1
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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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Svenning JB, Vasskog T, Campbell K, Bæverud AH, Myhre TN, Dalheim L, Forgereau ZL, Osanen JE, Hansen EH, Bernstein HC. Lipidome Plasticity Enables Unusual Photosynthetic Flexibility in Arctic vs. Temperate Diatoms. Mar Drugs 2024; 22:67. [PMID: 38393038 PMCID: PMC10890139 DOI: 10.3390/md22020067] [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: 01/05/2024] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The diatom lipidome actively regulates photosynthesis and displays a high degree of plasticity in response to a light environment, either directly as structural modifications of thylakoid membranes and protein-pigment complexes, or indirectly via photoprotection mechanisms that dissipate excess light energy. This acclimation is crucial to maintaining primary production in marine systems, particularly in polar environments, due to the large temporal variations in both the intensity and wavelength distributions of downwelling solar irradiance. This study investigated the hypothesis that Arctic marine diatoms uniquely modify their lipidome, including their concentration and type of pigments, in response to wavelength-specific light quality in their environment. We postulate that Arctic-adapted diatoms can adapt to regulate their lipidome to maintain growth in response to the extreme variability in photosynthetically active radiation. This was tested by comparing the untargeted lipidomic profiles, pigmentation, specific growth rates and carbon assimilation of the Arctic diatom Porosira glacialis vs. the temperate species Coscinodiscus radiatus during exponential growth under red, blue and white light. Here, we found that the chromatic wavelength influenced lipidome remodeling and growth in each strain, with P. glacialis showing effective utilization of red light coupled with increased inclusion of primary light-harvesting pigments and polar lipid classes. These results indicate a unique photoadaptation strategy that enables Arctic diatoms like P. glacialis to capitalize on a wide chromatic growth range and demonstrates the importance of active lipid regulation in the Arctic light environment.
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Affiliation(s)
- Jon Brage Svenning
- Norwegian College of Fishery Science, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; (L.D.); (E.H.H.); (H.C.B.)
- SINTEF Nord, Storgata 118, 9008 Tromsø, Norway
| | - Terje Vasskog
- Department of Pharmacy, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; (T.V.); (A.H.B.); (T.N.M.)
| | - Karley Campbell
- Department of Arctic and Marine Biology, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; (K.C.); (Z.L.F.); (J.E.O.)
| | - Agnethe Hansen Bæverud
- Department of Pharmacy, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; (T.V.); (A.H.B.); (T.N.M.)
| | - Torbjørn Norberg Myhre
- Department of Pharmacy, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; (T.V.); (A.H.B.); (T.N.M.)
| | - Lars Dalheim
- Norwegian College of Fishery Science, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; (L.D.); (E.H.H.); (H.C.B.)
| | - Zoé Lulu Forgereau
- Department of Arctic and Marine Biology, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; (K.C.); (Z.L.F.); (J.E.O.)
| | - Janina Emilia Osanen
- Department of Arctic and Marine Biology, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; (K.C.); (Z.L.F.); (J.E.O.)
| | - Espen Holst Hansen
- Norwegian College of Fishery Science, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; (L.D.); (E.H.H.); (H.C.B.)
| | - Hans C. Bernstein
- Norwegian College of Fishery Science, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; (L.D.); (E.H.H.); (H.C.B.)
- The Arctic Centre for Sustainable Energy—ARC, UiT—The Arctic University of Norway, 9037 Tromsø, Norway
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3
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Poirier M, Osmers P, Wilkins K, Morgan-Kiss RM, Cvetkovska M. Aberrant light sensing and motility in the green alga Chlamydomonas priscuii from the ice-covered Antarctic Lake Bonney. Plant Signal Behav 2023; 18:2184588. [PMID: 38126947 PMCID: PMC10012900 DOI: 10.1080/15592324.2023.2184588] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/20/2023] [Indexed: 12/23/2023]
Abstract
The Antarctic green alga Chlamydomonas priscuii is an obligate psychrophile and an emerging model for photosynthetic adaptation to extreme conditions. Endemic to the ice-covered Lake Bonney, this alga thrives at highly unusual light conditions characterized by very low light irradiance (<15 μmol m-2 s-1), a narrow wavelength spectrum enriched in blue light, and an extreme photoperiod. Genome sequencing of C. priscuii exposed an unusually large genome, with hundreds of highly similar gene duplicates and expanded gene families, some of which could be aiding its survival in extreme conditions. In contrast to the described expansion in the genetic repertoire in C. priscuii, here we suggest that the gene family encoding for photoreceptors is reduced when compared to related green algae. This alga also possesses a very small eyespot and exhibits an aberrant phototactic response, compared to the model Chlamydomonas reinhardtii. We also investigated the genome and behavior of the closely related psychrophilic alga Chlamydomonas sp. ICE-MDV, that is found throughout the photic zone of Lake Bonney and is naturally exposed to higher light levels. Our analyses revealed a photoreceptor gene family and a robust phototactic response similar to those in the model Chlamydomonas reinhardtii. These results suggest that the aberrant phototactic response in C. priscuii is a result of life under extreme shading rather than a common feature of all psychrophilic algae. We discuss the implications of these results on the evolution and survival of shade adapted polar algae.
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Affiliation(s)
| | - Pomona Osmers
- Department of Biology, University of Ottawa, Ottawa, OH, Canada
| | - Kieran Wilkins
- Department of Biology, University of Ottawa, Ottawa, OH, Canada
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4
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Lasek R, Piszczek I, Krolikowski M, Sówka A, Bartosik D. A Plasmid-Borne Gene Cluster Flanked by Two Restriction-Modification Systems Enables an Arctic Strain of Psychrobacter sp. to Decompose SDS. Int J Mol Sci 2023; 25:551. [PMID: 38203722 PMCID: PMC10779009 DOI: 10.3390/ijms25010551] [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: 11/23/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
The cold-adapted Psychrobacter sp. strain DAB_AL62B, isolated from ornithogenic deposits on the Arctic island of Spitsbergen, harbors a 34.5 kb plasmid, pP62BP1, which carries a genetic SLF module predicted to enable the host bacterium to metabolize alkyl sulfates including sodium dodecyl sulfate (SDS), a common anionic surfactant. In this work, we experimentally confirmed that the pP62BP1-harboring strain is capable of SDS degradation. The slfCHSL genes were shown to form an operon whose main promoter, PslfC, is negatively regulated by the product of the slfR gene in the absence of potential substrates. We showed that lauryl aldehyde acts as an inducer of the operon. The analysis of the draft genome sequence of the DAB_AL62B strain revealed that the crucial enzyme of the SDS degradation pathway-an alkyl sulfatase-is encoded only within the plasmid. The SLF module is flanked by two restriction-modification systems, which were shown to exhibit the same sequence specificity. We hypothesize that the maintenance of pP62BP1 may be dependent on this unique genetic organization.
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Affiliation(s)
- Robert Lasek
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (I.P.); (M.K.); (A.S.)
| | | | | | | | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (I.P.); (M.K.); (A.S.)
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Abstract
Despite common perception, most of Earth is what is often referred to as an 'extreme environment.' Yet to the organisms that call these places home, it is simply that (home). They have adapted to thrive in these environments and, in the process, have evolved many unique adaptations at the molecular- and 'omic-level. Scientists' interest in these organisms has typically been in how they and their products can be harnessed for biotechnological applications and the environments where they are found, while the general public's veers more toward a fascination with their deviation from the 'norm'. However, these organisms have so much more to tell us about Life and the myriad ways there are to perform 'simple' biological processes.
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Affiliation(s)
- James A Coker
- Center for Biotechnology Education, Advanced Academic Programs, Krieger School of Arts and Sciences, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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6
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Li AQ, Zhang C, Li DH, Qi XQ, Meng L, Wu LF, Li XG, Zhang WJ. Parasedimentitalea psychrophila sp. nov., a psychrophilic bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755238 DOI: 10.1099/ijsem.0.006046] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
A novel bacterium, strain QS115T, was isolated from deep-sea sediment collected from the South China Sea at a depth of 1151 m. Phylogenetic analyses based on 16S rRNA gene sequences indicated that QS115T was most closely related to Parasedimentitalea marina W43T, with similarity of 98.21 %. Strain QS115T shared 82.39 % average nucleotide identity, 26.3 % digital DNA-DNA hybridization and 85.32 % average amino acid identity with P. marina W43T. Cells of strain QS115T were Gram-stain-negative, rod-shaped and grew optimally at 10 °C, pH 7.5 and 2 % (w/v) NaCl. The principal fatty acids were summed feature 8 (C18 : 1 ω7c/ω6c), the major respiratory quinone was ubiquinone-10 and predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, glycophospholipid, phosphatidylglycerol and phosphatidylcholine. Polyphasic analyses of physiological and phenotypic characteristics and genomic studies suggested that strain QS115T represents a novel species of the genus Parasedimentitalea, for which the name Parasedimentitalea psychrophila sp. nov. is proposed (type strain QS115T=MCCC 1K04395T=JCM 34219T).
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Affiliation(s)
- An-Qi Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Chan Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, PR China
- Present address: Guangdong VTR BioTech Co., Ltd, Zhuhai, Guangdong, PR China
| | - Deng-Hui Li
- BGI Research, Qingdao, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, Hainan, PR China
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, PR China
- Present address: Hainan Research Academy of Environmental Sciences, Sanya, Hainan, PR China
| | - Liang Meng
- BGI Research, Qingdao, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, Hainan, PR China
| | - Long-Fei Wu
- Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, Hainan, PR China
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, Hainan, PR China
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7
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Broadwell ELM, Pickford RE, Perkins RG, Sgouridis F, Williamson CJ. Adaptation versus plastic responses to temperature, light, and nitrate availability in cultured snow algal strains. FEMS Microbiol Ecol 2023; 99:fiad088. [PMID: 37553143 PMCID: PMC10481995 DOI: 10.1093/femsec/fiad088] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/29/2023] [Accepted: 08/07/2023] [Indexed: 08/10/2023] Open
Abstract
Snow algal blooms are widespread, dominating low temperature, high light, and oligotrophic melting snowpacks. Here, we assessed the photophysiological and cellular stoichiometric responses of snow algal genera Chloromonas spp. and Microglena spp. in their vegetative life stage isolated from the Arctic and Antarctic to gradients in temperature (5 - 15°C), nitrate availability (1 - 10 µmol L-1), and light (50 and 500 µmol photons m-2 s-1). When grown under gradients in temperature, measured snow algal strains displayed Fv/Fm values increased by ∼115% and electron transport rates decreased by ∼50% at 5°C compared to 10 and 15°C, demonstrating how low temperatures can mimic high light impacts to photophysiology. When using carrying capacity as opposed to growth rate as a metric for determining the temperature optima, these snow algal strains can be defined as psychrophilic, with carrying capacities ∼90% higher at 5°C than warmer temperatures. All strains approached Redfield C:N stoichiometry when cultured under nutrient replete conditions regardless of temperature (5.7 ± 0.4 across all strains), whereas significant increases in C:N were apparent when strains were cultured under nitrate concentrations that reflected in situ conditions (17.8 ± 5.9). Intra-specific responses in photophysiology were apparent under high light with Chloromonas spp. more capable of acclimating to higher light intensities. These findings suggest that in situ conditions are not optimal for the studied snow algal strains, but they are able to dynamically adjust both their photochemistry and stoichiometry to acclimate to these conditions.
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Affiliation(s)
- Emily L M Broadwell
- School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, United Kingdom
| | - Rachel E Pickford
- School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, United Kingdom
| | - Rupert G Perkins
- School of Earth and Environmental Sciences, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Fotis Sgouridis
- School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, United Kingdom
| | - Christopher J Williamson
- School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, United Kingdom
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8
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Liu Y, Zhang N, Ma J, Zhou Y, Wei Q, Tian C, Fang Y, Zhong R, Chen G, Zhang S. Advances in cold-adapted enzymes derived from microorganisms. Front Microbiol 2023; 14:1152847. [PMID: 37180232 PMCID: PMC10169661 DOI: 10.3389/fmicb.2023.1152847] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
Cold-adapted enzymes, produced in cold-adapted organisms, are a class of enzyme with catalytic activity at low temperatures, high temperature sensitivity, and the ability to adapt to cold stimulation. These enzymes are largely derived from animals, plants, and microorganisms in polar areas, mountains, and the deep sea. With the rapid development of modern biotechnology, cold-adapted enzymes have been implemented in human and other animal food production, the protection and restoration of environments, and fundamental biological research, among other areas. Cold-adapted enzymes derived from microorganisms have attracted much attention because of their short production cycles, high yield, and simple separation and purification, compared with cold-adapted enzymes derived from plants and animals. In this review we discuss various types of cold-adapted enzyme from cold-adapted microorganisms, along with associated applications, catalytic mechanisms, and molecular modification methods, to establish foundation for the theoretical research and application of cold-adapted enzymes.
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Affiliation(s)
- Yehui Liu
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Na Zhang
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Jie Ma
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Yuqi Zhou
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Qiang Wei
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yi Fang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Rongzhen Zhong
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Guang Chen
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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Laye VJ, Solieva S, Voelz VA, DasSarma S. Effects of Salinity and Temperature on the Flexibility and Function of a Polyextremophilic Enzyme. Int J Mol Sci 2022; 23:ijms232415620. [PMID: 36555259 PMCID: PMC9779221 DOI: 10.3390/ijms232415620] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The polyextremophilic β-galactosidase enzyme of the haloarchaeon Halorubrum lacusprofundi functions in extremely cold and hypersaline conditions. To better understand the basis of polyextremophilic activity, the enzyme was studied using steady-state kinetics and molecular dynamics at temperatures ranging from 10 °C to 50 °C and salt concentrations from 1 M to 4 M KCl. Kinetic analysis showed that while catalytic efficiency (kcat/Km) improves with increasing temperature and salinity, Km is reduced with decreasing temperatures and increasing salinity, consistent with improved substrate binding at low temperatures. In contrast, kcat was similar from 2-4 M KCl across the temperature range, with the calculated enthalpic and entropic components indicating a threshold of 2 M KCl to lower the activation barrier for catalysis. With molecular dynamics simulations, the increase in per-residue root-mean-square fluctuation (RMSF) was observed with higher temperature and salinity, with trends like those seen with the catalytic efficiency, consistent with the enzyme's function being related to its flexibility. Domain A had the smallest change in flexibility across the conditions tested, suggesting the adaptation to extreme conditions occurs via regions distant to the active site and surface accessible residues. Increased flexibility was most apparent in the distal active sites, indicating their importance in conferring salinity and temperature-dependent effects.
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Affiliation(s)
- Victoria J. Laye
- Institute of Marine and Environmental Technology, University System of Maryland, Baltimore, MD 21202, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21202, USA
- Correspondence:
| | - Shahlo Solieva
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Shiladitya DasSarma
- Institute of Marine and Environmental Technology, University System of Maryland, Baltimore, MD 21202, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21202, USA
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10
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Szyszka-Mroz B, Ivanov AG, Trick CG, Hüner NPA. Palmelloid formation in the Antarctic psychrophile, Chlamydomonas priscuii, is photoprotective. Front Plant Sci 2022; 13:911035. [PMID: 36119589 PMCID: PMC9470844 DOI: 10.3389/fpls.2022.911035] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/01/2022] [Indexed: 05/27/2023]
Abstract
Cultures of the obligate, Antarctic psychrophile, Chlamydomonas priscuii grown at permissive low temperature (8°C) are composed of flagellated, single cells, as well as non-motile, multicellular palmelloids. The relative proportions of the two cell types are temperature dependent. However, the temperature dependence for palmelloid formation is not restricted to psychrophilic C. priscuii but appears to be a general response of mesophilic Chlamydomonas species (C. reinhardtii and C. raudensis) to non-permissive growth temperatures. To examine potential differences in photosynthetic performance between single cells versus palmelloids of the psychrophile, a cell filtration technique was developed to separate single cells from palmelloids of C. priscuii grown at 8°C. Flow cytometry was used to estimate the diameter of isolated single cells (≤5 μm) versus isolated palmelloids of varying size (≥8 μm). Compared to single cells, palmelloids of C. priscuii showed a decrease in the abundance of light-harvesting complex II (LHCII) proteins with a 2-fold higher Chl a/b ratio. A decrease in both lutein and β-carotene in palmelloids resulted in carotenoid pools which were 27% lower in palmelloids compared to single cells of the psychrophile. Chlorophyll fluorescence analyses of the isolated fractions revealed that maximum photochemical efficiency of PSII (Fv/Fm) was comparable for both single cells and palmelloids of C. priscuii. However, isolated palmelloids exhibited lower excitation pressure, measured as 1 - qL, but higher yield of PSII (ΦPSII) and 50% higher rates of electron transport (ETR) than single cells exposed to high light at 8°C. This decreased sensitivity to high light in isolated palmelloids compared to single cells was associated with greater non-regulated dissipation of excess absorbed energy (ΦNO) with minimal differences in ΦNPQ in C. priscuii in response to increasing irradiance at low temperature. The ratio ΦNO/ΦNPQ observed for isolated palmelloids of C. priscuii developed at 8°C (1.414 ± 0.036) was 1.38-fold higher than ΦNO/ΦNPQ of isolated single cells (1.021 ± 0.018) exposed to low temperature combined with high light (1,000 μmol m-2 s-1). The differences in the energy quenching capacities between palmelloids and single cells are discussed in terms of enhanced photoprotection of C. priscuii palmelloids against low-temperature photoinhibition.
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Affiliation(s)
- Beth Szyszka-Mroz
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, ON, Canada
| | - Alexander G. Ivanov
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, ON, Canada
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Charles G. Trick
- School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
| | - Norman P. A. Hüner
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, ON, Canada
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11
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Abstract
Biocatalysis is crucial for a green, sustainable, biobased economy, and this has driven major advances in biotechnology and biocatalysis over the past 2 decades. There are numerous benefits to biocatalysis, including increased selectivity and specificity, reduced operating costs and lower toxicity, all of which result in lower environmental impact of industrial processes. Most enzymes available commercially are active and stable under a narrow range of conditions, and quickly lose activity at extremes of ion concentration, temperature, pH, pressure, and solvent concentrations. Extremophilic microorganisms thrive under extreme conditions and produce robust enzymes with higher activity and stability under unconventional circumstances. The number of extremophilic enzymes, or extremozymes, currently available are insufficient to meet growing industrial demand. This is in part due to difficulty in cultivation of extremophiles in a laboratory setting. This review will present an overview of extremozymes and their biotechnological applications. Culture-independent and genomic-based methods for study of extremozymes will be presented.
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Affiliation(s)
- Noha M Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
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12
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Abstract
Diatoms, a key group of polar marine microbes, support highly productive ocean ecosystems. Like all life on earth, diatoms do not live in isolation, and they are therefore under constant biotic and abiotic pressures which directly influence their evolution through natural selection. Despite their importance in polar ecosystems, polar diatoms are understudied compared to temperate species. The observed rapid change in the polar climate, especially warming, has created increased research interest to discover the underlying causes and potential consequences on single species to entire ecosystems. Next-Generation Sequencing (NGS) technologies have greatly expanded our knowledge by revealing the molecular underpinnings of physiological adaptations to polar environmental conditions. Their genomes, transcriptomes, and proteomes together with the first eukaryotic meta-omics data of surface ocean polar microbiomes reflect the environmental pressures through adaptive responses such as the expansion of protein families over time as a consequence of selection. Polar regions and their microbiomes are inherently connected to climate cycles and their feedback loops. An integrated understanding built on “omics” resources centered around diatoms as key primary producers will enable us to reveal unifying concepts of microbial co-evolution and adaptation in polar oceans. This knowledge, which aims to relate past environmental changes to specific adaptations, will be required to improve climate prediction models for polar ecosystems because it provides a unifying framework of how interacting and co-evolving biological communities might respond to future environmental change.
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Affiliation(s)
- Reuben Gilbertson
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Emma Langan
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.,The Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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13
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Cvetkovska M, Zhang X, Vakulenko G, Benzaquen S, Szyszka-Mroz B, Malczewski N, Smith DR, Hüner NPA. A constitutive stress response is a result of low temperature growth in the Antarctic green alga Chlamydomonas sp. UWO241. Plant Cell Environ 2022; 45:156-177. [PMID: 34664276 DOI: 10.1111/pce.14203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
The Antarctic green alga Chlamydomonas sp. UWO241 is an obligate psychrophile that thrives in the cold (4-6°C) but is unable to survive at temperatures ≥18°C. Little is known how exposure to heat affects its physiology or whether it mounts a heat stress response in a manner comparable to mesophiles. Here, we dissect the responses of UWO241 to temperature stress by examining its growth, primary metabolome and transcriptome under steady-state low temperature and heat stress conditions. In comparison with Chlamydomonas reinhardtii, UWO241 constitutively accumulates metabolites and proteins commonly considered as stress markers, including soluble sugars, antioxidants, polyamines, and heat shock proteins to ensure efficient protein folding at low temperatures. We propose that this results from life at extreme conditions. A shift from 4°C to a non-permissive temperature of 24°C alters the UWO241 primary metabolome and transcriptome, but growth of UWO241 at higher permissive temperatures (10 and 15°C) does not provide enhanced heat protection. UWO241 also fails to induce the accumulation of HSPs when exposed to heat, suggesting that it has lost the ability to fine-tune its heat stress response. Our work adds to the growing body of research on temperature stress in psychrophiles, many of which are threatened by climate change.
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Affiliation(s)
- Marina Cvetkovska
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Xi Zhang
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, Ontario, Canada
| | - Galyna Vakulenko
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Samuel Benzaquen
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Beth Szyszka-Mroz
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, Ontario, Canada
| | - Nina Malczewski
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, Ontario, Canada
| | - David R Smith
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, Ontario, Canada
| | - Norman P A Hüner
- Department of Biology and the Biotron Centre for Experimental Climate Change Research, University of Western Ontario, London, Ontario, Canada
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14
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Abstract
Studies from cryoenvironments on Earth have demonstrated that microbial life is widespread and have identified microorganisms that are metabolically active and can replicate at subzero temperatures if liquid water is present. However, cryophiles (subzero-growing organisms) often exist in low densities in the environment and their growth rate is low, making them difficult to study. Compounding this, a large number of dormant and dead cells are preserved in frozen settings. Using integrated genomic and activity-based approaches is essential to understanding the cold limits of life on Earth, as well as how cryophilic microorganisms are poised to adapt and metabolize in warming settings, such as in thawing permafrost. An increased understanding of cryophilic lifestyles on Earth will also help inform how (and where) we look for potential microbial life on cold planetary bodies in our solar system such as Mars, Europa, and Enceladus.
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15
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Sysoev M, Grötzinger SW, Renn D, Eppinger J, Rueping M, Karan R. Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods. Front Microbiol 2021; 12:630013. [PMID: 33643258 PMCID: PMC7902512 DOI: 10.3389/fmicb.2021.630013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.
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Affiliation(s)
- Maksim Sysoev
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stefan W. Grötzinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jörg Eppinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Ram Karan
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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16
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Uetake J, Nagatsuka N, Onuma Y, Takeuchi N, Motoyama H, Aoki T. Bacterial community changes with granule size in cryoconite and their susceptibility to exogenous nutrients on NW Greenland glaciers. FEMS Microbiol Ecol 2020; 95:5499017. [PMID: 31132102 DOI: 10.1093/femsec/fiz075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/23/2019] [Indexed: 12/17/2022] Open
Abstract
Cryoconite granules are dark-colored biological aggregates on glaciers. Bacterial community varies with granule size, however, community change in space and their susceptibility to environmental factors has not been described yet. Therefore, we focused on bacterial community from four different granule sizes (30-249 μm, 250-750 μm, 750-1599 μm, more than 1600 μm diameter) in 10 glaciers in northwestern Greenland and their susceptibility to exogenous nutrients in cryoconite hole. A filamentous cyanobacterium Phormidesmis priestleyi, which has been frequently reported from glaciers in Arctic was abundant (10%-26%) across any size of granules on most of glaciers. Bacterial community across glaciers became similar with size increase, and whence smallest size fractions contain more unique genera in each glacier. Multivariate analysis revealed that effect of nutrients to beta diversity is larger in smaller granules (30-249 μm and 250-750 μm diameter), suggesting that bacterial susceptibility to nutrients changes with growth of granule (i.e. P. priestleyi was affected by nitrate in early growth stage).
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Affiliation(s)
- Jun Uetake
- National Institute of Polar Research, 10-3 Midoricho, Tachikawa, Tokyo, 190-8518 Japan
| | - Naoko Nagatsuka
- National Institute of Polar Research, 10-3 Midoricho, Tachikawa, Tokyo, 190-8518 Japan
| | - Yukihiko Onuma
- The University of Tokyo, Institute of Industrial Science, Institute of Industrial Science, 4-6-1 Komaba, Meguro, Tokyo, 153-8505 Japan
| | - Nozomu Takeuchi
- Chiba University, Department of Earth Science, 1-33, Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522 Japan
| | - Hideaki Motoyama
- National Institute of Polar Research, 10-3 Midoricho, Tachikawa, Tokyo, 190-8518 Japan
| | - Teruo Aoki
- National Institute of Polar Research, 10-3 Midoricho, Tachikawa, Tokyo, 190-8518 Japan.,Okayama University, Department of Earth Science, Department of Earth Science, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530 Japan
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17
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Wang J, Gu L, Su Y, Chang C, Xu L, Yang Y, Li J. Changes in microbial, physiochemical, and functional properties of pasteurized liquid whole egg during refrigerated storage. J Sci Food Agric 2020; 100:2873-2879. [PMID: 32020609 DOI: 10.1002/jsfa.10311] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Liquid eggs have the advantages of high hygiene security, easy use, and convenient transportation, but their shelf life is only limited to 2~3 weeks. The microbial, physiochemical, and functional properties of pasteurized LWE were investigated in this study to evaluate the quality of pasteurized liquid whole egg (LWE) during refrigerated storage. RESULTS The tested shelf life of the pasteurized LWE was 16 days when stored at 4 °C. During refrigerated storage, Pseudomonas gradually became the dominant bacterium in LWE following lactic acid bacteria, although the initial number of Pseudomonas after pasteurization was relatively limited (< 10 CFU mL-1 ). A total of 23 strains, including six Pseudomonas strains, were obtained. The pH of pasteurized LWE decreased with the growth of microorganisms, while the content of total volatile basic nitrogen (TVB-N) increased curvilinearly. The average particle size increased almost continuously until the sample reached its shelf life. The functional properties of pasteurized LWE were also reduced after a week of refrigerated storage at 4 °C when the microorganisms in pasteurized LWE entered an exponential growth period and the TVB-N content of pasteurized LWE reached its first peak. CONCLUSION During refrigerated storage, Pseudomonas was the dominant bacterium in LWE next to lactic acid bacteria. After a week of refrigerated storage at 4 °C, the particle size of LWE increased, while the functional properties of LWE reduced. This study provides a basis for extending the shelf life of liquid egg products in future research. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Luping Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Yujie Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Cuihua Chang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Lilan Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Yanjun Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Junhua Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
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18
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Liu Q, Tian JH, Liu HC, Zhou YG, Xin YH. Cryobacterium ruanii sp. nov. and Cryobacterium breve sp. nov., isolated from glaciers. Int J Syst Evol Microbiol 2020; 70:1918-1923. [PMID: 32100694 DOI: 10.1099/ijsem.0.003994] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains Sr36T and TMT4-23T were isolated from No. 1 glacier in Xinjiang Uygur Autonomous Region and Toumingmengke glacier in Gansu Province, PR China, respectively. They were Gram-stain-positive and rod-shaped micro-organisms. The optimum growth temperature of the two strains was 10-14 °C. Phylogenetic analysis showed that the two strains were related to members of the genus Cryobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain Sr36T and its close relatives Cryobacterium luteum Hh15T, Cryobacterium aureum Hh31T, Cryobacterium levicorallinum Hh34T and Cryobacterium flavum Hh8T were 81.16-87.24 and 28.0-32.5 %, respectively. The ANI and dDDH values between strain TMT4-23T and its close relative Cryobacterium psychrotolerans 0549T were 81.16 and 22.3 %. The polar lipids of strain Sr36T were diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid and three unidentified lipids. The polar lipids of strain TMT4-23T were diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid and six unidentified lipids. The major fatty acids of strain Sr36T were anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 1. The major fatty acids of strain TMT4-23T were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, anteiso-C15 : 1 and iso-C15 : 1. Both strains contained 2,4-diaminobutyric acid and their predominant menaquinone was MK-10. On the basis of the phenotypic, phylogenetic and genotypic data, two novel species Cryobacterium ruanii sp. nov. (type strain = Sr36T=CGMCC 1.9275T=NBRC 113797T) and Cryobacterium breve sp. nov. (type strain =TMT4-23T=CGMCC 1.9556T=NBRC 113800T) are proposed.
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Affiliation(s)
- Qing Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ji-Hui Tian
- Experimental School of Beihang University, Beijing 100083, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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19
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Abstract
Despite the typical human notion that the Earth is a habitable planet, over three quarters of our planet is uninhabitable by us without assistance. The organisms that live and thrive in these “inhospitable” environments are known by the name extremophiles and are found in all Domains of Life. Despite our general lack of knowledge about them, they have already assisted humans in many ways and still have much more to give. In this review, I describe how they have adapted to live/thrive/survive in their niches, helped scientists unlock major scientific discoveries, advance the field of biotechnology, and inform us about the boundaries of Life and where we might find it in the Universe.
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Affiliation(s)
- James A Coker
- Department of Sciences, University of Maryland Global Campus, Adelphi, MD, USA
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20
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Smith DR, Cvetkovska M, Hüner NPA, Morgan-Kiss R. Presence and absence of light-independent chlorophyll biosynthesis among Chlamydomonas green algae in an ice-covered Antarctic lake. Commun Integr Biol 2019; 12:148-150. [PMID: 31666915 PMCID: PMC6802932 DOI: 10.1080/19420889.2019.1676611] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/03/2022] Open
Abstract
The cold, permanently ice-covered waters of Lake Bonney, Antarctica, may seem like an uninviting place for an alga, but they are home to a diversity of photosynthetic life, including Chlamydomonas sp. UWO241, a psychrophile residing in the deep photic zone. Recently, we found that UWO241 has lost the genes responsible for light-independent chlorophyll biosynthesis, which is surprising given that this green alga comes from a light-limited environment and experiences extended periods of darkness during the Antarctic winter. Why discard such a process? We argued that it might be linked to the very high dissolved oxygen concentration of Lake Bonney at the depth at which UWO241 is found. Oxygen is the Achilles’ heel of the key enzyme involved in light-independent chlorophyll biosynthesis: DPOR. If this hypothesis is true, then other algae in Lake Bonney should also be susceptible to losing DPOR, such as Chlamydomonas sp. ICE-MDV, which predominantly resides in the chemocline, a depth with an even higher oxygen concentration than that where UWO241 exists. Here, we report that, contrary to our earlier prediction, ICE-MDV has maintained the genes encoding DPOR. We briefly discuss the implications of this finding in relation to the loss of light-independent chlorophyll synthesis in UWO241.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Marina Cvetkovska
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Norman P A Hüner
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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21
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Chrast L, Tratsiak K, Planas-Iglesias J, Daniel L, Prudnikova T, Brezovsky J, Bednar D, Kuta Smatanova I, Chaloupkova R, Damborsky J. Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17. Microorganisms 2019; 7:E498. [PMID: 31661858 PMCID: PMC6920932 DOI: 10.3390/microorganisms7110498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Haloalkane dehalogenases are enzymes with a broad application potential in biocatalysis, bioremediation, biosensing and cell imaging. The new haloalkane dehalogenase DmxA originating from the psychrophilic bacterium Marinobacter sp. ELB17 surprisingly possesses the highest thermal stability (apparent melting temperature Tm,app = 65.9 °C) of all biochemically characterized wild type haloalkane dehalogenases belonging to subfamily II. The enzyme was successfully expressed and its crystal structure was solved at 1.45 Å resolution. DmxA structure contains several features distinct from known members of haloalkane dehalogenase family: (i) a unique composition of catalytic residues; (ii) a dimeric state mediated by a disulfide bridge; and (iii) narrow tunnels connecting the enzyme active site with the surrounding solvent. The importance of narrow tunnels in such paradoxically high stability of DmxA enzyme was confirmed by computational protein design and mutagenesis experiments.
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Affiliation(s)
- Lukas Chrast
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
| | - Katsiaryna Tratsiak
- Institute of Chemistry and Biochemistry, Faculty of Science, University of South Bohemia Ceske Budejovice and Institute of Microbiology Academy of Sciences of the Czech Republic, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
| | - Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
| | - Lukas Daniel
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
| | - Tatyana Prudnikova
- Institute of Chemistry and Biochemistry, Faculty of Science, University of South Bohemia Ceske Budejovice and Institute of Microbiology Academy of Sciences of the Czech Republic, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
| | - Ivana Kuta Smatanova
- Institute of Chemistry and Biochemistry, Faculty of Science, University of South Bohemia Ceske Budejovice and Institute of Microbiology Academy of Sciences of the Czech Republic, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
- Enantis Ltd., Biotechnology Incubator INBIT, Kamenice 771/34, 625 00 Brno, Czech Republic.
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
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22
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Ciok A, Cegielski A, Bartosik D, Dziewit L. Benefits and Drawbacks of Harboring Plasmid pP32BP2, Identified in Arctic Psychrophilic Bacterium Psychrobacter sp. DAB_AL32B. Int J Mol Sci 2019; 20:E2015. [PMID: 31022896 DOI: 10.3390/ijms20082015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/11/2019] [Accepted: 04/22/2019] [Indexed: 12/18/2022] Open
Abstract
Psychrobacter sp. DAB_AL32B, originating from Spitsbergen island (Arctic), carries the large plasmid pP32BP2 (54,438 bp). Analysis of the pP32BP2 nucleotide sequence revealed the presence of three predicted phenotypic modules that comprise nearly 30% of the plasmid genome. These modules appear to be involved in fimbriae synthesis via the chaperone-usher pathway (FIM module) and the aerobic and anaerobic metabolism of carnitine (CAR and CAI modules, respectively). The FIM module was found to be functional in diverse hosts since it facilitated the attachment of bacterial cells to abiotic surfaces, enhancing biofilm formation. The CAI module did not show measurable activity in any of the tested strains. Interestingly, the CAR module enabled the enzymatic breakdown of carnitine, but this led to the formation of the toxic by-product trimethylamine, which inhibited bacterial growth. Thus, on the one hand, pP32BP2 can enhance biofilm formation, a highly advantageous feature in cold environments, while on the other, it may prevent bacterial growth under certain environmental conditions. The detrimental effect of harboring pP32BP2 (and its CAR module) seems to be conditional, since this replicon may also confer the ability to use carnitine as an alternative carbon source, although a pathway to utilize trimethylamine is most probably necessary to make this beneficial. Therefore, the phenotype determined by this CAR-containing plasmid depends on the metabolic background of the host strain.
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23
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Cvetkovska M, Orgnero S, Hüner NPA, Smith DR. The enigmatic loss of light-independent chlorophyll biosynthesis from an Antarctic green alga in a light-limited environment. New Phytol 2019; 222:651-656. [PMID: 30506801 DOI: 10.1111/nph.15623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Marina Cvetkovska
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Shane Orgnero
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Norman P A Hüner
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
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24
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Huang Q, Rodgers JM, Hemley RJ, Ichiye T. Adaptations for Pressure and Temperature Effects on Loop Motion in Escherichia coli and Moritella profunda Dihydrofolate Reductase. High Press Res 2019; 39:225-237. [PMID: 31359910 PMCID: PMC6662930 DOI: 10.1080/08957959.2019.1584799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/13/2019] [Indexed: 06/10/2023]
Abstract
Determining how enzymes in piezophilic microbes function at high pressure can give insights into how life adapts to living at high pressure. Here, the effects of pressure and temperature on loop motions are compared Escherichia coli (Ec) and Moritella profunda (Mp) dihydrofolate reductase (DHFR) via molecular dynamics simulations at combinations of the growth temperature and pressure of the two organisms. Analysis indicates that a flexible CD loop in MpDHFR is an adaptation for cold because it makes the adenosine binding subdomain more flexible. Also, analysis indicates that the Thr113-Glu27 hydrogen bond in MpDHFR is an adaptation for high pressure because it provides flexibility within the loop subdomain compared to the very strong Thr113-Asp27 hydrogen bond in EcDHFR, and affects the correlation of the Met20 and GH loops. In addition, the results suggest that temperature might affect external loops more strongly while pressure might affect motion between elements within the protein.
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Affiliation(s)
- Qi Huang
- Department of Chemistry, Georgetown University, Washington, DC 20057
| | | | - Russell J. Hemley
- Department of Civil and Environmental Engineering and Institute for Materials Science, George Washington University, Washington, DC 20052
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC 20057
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Casillo A, Di Guida R, Carillo S, Chen C, Kamasaka K, Kawamoto J, Kurihara T, Corsaro MM. Structural Elucidation of a Novel Lipooligosaccharide from the Antarctic Bacterium OMVs Producer Shewanella sp. HM13. Mar Drugs 2019; 17:E34. [PMID: 30626008 PMCID: PMC6357163 DOI: 10.3390/md17010034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 12/11/2018] [Revised: 12/23/2018] [Accepted: 01/03/2019] [Indexed: 01/08/2023] Open
Abstract
Shewanella sp. HM13 is a cold-adapted Gram-negative bacterium isolated from the intestine of a horse mackerel. It produces a large amount of outer membrane vesicles (OMVs), which are particles released in the medium where the bacterium is cultured. This strain biosynthesizes a single major cargo protein in the OMVs, a fact that makes Shewanella sp. HM13 a good candidate for the production of extracellular recombinant proteins. Therefore, the structural characterization of the components of the vesicles, such as lipopolysaccharides, takes on a fundamental role for understanding the mechanism of biogenesis of the OMVs and their applications. The aim of this study was to investigate the structure of the oligosaccharide (OS) isolated from Shewanella sp. HM13 cells as the first step for a comparison with that from the vesicles. The lipooligosaccharide (LOS) was isolated from dry cells, purified, and hydrolyzed by alkaline treatment. The obtained OS was analyzed completely, and the composition of fatty acids was obtained by chemical methods. In particular, the OS was investigated in detail by ¹H and 13C NMR spectroscopy and MALDI-TOF mass spectrometry. The oligosaccharide was characterized by the presence of a residue of 8-amino-3,8-dideoxy-manno-oct-2-ulosonic acid (Kdo8N) and of a d,d-heptose, with both residues being identified in other oligosaccharides from Shewanella species.
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Affiliation(s)
- Angela Casillo
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy.
| | - Rossella Di Guida
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy.
| | - Sara Carillo
- Characterisation and Comparability Laboratory, National Institute for Bioprocessing Research and Training. Fosters Avenue, Mount Merrion. Blackrock, Co., A94 X099 Dublin, Ireland.
| | - Chen Chen
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Kouhei Kamasaka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Jun Kawamoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Tatsuo Kurihara
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Maria Michela Corsaro
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy.
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Bierma JC, Roskamp KW, Ledray AP, Kiss AJ, Cheng CHC, Martin RW. Controlling Liquid-Liquid Phase Separation of Cold-Adapted Crystallin Proteins from the Antarctic Toothfish. J Mol Biol 2018; 430:5151-5168. [PMID: 30414964 DOI: 10.1016/j.jmb.2018.10.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 07/14/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022]
Abstract
Liquid-liquid phase separation (LLPS) of proteins is important to a variety of biological processes both functional and deleterious, including the formation of membraneless organelles, molecular condensations that sequester or release molecules in response to stimuli, and the early stages of disease-related protein aggregation. In the protein-rich, crowded environment of the eye lens, LLPS manifests as cold cataract. We characterize the LLPS behavior of six structural γ-crystallins from the eye lens of the Antarctic toothfish Dissostichus mawsoni, whose intact lenses resist cold cataract in subzero waters. Phase separation of these proteins is not strongly correlated with thermal stability, aggregation propensity, or cross-species chaperone protection from heat denaturation. Instead, LLPS is driven by protein-protein interactions involving charged residues. The critical temperature of the phase transition can be tuned over a wide temperature range by selective substitution of surface residues, suggesting general principles for controlling this phenomenon, even in compactly folded proteins.
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Affiliation(s)
- Jan C Bierma
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92697, USA
| | - Kyle W Roskamp
- Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - Aaron P Ledray
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92697, USA
| | - Andor J Kiss
- Center for Bioinformatics and Functional Genomics, Miami University, Oxford, OH 45056,USA.
| | - C-H Christina Cheng
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801,USA
| | - Rachel W Martin
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, CA 92697, USA.
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27
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Mohamadnezhadi H, Beiramzadeh A, Shadman Lakmehsari M, Khalifeh K, Heshmati E. Temperature dependent dynamics in highly homologous adenylate kinases. J Biomol Struct Dyn 2018; 37:2110-2117. [PMID: 30044184 DOI: 10.1080/07391102.2018.1477622] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
To correlate the structural features of enzymes to temperature adaptation, we studied psychrophile, mesophile, and thermophile adenylate kinases as model enzymes using bioinformatics and computational tools. Phylogenetic analysis revealed that mesophile and thermophile variants are clustered in one stem of phylogenetic tree and are close to contemporary time, while psychrophile enzyme is more close to their common ancestor. This finding is in good agreement with the process of environmental changes from ice age toward current warm conditions on the earth. We also performed Molecular Dynamics simulation at corresponding temperatures of all enzyme variants including 308, 318, and 328 K. It was found that mesophile enzyme has no distinct deviation of Root Mean Square Deviation (RMSD) and Radius of Gyration (Rg) values from equilibrium states at operating temperature of thermophile enzyme as well as its own optimum temperature. However, psychrophile enzyme undergoes more fluctuations with higher amplitude of change; particularly at 328 K. It was also found that initial increasing of RMSD and Rg for Psychrophile enzyme at all temperatures is occurred gradually; while, the increment of this structural parameters for thermophile enzyme at 328 K is occurred in a highly cooperative and switching manner demonstrating snap structural change of thermophile enzyme in its own temperature. By analysis of Root Mean Square Fluctuation values at different temperatures, we identified two flexible fragments in adenylate kinases so that different dynamic behavior of these regions in mesophile enzyme against operating temperatures of psychrophile and thermophile variants is critical in compensation of flexibility challenges at respective temperatures.
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Affiliation(s)
- Himan Mohamadnezhadi
- a Faculty of Science, Department of Biology , University of Zanjan , Zanjan , Iran
| | - Alireza Beiramzadeh
- a Faculty of Science, Department of Biology , University of Zanjan , Zanjan , Iran
| | - Muhammad Shadman Lakmehsari
- b Faculty of Science, Department of Chemistry , University of Zanjan , Zanjan , Iran Communicated by Ramaswamy H. Sarma
| | - Khosrow Khalifeh
- a Faculty of Science, Department of Biology , University of Zanjan , Zanjan , Iran
| | - Emran Heshmati
- a Faculty of Science, Department of Biology , University of Zanjan , Zanjan , Iran
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28
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Abstract
It is well known that cold environments are predominant over the Earth and there are a great number of reports analyzing bacterial adaptations to cold. Most of these works are focused on characteristics traditionally involved in cold adaptation, such as the structural adjustment of enzymes, maintenance of membrane fluidity, expression of cold shock proteins and presence of compatible solutes. Recent works based mainly on novel "omic" technologies have presented evidence of the presence of other important features to thrive in cold. In this work, we analyze cold-adapted bacteria, looking for strategies involving novel features, and/or activation of non-classical metabolisms for a cold lifestyle. Metabolic traits related to energy generation, compounds and mechanisms involved in stress resistance and cold adaptation, as well as characteristics of the cell envelope, are analyzed in heterotrophic cold-adapted bacteria. In addition, metagenomic, metatranscriptomic and metaproteomic data are used to detect key functions in bacterial communities inhabiting cold environments.
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Affiliation(s)
- Paula M Tribelli
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina.
- IQUIBICEN, CONICET, C1428EGA Buenos Aires, Argentina.
| | - Nancy I López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina.
- IQUIBICEN, CONICET, C1428EGA Buenos Aires, Argentina.
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29
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Vincent AT, Rouleau FD, Moineau S, Charette SJ. Study of mesophilic Aeromonas salmonicida A527 strain sheds light on the species' lifestyles and taxonomic dilemma. FEMS Microbiol Lett 2018; 364:4604818. [PMID: 29126137 DOI: 10.1093/femsle/fnx239] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/07/2017] [Indexed: 12/20/2022] Open
Abstract
The Gram-negative bacterium Aeromonas salmonicida contains five subspecies: salmonicida, smithia, achromogenes, masoucida and pectinolytica. Pectinolytica is a mesophilic subspecies with the ability to thrive at a wide range of temperatures, including 37°C, while the four other subspecies are psychrophilic, restricted to lower temperatures. The psychrophilic subspecies are known to infect a wide range of fishes. However, there is no evidence of pathogenicity for the mesophilic subspecies pectinolytica. Study of the differences between the mesophilic and psychrophilic subspecies is hampered by the lack of completely sequenced and closed genomes from the mesophilic subspecies. A previous study reported that insertion sequences, which can induce genomic rearrangements at temperatures around 25°C, could be one of the determinants explaining the differences in lifestyle (mesophilic or psychrophilic) between the subspecies. In this study, the genome of mesophilic strain A527 of A. salmonicida was sequenced, closed and analyzed to investigate the mesophilic-psychrophilic discrepancy. This reference genome supports the hypothesis that insertion sequences are major determinants of the lifestyle differences between the A. salmonicida subspecies. Moreover, the phylogenetic analysis performed to position strain A527 within the taxonomy raises an issue regarding the intraspecies structure of A. salmonicida.
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Affiliation(s)
- Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada, G1V 0A6.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada, G1V 0A6.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, Canada, G1V 4G5
| | - François D Rouleau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada, G1V 0A6.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada, G1V 0A6.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, Canada, G1V 4G5
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada, G1V 0A6.,Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada, G1V 0A6.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada, G1V 0A6
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada, G1V 0A6.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada, G1V 0A6.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, Canada, G1V 4G5
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Laye VJ, Karan R, Kim JM, Pecher WT, DasSarma P, DasSarma S. Key amino acid residues conferring enhanced enzyme activity at cold temperatures in an Antarctic polyextremophilic β-galactosidase. Proc Natl Acad Sci U S A 2017; 114:12530-5. [PMID: 29109294 DOI: 10.1073/pnas.1711542114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Antarctic microorganism Halorubrum lacusprofundi harbors a model polyextremophilic β-galactosidase that functions in cold, hypersaline conditions. Six amino acid residues potentially important for cold activity were identified by comparative genomics and substituted with evolutionarily conserved residues (N251D, A263S, I299L, F387L, I476V, and V482L) in closely related homologs from mesophilic haloarchaea. Using a homology model, four residues (N251, A263, I299, and F387) were located in the TIM barrel around the active site in domain A, and two residues (I476 and V482) were within coiled or β-sheet regions in domain B distant to the active site. Site-directed mutagenesis was performed by partial gene synthesis, and enzymes were overproduced from the cold-inducible cspD2 promoter in the genetically tractable Haloarchaeon, Halobacterium sp. NRC-1. Purified enzymes were characterized by steady-state kinetic analysis at temperatures from 0 to 25 °C using the chromogenic substrate o-nitrophenyl-β-galactoside. All substitutions resulted in altered temperature activity profiles compared with wild type, with five of the six clearly exhibiting reduced catalytic efficiency (kcat/Km) at colder temperatures and/or higher efficiency at warmer temperatures. These results could be accounted for by temperature-dependent changes in both Km and kcat (three substitutions) or either Km or kcat (one substitution each). The effects were correlated with perturbation of charge, hydrogen bonding, or packing, likely affecting the temperature-dependent flexibility and function of the enzyme. Our interdisciplinary approach, incorporating comparative genomics, mutagenesis, enzyme kinetics, and modeling, has shown that divergence of a very small number of amino acid residues can account for the cold temperature function of a polyextremophilic enzyme.
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Abstract
We collected snow blight of moss, Polytrichum juniperinum on King George Island, maritime Antarctica. Host died in a circle of about 10-30 cm after snow melts. Clamp connected hyphae and no sclerotia were observed on tip of host leaves. DNA sequence of ITS region from moss symptoms were perfectly matched with fruit bodies of Typhula sp. on Macquarie Island in the maritime Antarctica and high homology with Typhula cf. subvariabilis from Iran. Therefore, we suggested that T. cf. subvariabilis caused snow blight on moss in Antarctica, and this is first record of Typhula snow blight in Southern Hemisphere. These results also suggested that fungi in same genera gained similar ecological niche in both Polar Regions.
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Affiliation(s)
- Yuka Yajima
- College of Environmental Technology, Muroran Institute of Technology, Muroran, Japan
| | - Motoaki Tojo
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Tamotsu Hoshino
- Research Institute of Sustainable Chemistry, National Institute of Advanced Industrial Technology (AIST), Higashi-Hiroshima, Japan.,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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32
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Pankowski JA. Use of essential gene, encoding prophobilinogen deaminase from extreme psychrophilic Colwellia sp. C1, to generate temperature-sensitive strain of Francisella novicida. Lett Appl Microbiol 2017; 63:124-30. [PMID: 27248501 DOI: 10.1111/lam.12598] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 11/28/2022]
Abstract
UNLABELLED Previously, several essential genes from psychrophilic bacteria have been substituted for their homologues in mesophilic bacterial pathogens to make the latter temperature sensitive. It has been noted that an essential ligA gene from an extreme psychrophile, Colwellia sp. C1, yielded a gene product that is inactivated at 27°C, the lowest that has been observed for any psychrophilic enzyme, and hypothesized that other essential proteins of that strain would also have low inactivation temperatures. This work describes the partial sequencing of the genome of Colwellia sp. C1 strain and the identification of 24 open reading frames encoding homologues of highly conserved bacterial essential genes. The gene encoding porphobilinogen deaminase (hemC), which is involved in the pathway of haem synthesis, has been tested for its ability to convert Francisella novicida into a temperature-sensitive strain. The hybrid strain carrying the C1-derived hemC gene exhibited a temperature-sensitive phenotype with a restrictive temperature of 36°C. These results support the conclusion that Colwellia sp. C1 is a rich source of heat-labile enzymes. SIGNIFICANCE AND IMPACT OF THE STUDY The issue of biosafety is often raised when it comes to work with pathogenic organisms. The main concern is caused by the risk of researchers being exposed to infectious doses of dangerous microbes. This paper analyses essential genes identified in partial genomic sequence of the psychrophilic bacterium Collwelia sp. C1. These sequences can be used as a mean of generating temperature-sensitive strains of pathogenic bacteria. Such strains are incapable of surviving at the temperature of human body. This means they could be applied as vaccines or for safer work with dangerous organisms.
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Affiliation(s)
- J A Pankowski
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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33
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Baker JM, Riester CJ, Skinner BM, Newell AW, Swingley WD, Madigan MT, Jung DO, Asao M, Chen M, Loughlin PC, Pan H, Lin Y, Li Y, Shaw J, Prado M, Sherman C, Tang JK, Blankenship RE, Zhao T, Touchman JW, Sattley WM. Genome Sequence of Rhodoferax antarcticus ANT.BR T; A Psychrophilic Purple Nonsulfur Bacterium from an Antarctic Microbial Mat. Microorganisms 2017; 5:E8. [PMID: 28230808 DOI: 10.3390/microorganisms5010008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/16/2017] [Accepted: 02/18/2017] [Indexed: 12/23/2022] Open
Abstract
Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BRT, isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp) of Rfx. antarcticus has a 59.1% guanine + cytosine (GC) content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames) that comprises about 5% of the total genetic content. Surprisingly, genes encoding light-harvesting complexes 1 and 3 (LH1 and LH3), but not light-harvesting complex 2 (LH2), were identified in the photosynthesis gene cluster of the Rfx. antarcticus genome, a feature that is unique among purple phototrophs. Consistent with physiological studies that showed a strong capacity for nitrogen fixation in Rfx. antarcticus, a nitrogen fixation gene cluster encoding a molybdenum-type nitrogenase was present, but no alternative nitrogenases were identified despite the cold-active phenotype of this phototroph. Genes encoding two forms of ribulose 1,5-bisphosphate carboxylase/oxygenase were present in the Rfx. antarcticus genome, a feature that likely provides autotrophic flexibility under varying environmental conditions. Lastly, genes for assembly of both type IV pili and flagella are present, with the latter showing an unusual degree of clustering. This report represents the first genomic analysis of a psychrophilic anoxygenic phototroph and provides a glimpse of the genetic basis for maintaining a phototrophic lifestyle in a permanently cold, yet highly variable, environment.
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Han SJ, Park H, Kim S, Kim D, Park HJ, Yim JH. Enhanced production of protease by Pseudoalteromonas arctica PAMC 21717 via statistical optimization of mineral components and fed-batch fermentation. Prep Biochem Biotechnol 2016; 46:328-35. [PMID: 25830556 DOI: 10.1080/10826068.2015.1031390] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The objective of this study was to statistically optimize the mineral components of the nutritional medium required for enhancing the production of a cold-active extracellular serine-type protease, W-Pro21717, by the Antarctic bacterium Pseudoalteromonas arctica PAMC 21717. Skim milk was identified as the major efficient inducer. Among the 12 components included in the unoptimized medium, skim milk, NaCl, Na2SO4, Fe(C6H5O7) (ferric citrate), and KCl were determined, by the Plackett-Burman and Box-Behnken design, to have a major effect on W-Pro21717 production. Fed-batch fermentation (5 L scale) using the mineral-optimized medium supplemented with concentrated skim milk (critical medium component) resulted in a W-Pro21717 activity of 53.4 U/L, a 15-fold increment in production over that obtained using unoptimized flask culture conditions. These findings could be applied to scale up the production of cold-active protease.
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Affiliation(s)
- Se Jong Han
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea.,b Department of Polar Sciences , University of Science and Technology , Incheon , South Korea
| | - Heeyong Park
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Sunghui Kim
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Dockyu Kim
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Ha Ju Park
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
| | - Joung Han Yim
- a Division of Polar Life Sciences , Korea Polar Research Institute , Incheon , South Korea
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35
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Taubner RS, Rittmann SKMR. Method for Indirect Quantification of CH4 Production via H2O Production Using Hydrogenotrophic Methanogens. Front Microbiol 2016; 7:532. [PMID: 27199898 PMCID: PMC4850170 DOI: 10.3389/fmicb.2016.00532] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/31/2016] [Indexed: 01/01/2023] Open
Abstract
Hydrogenotrophic methanogens are an intriguing group of microorganisms from the domain Archaea. Methanogens exhibit extraordinary ecological, biochemical, and physiological characteristics and possess a huge biotechnological potential. Yet, the only possibility to assess the methane (CH4) production potential of hydrogenotrophic methanogens is to apply gas chromatographic quantification of CH4. In order to be able to effectively screen pure cultures of hydrogenotrophic methanogens regarding their CH4 production potential we developed a novel method for indirect quantification of the volumetric CH4 production rate by measuring the volumetric water production rate. This method was established in serum bottles for cultivation of methanogens in closed batch cultivation mode. Water production was estimated by determining the difference in mass increase in a quasi-isobaric setting. This novel CH4 quantification method is an accurate and precise analytical technique, which can be used to rapidly screen pure cultures of methanogens regarding their volumetric CH4 evolution rate. It is a cost effective alternative determining CH4 production of methanogens over CH4 quantification by using gas chromatography, especially if applied as a high throughput quantification method. Eventually, the method can be universally applied for quantification of CH4 production from psychrophilic, thermophilic and hyperthermophilic hydrogenotrophic methanogens.
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Affiliation(s)
- Ruth-Sophie Taubner
- Research Platform: ExoLife, University of ViennaVienna, Austria; Institute of Astrophysics, University of ViennaVienna, Austria; Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Simon K-M R Rittmann
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
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36
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Ciok A, Dziewit L, Grzesiak J, Budzik K, Gorniak D, Zdanowski MK, Bartosik D. Identification of miniature plasmids in psychrophilic Arctic bacteria of the genus Variovorax. FEMS Microbiol Ecol 2016; 92:fiw043. [PMID: 26917781 DOI: 10.1093/femsec/fiw043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2016] [Indexed: 11/13/2022] Open
Abstract
The Svalbard archipelago (Spitsbergen Island) is the northernmost landmass in the European Arctic and has a variety of small- and medium-sized glaciers. The plasmidome of eleven psychrophilic strains of Variovorax spp. isolated from the ice surface of Hans and Werenskiold Glaciers of Spitsbergen Island, was defined. This analysis revealed the presence of six plasmids whose nucleotide sequences have been determined. Four of them, exhibiting high reciprocal sequence similarity, possess unique structures, since their genomes lack any recognized genes. These miniature replicons, not exceeding 1 kb in size, include pHW69V1 (746 bp), which is the smallest autonomous replicon so far identified in free-living bacteria. The miniature plasmids share no similarity with known sequences present in the databases. In silico and experimental analyses identified conserved DNA regions essential for the initiation of replication of these replicons.
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Affiliation(s)
- Anna Ciok
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Karol Budzik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Dorota Gorniak
- Department of Microbiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Marek K Zdanowski
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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37
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Do H, Yun JS, Lee CW, Choi YJ, Kim HY, Kim YJ, Park H, Chang JH, Lee JH. Crystal Structure and Comparative Sequence Analysis of GmhA from Colwellia psychrerythraea Strain 34H Provides Insight into Functional Similarity with DiaA. Mol Cells 2015; 38:1086-95. [PMID: 26612680 PMCID: PMC4697000 DOI: 10.14348/molcells.2015.0191] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 07/02/2015] [Revised: 09/01/2015] [Accepted: 09/15/2015] [Indexed: 11/27/2022] Open
Abstract
The psychrophilic organism Colwellia psychrerythraea strain 34H produces extracellular polysaccharide substances to tolerate cold environments. Sedoheptulose 7-phosphate isomerase (GmhA) is essential for producing d-glycero-d-mannoheptose 7-phosphate, a key mediator in the lipopolysaccharide biosynthetic pathway. We determined the crystal structure of GmhA from C. psychrerythraea strain 34H (CpsGmhA, UniProtKB code: Q47VU0) at a resolution of 2.8 Å. The tetrameric structure is similar to that of homologous GmhA structures. Interestingly, one of the catalytic residues, glutamate, which has been reported to be critical for the activity of other homologous GmhA enzymes, is replaced by a glutamine residue in the CpsGmhA protein. We also found differences in the conformations of several other catalytic residues. Extensive structural and sequence analyses reveal that CpsGmhA shows high similarity to Escherichia coli DnaA initiator-associating protein A (DiaA). Therefore, the CpsGmhA structure reported here may provide insight into the structural and functional correlations between GmhA and DiaA among specific microorganisms.
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Affiliation(s)
- Hackwon Do
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840,
Korea
| | - Ji-Sook Yun
- Department of Biology Education, Kyungpook National University, Daegu 702-701,
Korea
| | - Chang Woo Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840,
Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840,
Korea
| | - Young Jun Choi
- Department of Biology Education, Kyungpook National University, Daegu 702-701,
Korea
| | - Hye-Yeon Kim
- Protein Structure Group, Korea Basic Science Institute, Chungbuk 363-883,
Korea
| | - Youn-Jung Kim
- Department of Marine Science, Incheon National University, Incheon 406-772,
Korea
| | - Hyun Park
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840,
Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840,
Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 702-701,
Korea
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840,
Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840,
Korea
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38
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Pinto CT, Nano FE. Stable, temperature-sensitive recombinant strain of Mycobacterium smegmatis generated through the substitution of a psychrophilic ligA gene. FEMS Microbiol Lett 2015; 362:fnv152. [PMID: 26337150 DOI: 10.1093/femsle/fnv152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2015] [Indexed: 02/03/2023] Open
Abstract
A synthetic version of the ligA gene encoding the NAD-dependent DNA ligase from the Arctic bacterium Pseudoalteromonas haloplanktis was substituted for its homolog in the chromosome of Mycobacterium smegmatis. The resulting recombinant strain grew identically to the parent strain at permissive temperatures but failed to grow above 37°C. The temperature-sensitive phenotype was stable, and the strain failed to generate temperature-resistant forms at a detectable level. Repeated passage of the hybrid strain resulted in no changes in the psychrophilic ligA gene. Given the high identity of the DNA ligases among mycobacterial species, these results suggest that a stable temperature-sensitive strain of M. tuberculosis could be generated using the approach described here.
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Affiliation(s)
- Crystal T Pinto
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V6P 4W8, Canada
| | - Francis E Nano
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V6P 4W8, Canada
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Pucciarelli S, Devaraj RR, Mancini A, Ballarini P, Castelli M, Schrallhammer M, Petroni G, Miceli C. Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences. Microb Ecol 2015; 70:484-97. [PMID: 25704316 PMCID: PMC4494151 DOI: 10.1007/s00248-015-0568-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/08/2015] [Indexed: 05/23/2023]
Abstract
We report the characterization of the bacterial consortium associated to Euplotes focardii, a strictly psychrophilic marine ciliate that was maintained in laboratory cultures at 4 °C after its first isolation from Terra Nova Bay, in Antarctica. By Illumina genome analyser, we obtained 11,179 contigs of potential prokaryotic origin and classified them according to the NCBI's prokaryotic attributes table. The majority of these sequences correspond to either Bacteroidetes (16 %) or Proteobacteria (78 %). The latter were dominated by gamma- (39 %, including sequences related to the pathogenic genus Francisella), and alpha-proteobacterial (30 %) sequences. Analysis of the Pfam domain family and Gene Ontology term variation revealed that the most frequent terms that appear unique to this consortium correspond to proteins involved in "transmembrane transporter activity" and "oxidoreductase activity". Furthermore, we identified genes that encode for enzymes involved in the catabolism of complex substance for energy reserves. We also characterized members of the transposase and integrase superfamilies, whose role in bacterial evolution is well documented, as well as putative antifreeze proteins. Antibiotic treatments of E. focardii cultures delayed the cell division of the ciliate. To conclude, our results indicate that this consortium is largely represented by bacteria derived from the original Antarctic sample and may contribute to the survival of E. focardii in laboratory condition. Furthermore, our results suggest that these bacteria may have a more general role in E. focardii survival in its natural cold and oxidative environment.
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Affiliation(s)
- Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, 62032, Italy,
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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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Kim S, Wi AR, Park HJ, Kim D, Kim HW, Yim JH, Han SJ. Enhancing extracellular lipolytic enzyme production in an arctic bacterium, Psychrobacter sp. ArcL13, by using statistical optimization and fed-batch fermentation. Prep Biochem Biotechnol 2014; 45:348-64. [PMID: 25035942 DOI: 10.1080/10826068.2014.940964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A strain isolated from seawater samples in the Chuckchi Sea and exhibiting extracellular lipolytic activity was identified using 16S rRNA gene sequence analysis as Psychrobacter sp. ArcL13. The lipolytic enzyme exhibited cold-active properties and high hydrolytic activity toward p-nitrophenyl caprylate (C8), p-nitrophenyl decanoate (C10), and sunflower oil. Statistical optimization of the medium components was performed to enhance the production of cold-active extracellular lipolytic activity. Glucose, yeast extract (YE), and NaCl were selected as the main efficient nutrient sources. Fed-batch fermentation using optimized medium with concentrated YE as the main feeding material showed a maximum lipolytic activity of 10.7 U/mL, which was a 21-fold increase in production over unoptimized flask culture conditions. The information obtained in the present study could prove applicable to the production of cold-active lipase on a large scale.
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Affiliation(s)
- Sunghui Kim
- a Division of Life Sciences , Korea Polar Research Institute , KIOST , Incheon , South Korea
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42
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Wells SA, Crennell SJ, Danson MJ. Structures of mesophilic and extremophilic citrate synthases reveal rigidity and flexibility for function. Proteins 2014; 82:2657-70. [PMID: 24948467 DOI: 10.1002/prot.24630] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 05/23/2014] [Accepted: 06/11/2014] [Indexed: 11/07/2022]
Abstract
Citrate synthase (CS) catalyses the entry of carbon into the citric acid cycle and is highly-conserved structurally across the tree of life. Crystal structures of dimeric CSs are known in both "open" and "closed" forms, which differ by a substantial domain motion that closes the substrate-binding clefts. We explore both the static rigidity and the dynamic flexibility of CS structures from mesophilic and extremophilic organisms from all three evolutionary domains. The computational expense of this wide-ranging exploration is kept to a minimum by the use of rigidity analysis and rapid all-atom simulations of flexible motion, combining geometric simulation and elastic network modeling. CS structures from thermophiles display increased structural rigidity compared with the mesophilic enzyme. A CS structure from a psychrophile, stabilized by strong ionic interactions, appears to display likewise increased rigidity in conventional rigidity analysis; however, a novel modified analysis, taking into account the weakening of the hydrophobic effect at low temperatures, shows a more appropriate decreased rigidity. These rigidity variations do not, however, affect the character of the flexible dynamics, which are well conserved across all the structures studied. Simulation trajectories not only duplicate the crystallographically observed symmetric open-to-closed transitions, but also identify motions describing a previously unidentified antisymmetric functional motion. This antisymmetric motion would not be directly observed in crystallography but is revealed as an intrinsic property of the CS structure by modeling of flexible motion. This suggests that the functional motion closing the binding clefts in CS may be independent rather than symmetric and cooperative.
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Affiliation(s)
- Stephen A Wells
- Department of Chemistry/Department of Physics, University of Bath, BATH, BA2 7AY, United Kingdom
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43
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Mitsuya D, Tanaka SI, Matsumura H, Urano N, Takano K, Ogasahara K, Takehira M, Yutani K, Ishida M. Strategy for cold adaptation of the tryptophan synthase α subunit from the psychrophile Shewanella frigidimarina K14-2: crystal structure and physicochemical properties. J Biochem 2013; 155:73-82. [PMID: 24163283 DOI: 10.1093/jb/mvt098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To investigate the molecular basis of cold adaptation of enzymes, we determined the crystal structure of the tryptophan synthase α subunit (SfTSA) from the psychrophile Shewanella frigidimarina K14-2 by X-ray analysis at 2.6-Å resolution and also examined its physicochemical properties. SfTSA was found to have the following characteristics: (i) The stabilities against heat and denaturant of SfTSA were lower than those of an α subunit (EcTSA) from Escherichia coli. This lower equilibrium stability originated from both a faster unfolding rate and a slower refolding rate; (ii) the heat denaturation of SfTSA was completely reversible at pH 7.0 and the solubility of denatured SfTSA was higher than that of denatured EcTSA. The two-state transition of denaturation for SfTSA was highly cooperative, whereas the denaturation process of EcTSA was considerably more complex and (iii) the global structure of SfTSA was quite similar to those of α subunits from other species. Relative to those other proteins, SfTSA exhibited an increase in cavity volume and a decrease in the number of ion pairs. SfTSA also lacks a hydrogen bond near loop B, related to catalytic function. These characteristics of SfTSA might provide the conformational flexibility required for catalytic activity at low temperatures.
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Affiliation(s)
- Daisuke Mitsuya
- Department of Ocean Sciences, Graduate school of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato, Tokyo 108-8477; Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871; Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871; Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871; Department of Life Science, University of Hyogo, 3-2-1, Kouto, Kamigori, Ako-gun, Hyogo 678-1297; and RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148
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44
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Karan R, Capes MD, DasSarma S. Function and biotechnology of extremophilic enzymes in low water activity. Aquat Biosyst 2012; 8:4. [PMID: 22480329 PMCID: PMC3310334 DOI: 10.1186/2046-9063-8-4] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 02/02/2012] [Indexed: 05/31/2023]
Abstract
Enzymes from extremophilic microorganisms usually catalyze chemical reactions in non-standard conditions. Such conditions promote aggregation, precipitation, and denaturation, reducing the activity of most non-extremophilic enzymes, frequently due to the absence of sufficient hydration. Some extremophilic enzymes maintain a tight hydration shell and remain active in solution even when liquid water is limiting, e.g. in the presence of high ionic concentrations, or at cold temperature when water is close to the freezing point. Extremophilic enzymes are able to compete for hydration via alterations especially to their surface through greater surface charges and increased molecular motion. These properties have enabled some extremophilic enzymes to function in the presence of non-aqueous organic solvents, with potential for design of useful catalysts. In this review, we summarize the current state of knowledge of extremophilic enzymes functioning in high salinity and cold temperatures, focusing on their strategy for function at low water activity. We discuss how the understanding of extremophilic enzyme function is leading to the design of a new generation of enzyme catalysts and their applications to biotechnology.
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Affiliation(s)
- Ram Karan
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute of Marine and Environmental Technology, University System of Maryland, Baltimore, MD, USA
| | - Melinda D Capes
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute of Marine and Environmental Technology, University System of Maryland, Baltimore, MD, USA
| | - Shiladitya DasSarma
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute of Marine and Environmental Technology, University System of Maryland, Baltimore, MD, USA
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45
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Merlino A, Russo Krauss I, Albino A, Pica A, Vergara A, Masullo M, De Vendittis E, Sica F. Improving protein crystal quality by the without-oil microbatch method: crystallization and preliminary X-ray diffraction analysis of glutathione synthetase from Pseudoalteromonas haloplanktis. Int J Mol Sci 2011; 12:6312-9. [PMID: 22016660 DOI: 10.3390/ijms12096312] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/05/2011] [Accepted: 09/14/2011] [Indexed: 11/17/2022] Open
Abstract
Glutathione synthetases catalyze the ATP-dependent synthesis of glutathione from l-γ-glutamyl- l-cysteine and glycine. Although these enzymes have been sequenced and characterized from a variety of biological sources, their exact catalytic mechanism is not fully understood and nothing is known about their adaptation at extremophilic environments. Glutathione synthetase from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhGshB) has been expressed, purified and successfully crystallized. An overall improvement of the crystal quality has been obtained by adapting the crystal growth conditions found with vapor diffusion experiments to the without-oil microbatch method. The best crystals of PhGshB diffract to 2.34 Å resolution and belong to space group P212121, with unit-cell parameters a = 83.28 Å, b = 119.88 Å, c = 159.82 Å. Refinement of the model, obtained using phases derived from the structure of the same enzyme from Escherichia coli by molecular replacement, is in progress. The structural determination will provide the first structural characterization of a psychrophilic glutathione synthetase reported to date.
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46
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Araújo LS, Kagohara E, Garcia TP, Pellizari VH, Andrade LH. Screening of microorganisms producing cold-active oxidoreductases to be applied in enantioselective alcohol oxidation. An Antarctic survey. Mar Drugs 2011; 9:889-905. [PMID: 21673897 PMCID: PMC3111190 DOI: 10.3390/md9050889] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [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: 04/20/2011] [Revised: 05/17/2011] [Accepted: 05/20/2011] [Indexed: 11/16/2022] Open
Abstract
Several microorganisms were isolated from soil/sediment samples of Antarctic Peninsula. The enrichment technique using (RS)-1-(phenyl)ethanol as a carbon source allowed us to isolate 232 psychrophile/psychrotroph microorganisms. We also evaluated the enzyme activity (oxidoreductases) for enantioselective oxidation reactions, by using derivatives of (RS)-1-(phenyl)ethanol as substrates. Among the studied microorganisms, 15 psychrophile/psychrotroph strains contain oxidoreductases that catalyze the (S)-enantiomer oxidation from racemic alcohols to their corresponding ketones. Among the identified microorganisms, Flavobacterium sp. and Arthrobacter sp. showed excellent enzymatic activity. These new bacteria strains were selected for optimization study, in which the (RS)-1-(4-methyl-phenyl)ethanol oxidation was evaluated in several reaction conditions. From these studies, it was observed that Flavobacterium sp. has an excellent enzymatic activity at 10 °C and Arthrobacter sp. at 15 and 25 °C. We have also determined the growth curves of these bacteria, and both strains showed optimum growth at 25 °C, indicating that these bacteria are psychrotroph.
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Affiliation(s)
- Lidiane S. Araújo
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, SP 05508-900, São Paulo, Brazil; E-Mails: (L.S.A); (E.K.); (T.P.G)
| | - Edna Kagohara
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, SP 05508-900, São Paulo, Brazil; E-Mails: (L.S.A); (E.K.); (T.P.G)
| | - Thaís P. Garcia
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, SP 05508-900, São Paulo, Brazil; E-Mails: (L.S.A); (E.K.); (T.P.G)
| | - Vivian H. Pellizari
- Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico 191, SP 05508-120, São Paulo, Brazil; E-Mail: (V.H.P.)
| | - Leandro H. Andrade
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, SP 05508-900, São Paulo, Brazil; E-Mails: (L.S.A); (E.K.); (T.P.G)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +55-11-3091-2287; Fax: +55-11-3815-5579
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Morrison BA, Shain DH. An AMP nucleosidase gene knockout in Escherichia coli elevates intracellular ATP levels and increases cold tolerance. Biol Lett 2008; 4:53-6. [PMID: 18029299 PMCID: PMC2412920 DOI: 10.1098/rsbl.2007.0432] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [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: 08/17/2007] [Revised: 10/22/2007] [Accepted: 10/23/2007] [Indexed: 11/12/2022] Open
Abstract
Disparate psychrophiles (e.g. glacier ice worms, bacteria, algae and fungi) elevate steady-state intracellular ATP levels as temperatures decline, which has been interpreted as a compensatory mechanism to offset reductions in molecular motion and Gibb's free energy of ATP hydrolysis. In this study, we sought to manipulate steady-state ATP levels in the mesophilic bacterium, Escherichia coli, to investigate the relationship between cold temperature survivability and elevated intracellular ATP. Based on known energetic pathways and feedback loops, we targeted the AMP nucleotidase (amn) gene, which is thought to encode the primary AMP degradative enzyme in prokaryotes. By knocking out amn in wild-type E. coli DY330 cells using recombineering methodology, we generated a mutant (AMNk) that elevated intracellular ATP levels by more than 30% across its viable temperature range. As temperature was lowered, the relative ATP disparity between AMNk and DY330 cells increased to approximately 66% at 10 degrees C, and was approximately 100% after storage at 0 degrees C for 5-7 days. AMNk cells stored at 0 degrees C for 7 days displayed approximately fivefold higher cell viability than wild-type DY330 cells treated in the same manner.
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Affiliation(s)
| | - Daniel H Shain
- Biology Department, Rutgers The State University of New JerseyCamden, NJ 08102, USA
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Fujii T, Oikawa T, Muraoka I, Soda K, Hata Y. Crystallization and preliminary X-ray diffraction studies of tetrameric malate dehydrogenase from the novel Antarctic psychrophile Flavobacterium frigidimaris KUC-1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:983-6. [PMID: 18007057 PMCID: PMC2339744 DOI: 10.1107/s1744309107051524] [Citation(s) in RCA: 4] [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: 09/14/2007] [Accepted: 10/18/2007] [Indexed: 05/25/2023]
Abstract
Flavobacterium frigidimaris KUC-1 is a novel psychrotolerant bacterium isolated from Antarctic seawater. Malate dehydrogenase (MDH) is an essential metabolic enzyme in the citric acid cycle and has been cloned, overexpressed and purified from F. frigidimaris KUC-1. In contrast to the already known dimeric form of MDH from the psychrophile Aquaspirillium arcticum, F. frigidimaris MDH exists as a tetramer. It was crystallized at 288 K by the hanging-drop vapour-diffusion method using ammonium sulfate as the precipitating agent. The crystal diffracted to a maximum resolution of 1.80 A. It contains one tetrameric molecule in the asymmetric unit.
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Affiliation(s)
- Tomomi Fujii
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tadao Oikawa
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680, Japan
| | - Ikuo Muraoka
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680, Japan
| | - Kenji Soda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680, Japan
| | - Yasuo Hata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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Garsoux G, Lamotte J, Gerday C, Feller G. Kinetic and structural optimization to catalysis at low temperatures in a psychrophilic cellulase from the Antarctic bacterium Pseudoalteromonas haloplanktis. Biochem J 2004; 384:247-53. [PMID: 15287848 PMCID: PMC1134107 DOI: 10.1042/bj20040325] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [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: 03/01/2004] [Revised: 07/23/2004] [Accepted: 08/03/2004] [Indexed: 11/17/2022]
Abstract
The cold-adapted cellulase CelG has been purified from the culture supernatant of the Antarctic bacterium Pseudoalteromonas haloplanktis and the gene coding for this enzyme has been cloned, sequenced and expressed in Escherichia coli. This cellulase is composed of three structurally and functionally distinct regions: an N-terminal catalytic domain belonging to glycosidase family 5 and a C-terminal cellulose-binding domain belonging to carbohydrate-binding module family 5. The linker of 107 residues connecting both domains is one of the longest found in cellulases, and optimizes substrate accessibility to the catalytic domain by drastically increasing the surface of cellulose available to a bound enzyme molecule. The psychrophilic enzyme is closely related to the cellulase Cel5 from Erwinia chrysanthemi. Both kcat and kcat/K(m) values at 4 degrees C for the psychrophilic cellulase are similar to the values for Cel5 at 30-35 degrees C, suggesting temperature adaptation of the kinetic parameters. The thermodynamic parameters of activation of CelG suggest a heat-labile, relatively disordered active site with low substrate affinity, in agreement with the experimental data. The structure of CelG has been constructed by homology modelling with a molecule of cellotetraose docked into the active site. No structural alteration related to cold-activity can be found in the catalytic cleft, whereas several structural factors in the overall structure can explain the weak thermal stability, suggesting that the loss of stability provides the required active-site mobility at low temperatures.
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Affiliation(s)
- Geneviève Garsoux
- *Laboratory of Biochemistry, Institute of Chemistry B6a, University of Liège, B-4000 Liège, Belgium
| | - Josette Lamotte
- †Center for Protein Engineering, Institute of Chemistry B6a, University of Liège, B-4000 Liège, Belgium
| | - Charles Gerday
- *Laboratory of Biochemistry, Institute of Chemistry B6a, University of Liège, B-4000 Liège, Belgium
| | - Georges Feller
- *Laboratory of Biochemistry, Institute of Chemistry B6a, University of Liège, B-4000 Liège, Belgium
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