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Zhou J, Feng Y, Wu X, Feng Y, Zhao Y, Pan J, Liu S. Communication leads to bacterial heterogeneous adaptation to changing conditions in partial nitrification reactor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172110. [PMID: 38565348 DOI: 10.1016/j.scitotenv.2024.172110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
Recently, it is reported that bacterial communication coordinates the whole consortia to jointly resist the adverse environments. Here, we found the bacterial communication inevitably distinguished bacterial adaptation among different species in partial nitrification reactor under decreasing temperatures. We operated a partial nitrification reactor under temperature gradient from 30 °C to 5 °C and found the promotion of bacterial communication on adaptation of ammonia-oxidizing bacteria (AOB) was greater than that of nitrite-oxidizing bacteria (NOB). Signal pathways with single-component sensing protein in AOB can regulate more genes involved in bacterial adaptation than that with two-component sensing protein in NOB. The negative effects of bacterial communication, which were seriously ignored, have been highlighted, and Clp regulator downstream diffusible signal factor (DSF) based signal pathways worked as transcription activators and inhibitors of adaptation genes in AOB and NOB respectively. Bacterial communication can induce differential adaptation through influencing bacterial interactions. AOB inclined to cooperate with DSF synthesis bacteria as temperature declined, however, cooperation between NOB and DSF synthesis bacteria inclined to get weakening. According to the regulatory effects of signal pathways, bacterial survival strategies for self-protection were revealed. This study hints a potential way to govern niche differentiation in the microbiota by bacterial communication, contributing to forming an efficient artificial ecosystem.
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Affiliation(s)
- Jianhang Zhou
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Ying Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Xiaogang Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yiming Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yunpeng Zhao
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Juejun Pan
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Sitong Liu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China.
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2
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Zhang D, Wang L, Wang W, Liu D. The Role of lncRNAs in Pig Muscle in Response to Cold Exposure. Genes (Basel) 2023; 14:1901. [PMID: 37895249 PMCID: PMC10606478 DOI: 10.3390/genes14101901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Cold exposure is an essential factor affecting breeding efforts in cold regions. Muscle, as an important tissue for homeothermic animals, can produce heat through shivering thermogenesis (ST) and non-shivering thermogenesis (NST) under cold exposure. Long non-coding RNAs (lncRNAs) play important roles in regulating gene expression. However, the regulatory mechanisms of lncRNAs and their role in the thermogenesis of pigs are unclear. We examined lncRNAs in the skeletal muscle of an indigenous pig breed, the Enshi black pig, when the pigs were exposed to acute or chronic cold. Three pigs were maintained inside a pig house (control group), three pigs were maintained outside the pig house for 55 d (chronic cold group), and three pigs were suddenly exposed to the conditions outside the pig house for 3 days (acute cold group). After the experiment, the longissimus dorsi of each pig were collected, and their lncRNA profiles were sequenced and analyzed. Each sample obtained nearly 12.56 Gb of clean data. A total of 11,605 non-coding RNAs were obtained, including 10,802 novel lncRNAs. The number of differentially expressed lncRNAs (DElncRNAs) was identified under acute cold (427) and cold acclimation (376), with 215 and 192 upregulated lncRNAs, respectively. However, only 113 lncRNAs were commonly upregulated by acute cold and cold acclimation. In addition, 65% of the target genes were trans-regulated by DElncRNAs. The target genes were enriched in signal transduction, immune system, cell growth and death pathways, and amino acid and carbohydrate metabolism. Compared to cold acclimation, acute cold stress-induced more DElncRNAs and response pathways. In conclusion, low temperatures altered the expression levels of lncRNAs and their target genes in muscle tissue. Some potential mechanisms were revealed, including ion migration and the metabolism of amino acids and carbohydrates.
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Affiliation(s)
| | | | | | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (D.Z.); (L.W.); (W.W.)
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3
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Gebhard LJ, Duggin IG, Erdmann S. Improving the genetic system for Halorubrum lacusprofundi to allow in-frame deletions. Front Microbiol 2023; 14:1095621. [PMID: 37065119 PMCID: PMC10102395 DOI: 10.3389/fmicb.2023.1095621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Halorubrum lacusprofundi is a cold-adapted halophilic archaeon isolated from Deep Lake, Antarctica. Hrr. lacusprofundi is commonly used to study adaptation to cold environments and thereby a potential source for biotechnological products. Additionally, in contrast to other haloarchaeal model organisms, Hrr. lacusprofundi is also susceptible to a range of different viruses and virus-like elements, making it a great model to study virus-host interactions in a cold-adapted organism. A genetic system has previously been reported for Hrr. lacusprofundi; however, it does not allow in-frame deletions and multiple gene knockouts. Here, we report the successful generation of uracil auxotrophic (pyrE2) mutants of two strains of Hrr. lacusprofundi. Subsequently, we attempted to generate knockout mutants using the auxotrophic marker for selection. However, surprisingly, only the combination of the auxotrophic marker and antibiotic selection allowed the timely and clean in-frame deletion of a target gene. Finally, we show that vectors established for the model organism Haloferax volcanii are deployable for genetic manipulation of Hrr. lacusprofundi, allowing the use of the portfolio of genetic tools available for H. volcanii in Hrr. lacusprofundi.
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Affiliation(s)
- L. Johanna Gebhard
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Iain G. Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Susanne Erdmann
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen, Germany
- *Correspondence: Susanne Erdmann,
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4
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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] [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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5
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Palumbo RJ, McKean N, Leatherman E, Namitz KEW, Connell L, Wolfe A, Moody K, Gostinčar C, Gunde-Cimerman N, Bah A, Hanes SD. Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance. SCIENCE ADVANCES 2022; 8:eabq3235. [PMID: 36070379 PMCID: PMC9451162 DOI: 10.1126/sciadv.abq3235] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/21/2022] [Indexed: 06/14/2023]
Abstract
Most of the world's biodiversity lives in cold (-2° to 4°C) and hypersaline environments. To understand how cells adapt to such conditions, we isolated two key components of the transcription machinery from fungal species that live in extreme polar environments: the Ess1 prolyl isomerase and its target, the carboxy-terminal domain (CTD) of RNA polymerase II. Polar Ess1 enzymes are conserved and functional in the model yeast, Saccharomyces cerevisiae. By contrast, polar CTDs diverge from the consensus (YSPTSPS)26 and are not fully functional in S. cerevisiae. These CTDs retain the critical Ess1 Ser-Pro target motifs, but substitutions at Y1, T4, and S7 profoundly affected their ability to undergo phase separation in vitro and localize in vivo. We propose that environmentally tuned phase separation by the CTD and other intrinsically disordered regions plays an adaptive role in cold tolerance by concentrating enzymes and substrates to overcome energetic barriers to metabolic activity.
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Affiliation(s)
- Ryan J. Palumbo
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Nathan McKean
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Erinn Leatherman
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Kevin E. W. Namitz
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Laurie Connell
- School of Marine Sciences and Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - Aaron Wolfe
- Ichor Life Sciences Inc., 2651 US Route 11, LaFayette, NY 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Kelsey Moody
- Ichor Life Sciences Inc., 2651 US Route 11, LaFayette, NY 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Alaji Bah
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Steven D. Hanes
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
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6
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Extracellular Enzymatic Activities of Oceanic Pelagic Fungal Strains and the Influence of Temperature. J Fungi (Basel) 2022; 8:jof8060571. [PMID: 35736054 PMCID: PMC9225461 DOI: 10.3390/jof8060571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 11/20/2022] Open
Abstract
Although terrestrial and aquatic fungi are well-known decomposers of organic matter, the role of marine fungi remains largely unknown. Recent studies based on omics suggest that marine fungi potentially play a major role in elemental cycles. However, there is very limited information on the diversity of extracellular enzymatic activities performed by pelagic fungi in the ocean and how these might be affected by community composition and/or critical environmental parameters such as temperature. In order to obtain information on the potential metabolic activity of marine fungi, extracellular enzymatic activities (EEA) were investigated. Five marine fungal species belonging to the most abundant pelagic phyla (Ascomycota and Basidiomycota) were grown at 5 °C and 20 °C, and fluorogenic enzymatic assays were performed using six substrate analogues for the hydrolysis of carbohydrates (β-glucosidase, β-xylosidase, and N-acetyl-β-D-glucosaminidase), amino acids (leucine aminopeptidase), and of organic phosphorus (alkaline phosphatase) and sulfur compounds (sulfatase). Remarkably, all fungal strains were capable of hydrolyzing all the offered substrates. However, the hydrolysis rate (Vmax) and half-saturation constant (Km) varied among the fungal strains depending on the enzyme type. Temperature had a strong impact on the EEAs, resulting in Q10 values of up to 6.1 and was species and substrate dependent. The observed impact of temperature on fungal EEA suggests that warming of the global ocean might alter the contribution of pelagic fungi in marine biogeochemical cycles.
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Zhou J, Huo T, Sun J, Feng Y, Pan J, Zhao Y, Liu S. Response of amino acid metabolism to decreased temperatures in anammox consortia: Strong, efficient and flexible. BIORESOURCE TECHNOLOGY 2022; 352:127099. [PMID: 35367607 DOI: 10.1016/j.biortech.2022.127099] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/26/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Although amino acid (AA) metabolism is basis of bacterial activities, unique characteristics of its response to decreased temperatures are not fully understood. Achieving nitrogen removal rate of 130-150 mg N/ (L∙d), metabolic differences of anammox consortia between 35 °C and four decreased temperatures (15-30 °C) were revealed respectively. 0-11.4-fold abundance variation of marker metabolites evidenced change of key metabolism (metabolism of AA, lipid and energy production) at decreased temperatures. However, AA metabolism varied more obviously than others, implying stronger response and higher functional potential. Efficiently, network topology confirmed more cellular processes represented by growth metabolism and biofilm formation were influenced by AA metabolism. Flexibly, down-regulated biosynthesis of unfavorable AAs for psychrophilic enzyme differed from enhanced biosynthesis of costly AAs, which only matched partial decreased temperatures to save energy. This work elucidates advantages of AA metabolism over others, exogenous amino acids could significantly promote activity of anammox bacteria at decreased temperatures.
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Affiliation(s)
- Jianhang Zhou
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Tangran Huo
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Jingqi Sun
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yiming Feng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Juejun Pan
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yunpeng Zhao
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Sitong Liu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China.
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8
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Martínez GM, Pire C, Martínez-Espinosa RM. Hypersaline environments as natural sources of microbes with potential applications in biotechnology: the case of solar evaporation systems to produce salt in Alicante County (Spain). CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100136. [PMID: 35909606 PMCID: PMC9325878 DOI: 10.1016/j.crmicr.2022.100136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/14/2022] [Accepted: 04/24/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guillermo Martínez Martínez
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Corresponding author.
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9
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Laye VJ, DasSarma S. Double mutations far from the active site affect cold activity in an Antarctic halophilic β-galactosidase. Protein Sci 2022; 31:677-687. [PMID: 34939242 PMCID: PMC8862438 DOI: 10.1002/pro.4264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022]
Abstract
The Antarctic haloarchaeon, Halorubrum lacusprofundi, contains a polyextremophilic family 42 β-galactosidase, which we are using as a model for cold-active enzymes. Divergent amino acid residues in this 78 kDa protein were identified through comparative genomics and hypothesized to be important for cold activity. Six amino acid residues were previously mutated and five were shown by steady-state kinetic analysis to have altered temperature-dependent catalytic activity profiles via effects on Km and/or kcat compared to the wild-type enzyme. In this follow-up study, double-mutated enzymes were constructed and tested for temperature effects, including two new tandem residue pairs (N180T/A181T and T383A/S384A), and pairwise combination of the single residue mutations (N251D, F387L, I476V, and V482L). All double-mutated enzymes were found to be more catalytically active at moderate and/or less active at colder temperatures than wild-type, with both Km and kcat effects observed for the two tandem mutations. For pairwise combinations, a Km effect was seen when the surface exposed F387L mutation located in a domain A TIM barrel α helix 19 Å from the active site was combined with two internal residues, N251D or V482L. When another surface exposed mutation I476V located in a coiled region of domain B 25 Å from the active site was paired with N251D or V482L, a kcat effect was observed. These results indicate that temperature-dependent kinetic effects may be complex and subtle and are mediated by a combination of a small number of residues distant from the active site via changes to the hydration shell and/or perturbation of internal packing.
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Affiliation(s)
- Victoria J. Laye
- Institute of Marine and Environmental TechnologyUniversity System of MarylandBaltimoreMarylandUSA,Department of Microbiology and ImmunologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Shiladitya DasSarma
- Institute of Marine and Environmental TechnologyUniversity System of MarylandBaltimoreMarylandUSA,Department of Microbiology and ImmunologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
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10
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Comparative Genomic Analyses of the Genus Nesterenkonia Unravels the Genomic Adaptation to Polar Extreme Environments. Microorganisms 2022; 10:microorganisms10020233. [PMID: 35208688 PMCID: PMC8875376 DOI: 10.3390/microorganisms10020233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
The members of the Nesterenkonia genus have been isolated from various habitats, like saline soil, salt lake, sponge-associated and the human gut, some of which are even located in polar areas. To identify their stress resistance mechanisms and draw a genomic profile across this genus, we isolated four Nesterenkonia strains from the lakes in the Tibetan Plateau, referred to as the third pole, and compared them with all other 30 high-quality Nesterenkonia genomes that are deposited in NCBI. The Heaps’ law model estimated that the pan-genome of this genus is open and the number of core, shell, cloud, and singleton genes were 993 (6.61%), 2782 (18.52%), 4117 (27.40%), and 7132 (47.47%), respectively. Phylogenomic and ANI/AAI analysis indicated that all genomes can be divided into three main clades, named NES-1, NES-2, and NES-3. The strains isolated from lakes in the Tibetan Plateau were clustered with four strains from different sources in the Antarctic and formed a subclade within NES-2, described as NES-AT. Genome features of this subclade, including GC (guanine + cytosine) content, tRNA number, carbon/nitrogen atoms per residue side chain (C/N-ARSC), and amino acid composition, in NES-AT individuals were significantly different from other strains, indicating genomic adaptation to cold, nutrient-limited, osmotic, and ultraviolet conditions in polar areas. Functional analysis revealed the enrichment of specific genes involved in bacteriorhodopsin synthesis, biofilm formation, and more diverse nutrient substance metabolism genes in the NES-AT clade, suggesting potential adaptation strategies for energy metabolism in polar environments. This study provides a comprehensive profile of the genomic features of the Nesterenkonia genus and reveals the possible mechanism for the survival of Nesterenkonia isolates in polar areas.
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Piszkin L, Bowman J. Extremophile enzyme optimization for low temperature and high salinity are fundamentally incompatible. Extremophiles 2021; 26:5. [PMID: 34940913 DOI: 10.1007/s00792-021-01254-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/09/2021] [Indexed: 11/25/2022]
Abstract
The evolutionary mechanisms behind cold and high-saline co-adaptation of proteins are not thoroughly understood. To explore how enzymes evolve in response to multiple environmental pressures we developed a novel in silico method to model the directed evolution of proteins, the Protein Evolution Parameter Calculator (PEPC). PEPC carries out single amino acid substitutions that lead to improvements in the selected user-defined parameters. To investigate the evolutionary relationship between increased flexibility and decreased isoelectric point, which are presumed indicators of cold and saline adaptation in proteins, we applied PEPC to a subset of core haloarchaea orthologous group (cHOG) proteins from the mesophilic Halobacterium salinarum NRC-1 and cold-tolerant Halorubrum lacusprofundi strain ATCC 49239. The results suggest that mutations that increase flexibility will also generally increase isoelectric point. These findings suggest that enzyme adaptation to low temperature and high salinity might be evolutionarily counterposed based on the structural characteristics of probable amino acid mutations. This may help to explain the apparent lack of truly psychrophilic halophiles in nature, and why microbes adapted to polar hypersaline environments typically have mesophilic temperature optima. A better understanding of protein evolution to extremely cold and salty conditions will aid in our understanding of where and how life is distributed on Earth and in our solar system.
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Affiliation(s)
- Luke Piszkin
- Department of Physics, UC San Diego, La Jolla, CA, USA.
| | - Jeff Bowman
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
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12
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Yusof NA, Hashim NHF, Bharudin I. Cold Adaptation Strategies and the Potential of Psychrophilic Enzymes from the Antarctic Yeast, Glaciozyma antarctica PI12. J Fungi (Basel) 2021; 7:jof7070528. [PMID: 34209103 PMCID: PMC8306469 DOI: 10.3390/jof7070528] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/19/2021] [Accepted: 06/25/2021] [Indexed: 12/20/2022] Open
Abstract
Psychrophilic organisms possess several adaptive strategies which allow them to sustain life at low temperatures between −20 to 20 °C. Studies on Antarctic psychrophiles are interesting due to the multiple stressors that exist on the permanently cold continent. These organisms produce, among other peculiarities, cold-active enzymes which not only have tremendous biotechnological potential but are valuable models for fundamental research into protein structure and function. Recent innovations in omics technologies such as genomics, transcriptomics, proteomics and metabolomics have contributed a remarkable perspective of the molecular basis underpinning the mechanisms of cold adaptation. This review critically discusses similar and different strategies of cold adaptation in the obligate psychrophilic yeast, Glaciozyma antarctica PI12 at the molecular (genome structure, proteins and enzymes, gene expression) and physiological (antifreeze proteins, membrane fluidity, stress-related proteins) levels. Our extensive studies on G. antarctica have revealed significant insights towards the innate capacity of- and the adaptation strategies employed by this psychrophilic yeast for life in the persistent cold. Furthermore, several cold-active enzymes and proteins with biotechnological potential are also discussed.
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Affiliation(s)
- Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia;
| | - Noor Haza Fazlin Hashim
- Water Quality Laboratory, National Water Research Institute Malaysia (NAHRIM), Ministry of Environment and Water, Jalan Putra Permai, Seri Kembangan 43300, Selangor, Malaysia;
| | - Izwan Bharudin
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
- Correspondence:
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13
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Blanquart S, Groussin M, Le Roy A, Szöllosi GJ, Girard E, Franzetti B, Gouy M, Madern D. Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties. Mol Biol Evol 2021; 38:3754-3774. [PMID: 33974066 PMCID: PMC8382911 DOI: 10.1093/molbev/msab146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Extreme halophilic Archaea thrive in high salt, where, through proteomic adaptation, they cope with the strong osmolarity and extreme ionic conditions of their environment. In spite of wide fundamental interest, however, studies providing insights into this adaptation are scarce, because of practical difficulties inherent to the purification and characterization of halophilic enzymes. In this work, we describe the evolutionary history of malate dehydrogenases (MalDH) within Halobacteria (a class of the Euryarchaeota phylum). We resurrected nine ancestors along the inferred halobacterial MalDH phylogeny, including the Last Common Ancestral MalDH of Halobacteria (LCAHa) and compared their biochemical properties with those of five modern halobacterial MalDHs. We monitored the stability of these various MalDHs, their oligomeric states and enzymatic properties, as a function of concentration for different salts in the solvent. We found that a variety of evolutionary processes such as amino acid replacement, gene duplication, loss of MalDH gene and replacement owing to horizontal transfer resulted in significant differences in solubility, stability and catalytic properties between these enzymes in the three Halobacteriales, Haloferacales and Natrialbales orders since the LCAHa MalDH.We also showed how a stability trade-off might favor the emergence of new properties during adaptation to diverse environmental conditions. Altogether, our results suggest a new view of halophilic protein adaptation in Archaea.
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Affiliation(s)
| | - Mathieu Groussin
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, Villeurbanne, F-69622, France.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Aline Le Roy
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France
| | - Gergely J Szöllosi
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, Villeurbanne, F-69622, France.,MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Budapest, H-1117, Hungary
| | - Eric Girard
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France
| | - Bruno Franzetti
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France
| | - Manolo Gouy
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, Villeurbanne, F-69622, France
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14
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Ando N, Barquera B, Bartlett DH, Boyd E, Burnim AA, Byer AS, Colman D, Gillilan RE, Gruebele M, Makhatadze G, Royer CA, Shock E, Wand AJ, Watkins MB. The Molecular Basis for Life in Extreme Environments. Annu Rev Biophys 2021; 50:343-372. [PMID: 33637008 DOI: 10.1146/annurev-biophys-100120-072804] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.
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Affiliation(s)
- Nozomi Ando
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Blanca Barquera
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Audrey A Burnim
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Amanda S Byer
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Daniel Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Richard E Gillilan
- Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York 14853, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Everett Shock
- GEOPIG, School of Earth & Space Exploration, School of Molecular Sciences, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona 85287, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77845, USA.,Department of Chemistry, Texas A&M University, College Station, Texas 77845, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, Texas 77845, USA
| | - Maxwell B Watkins
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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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] [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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Karan R, Mathew S, Muhammad R, Bautista DB, Vogler M, Eppinger J, Oliva R, Cavallo L, Arold ST, Rueping M. Understanding High-Salt and Cold Adaptation of a Polyextremophilic Enzyme. Microorganisms 2020; 8:microorganisms8101594. [PMID: 33081237 PMCID: PMC7602713 DOI: 10.3390/microorganisms8101594] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/27/2022] Open
Abstract
The haloarchaeon Halorubrum lacusprofundi is among the few polyextremophilic organisms capable of surviving in one of the most extreme aquatic environments on Earth, the Deep Lake of Antarctica (−18 °C to +11.5 °C and 21–28%, w/v salt content). Hence, H. lacusprofundi has been proposed as a model for biotechnology and astrobiology to investigate potential life beyond Earth. To understand the mechanisms that allow proteins to adapt to both salinity and cold, we structurally (including X-ray crystallography and molecular dynamics simulations) and functionally characterized the β-galactosidase from H. lacusprofundi (hla_bga). Recombinant hla_bga (produced in Haloferax volcanii) revealed exceptional stability, tolerating up to 4 M NaCl and up to 20% (v/v) of organic solvents. Despite being cold-adapted, hla_bga was also stable up to 60 °C. Structural analysis showed that hla_bga combined increased surface acidity (associated with halophily) with increased structural flexibility, fine-tuned on a residue level, for sustaining activity at low temperatures. The resulting blend enhanced structural flexibility at low temperatures but also limited protein movements at higher temperatures relative to mesophilic homologs. Collectively, these observations help in understanding the molecular basis of a dual psychrophilic and halophilic adaptation and suggest that such enzymes may be intrinsically stable and functional over an exceptionally large temperature range.
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Affiliation(s)
- Ram Karan
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
- Correspondence: (R.K.); (S.T.A.); (M.R.)
| | - Sam Mathew
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Reyhan Muhammad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia;
| | - Didier B. Bautista
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Malvina Vogler
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Jorg Eppinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Romina Oliva
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Luigi Cavallo
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia;
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
- Correspondence: (R.K.); (S.T.A.); (M.R.)
| | - Magnus Rueping
- KAUST Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (S.M.); (D.B.B.); (M.V.); (J.E.); (R.O.); (L.C.)
- Correspondence: (R.K.); (S.T.A.); (M.R.)
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17
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Dawson HM, Heal KR, Torstensson A, Carlson LT, Ingalls AE, Young JN. Large Diversity in Nitrogen- and Sulfur-Containing Compatible Solute Profiles in Polar and Temperate Diatoms. Integr Comp Biol 2020; 60:1401-1413. [PMID: 32960956 DOI: 10.1093/icb/icaa133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Intense bottom-ice algal blooms, often dominated by diatoms, are an important source of food for grazers, organic matter for export during sea ice melt, and dissolved organic carbon. Sea-ice diatoms have a number of adaptations, including accumulation of compatible solutes, that allows them to inhabit this highly variable environment characterized by extremes in temperature, salinity, and light. In addition to protecting them from extreme conditions, these compounds present a labile, nutrient-rich source of organic matter, and include precursors to climate active compounds (e.g., dimethyl sulfide [DMS]), which are likely regulated with environmental change. Here, intracellular concentrations of 45 metabolites were quantified in three sea-ice diatom species and were compared to two temperate diatom species, with a focus on compatible solutes and free amino acid pools. There was a large diversity of metabolite concentrations between diatoms with no clear pattern identifiable for sea-ice species. Concentrations of some compatible solutes (isethionic acid, homarine) approached 1 M in the sea-ice diatoms, Fragilariopsis cylindrus and Navicula cf. perminuta, but not in the larger sea-ice diatom, Nitzschia lecointei or in the temperate diatom species. The differential use of compatible solutes in sea-ice diatoms suggests different adaptive strategies and highlights which small organic compounds may be important in polar biogeochemical cycles.
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Affiliation(s)
- H M Dawson
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - K R Heal
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - A Torstensson
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
| | - L T Carlson
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - A E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - J N Young
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
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18
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Vogler M, Karan R, Renn D, Vancea A, Vielberg MT, Grötzinger SW, DasSarma P, DasSarma S, Eppinger J, Groll M, Rueping M. Crystal Structure and Active Site Engineering of a Halophilic γ-Carbonic Anhydrase. Front Microbiol 2020; 11:742. [PMID: 32411108 PMCID: PMC7199487 DOI: 10.3389/fmicb.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/30/2020] [Indexed: 11/27/2022] Open
Abstract
Environments previously thought to be uninhabitable offer a tremendous wealth of unexplored microorganisms and enzymes. In this paper, we present the discovery and characterization of a novel γ-carbonic anhydrase (γ-CA) from the polyextreme Red Sea brine pool Discovery Deep (2141 m depth, 44.8°C, 26.2% salt) by single-cell genome sequencing. The extensive analysis of the selected gene helps demonstrate the potential of this culture-independent method. The enzyme was expressed in the bioengineered haloarchaeon Halobacterium sp. NRC-1 and characterized by X-ray crystallography and mutagenesis. The 2.6 Å crystal structure of the protein shows a trimeric arrangement. Within the γ-CA, several possible structural determinants responsible for the enzyme's salt stability could be highlighted. Moreover, the amino acid composition on the protein surface and the intra- and intermolecular interactions within the protein differ significantly from those of its close homologs. To gain further insights into the catalytic residues of the γ-CA enzyme, we created a library of variants around the active site residues and successfully improved the enzyme activity by 17-fold. As several γ-CAs have been reported without measurable activity, this provides further clues as to critical residues. Our study reveals insights into the halophilic γ-CA activity and its unique adaptations. The study of the polyextremophilic carbonic anhydrase provides a basis for outlining insights into strategies for salt adaptation, yielding enzymes with industrially valuable properties, and the underlying mechanisms of protein evolution.
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Affiliation(s)
- Malvina Vogler
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Ram Karan
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Stefan W. Grötzinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Priya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shiladitya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jörg Eppinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael Groll
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Magnus Rueping
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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19
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DasSarma S, DasSarma P, Laye VJ, Schwieterman EW. Extremophilic models for astrobiology: haloarchaeal survival strategies and pigments for remote sensing. Extremophiles 2019; 24:31-41. [PMID: 31463573 DOI: 10.1007/s00792-019-01126-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022]
Abstract
Recent progress in extremophile biology, exploration of planetary bodies in the solar system, and the detection and characterization of extrasolar planets are leading to new insights in the field of astrobiology and possible distribution of life in the universe. Among the many extremophiles on Earth, the halophilic Archaea (Haloarchaea) are especially attractive models for astrobiology, being evolutionarily ancient and physiologically versatile, potentially surviving in a variety of planetary environments and with relevance for in situ life detection. Haloarchaea are polyextremophilic with tolerance of saturating salinity, anaerobic conditions, high levels of ultraviolet and ionizing radiation, subzero temperatures, desiccation, and toxic ions. Haloarchaea survive launches into Earth's stratosphere encountering conditions similar to those found on the surface of Mars. Studies of their unique proteins are revealing mechanisms permitting activity and function in high ionic strength, perchlorates, and subzero temperatures. Haloarchaea also produce spectacular blooms visible from space due to synthesis of red-orange isoprenoid carotenoids used for photoprotection and photorepair processes and purple retinal chromoproteins for phototrophy and phototaxis. Remote sensing using visible and infrared spectroscopy has shown that haloarchaeal pigments exhibit both a discernable peak of absorption and a reflective "green edge". Since the pigments produce remotely detectable features, they may influence the spectrum from an inhabited exoplanet imaged by a future large space-based telescope. In this review, we focus primarily on studies of two Haloarchaea, Halobacterium sp. NRC-1 and Halorubrum lacusprofundi.
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Affiliation(s)
- Shiladitya DasSarma
- Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Priya DasSarma
- Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Victoria J Laye
- Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Edward W Schwieterman
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA
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20
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Kumar R, Goomber S, Kaur J. Engineering lipases for temperature adaptation: Structure function correlation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140261. [PMID: 31401312 DOI: 10.1016/j.bbapap.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 01/13/2023]
Abstract
Bacillus lipases are industrially attractive enzymes due to their broad substrate specificity and optimum alkaline pH. However, narrow temperature range of action and low thermostability restrain their optimal use and thus, necessitate attention. Several laboratories are engaged in protein engineering of Bacillus lipases to generate variants with improved attributes for decades using techniques such as directed evolution or rational design. This review summarizes the effect of mutations on the conformational changes through in silico modeling and their manifestation with respect to various biochemical parameters. Various studies have been put together to develop a perspective on the molecular basis of biocatalysis of lipases holding industrial importance.
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Affiliation(s)
- Rakesh Kumar
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; Department of Microbiology and Cell Biology, Indian Institute Of Science, Bangalore, Karnataka 560012, India
| | - Shelly Goomber
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; National Institute of Malaria Research, Dwarka, New Delhi, Delhi 110077, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh 160014, India.
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21
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Torregrosa-Crespo J, Pire C, Martínez-Espinosa RM, Bergaust L. Denitrifying haloarchaea within the genus Haloferax display divergent respiratory phenotypes, with implications for their release of nitrogenous gases. Environ Microbiol 2018; 21:427-436. [PMID: 30421557 DOI: 10.1111/1462-2920.14474] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/05/2018] [Indexed: 11/30/2022]
Abstract
Haloarchaea are extremophiles, generally thriving at high temperatures and salt concentrations, thus, with limited access to oxygen. As a strategy to maintain a respiratory metabolism, many halophilic archaea are capable of denitrification. Among them are members of the genus Haloferax, which are abundant in saline/hypersaline environments. Three reported haloarchaeal denitrifiers, Haloferax mediterranei, Haloferax denitrificans and Haloferax volcanii, were characterized with respect to their denitrification phenotype. A semi-automatic incubation system was used to monitor the depletion of electron acceptors and accumulation of gaseous intermediates in batch cultures under a range of conditions. Out of the species tested, only H. mediterranei was able to consistently reduce all available N-oxyanions to N2 , while the other two released significant amounts of NO and N2 O, which affect tropospheric and stratospheric chemistries respectively. The prevalence and magnitude of hypersaline ecosystems are on the rise due to climate change and anthropogenic activity. Thus, the biology of halophilic denitrifiers is inherently interesting, due to their contribution to the global nitrogen cycle, and potential application in bioremediation. This work is the first detailed physiological study of denitrification in haloarchaea, and as such a seed for our understanding of the drivers of nitrogen turnover in hypersaline systems.
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Affiliation(s)
- Javier Torregrosa-Crespo
- Departamento de Agroquímica y Bioquímica, División de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Alicante, Carretera San Vicente del Raspeig s/n - 03690 San Vicente del Raspeig, Alicante, Spain
| | - Carmen Pire
- Departamento de Agroquímica y Bioquímica, División de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Alicante, Carretera San Vicente del Raspeig s/n - 03690 San Vicente del Raspeig, Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Departamento de Agroquímica y Bioquímica, División de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Alicante, Carretera San Vicente del Raspeig s/n - 03690 San Vicente del Raspeig, Alicante, Spain
| | - Linda Bergaust
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences. Chr. M, Falsens vei 1 - 1430, Ås, Norway
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22
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Cold survival strategies for bacteria, recent advancement and potential industrial applications. Arch Microbiol 2018; 201:1-16. [PMID: 30478730 DOI: 10.1007/s00203-018-1602-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/04/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022]
Abstract
Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.
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23
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See-Too WS, Convey P, Pearce DA, Chan KG. Characterization of a novel N-acylhomoserine lactonase, AidP, from Antarctic Planococcus sp. Microb Cell Fact 2018; 17:179. [PMID: 30445965 PMCID: PMC6240239 DOI: 10.1186/s12934-018-1024-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 11/07/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND N-acylhomoserine lactones (AHLs) are well-studied signalling molecules produced by some Gram-negative Proteobacteria for bacterial cell-to-cell communication or quorum sensing. We have previously demonstrated the degradation of AHLs by an Antarctic bacterium, Planococcus versutus L10.15T, at low temperature through the production of an AHL lactonase. In this study, we cloned the AHL lactonase gene and characterized the purified novel enzyme. RESULTS Rapid resolution liquid chromatography analysis indicated that purified AidP possesses high AHL-degrading activity on unsubstituted, and 3-oxo substituted homoserine lactones. Liquid chromatography-mass spectrometry analysis confirmed that AidP functions as an AHL lactonase that hydrolyzes the ester bond of the homoserine lactone ring of AHLs. Multiple sequence alignment analysis and phylogenetic analysis suggested that the aidP gene encodes a novel AHL lactonase enzyme. The amino acid composition analysis of aidP and the homologous genes suggested that it might be a cold-adapted enzyme, however, the optimum temperature is 28 °C, even though the thermal stability is low (reduced drastically above 32 °C). Branch-site analysis of several aidP genes of Planococcus sp. branch on the phylogenetic trees also showed evidence of episodic positive selection of the gene in cold environments. Furthermore, we demonstrated the effects of covalent and ionic bonding, showing that Zn2+ is important for activity of AidP in vivo. The pectinolytic inhibition assay confirmed that this enzyme attenuated the pathogenicity of the plant pathogen Pectobacterium carotovorum in Chinese cabbage. CONCLUSION We demonstrated that AidP is effective in attenuating the pathogenicity of P. carotovorum, a plant pathogen that causes soft-rot disease. This anti-quorum sensing agent is an enzyme with low thermal stability that degrades the bacterial signalling molecules (AHLs) that are produced by many pathogens. Since the enzyme is most active below human body temperature (below 28 °C), and lose its activity drastically above 32 °C, the results of a pectinolytic inhibition assay using Chinese cabbage indicated the potential of this anti-quorum sensing agent to be safely applied in the field trials.
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Affiliation(s)
- Wah Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- National Antarctic Research Centre, IPS Building, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Peter Convey
- National Antarctic Research Centre, IPS Building, University Malaya, 50603, Kuala Lumpur, Malaysia
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - David A Pearce
- National Antarctic Research Centre, IPS Building, University Malaya, 50603, Kuala Lumpur, Malaysia
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 OET, UK
- Applied Sciences, University of Northumbria at Newcastle, Newcastle-upon-Tyne, NE1 8ST, UK
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- International Genome Centre, Jiangsu University, Zhenjiang, China.
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Mokashe N, Chaudhari B, Patil U. Operative utility of salt-stable proteases of halophilic and halotolerant bacteria in the biotechnology sector. Int J Biol Macromol 2018; 117:493-522. [DOI: 10.1016/j.ijbiomac.2018.05.217] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 09/30/2022]
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Laye VJ, DasSarma S. An Antarctic Extreme Halophile and Its Polyextremophilic Enzyme: Effects of Perchlorate Salts. ASTROBIOLOGY 2018; 18:412-418. [PMID: 29189043 PMCID: PMC5910040 DOI: 10.1089/ast.2017.1766] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/26/2017] [Indexed: 06/07/2023]
Abstract
Effects of perchlorate salts prevalent on the surface of Mars are of significant interest to astrobiology from the perspective of potential life on the Red Planet. Halorubrum lacusprofundi, a cold-adapted halophilic Antarctic archaeon, was able to grow anaerobically on 0.04 M concentration of perchlorate. With increasing concentrations of perchlorate, growth was inhibited, with half-maximal growth rate in ca. 0.3 M NaClO4 and 0.1 M Mg(ClO4)2 under aerobic conditions. Magnesium ions were also inhibitory for growth, but at considerably higher concentrations, with half-maximal growth rate above 1 M. For a purified halophilic β-galactosidase enzyme of H. lacusprofundi expressed in Halobacterium sp. NRC-1, 50% inhibition of catalytic activity was observed at 0.88 M NaClO4 and 0.13 M Mg(ClO4)2. Magnesium ions were a more potent inhibitor of the enzyme than of cell growth. Steady-state kinetic analysis showed that Mg(ClO4)2 acts as a mixed inhibitor (KI = 0.04 M), with magnesium alone being a competitive inhibitor (KI = 0.3 M) and perchlorate alone acting as a very weak noncompetitive inhibitor (KI = 2 M). Based on the estimated concentrations of perchlorate salts on the surface of Mars, our results show that neither sodium nor magnesium perchlorates would significantly inhibit growth and enzyme activity of halophiles. This is the first study of perchlorate effects on a purified enzyme. Key Words: Halophilic archaea-Perchlorate-Enzyme inhibition-Magnesium. Astrobiology 18, 412-418.
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Affiliation(s)
- Victoria J Laye
- University of Maryland School of Medicine, Institute of Marine and Environmental Technology , Baltimore, Maryland
| | - Shiladitya DasSarma
- University of Maryland School of Medicine, Institute of Marine and Environmental Technology , Baltimore, Maryland
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26
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Hashim NHF, Mahadi NM, Illias RM, Feroz SR, Abu Bakar FD, Murad AMA. Biochemical and structural characterization of a novel cold-active esterase-like protein from the psychrophilic yeast Glaciozyma antarctica. Extremophiles 2018; 22:607-616. [DOI: 10.1007/s00792-018-1021-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 03/11/2018] [Indexed: 02/04/2023]
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Kumar A, Alam A, Tripathi D, Rani M, Khatoon H, Pandey S, Ehtesham NZ, Hasnain SE. Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome. Semin Cell Dev Biol 2018; 84:147-157. [PMID: 29331642 DOI: 10.1016/j.semcdb.2018.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/01/2017] [Accepted: 01/09/2018] [Indexed: 02/02/2023]
Abstract
The biological paradox about how extremophiles persist at extreme ecological conditions throws a fascinating picture of the enormous potential of a single cell to adapt to homeostatic conditions in order to propagate. Unicellular organisms face challenges from both environmental factors and the ecological niche provided by the host tissue. Although the existence of extremophiles and their physiological properties were known for a long time, availability of whole genome sequence has catapulted the study on mechanisms of adaptation and the underlying principles that have enabled these unique organisms to withstand evolutionary and environmental pressures. Comparative genomics has shown that extremophiles possess the unique set of genes and proteins that empower them with biochemical machinery necessary to thrive in extreme environments. The presence of these proteins safeguards the cell against a wide array of extreme conditions such as temperature, pressure, radiations, chemicals, drugs etc. An insight into these adaptive mechanisms in extremophiles may help us to devise strategies to alter the genes and proteins that may have therapeutic potential and commercial value. Here we present an overview of the various adaptations in extremophiles. We also try to explain how mycobacterium channelizes its proteome to survive in stress conditions posed by host immune system.
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Affiliation(s)
- Ashutosh Kumar
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Anwar Alam
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Deeksha Tripathi
- Department of Microbiology, Central University of Rajasthan, Bandar Sindri, Ajmer, Rajasthan, India
| | - Mamta Rani
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, India
| | - Hafeeza Khatoon
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Saurabh Pandey
- National Institute of Pathology, Safdarjang Hospital Campus, New Delhi, India
| | - Nasreen Z Ehtesham
- National Institute of Pathology, Safdarjang Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India; JH-Institute of Molecular Medicine, Hamdard Nagar, New Delhi, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India.
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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; 114:12530-12535. [PMID: 29109294 DOI: 10.1073/pnas.1711542114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [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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Structural and Mechanistic Insights into the Improvement of the Halotolerance of a Marine Microbial Esterase by Increasing Intra- and Interdomain Hydrophobic Interactions. Appl Environ Microbiol 2017; 83:AEM.01286-17. [PMID: 28733281 DOI: 10.1128/aem.01286-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/12/2017] [Indexed: 11/20/2022] Open
Abstract
Halotolerant enzymes are beneficial for industrial processes requiring high salt concentrations and low water activity. Most halophilic proteins are evolved to have reduced hydrophobic interactions on the surface and in the hydrophobic cores for their haloadaptation. However, in this study, we improved the halotolerance of a thermolabile esterase, E40, by increasing intraprotein hydrophobic interactions. E40 was quite unstable in buffers containing more than 0.3 M NaCl, and its kcat and substrate affinity were both significantly reduced in 0.5 M NaCl. By introducing hydrophobic residues in loop 1 of the CAP domain and/or α7 of the catalytic domain in E40, we obtained several mutants with improved halotolerance, and the M3 S202W I203F mutant was the most halotolerant. ("M3" represents a mutation in loop 1 of the CAP domain in which residues R22-K23-T24 of E40 are replaced by residues Y22-K23-H24-L25-S26 of Est2.) Then we solved the crystal structures of the S202W I203F and M3 S202W I203F mutants to reveal the structural basis for their improved halotolerance. Structural analysis revealed that the introduction of hydrophobic residues W202 and F203 in α7 significantly improved E40 halotolerance by strengthening intradomain hydrophobic interactions of F203 with W202 and other residues in the catalytic domain. By further introducing hydrophobic residues in loop 1, the M3 S202W I203F mutant became more rigid and halotolerant due to the formation of additional interdomain hydrophobic interactions between the introduced Y22 in loop 1 and W204 in α7. These results indicate that increasing intraprotein hydrophobic interactions is also a way to improve the halotolerance of enzymes with industrial potential under high-salt conditions.IMPORTANCE Esterases and lipases for industrial application are often subjected to harsh conditions such as high salt concentrations, low water activity, and the presence of organic solvents. However, reports on halotolerant esterases and lipases are limited, and the underlying mechanism for their halotolerance is still unclear due to the lack of structures. In this study, we focused on the improvement of the halotolerance of a salt-sensitive esterase, E40, and the underlying mechanism. The halotolerance of E40 was significantly improved by introducing hydrophobic residues. Comparative structural analysis of E40 and its halotolerant mutants revealed that increased intraprotein hydrophobic interactions make these mutants more rigid and more stable than the wild type against high concentrations of salts. This study shows a new way to improve enzyme halotolerance, which is helpful for protein engineering of salt-sensitive enzymes.
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Medvedev KE, Kolchanov NA, Afonnikov DA. Identification of residues of the archaeal RNA-binding Nip7 proteins specific to environmental conditions. J Bioinform Comput Biol 2017; 15:1650036. [DOI: 10.1142/s0219720016500360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The understanding of biological and molecular mechanisms providing survival of cells under extreme temperatures and pressures will help to answer fundamental questions related to the origin of life and to design of biotechnologically important enzymes with new properties. Here, we analyze amino acid sequences of the Nip7 proteins from 35 archaeal species to identify positions containing mutations specific to the hydrostatic pressure and temperature of organism’s habitat. The number of such positions related to pressure change is much lower than related to temperature change. The results suggest that adaptation to temperature changes of the Nip7 protein cause more pronounced modifications in sequence and structure, than to the pressure changes. Structural analysis of residues at these positions demonstrated their involvement in salt-bridge formation, which may reflect the importance of protein structure stabilization by salt-bridges at extreme environmental conditions.
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Affiliation(s)
- Kirill E. Medvedev
- Department of Biophysics, University of Texas Southwestern, Medical Center, Dallas, Texas 75390, USA
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl., 1, Moscow 123182, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Dmitry A. Afonnikov
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
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31
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Zhang Y, Hao J, Zhang YQ, Chen XL, Xie BB, Shi M, Zhou BC, Zhang YZ, Li PY. Identification and Characterization of a Novel Salt-Tolerant Esterase from the Deep-Sea Sediment of the South China Sea. Front Microbiol 2017; 8:441. [PMID: 28386249 PMCID: PMC5362591 DOI: 10.3389/fmicb.2017.00441] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/03/2017] [Indexed: 12/02/2022] Open
Abstract
Marine esterases play an important role in marine organic carbon degradation and cycling. Halotolerant esterases from the sea may have good potentials in industrial processes requiring high salts. Although a large number of marine esterases have been characterized, reports on halotolerant esterases are only a few. Here, a fosmid library containing 7,200 clones was constructed from a deep-sea sediment sample from the South China Sea. A gene H8 encoding an esterase was identified from this library by functional screening and expressed in Escherichia coli. Phylogenetic analysis showed that H8 is a new member of family V of bacterial lipolytic enzymes. H8 could effectively hydrolyze short-chain monoesters (C4–C10), with the highest activity toward p-nitrophenyl hexanoate. The optimal temperature and pH for H8 activity were 35°C and pH 10.0, respectively. H8 had high salt tolerance, remaining stable in 4.5 M NaCl, which suggests that H8 is well adapted to the marine saline environment and that H8 may have industrial potentials. Unlike reported halophilic/halotolerant enzymes with high acidic/basic residue ratios and low pI values, H8 contains a large number of basic residues, leading to its high basic/acidic residue ratio and high predicted pI (9.09). Moreover, more than 10 homologous sequences with similar basic/acidic residue ratios and predicted pI values were found in database, suggesting that H8 and its homologs represent a new group of halotolerant esterases. We also investigated the role of basic residues in H8 halotolerance by site-directed mutation. Mutation of Arg195, Arg203 or Arg236 to acidic Glu significantly decreased the activity and/or stability of H8 under high salts, suggesting that these basic residues play a role in the salt tolerance of H8. These results shed light on marine bacterial esterases and halotolerant enzymes.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University Jinan, China
| | - Jie Hao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University Jinan, China
| | - Yan-Qi Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University Jinan, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University Jinan, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University Jinan, China
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University Jinan, China
| | - Bai-Cheng Zhou
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University Jinan, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University Jinan, China
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Liao Y, Williams TJ, Walsh JC, Ji M, Poljak A, Curmi PMG, Duggin IG, Cavicchioli R. Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function. Sci Rep 2016; 6:34639. [PMID: 27708407 PMCID: PMC5052560 DOI: 10.1038/srep34639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/16/2016] [Indexed: 01/04/2023] Open
Abstract
No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
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Affiliation(s)
- Y Liao
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - T J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J C Walsh
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia.,The ithree institute, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - M Ji
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - A Poljak
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - P M G Curmi
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - I G Duggin
- The ithree institute, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - R Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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Anderson IJ, DasSarma P, Lucas S, Copeland A, Lapidus A, Del Rio TG, Tice H, Dalin E, Bruce DC, Goodwin L, Pitluck S, Sims D, Brettin TS, Detter JC, Han CS, Larimer F, Hauser L, Land M, Ivanova N, Richardson P, Cavicchioli R, DasSarma S, Woese CR, Kyrpides NC. Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34. Stand Genomic Sci 2016; 11:70. [PMID: 27617060 PMCID: PMC5018182 DOI: 10.1186/s40793-016-0194-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/03/2016] [Indexed: 01/26/2023] Open
Abstract
Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.
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Affiliation(s)
| | - Priya DasSarma
- Institute of Marine and Environmental Technology, Columbus Center, University of Maryland School of Medicine, University System of Maryland, Baltimore, MD 21202 USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | | | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Eileen Dalin
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - David C Bruce
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - David Sims
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Thomas S Brettin
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - John C Detter
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Cliff S Han
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Frank Larimer
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | | | | | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052 Australia
| | - Shiladitya DasSarma
- Institute of Marine and Environmental Technology, Columbus Center, University of Maryland School of Medicine, University System of Maryland, Baltimore, MD 21202 USA
| | - Carl R Woese
- B103 Chemical and Life Sciences Laboratory, University of Illinois at Urbana-Champaign, MC-110, 601 South Goodwin Avenue, Urbana, IL 61801 USA
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Chrismas NAM, Barker G, Anesio AM, Sánchez-Baracaldo P. Genomic mechanisms for cold tolerance and production of exopolysaccharides in the Arctic cyanobacterium Phormidesmis priestleyi BC1401. BMC Genomics 2016; 17:533. [PMID: 27485510 PMCID: PMC4971617 DOI: 10.1186/s12864-016-2846-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanobacteria are major primary producers in extreme cold ecosystems. Many lineages of cyanobacteria thrive in these harsh environments, but it is not fully understood how they survive in these conditions and whether they have evolved specific mechanisms of cold adaptation. Phormidesmis priestleyi is a cyanobacterium found throughout the cold biosphere (Arctic, Antarctic and alpine habitats). Genome sequencing of P. priestleyi BC1401, an isolate from a cryoconite hole on the Greenland Ice Sheet, has allowed for the examination of genes involved in cold shock response and production of extracellular polymeric substances (EPS). EPSs likely enable cyanobacteria to buffer the effects of extreme cold and by identifying mechanisms for EPS production in P. priestleyi BC1401 this study lays the way for investigating transcription and regulation of EPS production in an ecologically important cold tolerant cyanobacterium. RESULTS We sequenced the draft genome of P. priestleyi BC1401 and implemented a new de Bruijn graph visualisation approach combined with BLAST analysis to separate cyanobacterial contigs from a simple metagenome generated from non-axenic cultures. Comparison of known cold adaptation genes in P. priestleyi BC1401 with three relatives from other environments revealed no clear differences between lineages. Genes involved in EPS biosynthesis were identified from the Wzy- and ABC-dependent pathways. The numbers of genes involved in cell wall and membrane biogenesis in P. priestleyi BC1401 were typical relative to the genome size. A gene cluster implicated in biofilm formation was found homologous to the Wps system, although the intracellular signalling pathways by which this could be regulated remain unclear. CONCLUSIONS Results show that the genomic characteristics and complement of known cold shock genes in P. priestleyi BC1401 are comparable to related lineages from a wide variety of habitats, although as yet uncharacterised cold shock genes in this organism may still exist. EPS production by P. priestleyi BC1401 likely contributes to its ability to survive efficiently in cold environments, yet this mechanism is widely distributed throughout the cyanobacterial phylum. Discovering how these EPS related mechanisms are regulated may help explain why P. priestleyi BC1401 is so successful in cold environments where related lineages are not.
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Affiliation(s)
- Nathan A M Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS, UK.
| | - Gary Barker
- Cereal Genomics, School of Biological Sciences, University of Bristol, Bristol, BS8 1SS, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS, UK
| | - Patricia Sánchez-Baracaldo
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS, UK.
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Some like it hot, some like it cold: Temperature dependent biotechnological applications and improvements in extremophilic enzymes. Biotechnol Adv 2015; 33:1912-22. [DOI: 10.1016/j.biotechadv.2015.11.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/12/2015] [Accepted: 11/12/2015] [Indexed: 11/23/2022]
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36
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Point Mutation Ile137-Met Near Surface Conferred Psychrophilic Behaviour and Improved Catalytic Efficiency to Bacillus Lipase of 1.4 Subfamily. Appl Biochem Biotechnol 2015; 178:753-65. [DOI: 10.1007/s12010-015-1907-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
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Goomber S, Kumar A, Kaur J. Disruption of N terminus long range non covalent interactions shifted temp.opt 25°C to cold: Evolution of point mutant Bacillus lipase by error prone PCR. Gene 2015; 576:237-43. [PMID: 26456196 DOI: 10.1016/j.gene.2015.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/17/2015] [Accepted: 10/05/2015] [Indexed: 11/19/2022]
Abstract
Cold adapted enzymes have applications in detergent, textile, food, bioremediation and biotechnology processes. Bacillus lipases are 'generally recognized as safe' (GRAS) and hence are industrially attractive. Bacillus lipase of 1.4 subfamily are of lowest molecular weight and are reversibly unfolded due to absence of disulphide bonds. Therefore these are largely used to study energetic of protein stability that represents unfolding of native protein to fully unfolded state. In present study, metagenomically isolated Bacillus LipJ was laboratory evolved for cold adaptation by error Prone PCR. Library of variants were screened for high relative activity at low temperature of 10°C compared to native protein LipJ. Point mutant sequenced as Phe19→Leu was determined to be active at cold and was selected for extensive biochemical, biophysical characterization. Variant F19L showed its maximum activity at 10°C where parent protein LipJ had 20% relative activity. Psychrophilic nature of F19L was established with about 50% relative active at 5°C where native protein was frozen to act. Variant F19L showed no activity at temperature 40°C and above, establishing its thermolabile nature. Thermostability studies determined mutant to be unstable above 20°C and three fold decrease in its half life at 30°C compared to native protein. Far UV-CD and intrinsic fluorescence study demonstrated unstable tertiary structure of point variant F19L leading to its unfolding at low temperature of 20°C. Cold adaptation of mutant F19L is accompanied with increased specific activity. Mutant was catalytically more efficient with 1.3 fold increase in kcat. Homologue structure modelling predicted disruption of intersecondary hydrophobic core formed by aromatic ring of Phe19 with non polar residues placed at β3, β4, β5, β6, αF. Increased local flexibility of variant F19L explains molecular basis of its psychrophilic nature.
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Affiliation(s)
- Shelly Goomber
- Department of Biotechnology, Panjab University, Chandigarh 160014, India.
| | - Arbind Kumar
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
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38
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Badet T, Peyraud R, Raffaele S. Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae. FRONTIERS IN PLANT SCIENCE 2015; 6:776. [PMID: 26442085 DOI: 10.3389/fpls.2015.00776issn=1664-462x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/10/2015] [Indexed: 05/25/2023]
Abstract
Fungal plant pathogens produce secreted proteins adapted to function outside fungal cells to facilitate colonization of their hosts. In many cases such as for fungi from the Sclerotiniaceae family the repertoire and function of secreted proteins remains elusive. In the Sclerotiniaceae, whereas Sclerotinia sclerotiorum and Botrytis cinerea are cosmopolitan broad host-range plant pathogens, Sclerotinia borealis has a psychrophilic lifestyle with a low optimal growth temperature, a narrow host range and geographic distribution. To spread successfully, S. borealis must synthesize proteins adapted to function in its specific environment. The search for signatures of adaptation to S. borealis lifestyle may therefore help revealing proteins critical for colonization of the environment by Sclerotiniaceae fungi. Here, we analyzed amino acids usage and intrinsic protein disorder in alignments of groups of orthologous proteins from the three Sclerotiniaceae species. We found that enrichment in Thr, depletion in Glu and Lys, and low disorder frequency in hot loops are significantly associated with S. borealis proteins. We designed an index to report bias in these properties and found that high index proteins were enriched among secreted proteins in the three Sclerotiniaceae fungi. High index proteins were also enriched in function associated with plant colonization in S. borealis, and in in planta-induced genes in S. sclerotiorum. We highlight a novel putative antifreeze protein and a novel putative lytic polysaccharide monooxygenase identified through our pipeline as candidate proteins involved in colonization of the environment. Our findings suggest that similar protein signatures associate with S. borealis lifestyle and with secretion in the Sclerotiniaceae. These signatures may be useful for identifying proteins of interest as targets for the management of plant diseases.
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Affiliation(s)
- Thomas Badet
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France
| | - Rémi Peyraud
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France
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DasSarma S, DasSarma P. Halophiles and their enzymes: negativity put to good use. Curr Opin Microbiol 2015; 25:120-6. [PMID: 26066288 PMCID: PMC4729366 DOI: 10.1016/j.mib.2015.05.009] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 04/20/2015] [Accepted: 05/15/2015] [Indexed: 12/24/2022]
Abstract
Halophilic microorganisms possess stable enzymes that function in very high salinity, an extreme condition that leads to denaturation, aggregation, and precipitation of most other proteins. Genomic and structural analyses have established that the enzymes of halophilic Archaea and many halophilic Bacteria are negatively charged due to an excess of acidic over basic residues, and altered hydrophobicity, which enhance solubility and promote function in low water activity conditions. Here, we provide an update on recent bioinformatic analysis of predicted halophilic proteomes as well as experimental molecular studies on individual halophilic enzymes. Recent efforts on discovery and utilization of halophiles and their enzymes for biotechnology, including biofuel applications are also considered.
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Affiliation(s)
- Shiladitya DasSarma
- Institute of Marine and Environmental Technology, Department of Microbiology and Immunology, University of Maryland School of Medicine, 701 East Pratt Street, Columbus Center, Baltimore, MD 21202, USA.
| | - Priya DasSarma
- Institute of Marine and Environmental Technology, Department of Microbiology and Immunology, University of Maryland School of Medicine, 701 East Pratt Street, Columbus Center, Baltimore, MD 21202, USA
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40
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Carbon monoxide as a metabolic energy source for extremely halophilic microbes: implications for microbial activity in Mars regolith. Proc Natl Acad Sci U S A 2015; 112:4465-70. [PMID: 25831529 DOI: 10.1073/pnas.1424989112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbon monoxide occurs at relatively high concentrations (≥800 parts per million) in Mars' atmosphere, where it represents a potentially significant energy source that could fuel metabolism by a localized putative surface or near-surface microbiota. However, the plausibility of CO oxidation under conditions relevant for Mars in its past or at present has not been evaluated. Results from diverse terrestrial brines and saline soils provide the first documentation, to our knowledge, of active CO uptake at water potentials (-41 MPa to -117 MPa) that might occur in putative brines at recurrent slope lineae (RSL) on Mars. Results from two extremely halophilic isolates complement the field observations. Halorubrum str. BV1, isolated from the Bonneville Salt Flats, Utah (to our knowledge, the first documented extremely halophilic CO-oxidizing member of the Euryarchaeota), consumed CO in a salt-saturated medium with a water potential of -39.6 MPa; activity was reduced by only 28% relative to activity at its optimum water potential of -11 MPa. A proteobacterial isolate from hypersaline Mono Lake, California, Alkalilimnicola ehrlichii MLHE-1, also oxidized CO at low water potentials (-19 MPa), at temperatures within ranges reported for RSL, and under oxic, suboxic (0.2% oxygen), and anoxic conditions (oxygen-free with nitrate). MLHE-1 was unaffected by magnesium perchlorate or low atmospheric pressure (10 mbar). These results collectively establish the potential for microbial CO oxidation under conditions that might obtain at local scales (e.g., RSL) on contemporary Mars and at larger spatial scales earlier in Mars' history.
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41
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Badet T, Peyraud R, Raffaele S. Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae. FRONTIERS IN PLANT SCIENCE 2015; 6:776. [PMID: 26442085 PMCID: PMC4585107 DOI: 10.3389/fpls.2015.00776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/10/2015] [Indexed: 05/04/2023]
Abstract
Fungal plant pathogens produce secreted proteins adapted to function outside fungal cells to facilitate colonization of their hosts. In many cases such as for fungi from the Sclerotiniaceae family the repertoire and function of secreted proteins remains elusive. In the Sclerotiniaceae, whereas Sclerotinia sclerotiorum and Botrytis cinerea are cosmopolitan broad host-range plant pathogens, Sclerotinia borealis has a psychrophilic lifestyle with a low optimal growth temperature, a narrow host range and geographic distribution. To spread successfully, S. borealis must synthesize proteins adapted to function in its specific environment. The search for signatures of adaptation to S. borealis lifestyle may therefore help revealing proteins critical for colonization of the environment by Sclerotiniaceae fungi. Here, we analyzed amino acids usage and intrinsic protein disorder in alignments of groups of orthologous proteins from the three Sclerotiniaceae species. We found that enrichment in Thr, depletion in Glu and Lys, and low disorder frequency in hot loops are significantly associated with S. borealis proteins. We designed an index to report bias in these properties and found that high index proteins were enriched among secreted proteins in the three Sclerotiniaceae fungi. High index proteins were also enriched in function associated with plant colonization in S. borealis, and in in planta-induced genes in S. sclerotiorum. We highlight a novel putative antifreeze protein and a novel putative lytic polysaccharide monooxygenase identified through our pipeline as candidate proteins involved in colonization of the environment. Our findings suggest that similar protein signatures associate with S. borealis lifestyle and with secretion in the Sclerotiniaceae. These signatures may be useful for identifying proteins of interest as targets for the management of plant diseases.
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Affiliation(s)
- Thomas Badet
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594Castanet-Tolosan, France
| | - Rémi Peyraud
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594Castanet-Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594Castanet-Tolosan, France
- *Correspondence: Sylvain Raffaele, Laboratoire des Interactions Plante Micro-organismes, 24 Chemin de Borde Rouge – Auzeville, 31326 Castanet Tolosan, France
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Molecular bases of protein halotolerance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:850-8. [DOI: 10.1016/j.bbapap.2014.02.018] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 02/04/2023]
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De Maayer P, Anderson D, Cary C, Cowan DA. Some like it cold: understanding the survival strategies of psychrophiles. EMBO Rep 2014; 15:508-17. [PMID: 24671034 DOI: 10.1002/embr.201338170] [Citation(s) in RCA: 296] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Much of the Earth's surface, both marine and terrestrial, is either periodically or permanently cold. Although habitats that are largely or continuously frozen are generally considered to be inhospitable to life, psychrophilic organisms have managed to survive in these environments. This is attributed to their innate adaptive capacity to cope with cold and its associated stresses. Here, we review the various environmental, physiological and molecular adaptations that psychrophilic microorganisms use to thrive under adverse conditions. We also discuss the impact of modern "omic" technologies in developing an improved understanding of these adaptations, highlighting recent work in this growing field.
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Affiliation(s)
- Pieter De Maayer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
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44
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Fedyukina DV, Jennaro TS, Cavagnero S. Charge segregation and low hydrophobicity are key features of ribosomal proteins from different organisms. J Biol Chem 2014; 289:6740-6750. [PMID: 24398678 PMCID: PMC3945335 DOI: 10.1074/jbc.m113.507707] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Ribosomes are large and highly charged macromolecular complexes consisting of RNA and proteins. Here, we address the electrostatic and nonpolar properties of ribosomal proteins that are important for ribosome assembly and interaction with other cellular components and may influence protein folding on the ribosome. We examined 50 S ribosomal subunits from 10 species and found a clear distinction between the net charge of ribosomal proteins from halophilic and non-halophilic organisms. We found that ∼67% ribosomal proteins from halophiles are negatively charged, whereas only up to ∼15% of ribosomal proteins from non-halophiles share this property. Conversely, hydrophobicity tends to be lower for ribosomal proteins from halophiles than for the corresponding proteins from non-halophiles. Importantly, the surface electrostatic potential of ribosomal proteins from all organisms, especially halophiles, has distinct positive and negative regions across all the examined species. Positively and negatively charged residues of ribosomal proteins tend to be clustered in buried and solvent-exposed regions, respectively. Hence, the majority of ribosomal proteins is characterized by a significant degree of intramolecular charge segregation, regardless of the organism of origin. This key property enables the ribosome to accommodate proteins within its complex scaffold regardless of their overall net charge.
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Affiliation(s)
- Daria V Fedyukina
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Theodore S Jennaro
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706.
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45
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Oswald VF, Chen W, Harvilla PB, Magyar JS. Overexpression, purification, and enthalpy of unfolding of ferricytochrome c552 from a psychrophilic microorganism. J Inorg Biochem 2014; 131:76-8. [PMID: 24275750 PMCID: PMC3885257 DOI: 10.1016/j.jinorgbio.2013.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 11/04/2013] [Accepted: 11/05/2013] [Indexed: 11/28/2022]
Abstract
The psychrophilic, hydrocarbonoclastic microorganism Colwellia psychrerythraea is important in global nutrient cycling and bioremediation. In order to investigate how this organism can live so efficiently at low temperatures (~4°C), thermal denaturation studies of a small electron transfer protein from Colwellia were performed. Colwellia cytochrome c552 was overexpressed in Escherichia coli, isolated, purified, and characterized by UV-visible absorption spectroscopy. The melting temperature (Tm) and the van't Hoff enthalpy (ΔHvH) were determined. These values suggest an unexpectedly high stability for this psychrophilic cytochrome.
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Affiliation(s)
- Victoria F Oswald
- Department of Chemistry, Barnard College, Columbia University, New York, NY 10027, United States
| | - WeiTing Chen
- Department of Chemistry, Barnard College, Columbia University, New York, NY 10027, United States
| | - Paul B Harvilla
- Department of Chemistry, Barnard College, Columbia University, New York, NY 10027, United States; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, United States
| | - John S Magyar
- Department of Chemistry, Barnard College, Columbia University, New York, NY 10027, United States.
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46
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Protein adaptations in archaeal extremophiles. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:373275. [PMID: 24151449 PMCID: PMC3787623 DOI: 10.1155/2013/373275] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/26/2013] [Accepted: 08/14/2013] [Indexed: 12/25/2022]
Abstract
Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.
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