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Liu H, Liu WW, Haro-Moreno JM, Xu B, Zheng Y, Liu J, Tian J, Zhang XH, Zhou NY, Qin L, Zhu Y, Rodriguez-Valera F, Zhang C. A moderately thermophilic origin of a novel family of marine group II euryarchaeota from deep ocean. iScience 2023; 26:107664. [PMID: 37680465 PMCID: PMC10480650 DOI: 10.1016/j.isci.2023.107664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/30/2022] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
Marine group II (MGII) is the most abundant planktonic heterotrophic archaea in the ocean. The evolutionary history of MGII archaea is elusive. In this study, 13 new MGII metagenome-assembled genomes were recovered from surface to the hadal zone in Challenger Deep of the Mariana Trench; four of them from the deep ocean represent a novel group. The optimal growth temperature (OGT) of the common ancestor of MGII has been estimated to be at about 60°C and OGTs of MGIIc, MGIIb, and MGIIa at 47°C-50ºC, 37°C-44ºC, and 30°C-37ºC, respectively, suggesting the adaptation of these species to different temperatures during evolution. The estimated OGT range of MGIIc was supported by experimental measurements of cloned β-galactosidase that showed optimal enzyme activity around 50°C. These results indicate that MGIIc may have originated from a common ancestor that lived in warm or even hot marine environment, such as hydrothermal vents.
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Affiliation(s)
- Haodong Liu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
- CAS Key Laboratory of Crust-Mantle Materials and Environments, University of Science and Technology of China, Hefei 230026, China
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei-Wei Liu
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jose M. Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
| | - Bu Xu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
| | - Yanfen Zheng
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ocean University of China, Qingdao 266100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liping Qin
- CAS Key Laboratory of Crust-Mantle Materials and Environments, University of Science and Technology of China, Hefei 230026, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai 200062, China
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
- Laboratory for Theoretical and Computer Studies of Biological Macromolecules and Genomes, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai 200062, China
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Yao J, Zhen X, Tang K, Liu T, Xu X, Chen Z, Guo Y, Liu X, Wood TK, Ouyang S, Wang X. Novel polyadenylylation-dependent neutralization mechanism of the HEPN/MNT toxin/antitoxin system. Nucleic Acids Res 2020; 48:11054-11067. [PMID: 33045733 PMCID: PMC7641770 DOI: 10.1093/nar/gkaa855] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/20/2020] [Accepted: 09/27/2020] [Indexed: 12/25/2022] Open
Abstract
The two-gene module HEPN/MNT is predicted to be the most abundant toxin/antitoxin (TA) system in prokaryotes. However, its physiological function and neutralization mechanism remains obscure. Here, we discovered that the MntA antitoxin (MNT-domain protein) acts as an adenylyltransferase and chemically modifies the HepT toxin (HEPN-domain protein) to block its toxicity as an RNase. Biochemical and structural studies revealed that MntA mediates the transfer of three AMPs to a tyrosine residue next to the RNase domain of HepT in Shewanella oneidensis. Furthermore, in vitro enzymatic assays showed that the three AMPs are transferred to HepT by MntA consecutively with ATP serving as the substrate, and this polyadenylylation is crucial for reducing HepT toxicity. Additionally, the GSX10DXD motif, which is conserved among MntA proteins, is the key active motif for polyadenylylating and neutralizing HepT. Thus, HepT/MntA represents a new type of TA system, and the polyadenylylation-dependent TA neutralization mechanism is prevalent in bacteria and archaea.
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Affiliation(s)
- Jianyun Yao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Xiangkai Zhen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolong Xu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Zhe Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Xiaoxiao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802-4400, USA
| | - Songying Ouyang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China.,University of Chinese Academy of Sciences, Beijing, China
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Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification. J Virol 2017; 91:JVI.02275-16. [PMID: 28122979 PMCID: PMC5375668 DOI: 10.1128/jvi.02275-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/13/2017] [Indexed: 11/20/2022] Open
Abstract
Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly, we detected similarity at the nucleotide level between capsid protein-coding regions from viruses infecting cells belonging to all three domains of life, reproducing a previously established structure-based classification of icosahedral viral capsids.
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Cossu M, Da Cunha V, Toffano-Nioche C, Forterre P, Oberto J. Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes. Biochimie 2015; 118:313-21. [PMID: 26166067 PMCID: PMC4640148 DOI: 10.1016/j.biochi.2015.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/08/2015] [Indexed: 12/01/2022]
Abstract
The genomes of the 21 completely sequenced Thermococcales display a characteristic high level of rearrangements. As a result, the prediction of their origin and termination of replication on the sole basis of chromosomal DNA composition or skew is inoperative. Using a different approach based on biologically relevant sequences, we were able to determine oriC position in all 21 genomes. The position of dif, the site where chromosome dimers are resolved before DNA segregation could be predicted in 19 genomes. Computation of the core genome uncovered a number of essential gene clusters with a remarkably stable chromosomal position across species, in sharp contrast with the scrambled nature of their genomes. The active chromosomal reorganization of numerous genes acquired by horizontal transfer, mainly from mobile elements, could explain this phenomenon. Thermococcales chromosomal landmarks were uncovered using biologically relevant sequences. Core genomes procedures predict integration of mobile elements on Thermococcales chromosomes. Thermococcales genomes are highly rearranged but core clusters positions remain invariable. Thermococcales core genes are more expressed and predominantly encoded on the leading strand.
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Affiliation(s)
- Matteo Cossu
- Institute of Integrative Cellular Biology, CEA, CNRS, Université Paris Sud, 91405 Orsay, France
| | - Violette Da Cunha
- Institute of Integrative Cellular Biology, CEA, CNRS, Université Paris Sud, 91405 Orsay, France
| | - Claire Toffano-Nioche
- Institute of Integrative Cellular Biology, CEA, CNRS, Université Paris Sud, 91405 Orsay, France
| | - Patrick Forterre
- Institute of Integrative Cellular Biology, CEA, CNRS, Université Paris Sud, 91405 Orsay, France
| | - Jacques Oberto
- Institute of Integrative Cellular Biology, CEA, CNRS, Université Paris Sud, 91405 Orsay, France
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5
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Hensley SA, Jung JH, Park CS, Holden JF. Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents. Int J Syst Evol Microbiol 2014; 64:3655-3659. [DOI: 10.1099/ijs.0.066100-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two heterotrophic hyperthermophilic strains, ES1T and CL1T, were isolated from Paralvinella sp. polychaete worms collected from active hydrothermal vent chimneys in the north-eastern Pacific Ocean. Both were obligately anaerobic and produced H2S in the presence of elemental sulfur and H2. Complete genome sequences are available for both strains. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strains are more than 97 % similar to most other species of the genus
Thermococcus
. Therefore, overall genome relatedness index analyses were performed to establish that these strains are novel species. For each analysis, strain ES1T was determined to be most similar to
Thermococcus barophilus
MPT, while strain CL1T was determined to be most similar to
Thermococcus sp.
4557. The average nucleotide identity scores for these strains were 84 % for strain ES1T and 81 % for strain CL1T, genome-to-genome direct comparison scores were 23 % for strain ES1T and 47 % for strain CL1T, and the species identification scores were 89 % for strain ES1T and 88 % for strain CL1T. For each analysis, strains ES1T and CL1T were below the species delineation cut-off. Therefore, based on their whole genome sequences, strains ES1T and CL1T are suggested to represent novel species of the genus
Thermococcus
for which the names Thermococcus
paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. are proposed, respectively. The type strains are ES1T ( = DSM 27261T = KACC 17923T) and CL1T ( = DSM 27260T = KACC 17922T).
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Affiliation(s)
- Sarah A. Hensley
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Jong-Hyun Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Cheon-Seok Park
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - James F. Holden
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
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Characterization of the frhAGB-encoding hydrogenase from a non-methanogenic hyperthermophilic archaeon. Extremophiles 2014; 19:109-18. [PMID: 25142159 DOI: 10.1007/s00792-014-0689-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
Abstract
The F420-reducing hydrogenase has been known as a key enzyme in methanogenesis. Its homologs have been identified in non-methanogenic hyperthermophilic archaea, including Thermococcus onnurineus NA1, but neither physiological function nor biochemical properties have been reported to date. The enzyme of T. onnurineus NA1 was distinguished from those of other methanogens and the members of the family Desulfurobacteriaceae with respect to the phylogenetic distribution of the α and β subunits, organization of frhAGB genes and conservation of F420-coordinating residues. RT-qPCR and Western blot analyses revealed frhA gene is not silent but is expressed in T. onnurineus NA1 grown in the presence of sulfur, carbon monoxide, or formate. The trimeric enzyme complex was purified to homogeneity via affinity chromatography from T. onnurineus NA1 and exhibited catalytic activity toward the electron acceptors such as viologens and flavins but not the deazaflavin coenzyme F420. This is the first biochemical study on the function of the frhAGB-encoding enzyme from a non-methanogenic archaea.
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Gorlas A, Croce O, Oberto J, Gauliard E, Forterre P, Marguet E. Thermococcus
nautili sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal deep-sea vent. Int J Syst Evol Microbiol 2014; 64:1802-1810. [DOI: 10.1099/ijs.0.060376-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thermococcus nautili, strain 30-1T (formerly reported as Thermococcus nautilus), was isolated from a hydrothermal chimney sample collected from the East Pacific Rise at a depth of 2633 m on the ‘La chainette PP57’ area. Cells were motile, irregular cocci with a polar tuft of flagella (0.8–1.5 µm) and divided by constriction. The micro-organism grew optimally at 87.5 °C (range 55–95 °C), at pH 7 (range pH 4–9) and with 2 % NaCl (range 1–4 %). Doubling time was 64 min in Zillig’s broth medium under optimal conditions. Growth was strictly anaerobic. It grew preferentially in the presence of elemental sulfur or cystine, which are reduced to H2S, on complex organic substrates such as yeast extract, tryptone, peptone, Casamino acids and casein. Slow growth was observed on starch and pyruvate. Strain 30-1T was resistant to chloramphenicol and tetracyclin (at 100 µg ml−1) but sensitive to kanamycin and rifampicin. The G+C content of the genomic DNA was 54 mol%. Strain 30-1T harboured three plasmids named pTN1, pTN2 and pTN3 and produced membrane vesicles that incorporate pTN1 and pTN3. As determined by 16S rRNA gene sequence analysis, strain 30-1T is related most closely to Thermococcus sp. AM4 (99.3 % similarity) and
Thermococcus gammatolerans
DSM 15229T (99.2 %). DNA–DNA hybridization values (in silico) with these two closest relatives were below the threshold value of 70 % (33 % with Thermococcus sp. AM4 and 32 % with
T. gammatolerans
DSM 15229T) and confirmed that strain 30-1 represents a novel species. On the basis of the data presented, strain 30-1T is considered to represent a novel species of the genus
Thermococcus
, for which the name Thermococcus nautili sp. nov. is proposed. The type strain is 30-1T ( = CNCM 4275 = JCM 19601).
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Affiliation(s)
- Aurore Gorlas
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Olivier Croce
- Université Aix-Marseille, Faculté de médecine, CNRS UMR7278, Marseille, France
| | - Jacques Oberto
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Emilie Gauliard
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Patrick Forterre
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Evelyne Marguet
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
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Jeon EJ, Jung JH, Seo DH, Jung DH, Holden JF, Park CS. Bioinformatic and biochemical analysis of a novel maltose-forming α-amylase of the GH57 family in the hyperthermophilic archaeon Thermococcus sp. CL1. Enzyme Microb Technol 2014; 60:9-15. [PMID: 24835094 DOI: 10.1016/j.enzmictec.2014.03.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 03/17/2014] [Accepted: 03/21/2014] [Indexed: 11/15/2022]
Abstract
Maltose-forming α-amylase is a glycoside hydrolase family 57 (GH57) member that is unique because it displays dual hydrolysis activity toward α-1,4- and α-1,6-glycosidic linkages and only recognizes maltose. This enzyme was previously identified only in Pyrococcus sp. ST04 (PSMA); however, we recently found two homologs subgroups in Thermococcus species. One subgroup (subgroup A) showed relatively high amino acid sequence similarity to PSMA (>71%), while the other subgroup (subgroup B) showed lower homology with PSMA (<59%). To characterize the subgroup B maltose-forming α-amylase from Thermococcus species (TCMA), we cloned the CL1_0868 gene from Thermococcus sp. CL1 and then successfully expressed the gene in Escherichia coli. Although TCMA has a different oligomeric state relative to PSMA, TCMA showed similar substrate specificity. However, TCMA was shown to hydrolyze maltooligosaccharides more easily than PSMA. Also, TCMA displayed different optimum conditions depending on the glycosidic linkage of the substrate. TCMA had the highest activity at 85°C and at pH 5.0 for α-1,4-glycosidic linkage hydrolysis whereas it showed its maximal activity to cleave α-1,6-glycosidic linkages at 98°C and pH 6.0.
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Affiliation(s)
- Eun-Jung Jeon
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Jong-Hyun Jung
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea; Research Division for Biotechnology, Korea Atomic Energy Research Institute (KAERI), Jeongeup 580-185, Republic of Korea
| | - Dong-Ho Seo
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Dong-Hyun Jung
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - James F Holden
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Cheon-Seok Park
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea.
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Norais C, Moisan A, Gaspin C, Clouet-d'Orval B. Diversity of CRISPR systems in the euryarchaeal Pyrococcales. RNA Biol 2013; 10:659-70. [PMID: 23422322 DOI: 10.4161/rna.23927] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Pyrococcales are members of the order Thermococcales, a group of hyperthermophilic euryarchaea that are frequently found in deep sea hydrothermal vents. Infectious genetic elements, such as plasmids and viruses, remain a threat even in this remote environment and these microorganisms have developed several ways to fight their genetic invaders. Among these are the recently discovered CRISPR systems. In this review, we have combined and condensed available information on genetic elements infecting the Thermococcales and on the multiple CRISPR systems found in the Pyrococcales to fight them. Their organization and mode of action will be presented with emphasis on the Type III-B system that is the only CRISPR system known to target RNA molecules in a process reminiscent of RNA interference. The intriguing case of Pyrococcus abyssi, which is among the rare strains to present a CRISPR system devoid of the universal cas1 and cas2 genes, is also discussed.
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Affiliation(s)
- Cédric Norais
- Laboratoire de Biochimie, UMR CNRS 7654, Département de Biologie, Ecole Polytechnique, Palaiseau, France
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