shioyasakiensis D1497, a psychrophile from the Yap trench, revealed that it contained a circle chromosome of 3,631,285 bp with 40.94% GC content and prefered to use codons with A/T in the third position. Additionally, the relative synonymous codon usage (RSCU) values indicated the codons with A and T in the third position were always the most used. Cultivation of P. shioyasakiensis D1497 presented lower substrate consumption rate, higher ATP pool and higher conversion rate of biomass per unit substrate consumed at low temperature (15 °C) than that of the room temperature (25 °C) culture. Comparative transcriptomic analysis revealed that the mRNA abundance of energy metabolism related genes was decreased in 15 °C culture compared with that of 25 °C culture. In addition to its codon usage biases profile, P. shioyasakiensis D1497 presented an energy saving metabolism strategy to cope with cold, converting more carbon source into biomass in cold environment.
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Affiliation(s)
- Jingjing Duan
- College of Environment and Ecology, Xiamen University, Xiamen 361005, Fujian, China
| | - Wenbin Guo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, China
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Acrylate protects a marine bacterium from grazing by a ciliate predator. Nat Microbiol 2021; 6:1351-1356. [PMID: 34697458 DOI: 10.1038/s41564-021-00981-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 09/16/2021] [Indexed: 12/26/2022]
Abstract
Cleavage of dimethylsulfoniopropionate (DMSP) can deter herbivores in DMSP-producing eukaryotic algae; however, it is unclear whether a parallel defence mechanism operates in marine bacteria. Here we demonstrate that the marine bacterium Puniceibacterium antarcticum SM1211, which does not use DMSP as a carbon source, has a membrane-associated DMSP lyase, DddL. At high concentrations of DMSP, DddL causes an accumulation of acrylate around cells through the degradation of DMSP, which protects against predation by the marine ciliate Uronema marinum. The presence of acrylate can alter the grazing preference of U. marinum to other bacteria in the community, thereby influencing community structure.
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7
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Qin QL, Wang ZB, Su HN, Chen XL, Miao J, Wang XJ, Li CY, Zhang XY, Li PY, Wang M, Fang J, Lidbury I, Zhang W, Zhang XH, Yang GP, Chen Y, Zhang YZ. Oxidation of trimethylamine to trimethylamine N-oxide facilitates high hydrostatic pressure tolerance in a generalist bacterial lineage. SCIENCE ADVANCES 2021; 7:7/13/eabf9941. [PMID: 33771875 PMCID: PMC7997507 DOI: 10.1126/sciadv.abf9941] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/05/2021] [Indexed: 06/01/2023]
Abstract
High hydrostatic pressure (HHP) is a characteristic environmental factor of the deep ocean. However, it remains unclear how piezotolerant bacteria adapt to HHP. Here, we identify a two-step metabolic pathway to cope with HHP stress in a piezotolerant bacterium. Myroides profundi D25T, obtained from a deep-sea sediment, can take up trimethylamine (TMA) through a previously unidentified TMA transporter, TmaT, and oxidize intracellular TMA into trimethylamine N-oxide (TMAO) by a TMA monooxygenase, MpTmm. The produced TMAO is accumulated in the cell, functioning as a piezolyte, improving both growth and survival at HHP. The function of the TmaT-MpTmm pathway was further confirmed by introducing it into Escherichia coli and Bacillus subtilis Encoded TmaT-like and MpTmm-like sequences extensively exist in marine metagenomes, and other marine Bacteroidetes bacteria containing genes encoding TmaT-like and MpTmm-like proteins also have improved HHP tolerance in the presence of TMA, implying the universality of this HHP tolerance strategy in marine Bacteroidetes.
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Affiliation(s)
- Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Zhi-Bin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jie Miao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiu-Juan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Weipeng Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Gui-Peng Yang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Chitin Degradation Machinery and Secondary Metabolite Profiles in the Marine Bacterium Pseudoalteromonas rubra S4059. Mar Drugs 2021; 19:md19020108. [PMID: 33673118 PMCID: PMC7917724 DOI: 10.3390/md19020108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
Genome mining of pigmented Pseudoalteromonas has revealed a large potential for the production of bioactive compounds and hydrolytic enzymes. The purpose of the present study was to explore this bioactivity potential in a potent antibiotic and enzyme producer, Pseudoalteromonas rubra strain S4059. Proteomic analyses (data are available via ProteomeXchange with identifier PXD023249) indicated that a highly efficient chitin degradation machinery was present in the red-pigmented P. rubra S4059 when grown on chitin. Four GH18 chitinases and two GH20 hexosaminidases were significantly upregulated under these conditions. GH19 chitinases, which are not common in bacteria, are consistently found in pigmented Pseudoalteromonas, and in S4059, GH19 was only detected when the bacterium was grown on chitin. To explore the possible role of GH19 in pigmented Pseudoalteromonas, we developed a protocol for genetic manipulation of S4059 and deleted the GH19 chitinase, and compared phenotypes of the mutant and wild type. However, none of the chitin degrading ability, secondary metabolite profile, or biofilm-forming capacity was affected by GH19 deletion. In conclusion, we developed a genetic manipulation protocol that can be used to unravel the bioactive potential of pigmented pseudoalteromonads. An efficient chitinolytic enzyme cocktail was identified in S4059, suggesting that this strain could be a candidate with industrial potential.
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Abstract
Chromosome replication is an essential process for cell division. The mode of chromosome replication has important impacts on the structure of the chromosome and replication speed. As typical bacterial replicons, circular chromosomes replicate bidirectionally and circular plasmids replicate either bidirectionally or unidirectionally. Whereas the finding of chromids (plasmid-derived chromosomes) in multiple bacterial lineages provides circumstantial evidence that chromosomes likely evolved from plasmids, all experimentally assayed chromids were shown to use bidirectional replication. Here, we employed a model system, the marine bacterial genus Pseudoalteromonas, members of which consistently carry a chromosome and a chromid. We provide experimental and bioinformatic evidence that while chromids in a few strains replicate bidirectionally, most replicate unidirectionally. This is the first experimental demonstration of the unidirectional replication mode in bacterial chromids. Phylogenomic and comparative genomic analyses showed that the bidirectional replication evolved only once from a unidirectional ancestor and that this transition was associated with insertions of exogenous DNA and relocation of the replication terminus region (ter2) from near the origin site (ori2) to a position roughly opposite it. This process enables a plasmid-derived chromosome to increase its size and expand the bacterium’s metabolic versatility while keeping its replication synchronized with that of the main chromosome. A major implication of our study is that the uni- and bidirectionally replicating chromids may represent two stages on the evolutionary trajectory from unidirectionally replicating plasmids to bidirectionally replicating chromosomes in bacteria. Further bioinformatic analyses predicted unidirectionally replicating chromids in several unrelated bacterial phyla, suggesting that evolution from unidirectionally to bidirectionally replicating replicons occurred multiple times in bacteria.
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Alterocin, an Antibiofilm Protein Secreted by Pseudoalteromonas sp. Strain 3J6. Appl Environ Microbiol 2020; 86:AEM.00893-20. [PMID: 32769182 DOI: 10.1128/aem.00893-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022] Open
Abstract
We sought to identify and study the antibiofilm protein secreted by the marine bacterium Pseudoalteromonas sp. strain 3J6. The latter is active against marine and terrestrial bacteria, including Pseudomonas aeruginosa clinical strains forming different biofilm types. Several amino acid sequences were obtained from the partially purified antibiofilm protein, named alterocin. The Pseudoalteromonas sp. 3J6 genome was sequenced, and a candidate alt gene was identified by comparing the genome-encoded proteins to the sequences from purified alterocin. Expressing the alt gene in another nonactive Pseudoalteromonas sp. strain, 3J3, demonstrated that it is responsible for the antibiofilm activity. Alterocin is a 139-residue protein that includes a predicted 20-residue signal sequence, which would be cleaved off upon export by the general secretion system. No sequence homology was found between alterocin and proteins of known functions. The alt gene is not part of an operon and adjacent genes do not seem related to alterocin production, immunity, or regulation, suggesting that these functions are not fulfilled by devoted proteins. During growth in liquid medium, the alt mRNA level peaked during the stationary phase. A single promoter was experimentally identified, and several inverted repeats could be binding sites for regulators. alt genes were found in about 30% of the Pseudoalteromonas genomes and in only a few instances of other marine bacteria of the Hahella and Paraglaciecola genera. Comparative genomics yielded the hypothesis that alt gene losses occurred within the Pseudoalteromonas genus. Overall, alterocin is a novel kind of antibiofilm protein of ecological and biotechnological interest.IMPORTANCE Biofilms are microbial communities that develop on solid surfaces or interfaces and are detrimental in a number of fields, including for example food industry, aquaculture, and medicine. In the latter, antibiotics are insufficient to clear biofilm infections, leading to chronic infections such as in the case of infection by Pseudomonas aeruginosa of the lungs of cystic fibrosis patients. Antibiofilm molecules are thus urgently needed to be used in conjunction with conventional antibiotics, as well as in other fields of application, especially if they are environmentally friendly molecules. Here, we describe alterocin, a novel antibiofilm protein secreted by a marine bacterium belonging to the Pseudoalteromonas genus, and its gene. Alterocin homologs were found in about 30% of Pseudoalteromonas strains, indicating that this new family of antibiofilm proteins likely plays an important albeit nonessential function in the biology of these bacteria. This study opens up the possibility of a variety of applications.
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Tang BL, Yang J, Chen XL, Wang P, Zhao HL, Su HN, Li CY, Yu Y, Zhong S, Wang L, Lidbury I, Ding H, Wang M, McMinn A, Zhang XY, Chen Y, Zhang YZ. A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria. Nat Commun 2020; 11:285. [PMID: 31941905 PMCID: PMC6962226 DOI: 10.1038/s41467-019-14133-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/13/2019] [Indexed: 12/23/2022] Open
Abstract
Predator-prey interactions play important roles in the cycling of marine organic matter. Here we show that a Gram-negative bacterium isolated from marine sediments (Pseudoalteromonas sp. strain CF6-2) can kill Gram-positive bacteria of diverse peptidoglycan (PG) chemotypes by secreting the metalloprotease pseudoalterin. Secretion of the enzyme requires a Type II secretion system. Pseudoalterin binds to the glycan strands of Gram positive bacterial PG and degrades the PG peptide chains, leading to cell death. The released nutrients, including PG-derived D-amino acids, can then be utilized by strain CF6-2 for growth. Pseudoalterin synthesis is induced by PG degradation products such as glycine and glycine-rich oligopeptides. Genes encoding putative pseudoalterin-like proteins are found in many other marine bacteria. This study reveals a new microbial interaction in the ocean. Predator-prey interactions play important roles in the cycling of marine organic matter. Here the authors show that a Gram-negative bacterium isolated from marine sediments can kill and feed on Gram-positive bacteria by secreting a peptidoglycan-degrading enzyme.
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Affiliation(s)
- Bai-Lu Tang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Jie Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Hui-Lin Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Yang Yu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Shuai Zhong
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Lei Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Haitao Ding
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, 200136, China
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yin Chen
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China. .,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China.
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12
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Parrilli E, Tedesco P, Fondi M, Tutino ML, Lo Giudice A, de Pascale D, Fani R. The art of adapting to extreme environments: The model system Pseudoalteromonas. Phys Life Rev 2019; 36:137-161. [PMID: 31072789 DOI: 10.1016/j.plrev.2019.04.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/10/2023]
Abstract
Extremophilic microbes have adapted to thrive in ecological niches characterized by harsh chemical/physical conditions such as, for example, very low/high temperature. Living organisms inhabiting these environments have developed peculiar mechanisms to cope with extreme conditions, in such a way that they mark the chemical-physical boundaries of life on Earth. Studying such mechanisms is stimulating from a basic research viewpoint and because of biotechnological applications. Pseudoalteromonas species are a group of marine gamma-proteobacteria frequently isolated from a range of extreme environments, including cold habitats and deep-sea sediments. Since deep-sea floors constitute almost 60% of the Earth's surface and cold temperatures represent the most common of the extreme conditions, the genus Pseudoalteromonas can be considered one of the most important model systems for studying microbial adaptation. Particularly, among all Pseudoalteromonas representatives, P. haloplanktis TAC125 has recently gained a central role. This bacterium was isolated from seawater sampled along the Antarctic ice-shell and is considered one of the model organisms of cold-adapted bacteria. It is capable of thriving in a wide temperature range and it has been suggested as an alternative host for the soluble overproduction of heterologous proteins, given its ability to rapidly multiply at low temperatures. In this review, we will present an overview of the recent advances in the characterization of Pseudoalteromonas strains and, more importantly, in the understanding of their evolutionary and chemical-physical strategies to face such a broad array of extreme conditions. A particular attention will be given to systems-biology approaches in the study of the above-mentioned topics, as genome-scale datasets (e.g. genomics, proteomics, phenomics) are beginning to expand for this group of organisms. In this context, a specific section dedicated to P. haloplanktis TAC125 will be presented to address the recent efforts in the elucidation of the metabolic rewiring of the organisms in its natural environment (Antarctica).
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Affiliation(s)
- Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Pietro Tedesco
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | | | - Donatella de Pascale
- Institute of Protein Biochemistry, CNR, Napoli, Italy, Stazione Zoologica "Anthon Dorn", Villa Comunale, I-80121 Napoli, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy.
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13
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Delavat F, Bidault A, Pichereau V, Paillard C. Rapid and efficient protocol to introduce exogenous DNA in Vibrio harveyi and Pseudoalteromonas sp. J Microbiol Methods 2018; 154:1-5. [PMID: 30287352 DOI: 10.1016/j.mimet.2018.09.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 02/08/2023]
Abstract
Vibrio campbellii BAA-1116 is renowned for its bioluminescence properties, and genetic tools are available to genetically track this strain. However, many other ecologically important V. harveyi strains exist, for which only few genetic tools are available. In this study, a rapid electroporation protocol was developed to transform replicative plasmids in various environmental V. harveyi and Pseudoalteromonas strains. Moreover, a mini-Tn7 delivery system was modified to site-specifically integrate mini-transposons in the genome of V. harveyi ORM4. As a proof-of-principle, replicative plasmids carrying bioreporters were introduced by electroporation in V. harveyi ORM4 cells, and gene expression was followed at the single cell level. We could demonstrate that a flagellar gene is subjected to bimodal gene expression in V. harveyi ORM4, being highly expressed in 10% of the population in stationary phase. This study extends the possibilities to study environmental Vibrio strains and uncovers the occurrence of phenotypic heterogeneity in flagellar expression in Vibrio.
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Affiliation(s)
- François Delavat
- Laboratoire des sciences de l'Environnement Marin, Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale - UMR6539 CNRS/UBO/IRD/Ifremer, Plouzané, France.
| | - Adeline Bidault
- Laboratoire des sciences de l'Environnement Marin, Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale - UMR6539 CNRS/UBO/IRD/Ifremer, Plouzané, France
| | - Vianney Pichereau
- Laboratoire des sciences de l'Environnement Marin, Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale - UMR6539 CNRS/UBO/IRD/Ifremer, Plouzané, France
| | - Christine Paillard
- Laboratoire des sciences de l'Environnement Marin, Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale - UMR6539 CNRS/UBO/IRD/Ifremer, Plouzané, France
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14
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Tortorella E, Tedesco P, Palma Esposito F, January GG, Fani R, Jaspars M, de Pascale D. Antibiotics from Deep-Sea Microorganisms: Current Discoveries and Perspectives. Mar Drugs 2018; 16:md16100355. [PMID: 30274274 PMCID: PMC6213577 DOI: 10.3390/md16100355] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 12/17/2022] Open
Abstract
The increasing emergence of new forms of multidrug resistance among human pathogenic bacteria, coupled with the consequent increase of infectious diseases, urgently requires the discovery and development of novel antimicrobial drugs with new modes of action. Most of the antibiotics currently available on the market were obtained from terrestrial organisms or derived semisynthetically from fermentation products. The isolation of microorganisms from previously unexplored habitats may lead to the discovery of lead structures with antibiotic activity. The deep-sea environment is a unique habitat, and deep-sea microorganisms, because of their adaptation to this extreme environment, have the potential to produce novel secondary metabolites with potent biological activities. This review covers novel antibiotics isolated from deep-sea microorganisms. The chemical classes of the compounds, their bioactivities, and the sources of organisms are outlined. Furthermore, the authors report recent advances in techniques and strategies for the exploitation of deep-sea microorganisms.
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Affiliation(s)
- Emiliana Tortorella
- Institute of Protein Biochemistry, National Research Council, I-80131 Naples, Italy.
| | - Pietro Tedesco
- Institute of Protein Biochemistry, National Research Council, I-80131 Naples, Italy.
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, INSA, 31400 Toulouse, France.
| | - Fortunato Palma Esposito
- Institute of Protein Biochemistry, National Research Council, I-80131 Naples, Italy.
- Stazione Zoologica "Anthon Dorn", Villa Comunale, I-80121 Naples, Italy.
| | - Grant Garren January
- Institute of Protein Biochemistry, National Research Council, I-80131 Naples, Italy.
| | - Renato Fani
- Department of Biology, University of Florence, Sesto Fiorentino, I-50019 Florence, Italy.
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen, Scotland AB24 3UE, UK.
| | - Donatella de Pascale
- Institute of Protein Biochemistry, National Research Council, I-80131 Naples, Italy.
- Stazione Zoologica "Anthon Dorn", Villa Comunale, I-80121 Naples, Italy.
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15
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Zeaiter Z, Mapelli F, Crotti E, Borin S. Methods for the genetic manipulation of marine bacteria. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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16
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Liao Y, Williams TJ, Walsh JC, Ji M, Poljak A, Curmi PMG, Duggin IG, Cavicchioli R. Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function. Sci Rep 2016; 6:34639. [PMID: 27708407 PMCID: PMC5052560 DOI: 10.1038/srep34639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/16/2016] [Indexed: 01/04/2023] Open
Abstract
No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
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Affiliation(s)
- Y Liao
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - T J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J C Walsh
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia.,The ithree institute, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - M Ji
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - A Poljak
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - P M G Curmi
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - I G Duggin
- The ithree institute, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - R Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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17
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Offret C, Desriac F, Le Chevalier P, Mounier J, Jégou C, Fleury Y. Spotlight on Antimicrobial Metabolites from the Marine Bacteria Pseudoalteromonas: Chemodiversity and Ecological Significance. Mar Drugs 2016; 14:E129. [PMID: 27399731 PMCID: PMC4962019 DOI: 10.3390/md14070129] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 12/17/2022] Open
Abstract
This review is dedicated to the antimicrobial metabolite-producing Pseudoalteromonas strains. The genus Pseudoalteromonas hosts 41 species, among which 16 are antimicrobial metabolite producers. To date, a total of 69 antimicrobial compounds belonging to 18 different families have been documented. They are classified into alkaloids, polyketides, and peptides. Finally as Pseudoalteromonas strains are frequently associated with macroorganisms, we can discuss the ecological significance of antimicrobial Pseudoalteromonas as part of the resident microbiota.
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Affiliation(s)
- Clément Offret
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Florie Desriac
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Patrick Le Chevalier
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Jérôme Mounier
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Camille Jégou
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Yannick Fleury
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
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18
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Liu A, Mi ZH, Zheng XY, Yu Y, Su HN, Chen XL, Xie BB, Zhou BC, Zhang YZ, Qin QL. Exopolysaccharides Play a Role in the Swarming of the Benthic Bacterium Pseudoalteromonas sp. SM9913. Front Microbiol 2016; 7:473. [PMID: 27092127 PMCID: PMC4820436 DOI: 10.3389/fmicb.2016.00473] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/21/2016] [Indexed: 12/01/2022] Open
Abstract
Most marine bacteria secrete exopolysaccharide (EPS), which is important for bacterial survival in the marine environment. However, it is still unclear whether the self-secreted EPS is involved in marine bacterial motility. Here we studied the role of EPS in the lateral flagella-driven swarming motility of benthic bacterium Pseudoalteromonas sp. SM9913 (SM9913) by a comparison of wild SM9913 and ΔepsT, an EPS synthesis defective mutant. Reduction of EPS production in ΔepsT did not affect the growth rate or the swimming motility, but significantly decreased the swarming motility on a swarming plate, suggesting that the EPS may play a role in SM9913 swarming. However, the expression and assembly of lateral flagella in ΔepsT were not affected. Instead, ΔepsT had a different swarming behavior from wild SM9913. The swarming of ΔepsT did not have an obvious rapid swarming period, and its rate became much lower than that of wild SM9913 after 35 h incubation. An addition of surfactin or SM9913 EPS on the surface of the swarming plate could rescue the swarming level. These results indicate that the self-secreted EPS is required for the swarming of SM9913. This study widens our understanding of the function of the EPS of benthic bacteria.
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Affiliation(s)
- Ang Liu
- Marine and Agricultural Biotechnology Laboratory, State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research CenterJinan, China
| | - Zi-Hao Mi
- Marine and Agricultural Biotechnology Laboratory, State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research CenterJinan, China
| | - Xiao-Yu Zheng
- Marine and Agricultural Biotechnology Laboratory, State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research CenterJinan, China
| | - Yang Yu
- Marine and Agricultural Biotechnology Laboratory, State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research CenterJinan, China
| | - Hai-Nan Su
- Marine and Agricultural Biotechnology Laboratory, State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research CenterJinan, China
| | - Xiu-Lan Chen
- Marine and Agricultural Biotechnology Laboratory, State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research CenterJinan, China
| | - Bin-Bin Xie
- Marine and Agricultural Biotechnology Laboratory, State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research CenterJinan, China
| | - Bai-Cheng Zhou
- Marine and Agricultural Biotechnology Laboratory, State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research CenterJinan, China
| | - Yu-Zhong Zhang
- Marine and Agricultural Biotechnology Laboratory, State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research CenterJinan, China
| | - Qi-Long Qin
- Marine and Agricultural Biotechnology Laboratory, State Key Laboratory of Microbial Technology, Shandong UniversityJinan, China; Marine Biotechnology Research CenterJinan, China
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19
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Yu ZC, Tang BL, Zhao DL, Pang X, Qin QL, Zhou BC, Zhang XY, Chen XL, Zhang YZ. Development of a Cold-Adapted Pseudoalteromonas Expression System for the Pseudoalteromonas Proteins Intractable for the Escherichia coli System. PLoS One 2015; 10:e0137384. [PMID: 26333173 PMCID: PMC4557933 DOI: 10.1371/journal.pone.0137384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/16/2015] [Indexed: 12/01/2022] Open
Abstract
Although the Escherichia coli expression system is the most commonly used expression system, some proteins are still difficult to be expressed by this system, such as proteins with high thermolability and enzymes that cannot mature by autoprocessing. Therefore, it is necessary to develop alternative expression systems. In this study, a cold-adapted Pseudoalteromonas expression system was developed. A shuttle vector was constructed, and a conjugational transfer system between E. coli and psychrophilic strain Pseudoalteromonas sp. SM20429 was established. Based on the shuttle vector, three reporter vectors were constructed to compare the strength of the cloned promoters at low temperature. The promoter of xylanase gene from Pseudoalteromonas sp. BSi20429 was chosen due to its high activity at 10–15°C. An expression vector pEV containing the chosen promoter, multiple cloning sites and a His tag was constructed for protein expression and purification. With pEV as expression vector and SM20429 as the host, a cold-adapted protease, pseudoalterin, which cannot be maturely expressed in E. coli, was successfully expressed as an active extracellular enzyme when induced by 2% oat spelt xylan at 15°C for 48 h. Recombinant pseudoalterin purified from the culture by Ni affinity chromatography had identical N-terminal sequence, similar molecular mass and substrate specificity as the native pseudoalterin. In addition, another two cold-adapted enzymes were also successfully expressed by this system. Our results indicate that this cold-adapted Pseudoalteromonas expression system will provide an alternative choice for protein expression, especially for the Pseudoalteromonas proteins intractable for the E. coli system.
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Affiliation(s)
- Zi-Chao Yu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Bai-Lu Tang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Dian-Li Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Xiuhua Pang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Marine Biotechnology Research Center, Shandong University, Jinan, China
- * E-mail:
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Marine Biotechnology Research Center, Shandong University, Jinan, China
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20
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Mi ZH, Yu ZC, Su HN, Wang L, Chen XL, Pang X, Qin QL, Xie BB, Zhang XY, Zhou BC, Zhang YZ. Physiological and genetic analyses reveal a mechanistic insight into the multifaceted lifestyles ofPseudoalteromonassp. SM9913 adapted to the deep-sea sediment. Environ Microbiol 2015; 17:3795-806. [DOI: 10.1111/1462-2920.12823] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/22/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Zi-Hao Mi
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Zi-Chao Yu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
- Collaborative Innovation Center of Deep Sea Biology; Shandong University; Jinan 250100 China
| | - Lei Wang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
- Collaborative Innovation Center of Deep Sea Biology; Shandong University; Jinan 250100 China
| | - Xiuhua Pang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
- Collaborative Innovation Center of Deep Sea Biology; Shandong University; Jinan 250100 China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
- Marine Biotechnology Research Center; Shandong University; Jinan 250100 China
- Collaborative Innovation Center of Deep Sea Biology; Shandong University; Jinan 250100 China
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21
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Wang P, Yu Z, Li B, Cai X, Zeng Z, Chen X, Wang X. Development of an efficient conjugation-based genetic manipulation system for Pseudoalteromonas. Microb Cell Fact 2015; 14:11. [PMID: 25612661 PMCID: PMC4318363 DOI: 10.1186/s12934-015-0194-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/10/2015] [Indexed: 11/10/2022] Open
Abstract
Pseudoalteromonas is commonly found throughout the world's oceans, and has gained increased attention due to the ecological and biological significance. Although over fifty Pseudoalteromonas genomes have been sequenced with an aim to explore the adaptive strategies in different habitats, in vivo studies are hampered by the lack of effective genetic manipulation systems for most strains in this genus. Here, nine Pseudoalteromonas strains isolated from different habitats were selected and used as representative strains to develop a universal genetic manipulation system. Erythromycin and chloramphenicol resistance were chosen as selection markers based on antibiotics resistance test of the nine strains. A conjugation protocol based on the RP4 conjugative machinery in E. coli WM3064 was developed to overcome current limitations of genetic manipulation in Pseudoalteromonas. Two mobilizable gene expression shuttle vectors (pWD2-oriT and pWD2Ery-oriT) were constructed, and conjugation efficiency of pWD2-oriT from E. coli to the nine Pseudoalteromonas strains ranged from 10(-6) to 10(-3) transconjugants per recipient cells. Two suicide vectors, pK18mobsacB-Cm and pK18mobsacB-Ery (with sacB for counter-selection), were constructed for gene knockout. To verify the feasibility of this system, we selected gene or operon that may lead to phenotypic change once disrupted as targets to facilitate in vivo functional confirmation. Successful deletions of two genes related to prodigiosin biosynthesis (pigMK) in P. rubra DSM 6842, one biofilm related gene (bsmA) in P. sp. SM9913, one gene related to melanin hyperproduction (hmgA) in P. lipolytica SCSIO 04301 and two flagella-related genes (fliF and fliG) in P. sp. SCSIO 11900 were verified, respectively. In addition, complementation of hmgA using shuttle vector pWD2-oriT was rescued the phenotype caused by deletion of chromosomal copy of hmgA in P. lipolytica SCSIO 04301. Taken together, we demonstrate that the vectors and the conjugative protocol developed here have potential to use in various Pseudoalteromonas strains.
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Affiliation(s)
- Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Zichao Yu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.
| | - Baiyuan Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xingsheng Cai
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Zhenshun Zeng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiulan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, 250100, China.
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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