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Sahtout N, Sanders DAR. Biophysical and biochemical characterization of the thioredoxin system from Colwellia psychrerythraea. Proteins 2024; 92:370-383. [PMID: 37909486 DOI: 10.1002/prot.26627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/24/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023]
Abstract
The thioredoxin system is a ubiquitous oxidoreductase system consisting of the enzyme thioredoxin reductase, the protein thioredoxin, and the cofactor nicotinamide adenine dinucleotide phosphate. The system has been comprehensively studied from many organisms, such as Escherichia coli; however, structural and functional analysis of this system from psychrophilic bacteria has not been as extensive. In this study, the thioredoxin system proteins of a psychrophilic bacterium, Colwellia psychrerythraea, were characterized using biophysical and biochemical techniques. Analysis of the complete genome sequence of the C. psychrerythraea thioredoxin system suggested the presence of a putative thioredoxin reductase and at least three thioredoxin. In this study, these identified putative thioredoxin system components were cloned, overexpressed, purified, and characterized. Our studies have indicated that the thioredoxin system proteins from E. coli were more stable than those from C. psychrerythraea. Consistent with these results, kinetic assays indicated that the thioredoxin reductase from E. coli had a higher optimal temperature than that from C. psychrerythraea.
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Affiliation(s)
- Naheda Sahtout
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - David A R Sanders
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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2
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Huang Y, Jiang Y, Zhao A, Liu Y, Chen X, Wang F, Liu H, Huang W, Ihsan YN, Jiang M, Jiang Y. Microbulbifer litoralis sp. nov., Isolated from Seashore of Weizhou Island. Curr Microbiol 2024; 81:105. [PMID: 38393402 DOI: 10.1007/s00284-023-03594-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 12/19/2023] [Indexed: 02/25/2024]
Abstract
A bacterium designated GXH0434T was isolated from sea shore samples collected from Weizhou Island, Beihai, Guangxi, China. The organism is motile, strictly aerobic, and possesses a rod-coccus cell cycle in association with the growth phase. It can grow at 15-45 °C (optimum 37 °C), at pH 6.0-11.0 (optimum 6.0), and at 0-20% (w/v) NaCl (optimum 5.0-8.0%). The strain is positive for peroxidase and oxidase activity, negative for Voges-Proskauer test, can hydrolyze Tween 20, Tween 60, Tween 80, casein, and is able to produce siderophore and has the function of nitrogen fixation. Molecular phylogenetic analysis based on 16S rRNA gene sequences indicated that GXH0434T was most closely related to Microbulbifer halophilus KCTC 12848T with the similarity of 97.2%, followed by Microbulbifer chitinilyticus JCM 16148T (97.1%) and Microbulbifer taiwanensis LMG 26125T (96.5%). The digital DNA-DNA hybridization and the average nucleotide identity values between GXH0434T and Microbulbifer halophilus KCTC 12848T were 28.90% and 83.38%, respectively, which were below thresholds of species delineation. The genomic DNA G+C content of the strain was 61.9%. The major fatty acids were iso-C15:0, C16:0, iso-C11:0 3-OH, iso-C11:0 and Summed features 8 (C18:0 ω7c and/or C18:0 ω6c). The major polar lipids detected in GXH0434T were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC). The major respiratory quinone was ubiquinone Q-8. Based on the above polyphasic classification indicated strain GXH0434T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer litoralis sp. nov. is proposed. The type strain is GXH0434T (= MCCC 1K07158T = KCTC 92169T).
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Affiliation(s)
- Ying Huang
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Yu Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, People's Republic of China
| | - Aolin Zhao
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Ying Liu
- School of Chemistry and Chemical Engineering, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Xuemei Chen
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Fang Wang
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Hongcun Liu
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China
| | - Wenshan Huang
- Guangxi Lvyounong Biological Technology Co., Ltd, Nanning, 530000, People's Republic of China
| | - Yudi N Ihsan
- Department of Marine Science, Universitas Padjadjaran, Jatinangor, Indonesia
| | - Mingguo Jiang
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory of Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning, 530008, People's Republic of China.
| | - Yi Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
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3
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Liu N, Kivenson V, Peng X, Cui Z, Lankiewicz TS, Gosselin KM, English CJ, Blair EM, O'Malley MA, Valentine DL. Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen. Appl Environ Microbiol 2024; 90:e0091423. [PMID: 38265213 PMCID: PMC10880615 DOI: 10.1128/aem.00914-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024] Open
Abstract
Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.
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Affiliation(s)
- Na Liu
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Veronika Kivenson
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Xuefeng Peng
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao, China
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Kelsey M. Gosselin
- Interdepartmental Graduate Program in Marine Science, University of California Santa Barbara, Santa Barbara, California, USA
| | - Chance J. English
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Ecology Evolution, and Marine Biology, University of California, Santa Barbara, California, USA
| | - Elaina M. Blair
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
- Biological Engineering Program, University of California, Santa Barbara, California, USA
| | - David L. Valentine
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Earth Science, University of California Santa Barbara, Santa Barbara, California, USA
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Zhang M, Wang J, Zeng R, Wang D, Wang W, Tong X, Qu W. Agarose-Degrading Characteristics of a Deep-Sea Bacterium Vibrio Natriegens WPAGA4 and Its Cold-Adapted GH50 Agarase Aga3420. Mar Drugs 2022; 20:692. [PMID: 36355015 PMCID: PMC9698624 DOI: 10.3390/md20110692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 11/23/2023] Open
Abstract
Up until now, the characterizations of GH50 agarases from Vibrio species have rarely been reported compared to GH16 agarases. In this study, a deep-sea strain, WPAGA4, was isolated and identified as Vibrio natriegens due to the maximum similarity of its 16S rRNA gene sequence, the values of its average nucleotide identity, and through digital DNA-DNA hybridization. Two circular chromosomes in V. natriegens WPAGA4 were assembled. A total of 4561 coding genes, 37 rRNA, 131 tRNA, and 59 other non-coding RNA genes were predicted in the genome of V. natriegens WPAGA4. An agarase gene belonging to the GH50 family was annotated in the genome sequence and expressed in E. coli cells. The optimum temperature and pH of the recombinant Aga3420 (rAga3420) were 40 °C and 7.0, respectively. Neoagarobiose (NA2) was the only product during the degradation process of agarose by rAga3420. rAga3420 had a favorable stability following incubation at 10-30 °C for 50 min. The Km, Vmax, and kcat values of rAga3420 were 2.8 mg/mL, 78.1 U/mg, and 376.9 s-1, respectively. rAga3420 displayed cold-adapted properties as 59.7% and 41.2% of the relative activity remained at 10 3 °C and 0 °C, respectively. This property ensured V. natriegens WPAGA4 could degrade and metabolize the agarose in cold deep-sea environments and enables rAga3420 to be an appropriate industrial enzyme for NA2 production, with industrial potential in medical and cosmetic fields.
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Affiliation(s)
- Mengyuan Zhang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Runying Zeng
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China
| | - Dingquan Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Wenxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Xiufang Tong
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
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5
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Sun XK, Gong Y, Shang DD, Liu BT, Du ZJ, Chen GJ. Degradation of Alginate by a Newly Isolated Marine Bacterium Agarivorans sp. B2Z047. Mar Drugs 2022; 20:254. [PMID: 35447927 PMCID: PMC9029943 DOI: 10.3390/md20040254] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 12/21/2022] Open
Abstract
Alginate is the main component of brown algae, which is an important primary production in marine ecosystems and represents a huge marine biomass. The efficient utilization of alginate depends on alginate lyases to catalyze the degradation, and remains to be further explored. In this study, 354 strains were isolated from the gut of adult abalones, which mainly feed on brown algae. Among them, 100 alginate-degrading strains were gained and the majority belonged to the Gammaproteobacteria, followed by the Bacteroidetes and Alphaproteobacteria. A marine bacterium, Agarivorans sp. B2Z047, had the strongest degradation ability of alginate with the largest degradation circle and the highest enzyme activity. The optimal alginate lyase production medium of strain B2Z047 was determined as 1.1% sodium alginate, 0.3% yeast extract, 1% NaCl, and 0.1% MgSO4 in artificial seawater (pH 7.0). Cells of strain B2Z047 were Gram-stain-negative, aerobic, motile by flagella, short rod-shaped, and approximately 0.7-0.9 µm width and 1.2-1.9 µm length. The optimal growth conditions were determined to be at 30 °C, pH 7.0-8.0, and in 3% (w/v) NaCl. A total of 12 potential alginate lyase genes were identified through whole genome sequencing and prediction, which belonged to polysaccharide lyase family 6, 7, 17, and 38 (PL6, PL7, PL17, and PL38, respectively). Furthermore, the degradation products of nine alginate lyases were detected, among which Aly38A was the first alginate lyase belonging to the PL38 family that has been found to degrade alginate. The combination of alginate lyases functioning in the alginate-degrading process was further demonstrated by the growth curve and alginate lyase production of strain B2Z047 cultivated with or without sodium alginate, as well as the content changes of total sugar and reducing sugar and the transcript levels of alginate lyase genes. A simplified model was proposed to explain the alginate utilization process of Agarivorans sp. B2Z047.
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Affiliation(s)
- Xun-Ke Sun
- Marine College, Shandong University, Weihai 264209, China; (X.-K.S.); (D.-D.S.); (B.-T.L.); (Z.-J.D.)
| | - Ya Gong
- Marine College, Shandong University, Weihai 264209, China; (X.-K.S.); (D.-D.S.); (B.-T.L.); (Z.-J.D.)
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Dan-Dan Shang
- Marine College, Shandong University, Weihai 264209, China; (X.-K.S.); (D.-D.S.); (B.-T.L.); (Z.-J.D.)
| | - Bang-Tao Liu
- Marine College, Shandong University, Weihai 264209, China; (X.-K.S.); (D.-D.S.); (B.-T.L.); (Z.-J.D.)
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, China; (X.-K.S.); (D.-D.S.); (B.-T.L.); (Z.-J.D.)
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Guan-Jun Chen
- Marine College, Shandong University, Weihai 264209, China; (X.-K.S.); (D.-D.S.); (B.-T.L.); (Z.-J.D.)
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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Aljandal S, Doyle SM, Bera G, Wade TL, Knap AH, Sylvan JB. Mesopelagic microbial community dynamics in response to increasing oil and Corexit 9500 concentrations. PLoS One 2022; 17:e0263420. [PMID: 35196352 PMCID: PMC8865645 DOI: 10.1371/journal.pone.0263420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/18/2022] [Indexed: 01/04/2023] Open
Abstract
Marine microbial communities play an important role in biodegradation of subsurface plumes of oil that form after oil is accidentally released from a seafloor wellhead. The response of these mesopelagic microbial communities to the application of chemical dispersants following oil spills remains a debated topic. While there is evidence that contrasting results in some previous work may be due to differences in dosage between studies, the impacts of these differences on mesopelagic microbial community composition remains unconstrained. To answer this open question, we exposed a mesopelagic microbial community from the Gulf of Mexico to oil alone, three concentrations of oil dispersed with Corexit 9500, and three concentrations of Corexit 9500 alone over long periods of time. We analyzed changes in hydrocarbon chemistry, cell abundance, and microbial community composition at zero, three and six weeks. The lowest concentration of dispersed oil yielded hydrocarbon concentrations lower than oil alone and microbial community composition more similar to control seawater than any other treatments with oil or dispersant. Higher concentrations of dispersed oil resulted in higher concentrations of microbe-oil microaggregates and similar microbial composition to the oil alone treatment. The genus Colwellia was more abundant when exposed to multiple concentrations of dispersed oil, but not when exposed to dispersant alone. Conversely, the most abundant Marinobacter amplicon sequence variant (ASV) was not influenced by dispersant when oil was present and showed an inverse relationship to the summed abundance of Alcanivorax ASVs. As a whole, the data presented here show that the concentration of oil strongly impacts microbial community response, more so than the presence of dispersant, confirming the importance of the concentrations of both oil and dispersant in considering the design and interpretation of results for oil spill simulation experiments.
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Affiliation(s)
- Shahd Aljandal
- Department of Oceanography, Texas A&M University, College Station, TX, United States of America
| | - Shawn M. Doyle
- Department of Oceanography, Texas A&M University, College Station, TX, United States of America
| | - Gopal Bera
- Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, United States of America
| | - Terry L. Wade
- Department of Oceanography, Texas A&M University, College Station, TX, United States of America
- Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, United States of America
| | - Anthony H. Knap
- Department of Oceanography, Texas A&M University, College Station, TX, United States of America
- Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, United States of America
| | - Jason B. Sylvan
- Department of Oceanography, Texas A&M University, College Station, TX, United States of America
- * E-mail:
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Abstract
Metagenomic analysis of food is becoming more routine and can provide important information pertaining to the shelf life potential and the safety of these products. However, less information is available on the microbiomes associated with low water activity foods. Pine nuts and sesame seeds, and food products which contain these ingredients, have been associated with recalls due to contamination with bacterial foodborne pathogens. The objective of this study was to identify the microbial community of pine nuts and sesame seeds using targeted 16S rRNA sequencing technology. Ten different brands of each seed type were assessed, and core microbiomes were determined. A total of 21 and 16 unique taxa with proportional abundances >1% in at least one brand were identified in the pine nuts and sesame seeds, respectively. Members of the core pine nut microbiome included the genera Alishewanella, Aminivibrio, Mycoplasma, Streptococcus, and unassigned OTUs in the families of Desulfobacteraceae and Xanthomonadaceae. For sesame seeds, the core microbiome included Aminivibrio, Chryseolina, Okibacterium, and unassigned OTUs in the family Flavobacteriaceae. The microbiomes of these seeds revealed that these products are dominated by environmental bacterial genera commonly isolated from soil, water, and plants; bacterial genera containing species known as commensal organisms were also identified. Understanding these microbiomes can aid in the risk assessment of these products by identifying food spoilage potential and community members which may co-enrich with foodborne bacterial pathogens.
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Affiliation(s)
- Megan Fay
- Division of Food Processing Science and Technology, U. S. Food and Drug Administration, Bedford Park, Illinois, United States of America
| | - Joelle K. Salazar
- Division of Food Processing Science and Technology, U. S. Food and Drug Administration, Bedford Park, Illinois, United States of America
| | - Padmini Ramachandran
- Division of Microbiology, U. S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Diana Stewart
- Division of Food Processing Science and Technology, U. S. Food and Drug Administration, Bedford Park, Illinois, United States of America
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8
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Abstract
The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs. Overall, 89 expanded 5S rRNAs of 15 structural types were identified in 15 archaeal and 36 bacterial genomes. Expansion segments ranging in length from 13 to 109 residues were found to be distributed among 17 insertion sites. The strains harboring the expanded 5S rRNAs belong to the bacterial orders Clostridiales, Halanaerobiales, Thermoanaerobacterales, and Alteromonadales as well as the archael order Halobacterales When several copies of a 5S rRNA gene are present in a genome, the expanded versions may coexist with normal 5S rRNA genes. The insertion sequences are typically capable of forming extended helices, which do not seemingly interfere with folding of the conserved core. The expanded 5S rRNAs have largely been overlooked in 5S rRNA databases.
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MESH Headings
- Alteromonadaceae/classification
- Alteromonadaceae/genetics
- Alteromonadaceae/metabolism
- Base Pairing
- Base Sequence
- Clostridiales/classification
- Clostridiales/genetics
- Clostridiales/metabolism
- Firmicutes/classification
- Firmicutes/genetics
- Firmicutes/metabolism
- Genome, Archaeal
- Genome, Bacterial
- Halobacteriales/classification
- Halobacteriales/genetics
- Halobacteriales/metabolism
- Nucleic Acid Conformation
- Phylogeny
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Thermoanaerobacterium/classification
- Thermoanaerobacterium/genetics
- Thermoanaerobacterium/metabolism
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Affiliation(s)
- Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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9
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Xue J, Fang J, Zhang H, Wei Y, Wang L, Liu R, Cao J. Complete genome sequence of a piezophilic bacterium Salinimonas sediminis N102 T, isolated from deep-sea sediment of the New Britain Trench. Mar Genomics 2020; 56:100807. [PMID: 33632424 DOI: 10.1016/j.margen.2020.100807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/22/2023]
Abstract
Salinimonas sediminis N102T is a cold-adapted, slightly halophilic piezophile isolated from deep-sea sediment (4700 m) of the New Britain Trench. In this study, we report the complete genome sequence of S. sediminis N102T, which is comprised of 4,440,293 base pairs with a mean G + C content of 48.2 mol%. The complete genome harbors 3851 predicted protein-coding genes, 70 tRNA genes and 15 rRNA genes. Abundant genes in the genome were predicted to be linked to bacterial deep-sea lifestyle. The complete genome sequence of S. sediminis N102T provides insights into the microbial adaptation strategies to the deep-sea environment.
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Affiliation(s)
- Junyi Xue
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
| | - Hongge Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China.
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10
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Cheng R, Wang X, Zhu H, Yan B, Shutes B, Xu Y, Fu B, Wen H. Isolation and characterization of a salt-tolerant denitrifying bacterium Alishewanella sp. F2 from seawall muddy water. Sci Rep 2020; 10:10002. [PMID: 32561802 PMCID: PMC7305158 DOI: 10.1038/s41598-020-66989-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/01/2020] [Indexed: 11/08/2022] Open
Abstract
A salt-tolerant denitrifying bacterium strain F2 was isolated from seawall muddy water in Dalian City, Liaoning Province, China. Strain F2 was identified by morphological observations, physiological and biochemical characteristics and 16 S rDNA identification. The salt tolerance of strain F2 was verified and the factors affecting the removal ability of strain F2 to nitrous nitrogen (NO2-N) and nitrate nitrogen (NO3-N) in saline conditions were investigated. Strain F2 was identified as Alishewanella sp., named Alishewanella sp. F2. Strain F2 can tolerate NaCl concentrations up to 70 g/L, and its most efficient denitrification capacity was observed at NaCl concentrations of 0-30 g/L. In the medium with NaCl concentrations of 0-30 g/L, strain F2 exhibited high removal efficiencies of NO2-N and NO3-N, with the removal percentages for both NO2-N and NO3-N of approximately 99%. In saline conditions with 30 g/L NaCl, the optimum culture pH, NaNO2 initial concentrations and inoculation sizes of strain F2 were 8-10, 0.4-0.8 g/L and 5-7%, respectively. Strain F2 was highly effective in removing NO2-N and NO3-N in saline conditions, and it has a good application potential in saline wastewater treatment.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, P R China
- University of Chinese Academy of Sciences, Beijing, 100049, P R China
- Jilin Provincial Engineering Center of CWs Design in Cold Region & Beautiful Country Construction, Changchun, 130102, P R China
| | - Xinyi Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, P R China
- Jilin Provincial Engineering Center of CWs Design in Cold Region & Beautiful Country Construction, Changchun, 130102, P R China
- School of Environment, Liaoning University, Shenyang, 110036, P R China
| | - Hui Zhu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, P R China.
- Jilin Provincial Engineering Center of CWs Design in Cold Region & Beautiful Country Construction, Changchun, 130102, P R China.
| | - Baixing Yan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, P R China
- Jilin Provincial Engineering Center of CWs Design in Cold Region & Beautiful Country Construction, Changchun, 130102, P R China
| | - Brian Shutes
- Urban Pollution Research Centre, Middlesex University, Hendon, London, NW4 4BT, UK
| | - Yingying Xu
- Key Laboratory of Songliao Aquatic Environment, Ministry of Education, Jilin Jianzhu University, Changchun, 130118, P R China
| | - Baorong Fu
- School of Environment, Liaoning University, Shenyang, 110036, P R China
| | - Huiyang Wen
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, P R China
- Jilin Provincial Engineering Center of CWs Design in Cold Region & Beautiful Country Construction, Changchun, 130102, P R China
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11
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Nagai S, Takada Y. Analysis of amino acid residues involved in the thermal properties of isocitrate dehydrogenases from a psychrophilic bacterium, Colwellia maris, and a psychrotrophic bacterium, Pseudomonas psychrophila. J Biosci Bioeng 2019; 129:284-290. [PMID: 31619337 DOI: 10.1016/j.jbiosc.2019.09.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 11/18/2022]
Abstract
Monomeric NADP+-dependent isocitrate dehydrogenase (IDH) from a psychrophilic bacterium, Colwella maris, (CmIDH) is a cold-adapted enzyme, whereas that of a psychrotrophic bacterium, Pseudomonas psychrophila, (PpIDH) is mesophilic. However, the amino acid sequence identity of the two IDHs is high (67%). To identify the amino acid residues involved in the differences in their thermal properties, such as optimum temperature and thermostability for activity, six amino acid residues located in the corresponding positions of their regions 2 and 3 were substituted by site-directed mutagenesis, and several thermal properties of the mutated IDHs were examined. CmIDH mutants, CmE538L, CmE596L and CmA741S, substituted at Glu538, Glu596 and Ala741 by the corresponding PpIDH residues of Leu, Leu and Ser, respectively, exhibited higher thermostability than wild-type CmIDH (CmWT). Furthermore, the specific activity of CmE596L and CmA741S was higher than that of CmWT. On the other hand, the corresponding mutants of PpIDH PpL536E, PpL594E and PpS739A were more thermolabile than wild-type PpIDH, and PpL594E had a lower specific activity at temperatures over 45°C. These results suggested that these amino acid residues of CmIDH and PpIDH are involved in their thermal properties.
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Affiliation(s)
- Shunsuke Nagai
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Kita 10-jo Nishi 8-chome, Kita-ku, Sapporo 060-0810, Japan
| | - Yasuhiro Takada
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita 10-jo Nishi 8-chome, Kita-ku, Sapporo 060-0810, Japan.
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12
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Liu J, Liu Z, Jiang C, Mao X. Biochemical Characterization and Substrate Degradation Mode of a Novel α-Agarase from Catenovulum agarivorans. J Agric Food Chem 2019; 67:10373-10379. [PMID: 31453692 DOI: 10.1021/acs.jafc.9b03073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Agarose can be hydrolyzed into agarooligosaccharides (AOSs) by α-agarase, which is an important enzyme for efficient saccharification of agarose or preparation of bioactive oligosaccharides from agarose. Although many β-agarases have been reported and characterized, there are only a few studies on α-agarases. Here, we cloned a novel α-agarase named CaLJ96 with a molecular weight of approximately 200 kDa belonging to glycoside hydrolase family 96 from Catenovulum agarivorans. CaLJ96 has good pH stability and exhibits maximum activity at 37 °C and pH 7.0. The hydrolyzed products of agarose by CaLJ96 are analyzed as agarobiose (A2), agarotetraose (A4), and agarohexaose (A6), in which A4 is the dominant product. CaLJ96 can hydrolyze agaropentaose (A5) into A2 and agarotriose (A3) and A6 into A2 and A4 but cannot act on A2, A3, or A4. This is the first report to characterize the α-agarase action on AOSs in detail. Therefore, CaLJ96 has potential for the manufacture of bioactive AOSs.
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Affiliation(s)
- Jie Liu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Zhen Liu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Chengcheng Jiang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xiangzhao Mao
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
- Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
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13
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Lee CW, Park SH, Jeong CS, Cha SS, Park H, Lee JH. Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H. Sci Rep 2019; 9:2649. [PMID: 30804410 PMCID: PMC6390093 DOI: 10.1038/s41598-019-39641-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/28/2019] [Indexed: 11/22/2022] Open
Abstract
Cells regulate their intracellular mRNA levels by using specific ribonucleases. Oligoribonuclease (ORN) is a 3'-5' exoribonuclease for small RNA molecules, important in RNA degradation and re-utilisation. However, there is no structural information on the ligand-binding form of ORNs. In this study, the crystal structures of oligoribonuclease from Colwellia psychrerythraea strain 34H (CpsORN) were determined in four different forms: unliganded-structure, thymidine 5'-monophosphate p-nitrophenyl ester (pNP-TMP)-bound, two separated uridine-bound, and two linked uridine (U-U)-bound forms. The crystal structures show that CpsORN is a tight dimer, with two separated active sites and one divalent metal cation ion in each active site. These structures represent several snapshots of the enzymatic reaction process, which allowed us to suggest a possible one-metal-dependent reaction mechanism for CpsORN. Moreover, the biochemical data support our suggested mechanism and identified the key residues responsible for enzymatic catalysis of CpsORN.
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Affiliation(s)
- Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Chang-Sook Jeong
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Woman's University, Seoul, 03760, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
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Pu W, Cui C, Guo C, Wu ZL. Characterization of two styrene monooxygenases from marine microbes. Enzyme Microb Technol 2018; 112:29-34. [PMID: 29499777 DOI: 10.1016/j.enzmictec.2018.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/29/2018] [Accepted: 02/01/2018] [Indexed: 12/16/2022]
Abstract
Styrene monooxygenases (SMOs) are highly stereoselective enzymes that catalyze the formation of chiral epoxides as versatile building blocks. To expand the enzyme toolbox, two bacterial SMOs were identified from the genome of marine microbes Paraglaciecola agarilytica NO2 and Marinobacterium litorale DSM 23545, and heterologously expressed in Escherichia coli in soluble form. Both of the resulting whole-cell biocatalysts exhibited maximal activity at 30 °C and pH 8.0. They catalyzed the sulfoxidation reactions, and the epoxidation of both conjugated and unconjugated styrene derivatives with up to >99%ee. MlSMO displayed higher activity toward most substrates tested. Compared to an established SMO from Pseudomonas species (PsSMO), MlSMO achieved 3.0-, 3.4- and 2.6-fold conversions for substrates styrene, cinnamyl alcohol and 4-vinyl-2, 3-dihydrobenzofuran, respectively.
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Affiliation(s)
- Wei Pu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Can Cui
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Guo
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Zhong-Liu Wu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
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15
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Liang Y, Ma X, Zhang L, Li F, Liu Z, Mao X. Biochemical Characterization and Substrate Degradation Mode of a Novel Exotype β-Agarase from Agarivorans gilvus WH0801. J Agric Food Chem 2017; 65:7982-7988. [PMID: 28817933 DOI: 10.1021/acs.jafc.7b01533] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Agarases are important hydrolytic enzymes for the biodegradation of agar. Understanding the degradation mode and hydrolysis products of agarases is essential for their utilization in oligosaccharide preparations. Herein, we cloned and expressed AgWH50B, a novel neoagarotetraose-forming β-agarase from Agarivorans gilvus WH0801 that has high specific activity and a fast reaction rate. AgWH50B consists of a C-terminal glycoside hydrolase family 50 catalytic domain with two tandem noncatalytic carbohydrate-binding modules (CBMs) in the N-terminus (residues 45-214 and 236-442). AgWH50B exhibited good enzymatic properties with high specific activity and catalytic efficiency (1523.2 U/mg and a Vmax of 1700 μmol/min/mg) under optimal hydrolysis conditions of pH 7.0 and 40 °C. Analysis of the hydrolysis products revealed that this enzyme is an exotype β-agarase and that the dominant product of agarose or oligosaccharide degradation was neoagarotetraose. These findings suggest that AgWH50B could be utilized to yield abundant neoagarotetraose.
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Affiliation(s)
- Yunxiao Liang
- College of Food Science and Engineering, Ocean University of China , Qingdao 266003, China
| | - Xiaoqing Ma
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101, China
| | - Lujia Zhang
- College of Food Science and Engineering, Ocean University of China , Qingdao 266003, China
- School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200241, China
| | - Fuli Li
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101, China
| | - Zhen Liu
- College of Food Science and Engineering, Ocean University of China , Qingdao 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China , Qingdao 266003, China
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16
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Park SH, Lee CW, Lee SG, Shin SC, Kim HJ, Park H, Lee JH. Crystal structure and functional characterization of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea strain 34H. PLoS One 2017; 12:e0181705. [PMID: 28723955 PMCID: PMC5517026 DOI: 10.1371/journal.pone.0181705] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/04/2017] [Indexed: 01/07/2023] Open
Abstract
Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the β-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea, both ligand-free and that complexed with β-isoaspartyl lysine, at 1.85-Å and 2.33-Å resolution, respectively. In both structures, CpsIadA formed an octamer with two Zn ions in the active site. A structural comparison with Escherichia coli isoaspartyl dipeptidase (EcoIadA) revealed a major difference in the structure of the active site. For metal ion coordination, CpsIadA has a Glu166 residue in the active site, whereas EcoIadA has a post-translationally carbamylated-lysine 162 residue. Site-directed mutagenesis studies confirmed that the Glu166 residue is critical for CpsIadA enzymatic activity. This residue substitution from lysine to glutamate induces the protrusion of the β12-α8 loop into the active site to compensate for the loss of length of the side chain. In addition, the α3-β9 loop of CpsIadA adopts a different conformation compared to EcoIadA, which induces a change in the structure of the substrate-binding pocket. Despite CpsIadA having a different active-site residue composition and substrate-binding pocket, there is only a slight difference in CpsIadA substrate specificity compared with EcoIadA. Comparative sequence analysis classified IadA-containing bacteria and archaea into two groups based on the active-site residue composition, with Type I IadAs having a glutamate residue and Type II IadAs having a carbamylated-lysine residue. CpsIadA has maximal activity at pH 8–8.5 and 45°C, and was completely inactivated at 60°C. Despite being isolated from a psychrophilic bacteria, CpsIadA is thermostable probably owing to its octameric structure. This is the first conclusive description of the structure and properties of a Type I IadA.
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Affiliation(s)
- Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Sung Gu Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Seung Chul Shin
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Hak Jun Kim
- Department of Chemistry, Pukyong National University, Busan, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
- * E-mail: (HP); (JHL)
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
- * E-mail: (HP); (JHL)
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17
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Sisinthy S, Chakraborty D, Adicherla H, Gundlapally SR. Emended description of the family Chromatiaceae, phylogenetic analyses of the genera Alishewanella, Rheinheimera and Arsukibacterium, transfer of Rheinheimera longhuensis LH2-2 T to the genus Alishewanella and description of Alishewanella alkalitolerans sp. nov. from Lonar Lake, India. Antonie Van Leeuwenhoek 2017; 110:1227-1241. [PMID: 28612170 DOI: 10.1007/s10482-017-0896-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/31/2017] [Indexed: 11/30/2022]
Abstract
Phylogenetic analyses were performed for members of the family Chromatiaceae, signature nucleotides deduced and the genus Alishewanella transferred to Chromatiaceae. Phylogenetic analyses were executed for the genera Alishewanella, Arsukibacterium and Rheinheimera and the genus Rheinheimera is proposed to be split, with the creation of the Pararheinheimera gen. nov. Furthermore, the species Rheinheimera longhuensis, is transferred to the genus Alishewanella as Alishewanella longhuensis comb. nov. Besides, the genera Alishewanella and Rheinheimera are also emended. Strain LNK-7.1T was isolated from a water sample from the Lonar Lake, India. Cells were Gram-negative, motile rods, positive for catalase, oxidase, phosphatase, contained C16:0, C17:1ω8c, summed feature3 (C16:1ω6c and/or C16:1ω7c) and summed feature 8 (C18:1ω7c) as major fatty acids, PE and PG as the major lipids and Q-8 as the sole respiratory quinone. Phylogenetic analyses using NJ, ME, ML and Maximum parsimony, based on 16S rRNA gene sequences, identified Alishewanella tabrizica RCRI4T as the closely related species of strain LNK-7.1T with a 16S rRNA gene sequence similarity of 98.13%. The DNA-DNA similarity between LNK-7.1T and the closely related species (A. tabrizica) was only 12.0% and, therefore, strain LNK-7.1T was identified as a novel species of the genus Alishewanella with the proposed name Alishewanella alkalitolerans sp. nov. In addition phenotypic characteristics confirmed the species status to strain LNK-7.1T. The type strain of A. alkalitolerans is LNK-7.1T (LMG 29592T = KCTC 52279T), isolated from a water sample collected from the Lonar lake, India.
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Affiliation(s)
- Shivaji Sisinthy
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Dwaipayan Chakraborty
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Harikrishna Adicherla
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Sathyanarayana Reddy Gundlapally
- Laboratory for Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
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18
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Michl SC, Ratten JM, Beyer M, Hasler M, LaRoche J, Schulz C. The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures. PLoS One 2017; 12:e0177735. [PMID: 28498878 PMCID: PMC5428975 DOI: 10.1371/journal.pone.0177735] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 05/02/2017] [Indexed: 12/31/2022] Open
Abstract
Plant-derived protein sources are the most relevant substitutes for fishmeal in aquafeeds. Nevertheless, the effects of plant based diets on the intestinal microbiome especially of juvenile Rainbow trout (Oncorhynchus mykiss) are yet to be fully investigated. The present study demonstrates, based on 16S rDNA bacterial community profiling, that the intestinal microbiome of juvenile Rainbow trout is strongly affected by dietary plant protein inclusion levels. After first feeding of juveniles with either 0%, 50% or 97% of total dietary protein content derived from plants, statistically significant differences of the bacterial gut community for the three diet-types were detected, both at phylum and order level. The microbiome of juvenile fish consisted mainly of the phyla Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria and Actinobacteria, and thus fits the salmonid core microbiome suggested in previous studies. Dietary plant proteins significantly enhanced the relative abundance of the orders Lactobacillales, Bacillales and Pseudomonadales. Animal proteins in contrast significantly promoted Bacteroidales, Clostridiales, Vibrionales, Fusobacteriales and Alteromonadales. The overall alpha diversity significantly decreased with increasing plant protein inclusion levels and with age of experimental animals. In order to investigate permanent effects of the first feeding diet-type on the early development of the microbiome, a diet change was included in the study after 54 days, but no such effects could be detected. Instead, the microbiome of juvenile trout fry was highly dependent on the actual diet fed at the time of sampling.
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Affiliation(s)
- Stéphanie Céline Michl
- Gesellschaft für Marine Aquakultur mbH (GMA) Büsum, Büsum, Germany
- Department of Marine Aquaculture, Institute of Animal Breeding and Husbandry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Matt Beyer
- Department of Biology, Dalhousie University, Halifax, Canada
| | - Mario Hasler
- Lehrfach Variationsstatistik, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Canada
| | - Carsten Schulz
- Gesellschaft für Marine Aquakultur mbH (GMA) Büsum, Büsum, Germany
- Department of Marine Aquaculture, Institute of Animal Breeding and Husbandry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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19
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Gourinchas G, Etzl S, Göbl C, Vide U, Madl T, Winkler A. Long-range allosteric signaling in red light-regulated diguanylyl cyclases. Sci Adv 2017; 3:e1602498. [PMID: 28275738 PMCID: PMC5336353 DOI: 10.1126/sciadv.1602498] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/10/2017] [Indexed: 05/06/2023]
Abstract
Nature has evolved an astonishingly modular architecture of covalently linked protein domains with diverse functionalities to enable complex cellular networks that are critical for cell survival. The coupling of sensory modules with enzymatic effectors allows direct allosteric regulation of cellular signaling molecules in response to diverse stimuli. We present molecular details of red light-sensing bacteriophytochromes linked to cyclic dimeric guanosine monophosphate-producing diguanylyl cyclases. Elucidation of the first crystal structure of a full-length phytochrome with its enzymatic effector, in combination with the characterization of light-induced changes in conformational dynamics, reveals how allosteric light regulation is fine-tuned by the architecture and composition of the coiled-coil sensor-effector linker and also the central helical spine. We anticipate that consideration of molecular principles of sensor-effector coupling, going beyond the length of the characteristic linker, and the appreciation of dynamically driven allostery will open up new directions for the design of novel red light-regulated optogenetic tools.
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Affiliation(s)
- Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Stefan Etzl
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Christoph Göbl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Uršula Vide
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Tobias Madl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
- Corresponding author.
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20
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Mehdizadeh Aghdam E, Sinn M, Tarhriz V, Barzegar A, Hartig JS, Hejazi MS. TPP riboswitch characterization in Alishewanella tabrizica and Alishewanella aestuarii and comparison with other TPP riboswitches. Microbiol Res 2016; 195:71-80. [PMID: 28024528 DOI: 10.1016/j.micres.2016.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/15/2016] [Accepted: 11/05/2016] [Indexed: 11/18/2022]
Abstract
Riboswitches are located in non-coding areas of mRNAs and act as sensors of cellular small molecules, regulating gene expression in response to ligand binding. The TPP riboswitch is the most widespread riboswitch occurring in all three domains of life. However, it has been rarely characterized in environmental bacteria other than Escherichia coli and Bacillus subtilis. In this study, TPP riboswitches located in the 5' UTR of thiC operon from Alishewanella tabrizica and Alishewanella aestuarii were identified and characterized. Moreover, affinity analysis of TPP binding to the TPP aptamer domains originated from A. tabrizica, A. aestuarii, E.coli, and B. subtilis were studied and compared using In-line probing and Surface Plasmon Resonance (SPR). TPP binding to the studied RNAs from A. tabrizica and A. aestuarii caused distinctive changes of the In-line cleavage pattern, demonstrating them as functional TPP riboswitches. With dissociation constant of 2-4nM (depending on the method utilized), the affinity of TPP binding was highest in A. tabrizica, followed by the motifs sourced from A. aestuarii, E. coli, and B. subtilis. The observed variation in their TPP-binding affinity might be associated with adaptation to the different environments of the studied bacteria.
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Affiliation(s)
- Elnaz Mehdizadeh Aghdam
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Malte Sinn
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Vahideh Tarhriz
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolfazl Barzegar
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran; The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Mohammad Saeid Hejazi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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21
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Sheu DS, Sheu SY, Lin KR, Chen YLL, Chen WM. Planctobacterium marinum gen. nov., sp. nov., a new member of the family Alteromonadaceae isolated from seawater. Int J Syst Evol Microbiol 2016; 67:974-980. [PMID: 27959781 DOI: 10.1099/ijsem.0.001726] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated K7T was isolated from the South China Sea and characterized using a polyphasic taxonomic approach. Cells of strain K7T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore forming rods surrounded by a thick capsule and forming yellow colonies. Growth occurred at 4-35 °C (optimum, 25-30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and with 0.5-10 % (w/v) NaCl [optimum, 1-4 % (w/v)]. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8 and the DNA G+C content was 46.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, one uncharacterized phospholipid, two uncharacterized aminophospholipids and five uncharacterized lipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain K7T formed a distinct lineage with respect to closely related genera in the family Alteromonadaceae. Strain K7T was most closely related to Aestuariibacter, Aliiglaciecola, Paraglaciecola and Glaciecola, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 95 %. On the basis of the genotypic and phenotypic data, strain K7T represents a novel species of a new genus of the family Alteromonadaceae, for which the name Planctobacterium marinum gen. nov., sp. nov. is proposed. The type strain of Planctobacterium marinum is K7T (=BCRC 80901T=LMG 28835T=KCTC 42657T).
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Affiliation(s)
- Der-Shyan Sheu
- Department of Marine Biotechnology, National KaohsiungMarine University, No. 142, Hai-ChuanRd. Nan-Tzu, Kaohsiung City 811, Taiwan ROC
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National KaohsiungMarine University, No. 142, Hai-ChuanRd. Nan-Tzu, Kaohsiung City 811, Taiwan ROC
| | - Kai-Rou Lin
- Laboratoryof Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan ROC
| | - Yuh-Ling Lee Chen
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung 80424, Taiwan ROC
| | - Wen-Ming Chen
- Laboratoryof Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan ROC
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Peng YF, Chen WC, Xiao K, Xu L, Wang L, Wan X. DHA Production in Escherichia coli by Expressing Reconstituted Key Genes of Polyketide Synthase Pathway from Marine Bacteria. PLoS One 2016; 11:e0162861. [PMID: 27649078 PMCID: PMC5029812 DOI: 10.1371/journal.pone.0162861] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/30/2016] [Indexed: 12/30/2022] Open
Abstract
The gene encoding phosphopantetheinyl transferase (PPTase), pfaE, a component of the polyketide synthase (PKS) pathway, is crucial for the production of docosahexaenoic acid (DHA, 22:6ω3), along with the other pfa cluster members pfaA, pfaB, pfaC and pfaD. DHA was produced in Escherichia coli by co-expressing pfaABCD from DHA-producing Colwellia psychrerythraea 34H with one of four pfaE genes from bacteria producing arachidonic acid (ARA, 20:4ω6), eicosapentaenoic acid (EPA, 20:5ω3) or DHA, respectively. Substitution of the pfaE gene from different strain source in E. coli did not influence the function of the PKS pathway producing DHA, although they led to different DHA yields and fatty acid profiles. This result suggested that the pfaE gene could be switchable between these strains for the production of DHA. The DHA production by expressing the reconstituted PKS pathway was also investigated in different E. coli strains, at different temperatures, or with the treatment of cerulenin. The highest DHA production, 2.2 mg of DHA per gram of dry cell weight or 4.1% of total fatty acids, was obtained by co-expressing pfaE(EPA) from the EPA-producing strain Shewanella baltica with pfaABCD in DH5α. Incubation at low temperature (10–15°C) resulted in higher accumulation of DHA compared to higher temperatures. The addition of cerulenin to the medium increased the proportion of DHA and saturated fatty acids, including C12:0, C14:0 and C16:0, at the expense of monounsaturated fatty acids, including C16:1 and C18:1. Supplementation with 1 mg/L cerulenin resulted in the highest DHA yield of 2.4 mg/L upon co-expression of pfaE(DHA) from C. psychrerythraea.
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Affiliation(s)
- Yun-Feng Peng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wen-Chao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Kang Xiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lin Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xia Wan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan, China
- * E-mail:
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23
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Verma A, Mual P, Mayilraj S, Krishnamurthi S. Tamilnaduibacter salinus gen. nov., sp. nov., a halotolerant gammaproteobacterium within the family Alteromonadaceae, isolated from a salt pan in Tamilnadu, India. Int J Syst Evol Microbiol 2015; 65:3248-3255. [PMID: 26296662 DOI: 10.1099/ijsem.0.000401] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-negative, slow-growing, halotolerant strains with rod-shaped cells, designated as strains Mi-7T and Mi-8, which formed pin-point colonies on halophilic media were isolated during a study into the microbial diversity of a salt pan in the state of Tamilnadu, India. Both the strains had an obligate requirement for 1 % (w/v) NaCl for growth and were halotolerant, growing at NaCl concentrations of up to 20 % (w/v) in media. The strains, however, showed an inability to utilize the majority of substrates tested as sole carbon sources for growth and in fermentation reactions. Molecular phylogenetic analyses, based on 16S rRNA gene sequence revealed their closest phylogenetic neighbours to be members of the genus Marinobacter, with whom they showed the highest sequence similarity of 93.6 % and even less with the type strain of the type species, Marinobacter hydrocarbonoclasticus DSM 8798T (91.1 %). Similarities with other genera within the family Alteromonadaceae were below 91.0 %. However, the two strains were very closely related to each other with 99.9 % sequence similarity, and DNA–DNA hybridization analyses confirmed their placement in the same species. The DNA G+C content of both strains was 65 mol%. Using the polyphasic taxonomic data obtained from this study, strains Mi-7T and Mi-8 represent two strains of the same species of a novel genus for which the name Tamilnaduibacter salinus gen. nov., sp. nov., is proposed; the type strain of the novel species is Mi-7T ( = MTCC 12009T = DSM 28688T).
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Affiliation(s)
- Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Poonam Mual
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
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24
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Sweet CR, Watson RE, Landis CA, Smith JP. Temperature-Dependence of Lipid A Acyl Structure in Psychrobacter cryohalolentis and Arctic Isolates of Colwellia hornerae and Colwellia piezophila. Mar Drugs 2015; 13:4701-20. [PMID: 26264000 PMCID: PMC4557000 DOI: 10.3390/md13084701] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 12/21/2022] Open
Abstract
Lipid A is a fundamental Gram-negative outer membrane component and the essential element of lipopolysaccharide (endotoxin), a potent immunostimulatory molecule. This work describes the metabolic adaptation of the lipid A acyl structure by Psychrobacter cryohalolentis at various temperatures in its facultative psychrophilic growth range, as characterized by MALDI-TOF MS and FAME GC-MS. It also presents the first elucidation of lipid A structure from the Colwellia genus, describing lipid A from strains of Colwellia hornerae and Colwellia piezophila, which were isolated as primary cultures from Arctic fast sea ice and identified by 16S rDNA sequencing. The Colwellia strains are obligate psychrophiles, with a growth range restricted to 15 °C or less. As such, these organisms have less need for fluidity adaptation in the acyl moiety of the outer membrane, and they do not display alterations in lipid A based on growth temperature. Both Psychrobacter and Colwellia make use of extensive single-methylene variation in the size of their lipid A molecules. Such single-carbon variations in acyl size were thought to be restricted to psychrotolerant (facultative) species, but its presence in these Colwellia species shows that odd-chain acyl units and a single-carbon variation in lipid A structure are present in obligate psychrophiles, as well.
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Affiliation(s)
- Charles R Sweet
- Chemistry Department, 572M Holloway Road, United States Naval Academy, Annapolis, MD 21402, USA.
| | - Rebecca E Watson
- Chemistry Department, 572M Holloway Road, United States Naval Academy, Annapolis, MD 21402, USA.
| | - Corinne A Landis
- Chemistry Department, 572M Holloway Road, United States Naval Academy, Annapolis, MD 21402, USA.
| | - Joseph P Smith
- Oceanography Department, 572C Holloway Road, United States Naval Academy, Annapolis, MD 21402, USA.
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25
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Pagé AP, Yergeau É, Greer CW. Salix purpurea Stimulates the Expression of Specific Bacterial Xenobiotic Degradation Genes in a Soil Contaminated with Hydrocarbons. PLoS One 2015; 10:e0132062. [PMID: 26161539 PMCID: PMC4498887 DOI: 10.1371/journal.pone.0132062] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/09/2015] [Indexed: 12/30/2022] Open
Abstract
The objectives of this study were to uncover Salix purpurea-microbe xenobiotic degradation systems that could be harnessed in rhizoremediation, and to identify microorganisms that are likely involved in these partnerships. To do so, we tested S. purpurea's ability to stimulate the expression of 10 marker microbial oxygenase genes in a soil contaminated with hydrocarbons. In what appeared to be a detoxification rhizosphere effect, transcripts encoding for alkane 1-monooxygenases, cytochrome P450 monooxygenases, laccase/polyphenol oxidases, and biphenyl 2,3-dioxygenase small subunits were significantly more abundant in the vicinity of the plant's roots than in bulk soil. This gene expression induction is consistent with willows' known rhizoremediation capabilities, and suggests the existence of S. purpurea-microbe systems that target many organic contaminants of interest (i.e. C4-C16 alkanes, fluoranthene, anthracene, benzo(a)pyrene, biphenyl, polychlorinated biphenyls). An enhanced expression of the 4 genes was also observed within the bacterial orders Actinomycetales, Rhodospirillales, Burkholderiales, Alteromonadales, Solirubrobacterales, Caulobacterales, and Rhizobiales, which suggest that members of these taxa are active participants in the exposed partnerships. Although the expression of the other 6 marker genes did not appear to be stimulated by the plant at the community level, signs of additional systems that rest on their expression by members of the orders Solirubrobacterales, Sphingomonadales, Actinomycetales, and Sphingobacteriales were observed. Our study presents the first transcriptomics-based identification of microbes whose xenobiotic degradation activity in soil appears stimulated by a plant. It paints a portrait that contrasts with the current views on these consortia's composition, and opens the door for the development of laboratory test models geared towards the identification of root exudate characteristics that limit the efficiency of current willow-based rhizoremediation applications.
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Affiliation(s)
- Antoine P. Pagé
- Department of Natural Resource Sciences, McGill University, Montréal, Québec, Canada
- * E-mail:
| | - Étienne Yergeau
- Energy, Mining and Environment, National Research Council Canada, Montréal, Québec, Canada
| | - Charles W. Greer
- Department of Natural Resource Sciences, McGill University, Montréal, Québec, Canada
- Energy, Mining and Environment, National Research Council Canada, Montréal, Québec, Canada
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26
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Qin QL, Xie BB, Yu Y, Shu YL, Rong JC, Zhang YJ, Zhao DL, Chen XL, Zhang XY, Chen B, Zhou BC, Zhang YZ. Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation. Environ Microbiol 2014; 16:1642-53. [PMID: 25009843 DOI: 10.1111/1462-2920.12318] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.
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Swift SM, Hudgens JW, Heselpoth RD, Bales PM, Nelson DC. Characterization of AlgMsp, an alginate lyase from Microbulbifer sp. 6532A. PLoS One 2014; 9:e112939. [PMID: 25409178 PMCID: PMC4237336 DOI: 10.1371/journal.pone.0112939] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 10/22/2014] [Indexed: 11/19/2022] Open
Abstract
Alginate is a polysaccharide produced by certain seaweeds and bacteria that consists of mannuronic acid and guluronic acid residues. Seaweed alginate is used in food and industrial chemical processes, while the biosynthesis of bacterial alginate is associated with pathogenic Pseudomonas aeruginosa. Alginate lyases cleave this polysaccharide into short oligo-uronates and thus have the potential to be utilized for both industrial and medicinal applications. An alginate lyase gene, algMsp, from Microbulbifer sp. 6532A, was synthesized as an E.coli codon-optimized clone. The resulting 37 kDa recombinant protein, AlgMsp, was expressed, purified and characterized. The alginate lyase displayed highest activity at pH 8 and 0.2 M NaCl. Activity of the alginate lyase was greatest at 50°C; however the enzyme was not stable over time when incubated at 50°C. The alginate lyase was still highly active at 25°C and displayed little or no loss of activity after 24 hours at 25°C. The activity of AlgMsp was not dependent on the presence of divalent cations. Comparing activity of the lyase against polymannuronic acid and polyguluronic acid substrates showed a higher turnover rate for polymannuronic acid. However, AlgMSP exhibited greater catalytic efficiency with the polyguluronic acid substrate. Prolonged AlgMsp-mediated degradation of alginate produced dimer, trimer, tetramer, and pentamer oligo-uronates.
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Affiliation(s)
- Steven M. Swift
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America
| | - Jeffrey W. Hudgens
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America
- National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, Maryland, United States of America
| | - Ryan D. Heselpoth
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America
| | - Patrick M. Bales
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America
| | - Daniel C. Nelson
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
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28
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Ohta Y, Nogi Y, Miyazaki M, Li Z, Hatada Y, Ito S, Horikoshi K. Enzymatic Properties and Nucleotide and Amino Acid Sequences of a Thermostable β-Agarase from the Novel Marine Isolate, JAMB-A94. Biosci Biotechnol Biochem 2014; 68:1073-81. [PMID: 15170112 DOI: 10.1271/bbb.68.1073] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A gene, agaA, for a novel beta-agarase from the marine bacterium JAMB-A94 was cloned and sequenced. The 16S rDNA of the isolate had the closest match, of only 94.8% homology, with that from Microbulbifer salipaludis JCM11542(T). The agaA gene encoded a protein with a calculated molecular mass of 48,203 Da. The deduced amino acid sequence showed 37-66% identity to those of known agarases in glycoside hydrolase family 16. A carbohydrate-binding module-like amino acid sequence was found in the C-terminal region. The recombinant enzyme was hyper-produced extracellularly when Bacillus subtilis was used as a host. The purified enzyme was an endo-type beta-agarase, yielding neoagarotetraose as the main final product. It was very thermostable up to 60 degrees C. The optimal pH and temperature for activity were around 7.0 and 55 degrees C respectively. The activity was not inhibited by EDTA (up to 100 mM) and sodium dodecyl sulfate (up to 30 mM).
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Affiliation(s)
- Yukari Ohta
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Cui F, Dong S, Shi X, Zhao X, Zhang XH. Overexpression and characterization of a novel thermostable β-agarase YM01-3, from marine bacterium Catenovulum agarivorans YM01(T). Mar Drugs 2014; 12:2731-47. [PMID: 24824021 PMCID: PMC4052312 DOI: 10.3390/md12052731] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 04/21/2014] [Accepted: 04/22/2014] [Indexed: 11/20/2022] Open
Abstract
Genome sequencing of Catenovulum agarivorans YM01T reveals 15 open-reading frames (ORFs) encoding various agarases. In this study, extracellular proteins of YM01T were precipitated by ammonium sulfate and separated by one-dimensional gel electrophoresis. The results of in-gel agarase activity assay and mass spectrometry analysis revealed that the protein, YM01-3, was an agarase with the most evident agarolytic activity. Agarase YM01-3, encoded by the YM01-3 gene, consisted of 420 amino acids with a calculated molecular mass of 46.9 kDa and contained a glycoside hydrolase family 16 β-agarase module followed by a RICIN superfamily in the C-terminal region. The YM01-3 gene was cloned and expressed in Escherichia coli. The recombinant agarase, YM01-3, showed optimum activity at pH 6.0 and 60 °C and had a K(m) of 3.78 mg mL⁻¹ for agarose and a Vmax of 1.14 × 10⁴ U mg⁻¹. YM01-3 hydrolyzed the β-1,4-glycosidic linkages of agarose, yielding neoagarotetraose and neoagarohexaose as the main products. Notably, YM01-3 was stable below 50 °C and retained 13% activity after incubation at 80 °C for 1 h, characteristics much different from other agarases. The present study highlights a thermostable agarase with great potential application value in industrial production.
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Affiliation(s)
- Fangyuan Cui
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Sujie Dong
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Xiaochong Shi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Xia Zhao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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Abstract
A Gram-stain-negative, motile, mesophilic, aerobic, rod-shaped bacterium, strain 8-8(T), was isolated from surface seawater at Muroto, Kochi, Japan. The strain exhibited agar-degrading activity. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Alteromonadaceae and clustered distantly with members of the genus Glaciecola (≤ 94.0% similarity). The DNA G+C content was 41.8 mol%. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c and the major hydroxy fatty acid was C12 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified polar lipid; lysophosphatidylethanolamine and unidentified polar lipids were found as minor components. The major quinone was Q-8. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 8-8(T) represents a novel species of a new genus, for which the name Agaribacter marinus gen. nov., sp. nov. is proposed. The type strain of Agaribacter marinus is 8-8(T) ( = NBRC 110023(T) = LMG 28167(T)).
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Affiliation(s)
- Maki Teramoto
- Oceanography Section, Kochi University, Kohasu, Oko, Nankoku, Kochi 783-8505, Japan
| | - Miyuki Nishijima
- TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan
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31
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Qin QL, Xie BB, Shu YL, Rong JC, Zhao DL, Zhang XY, Chen XL, Zhou BC, Zhang YZ. Genome sequence of proteorhodopsin-containing sea ice bacterium Glaciecola punicea ACAM 611T. J Bacteriol 2012; 194:3267. [PMID: 22628500 PMCID: PMC3370857 DOI: 10.1128/jb.00463-12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 03/29/2012] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft genome sequence of Antarctic sea ice bacterium Glaciecola punicea ACAM 611(T), the type species of the genus Glaciecola. A blue-light-absorbing proteorhodopsin gene is present in the 3.08-Mb genome. This genome sequence can facilitate the study of the physiological metabolisms and ecological roles of sea ice bacteria.
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Affiliation(s)
- Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
- Key Laboratory for Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Yan-Li Shu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Jin-Cheng Rong
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Dian-Li Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Bai-Cheng Zhou
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
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Ko HJ, Park E, Song J, Yang TH, Lee HJ, Kim KH, Choi IG. Functional cell surface display and controlled secretion of diverse Agarolytic enzymes by Escherichia coli with a novel ligation-independent cloning vector based on the autotransporter YfaL. Appl Environ Microbiol 2012; 78:3051-8. [PMID: 22344647 PMCID: PMC3346495 DOI: 10.1128/aem.07004-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Accepted: 02/08/2012] [Indexed: 11/20/2022] Open
Abstract
Autotransporters have been employed as the anchoring scaffold for cell surface display by replacing their passenger domains with heterologous proteins to be displayed. We adopted an autotransporter (YfaL) of Escherichia coli for the cell surface display system. The critical regions in YfaL for surface display were identified for the construction of a ligation-independent cloning (LIC)-based display system. The designed system showed no detrimental effect on either the growth of the host cell or overexpressing heterologous proteins on the cell surface. We functionally displayed monomeric red fluorescent protein (mRFP1) as a reporter protein and diverse agarolytic enzymes from Saccharophagus degradans 2-40, including Aga86C and Aga86E, which previously had failed to be functional expressed. The system could display different sizes of proteins ranging from 25.3 to 143 kDa. We also attempted controlled release of the displayed proteins by incorporating a tobacco etch virus protease cleavage site into the C termini of the displayed proteins. The maximum level of the displayed protein was 6.1 × 10(4) molecules per a single cell, which corresponds to 5.6% of the entire cell surface of actively growing E. coli.
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Affiliation(s)
- Hyeok-Jin Ko
- Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Eunhye Park
- Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Joseph Song
- Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Taek Ho Yang
- Chemical and Polymer Laboratory, R&D Center, GS Caltex Corporation, Daejeon, South Korea
| | - Hee Jong Lee
- Chemical and Polymer Laboratory, R&D Center, GS Caltex Corporation, Daejeon, South Korea
| | - Kyoung Heon Kim
- Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - In-Geol Choi
- Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
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Kim HT, Ko HJ, Kim N, Kim D, Lee D, Choi IG, Woo HC, Kim MD, Kim KH. Characterization of a recombinant endo-type alginate lyase (Alg7D) from Saccharophagus degradans. Biotechnol Lett 2012; 34:1087-92. [PMID: 22391735 DOI: 10.1007/s10529-012-0876-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 02/06/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Hee Taek Kim
- School of Life Sciences and Biotechnology, Korea University, Seoul, Korea
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34
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Wakabayashi M, Sakatoku A, Noda F, Noda M, Tanaka D, Nakamura S. Isolation and characterization of Microbulbifer species 6532A degrading seaweed thalli to single cell detritus particles. Biodegradation 2012; 23:93-105. [PMID: 21681519 DOI: 10.1007/s10532-011-9489-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 06/04/2011] [Indexed: 10/18/2022]
Abstract
To reduce the volume of seaweed wastes and extract polysaccharides, seaweed-degrading bacteria were isolated from drifting macroalgae harvested along the coast of Toyama Bay, Japan. Sixty-four bacterial isolates were capable of degrading "Wakame" (Undaria pinnatifida) thallus fragments into single cell detritus (SCD) particles. Amongst these, strain 6532A was the most active degrader of thallus fragments, and was capable of degrading thallus fragments to SCD particles within a day. Although the sequence similarity of the 16S rRNA gene of strain 6532A was 100% similar to that of Microbulbifer elongatus JAMB-A7, several distinct differences were observed between strains, including motility, morphology, and utilization of D: -arabinose and gelatin. Consequently, strain 6532A was classified as a new Microbulbifer strain, and was designated Microbulbifer sp. 6532A. Strain 6532A was capable of degrading both alginate and cellulose in the culture medium, zymogram analysis of which revealed the presence of multiple alginate lyases and cellulases. To the best of our knowledge, this is the first study to directly demonstrate the existence of these enzymes in Microbulbifer species. Shotgun cloning and sequencing of the alginate lyase gene in 6532A revealed a 1,074-bp open reading frame, which was designated algMsp. The reading frame encoded a PL family seven enzyme composed of 358 amino acids (38,181 Da). With a similarity of 74.2%, the deduced amino acid sequence was most similar to a Saccharophagus enzyme (alg 7C). These findings suggest that algMsp in strain 6532A is a novel alginate lyase gene.
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35
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Bian F, Qin QL, Xie BB, Shu YL, Zhang XY, Yu Y, Chen B, Chen XL, Zhou BC, Zhang YZ. Complete genome sequence of seawater bacterium Glaciecola nitratireducens FR1064(T). J Bacteriol 2011; 193:7006-7. [PMID: 22123761 PMCID: PMC3232840 DOI: 10.1128/jb.06296-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 09/30/2011] [Indexed: 11/20/2022] Open
Abstract
Glaciecola nitratireducens strain FR1064(T) was isolated from seawater and described as a new species by Baik et al. in 2006. The genome size is about 1.01 to 1.26 Mb smaller than two reported Glaciecola genomes, indicating the gain or loss of large genome segments in the evolution of Glaciecola strains.
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Affiliation(s)
- Fei Bian
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
- Key Laboratory for Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Yan-Li Shu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Bai-Cheng Zhou
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
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Hutcheson SW, Zhang H, Suvorov M. Carbohydrase systems of Saccharophagus degradans degrading marine complex polysaccharides. Mar Drugs 2011; 9:645-665. [PMID: 21731555 PMCID: PMC3124978 DOI: 10.3390/md9040645] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/01/2011] [Accepted: 04/13/2011] [Indexed: 11/16/2022] Open
Abstract
Saccharophagus degradans 2-40 is a γ-subgroup proteobacterium capable of using many of the complex polysaccharides found in the marine environment for growth. To utilize these complex polysaccharides, this bacterium produces a plethora of carbohydrases dedicated to the processing of a carbohydrate class. Aiding in the identification of the contributing genes and enzymes is the known genome sequence for this bacterium. This review catalogs the genes and enzymes of the S. degradans genome that are likely to function in the systems for the utilization of agar, alginate, α- and β-glucans, chitin, mannans, pectins, and xylans and discusses the cell biology and genetics of each system as it functions to transfer carbon back to the bacterium.
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Affiliation(s)
- Steven W. Hutcheson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Haitao Zhang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
- Zymetis, Inc., 387 Technology Drive, College Park, MD 20742, USA; E-Mails: (H.Z.); (M.S.)
| | - Maxim Suvorov
- Zymetis, Inc., 387 Technology Drive, College Park, MD 20742, USA; E-Mails: (H.Z.); (M.S.)
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Meron D, Atias E, Iasur Kruh L, Elifantz H, Minz D, Fine M, Banin E. The impact of reduced pH on the microbial community of the coral Acropora eurystoma. ISME J 2011; 5:51-60. [PMID: 20668489 PMCID: PMC3105665 DOI: 10.1038/ismej.2010.102] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 05/21/2010] [Accepted: 06/08/2010] [Indexed: 12/21/2022]
Abstract
Rising concentrations of atmospheric carbon dioxide are acidifying the world's oceans. Surface seawater pH is 0.1 units lower than pre-industrial values and is predicted to decrease by up to 0.4 units by the end of the century. This change in pH may result in changes in the physiology of ocean organisms, in particular, organisms that build their skeletons/shells from calcium carbonate, such as corals. This physiological change may also affect other members of the coral holobiont, for example, the microbial communities associated with the coral, which in turn may affect the coral physiology and health. In the present study, we examined changes in bacterial communities in the coral mucus, tissue and skeleton following exposure of the coral Acropora eurystoma to two different pH conditions: 7.3 and 8.2 (ambient seawater). The microbial community was different at the two pH values, as determined by denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis. Further analysis of the community in the corals maintained at the lower pH revealed an increase in bacteria associated with diseased and stressed corals, such as Vibrionaceae and Alteromonadaceae. In addition, an increase in the number of potential antibacterial activity was recorded among the bacteria isolated from the coral maintained at pH 7.3. Taken together, our findings highlight the impact that changes in the pH may have on the coral-associated bacterial community and their potential contribution to the coral host.
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Affiliation(s)
- Dalit Meron
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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Lee S, Lee JY, Ha SC, Jung J, Shin DH, Kim KH, Choi IG. Crystallization and preliminary X-ray analysis of neoagarobiose hydrolase from Saccharophagus degradans 2-40. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1299-301. [PMID: 20054134 PMCID: PMC2802886 DOI: 10.1107/s174430910904603x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 11/02/2009] [Indexed: 05/04/2023]
Abstract
Many agarolytic bacteria degrade agar polysaccharide into the disaccharide unit neoagarobiose [O-3,6-anhydro-alpha-L-galactopyranosyl-(1-->3)-D-galactose] using various beta-agarases. Neoagarobiose hydrolase is an enzyme that acts on the alpha-1,3 linkage in neoagarobiose to yield D-galactose and 3,6-anhydro-L-galactose. This activity is essential in both the metabolism of agar by agarolytic bacteria and the production of fermentable sugars from agar biomass for bioenergy production. Neoagarobiose hydrolase from the marine bacterium Saccharophagus degradans 2-40 was overexpressed in Escherichia coli and crystallized in the monoclinic space group C2, with unit-cell parameters a = 129.83, b = 76.81, c = 90.11 A, beta = 101.86 degrees . The crystals diffracted to 1.98 A resolution and possibly contains two molecules in the asymmetric unit.
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Affiliation(s)
- Saeyoung Lee
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea
| | - Jonas Yun Lee
- Division of Chemistry and Chemical Engineering 114-96, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sung Chul Ha
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jina Jung
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea
- College of Pharmacy, Ewha Womans University, Seoul, Republic of Korea
| | - Dong Hae Shin
- College of Pharmacy, Ewha Womans University, Seoul, Republic of Korea
| | - Kyoung Heon Kim
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea
| | - In-Geol Choi
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea
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Xie H, Han B, Dong W, Yang Y, Chang J, Peng Y, Liu W. [Isolation and characterization of a marine agarase]. Wei Sheng Wu Xue Bao 2009; 49:896-901. [PMID: 19873753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVE This study was carried out to isolate and characterize an agarase from a marine bacterium Agarivorans albus QM38. METHODS SDS-PAGE grade agarase was obtained from the fermentation broth after removing the bacteria by centrifugation, ammonium sulfate precipitation, DEAE-sepharose fast flow anion exchange chromatography and Sephacryl S-100 gel filtration. Enzyme's molecular weight was determined with SDS-PAGE. The catalysates of the isolated enzyme were determined withmass spectrography. RESULTS Agarase A was isolated. The molecular weight of agarase A was 127.80 kDa. More characterizations of agarase A were studied and the results showed that the optimal reaction condition for agarase A was at 35 degrees C, pH 7.6, and agar concentration of 0.9% (w/v), while most of the metal ions inhibited the activity of it. The catalysates of agarase A were mainly tetrose and hexose. CONCLUSION Agarase A was purified from the medium. It could hydrolyze jellied agar and yield simple catalysates. Its molecular weight is different from all the agarases reported so far.
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Affiliation(s)
- Hui Xie
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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Huang Y, Lai X, He X, Cao L, Zeng Z, Zhang J, Zhou S. Characterization of a deep-sea sediment metagenomic clone that produces water-soluble melanin in Escherichia coli. Mar Biotechnol (NY) 2009; 11:124-131. [PMID: 18648877 DOI: 10.1007/s10126-008-9128-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 06/13/2008] [Indexed: 05/26/2023]
Abstract
To access to the microbial genetic resources of deep-sea sediment by a culture-independent approach, the sediment DNA was extracted and cloned into fosmid vector (pCC1FOS) generating a library of 39,600 clones with inserts of 24-45 kb. The clone fss6 producing red-brown pigment was isolated and characterized. The pigment was identified as melanin according to its physico-chemical characteristics. Subcloning and sequences analyses of fss6 demonstrated that one open reading frame (ORF2) was responsible for the pigment production. The deduced protein from ORF2 revealed significant amino acid similarity to the 4-hydroxyphenylpyruvate dioxygenase (HPPD) from deep-sea bacteria Idiomarina loihiensis. Further study demonstrated that the production of melanin was correlated with homogentistic acid (HGA). The p-hydroxyphenylpyruvate produced by the Escherichia coli host was converted to HGA through the oxidation reaction of introduced HPPD. The results demonstrate that expression of DNA extracted directly from the environment might generate applicable microbial gene products. The construction and analysis of the metagenomic library from deep-sea sediment contributed to our understanding for the reservoir of unexploited deep-sea microorganisms.
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Affiliation(s)
- Yali Huang
- State Key Laboratory for Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
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Weiner RM, Taylor LE, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, Ekborg NA, Lamed R, Richardson PM, Borovok I, Hutcheson S. Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. PLoS Genet 2008; 4:e1000087. [PMID: 18516288 PMCID: PMC2386152 DOI: 10.1371/journal.pgen.1000087] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 05/01/2008] [Indexed: 01/02/2023] Open
Abstract
The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment. A segment of the global marine carbon cycle that has been poorly characterized is the mineralization of complex polysaccharides to carbon dioxide, a greenhouse gas. It also remained a mystery whether prokaryotes mineralize plant/algal cell walls and woody material in the oceans via carbohydrase systems and, if so, which organisms are involved. We have analyzed the complete genome sequence of the marine bacterium Saccharophagus degradans to better ascertain the potential role of prokaryotes in marine carbon transformation. We discovered that S. degradans, which is related to a number of other newly discovered marine strains, has an unprecedented quantity and diversity of carbohydrases, including the first characterized marine cellulose system. In fact, extensive analysis of the S. degradans genome sequence and functional followup experiments identified an extensive collection of complete enzyme systems that degrade more than 10 complex polysaccharides. These include agar, alginate, and chitin, altogether representing an extraordinary range of catabolic capability. Genomic analyses further demonstrated that the carbohydrases are unusually modular; sequence comparisons revealed that many of the functional modules were acquired by lateral transfer. These results suggest that the prokaryotic contribution to marine carbon fluxes is substantial and cannot be ignored in predictions of climate change.
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Affiliation(s)
- Ronald M. Weiner
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
- Marine and Estuarine Environmental Sciences Program, University of Maryland, College Park, Maryland, United States of America
- * E-mail: (RMW); (SH)
| | - Larry E. Taylor
- Marine and Estuarine Environmental Sciences Program, University of Maryland, College Park, Maryland, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Marseille, France
| | - Loren Hauser
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Miriam Land
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Marseille, France
| | - Corinne Rancurel
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Marseille, France
| | - Elizabeth H. Saunders
- Joint Genome Institute, Group B-5 Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Atkinson G. Longmire
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Haitao Zhang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Edward A. Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne, United Kingdom
| | - Frank Larimer
- Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America
| | - Igor B. Zhulin
- Joint Institute for Computational Sciences, University of Tennessee–Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Nathan A. Ekborg
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Paul M. Richardson
- DOE Joint Genome Institute, Production Genomics Facility, Walnut Creek, California, United States of America
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Steven Hutcheson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
- * E-mail: (RMW); (SH)
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Abstract
An Antarctic sea ice bacterium of the Gram-negative genus Colwellia, strain SLW05, produces an extracellular substance that changes the morphology of growing ice. The active substance was identified as a approximately 25-kDa protein that was purified through its affinity for ice. The full gene sequence was determined and was found to encode a 253-amino acid protein with a calculated molecular mass of 26,350 Da. The predicted amino acid sequence is similar to predicted sequences of ice-binding proteins recently found in two species of sea ice diatoms and a species of snow mold. A recombinant ice-binding protein showed ice-binding activity and ice recrystallization inhibition activity. The protein is much smaller than bacterial ice-nucleating proteins and antifreeze proteins that have been previously described. The function of the protein is unknown but it may act as an ice recrystallization inhibitor to protect membranes in the frozen state.
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Affiliation(s)
- James A Raymond
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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Yoon JH, Jung SY, Kang SJ, Oh TK. Microbulbifer celer sp. nov., isolated from a marine solar saltern of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2007; 57:2365-2369. [PMID: 17911312 DOI: 10.1099/ijs.0.65184-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile, rod-shaped, Microbulbifer-like bacterial strain, ISL-39T, was isolated from a marine solar saltern of the Yellow Sea in Korea and was subjected to a polyphasic taxonomic investigation. Strain ISL-39T grew optimally at pH 7.0–8.0 and 37 °C. It contained Q-8 as the predominant ubiquinone and iso-C15 : 0, C16 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C content was 57.7 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-39T belonged to the genus Microbulbifer. Strain ISL-39T exhibited 16S rRNA gene sequence similarity values of 94.7–97.5 % with respect to the type strains of four recognized Microbulbifer species. DNA–DNA relatedness data and the differential phenotypic properties and phylogenetic distinctiveness of ISL-39T make this strain distinguishable from the recognized Microbulbifer species. On the basis of the phenotypic, phylogenetic and genetic data, strain ISL-39T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer celer sp. nov. is proposed. The type strain is ISL-39T (=KCTC 12973T=CCUG 54356T).
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MESH Headings
- Alteromonadaceae/chemistry
- Alteromonadaceae/classification
- Alteromonadaceae/genetics
- Alteromonadaceae/isolation & purification
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Hydrogen-Ion Concentration
- Korea
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Temperature
- Ubiquinone/analysis
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Seo-Youn Jung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - So-Jung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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44
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Abstract
A bacterial strain named IMCC1877T was obtained from surface seawater collected near the coast of Deokjeok island (Yellow Sea), using a standard dilution-plating method. The strain was Gram-negative, chemoheterotrophic and facultatively anaerobic, requiring NaCl, and cells were motile rods with a single polar flagellum. Colonies on marine agar were very small (average diameter 0.1 mm). Based on 16S rRNA gene sequences, the most closely related species to strain IMCC1877T was Marinobacterium stanieri (93.7 % sequence similarity to the type strain). Phylogenetic analyses based on 16S rRNA gene sequences showed that this marine isolate belonged to the order Oceanospirillales and formed an independent phyletic line within the clade forming the genus Marinobacterium. The DNA G+C content of the strain was 60.7 mol% and the predominant constituents of the cellular fatty acids were C18 : 1
ω7c (36.6 %), C16 : 1
ω7c and/or iso-C15 : 0 2-OH (26.7 %) and C16 : 0 (24.3 %). Based on the taxonomic data, only a distant relationship could be established between strain IMCC1877T and other Marinobacterium species; the strain therefore represents a novel species of the genus Marinobacterium, for which the name Marinobacterium litorale sp. nov. is proposed. The type strain is IMCC1877T (=KCTC 12756T=LMG 23872T).
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MESH Headings
- Aerobiosis
- Alteromonadaceae/chemistry
- Alteromonadaceae/classification
- Alteromonadaceae/genetics
- Alteromonadaceae/isolation & purification
- Anaerobiosis
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Flagella
- Genes, rRNA
- Korea
- Locomotion
- Molecular Sequence Data
- Organic Chemicals/metabolism
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
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Affiliation(s)
- Hana Kim
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Yoe-Jin Choo
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Jaeho Song
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Republic of Korea
| | - Jang-Cheon Cho
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
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45
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Leiros HKS, Pey AL, Innselset M, Moe E, Leiros I, Steen IH, Martinez A. Structure of phenylalanine hydroxylase from Colwellia psychrerythraea 34H, a monomeric cold active enzyme with local flexibility around the active site and high overall stability. J Biol Chem 2007; 282:21973-86. [PMID: 17537732 DOI: 10.1074/jbc.m610174200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The characteristic of cold-adapted enzymes, high catalytic efficiency at low temperatures, is often associated with low thermostability and high flexibility. In this context, we analyzed the catalytic properties and solved the crystal structure of phenylalanine hydroxylase from the psychrophilic bacterium Colwellia psychrerythraea 34H (CpPAH). CpPAH displays highest activity with tetrahydrobiopterin (BH(4)) as cofactor and at 25 degrees C (15 degrees C above the optimal growth temperature). Although the enzyme is monomeric with a single L-Phe-binding site, the substrate binds cooperatively. In comparison with PAH from mesophilic bacteria and mammalian organisms, CpPAH shows elevated [S(0.5)](L-Phe) (= 1.1 +/- 0.1 mm) and K(m)(BH(4))(= 0.3 +/- 0.1 mm), as well as high catalytic efficiency at 10 degrees C. However, the half-inactivation and denaturation temperature is only slightly lowered (T(m) approximately 52 degrees C; where T(m) is half-denaturation temperature), in contrast to other cold-adapted enzymes. The crystal structure shows regions of local flexibility close to the highly solvent accessible binding sites for BH(4) (Gly(87)/Phe(88)/Gly(89)) and l-Phe (Tyr(114)-Pro(118)). Normal mode and COREX analysis also detect these and other areas with high flexibility. Greater mobility around the active site and disrupted hydrogen bonding abilities for the cofactor appear to represent cold-adaptive properties that do not markedly affect the thermostability of CpPAH.
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Affiliation(s)
- Hanna-Kirsti S Leiros
- Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, University of Tromsø, Tromsø
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46
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Arahal DR, Lekunberri I, González JM, Pascual J, Pujalte MJ, Pedrós-Alió C, Pinhassi J. Neptuniibacter caesariensis gen. nov., sp. nov., a novel marine genome-sequenced gammaproteobacterium. Int J Syst Evol Microbiol 2007; 57:1000-1006. [PMID: 17473248 DOI: 10.1099/ijs.0.64524-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, slightly halophilic, strictly aerobic, motile chemoorganotrophic bacterium, strain MED92T, was isolated from a surface water sample from the eastern Mediterranean Sea. Phylogenetic analysis based on its 16S rRNA gene sequence, retrieved from the whole-genome sequence, demonstrated that this isolate is unique, showing <93 % sequence similarity to species of the families Oceanospirillaceae and Alteromonadaceae. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol, an unknown aminophospholipid and diphosphatidylglycerol. Major fatty acids are 16 : 1ω7c/15 iso 2-OH (41.2 % relative amount), 18 : 1ω7c (35.9 %), 16 : 0 (16.1 %), 10 : 0 3-OH (5.0 %) and 18 : 0 (1.0 %). Preferred carbon sources are organic acids and amino acids. The DNA G+C content is 46.6 mol%. Based on a phenotypic, chemotaxonomic and phylogenetic analyses, it is proposed that this marine bacterium represents a novel genus and species, for which the name Neptuniibacter caesariensis gen. nov., sp. nov. is proposed. The type strain is MED92T (=CECT 7075T=CCUG 52065T).
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MESH Headings
- Alteromonadaceae/genetics
- Amino Acids/metabolism
- Bacterial Typing Techniques
- Base Composition
- Carboxylic Acids/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Gammaproteobacteria/chemistry
- Gammaproteobacteria/classification
- Gammaproteobacteria/cytology
- Gammaproteobacteria/genetics
- Gammaproteobacteria/metabolism
- Gammaproteobacteria/physiology
- Genes, rRNA/genetics
- Genome, Bacterial
- Mediterranean Sea
- Membrane Lipids/analysis
- Molecular Sequence Data
- Movement
- Oceanospirillaceae/genetics
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Campus de Burjassot, 46100 València, Spain
- Colección Española de Cultivos Tipo (CECT), Universitat de València, Campus de Burjassot, 46100 València, Spain
| | - Itziar Lekunberri
- Institut de Ciències del Mar-CMIMA (CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - José M González
- Departamento de Microbiología y Biología Celular, Facultad de Farmacia, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Javier Pascual
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Campus de Burjassot, 46100 València, Spain
- Departamento de Microbiología y Ecología, Universitat de València, Campus de Burjassot, 46100 València, Spain
| | - María J Pujalte
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Campus de Burjassot, 46100 València, Spain
- Departamento de Microbiología y Ecología, Universitat de València, Campus de Burjassot, 46100 València, Spain
| | - Carlos Pedrós-Alió
- Institut de Ciències del Mar-CMIMA (CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Jarone Pinhassi
- Marine Microbiology, Department of Biology and Environmental Sciences, University of Kalmar, SE-39182 Kalmar, Sweden
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47
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Yong JJ, Park SJ, Kim HJ, Rhee SK. Glaciecola agarilytica sp. nov., an agar-digesting marine bacterium from the East Sea, Korea. Int J Syst Evol Microbiol 2007; 57:951-953. [PMID: 17473239 DOI: 10.1099/ijs.0.64723-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on an isolate, strain NO2T, from marine sediment collected from the East Sea, Korea. Comparative 16S rRNA gene sequence studies showed that this strain belonged to the Gammaproteobacteria and was most closely related to Glaciecola mesophila KMM 241T and Glaciecola polaris LMG 21857T (98.6 and 98.0 % 16S rRNA gene sequence similarity, respectively). The isolate was Gram-negative, aerobic and slightly halophilic and grew in 2–8 % NaCl and at 7–30 °C. Strain NO2T shared some physiological and biochemical properties with G. mesophila KMM 241T and G. polaris LMG 21857T. The G+C content of the genomic DNA of strain NO2T was 45 mol%. Strain NO2T possessed C16 : 0, summed feature 4 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH) and summed feature 7 (C18 : 1
ω9c/ω12t/ω7c) as the major cellular fatty acids. DNA–DNA relatedness data indicated that strain NO2T represents a distinct species that is separate from G. mesophila and G. polaris. On the basis of polyphasic evidence, it is proposed that strain NO2T (=KCTC 12755T=LMG 23762T) represents the type strain of a novel species, Glaciecola agarilytica sp. nov.
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Affiliation(s)
- Jeong-Joong Yong
- Department of Microbiology and Biotechnology Research Institute, Chungbuk National University, 12 Gaeshin-dong, Cheongju 361-763, Republic of Korea
| | - Soo-Je Park
- Department of Microbiology and Biotechnology Research Institute, Chungbuk National University, 12 Gaeshin-dong, Cheongju 361-763, Republic of Korea
| | - Hyeon-Ju Kim
- Deep Ocean Water Application Research Center, Korea Ocean Research and Development Institute (KORDI), 245-7 Oho-ri, Jugwang-myeon, Goseong-gun 219-822, Republic of Korea
| | - Sung-Keun Rhee
- Department of Microbiology and Biotechnology Research Institute, Chungbuk National University, 12 Gaeshin-dong, Cheongju 361-763, Republic of Korea
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48
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Abstract
Nucleotide composition analyses of bacterial genomes such as cumulative GC skew highlight the atypical, strongly asymmetric architecture of the recently published chromosome of Idiomarina loihiensis L2TR, suggesting that an inversion of a 600-kb chromosomal segment occurred. The presence of 3.4-kb inverted repeated sequences at the borders of the putative rearrangement supports this hypothesis. Reverting in silico this segment restores (1) a symmetric chromosome architecture; (2) the co-orientation of transcription of all rRNA operons with DNA replication; and (3) a better conservation of gene order between this chromosome and other gamma-proteobacterial ones. Finally, long-range PCRs encompassing the ends of the 600-kb segment reveal the existence of the reverted configuration but not of the published one. This demonstrates how cumulative nucleotide-skew analyses can validate genome assemblies.
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Affiliation(s)
- François Collyn
- Département de Microbiologie Fondamentale, Faculté de Biologie et Médecine, Université de Lausanne, Switzerland
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49
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Prabagaran SR, Manorama R, Delille D, Shivaji S. Predominance of Roseobacter, Sulfitobacter, Glaciecola and Psychrobacter in seawater collected off Ushuaia, Argentina, Sub-Antarctica. FEMS Microbiol Ecol 2007; 59:342-55. [PMID: 17026513 DOI: 10.1111/j.1574-6941.2006.00213.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Bacterial diversity in sub-Antarctic seawater, collected off Ushuaia, Argentina, was examined using a culture independent approach. The composition of the 16S rRNA gene libraries from seawater and seawater contaminated with the water soluble fraction of crude oil was statistically different (P value 0.001). In both libraries, clones representing the Alphaproteobacteria, Gammaproteobacteria, the Cytophaga-Flavobacterium-Bacteroidetes group and unculturable bacteria were dominant. Clones associated with the genera Roseobacter, Sulfitobacter, Staleya, Glaciecola, Colwellia, Marinomonas, Cytophaga and Cellulophaga were common to both the libraries. However, clones associated with Psychrobacter, Arcobacter, Formosa algae, Polaribacter, Ulvibacter and Tenacibaculum were found only in seawater contaminated with hydrocarbons (Table 1). Further, the percentage of clones of Roseobacter, Sulfitobacter and Glaceicola was high in seawater (43%, 90% and 12% respectively) compared to seawater contaminated with hydrocarbons (35%, 4% and 9% respectively). One of the clones F2C63 showed 100% similarity with Marinomonas ushuaiensis a bacterium identified by us from the same site.
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50
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Zhang DC, Yu Y, Chen B, Wang HX, Liu HC, Dong XZ, Zhou PJ. Glaciecola psychrophila sp. nov., a novel psychrophilic bacterium isolated from the Arctic. Int J Syst Evol Microbiol 2006; 56:2867-2869. [PMID: 17158989 DOI: 10.1099/ijs.0.64575-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, designated 170T, was collected from high latitude Arctic locations (77° 30′ N to approximately 81° 12′ N), including the Canadian Basin and Greenland Sea. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain 170T was related to members of the genus Glaciecola and had the highest 16S rRNA gene sequence similarity to Glaciecola mesophila. Cells were Gram-negative, psychrophilic, motile rods. The temperature range for growth was 4–15 °C, with optimum growth at 12 °C and at approximately pH 6.0–9.0. Strain 170T contained C16 : 1
ω7c, C16 : 0, C12 : 1 3-OH and C18 : 1
ω7c as major fatty acids. The genomic DNA G+C content was 42.9 mol%. On the basis of phenotypic characterization, phylogenetic analysis and DNA–DNA relatedness data, strain 170T is considered to represent a novel species of the genus Glaciecola, for which the name Glaciecola psychrophila is proposed. The type strain is 170T (=CGMCC 1.6130T=JCM 13954T).
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Affiliation(s)
- De-Chao Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China
| | - He-Xiang Wang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Hong-Can Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
| | - Xiu-Zhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
| | - Pei-Jin Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
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