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Genomic and Transcriptomic Analysis Reveal Multiple Strategies for the Cadmium Tolerance in Vibrio parahaemolyticus N10-18 Isolated from Aquatic Animal Ostrea gigas Thunberg. Foods 2022; 11:foods11233777. [PMID: 36496584 PMCID: PMC9741282 DOI: 10.3390/foods11233777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/05/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
The waterborne Vibrio parahaemolyticus can cause acute gastroenteritis, wound infection, and septicemia in humans. Pollution of heavy metals in aquatic environments is proposed to link high incidence of the multidrug-resistant (MDR) pathogen. Nevertheless, the genome evolution and heavy metal tolerance mechanism of V. parahaemolyticus in aquatic animals remain to be largely unveiled. Here, we overcome the limitation by characterizing an MDR V. parahaemolyticus N10-18 isolate with high cadmium (Cd) tolerance using genomic and transcriptomic techniques. The draft genome sequence (4,910,080 bp) of V. parahaemolyticus N10-18 recovered from Ostrea gigas Thunberg was determined, and 722 of 4653 predicted genes had unknown function. Comparative genomic analysis revealed mobile genetic elements (n = 11) and heavy metal and antibiotic-resistance genes (n = 38 and 7). The bacterium significantly changed cell membrane structure to resist the Cd2+ (50 μg/mL) stress (p < 0.05). Comparative transcriptomic analysis revealed seven significantly altered metabolic pathways elicited by the stress. The zinc/Cd/mercury/lead transportation and efflux and the zinc ATP-binding cassette (ABC) transportation were greatly enhanced; metal and iron ABC transportation and thiamine metabolism were also up-regulated; conversely, propanoate metabolism and ribose and maltose ABC transportation were inhibited (p < 0.05). The results of this study demonstrate multiple strategies for the Cd tolerance in V. parahaemolyticus.
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Nizovoy P, Bellora N, Haridas S, Sun H, Daum C, Barry K, Grigoriev IV, Libkind D, Connell LB, Moliné M. Unique genomic traits for cold adaptation in Naganishia vishniacii, a polyextremophile yeast isolated from Antarctica. FEMS Yeast Res 2020; 21:6000217. [PMID: 33232451 DOI: 10.1093/femsyr/foaa056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/15/2020] [Indexed: 12/15/2022] Open
Abstract
Cold environments impose challenges to organisms. Polyextremophile microorganisms can survive in these conditions thanks to an array of counteracting mechanisms. Naganishia vishniacii, a yeast species hitherto only isolated from McMurdo Dry Valleys, Antarctica, is an example of a polyextremophile. Here we present the first draft genomic sequence of N. vishniacii. Using comparative genomics, we unraveled unique characteristics of cold associated adaptations. 336 putative genes (total: 6183) encoding solute transfers and chaperones, among others, were absent in sister species. Among genes shared by N. vishniacii and its closest related species we found orthologs encompassing possible evidence of positive selection (dN/dS > 1). Genes associated with photoprotection were found in agreement with high solar irradiation exposure. Also genes coding for desaturases and genomic features associated with cold tolerance (i.e. trehalose synthesis and lipid metabolism) were explored. Finally, biases in amino acid usage (namely an enrichment of glutamine and a trend in proline reduction) were observed, possibly conferring increased protein flexibility. To the best of our knowledge, such a combination of mechanisms for cold tolerance has not been previously reported in fungi, making N. vishniacii a unique model for the study of the genetic basis and evolution of cold adaptation strategies.
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Affiliation(s)
- Paula Nizovoy
- Centro de Referencia en Levaduras y Tecnologı́a Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologı́as Biológicas y Geoambientales (IPATEC) - CONICET / Universidad Nacional del Comahue, San Carlos de Bariloche, Rı́o Negro 8400, Argentina
| | - Nicolás Bellora
- Centro de Referencia en Levaduras y Tecnologı́a Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologı́as Biológicas y Geoambientales (IPATEC) - CONICET / Universidad Nacional del Comahue, San Carlos de Bariloche, Rı́o Negro 8400, Argentina
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598, USA
| | - Hui Sun
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnologı́a Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologı́as Biológicas y Geoambientales (IPATEC) - CONICET / Universidad Nacional del Comahue, San Carlos de Bariloche, Rı́o Negro 8400, Argentina
| | - Laurie B Connell
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Martín Moliné
- Centro de Referencia en Levaduras y Tecnologı́a Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologı́as Biológicas y Geoambientales (IPATEC) - CONICET / Universidad Nacional del Comahue, San Carlos de Bariloche, Rı́o Negro 8400, Argentina
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Perera E, Rodriguez-Viera L, Montero-Alejo V, Perdomo-Morales R. Crustacean Proteases and Their Application in Debridement. Trop Life Sci Res 2020; 31:187-209. [PMID: 32922675 PMCID: PMC7470474 DOI: 10.21315/tlsr2020.31.2.10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Digestive proteases from marine organisms have been poorly applied to biomedicine. Exceptions are trypsin and other digestive proteases from a few cold-adapted or temperate fish and crustacean species. These enzymes are more efficient than enzymes from microorganism and higher vertebrates that have been used traditionally. However, the biomedical potential of digestive proteases from warm environment species has received less research attention. This review aims to provide an overview of this unrealised biomedical potential, using the debridement application as a paradigm. Debridement is intended to remove nonviable, necrotic and contaminated tissue, as well as fibrin clots, and is a key step in wound treatment. We discuss the physiological role of enzymes in wound healing, the use of exogenous enzymes in debridement, and the limitations of cold-adapted enzymes such as their poor thermal stability. We show that digestive proteases from tropical crustaceans may have advantages over their cold-adapted counterparts for this and similar uses. Differences in thermal stability, auto-proteolytic stability, and susceptibility to proteinase inhibitors are discussed. Furthermore, it is proposed that the feeding behaviour of the source organism may direct the evaluation of enzymes for particular applications, as digestive proteases have evolved to fill a wide variety of feeding habitats, natural substrates, and environmental conditions. We encourage more research on the biomedical application of digestive enzymes from tropical marine crustaceans.
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Affiliation(s)
- Erick Perera
- Nutrigenomics and Fish Growth Endocrinology, Institute of Aquaculture Torre de la Sal, IATS-CSIC, Castellón, Valencia, Spain
| | | | - Vivian Montero-Alejo
- Department of Biochemistry, Center for Pharmaceuticals Research and Development, Havana, Cuba
| | - Rolando Perdomo-Morales
- Department of Biochemistry, Center for Pharmaceuticals Research and Development, Havana, Cuba
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Zeng J, Huang Z. From Levinthal's Paradox to the Effects of Cell Environmental Perturbation on Protein Folding. Curr Med Chem 2018; 26:7537-7554. [PMID: 30332937 DOI: 10.2174/0929867325666181017160857] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/04/2018] [Accepted: 08/03/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND The rapidly increasing number of known protein sequences calls for more efficient methods to predict the Three-Dimensional (3D) structures of proteins, thus providing basic knowledge for rational drug design. Understanding the folding mechanism of proteins is valuable for predicting their 3D structures and for designing proteins with new functions and medicinal applications. Levinthal's paradox is that although the astronomical number of conformations possible even for proteins as small as 100 residues cannot be fully sampled, proteins in nature normally fold into the native state within timescales ranging from microseconds to hours. These conflicting results reveal that there are factors in organisms that can assist in protein folding. METHODS In this paper, we selected a crowded cell-like environment and temperature, and the top three Posttranslational Modifications (PTMs) as examples to show that Levinthal's paradox does not reflect the folding mechanism of proteins. We then revealed the effects of these factors on protein folding. RESULTS The results summarized in this review indicate that a crowded cell-like environment, temperature, and the top three PTMs reshape the Free Energy Landscapes (FELs) of proteins, thereby regulating the folding process. The balance between entropy and enthalpy is the key to understanding the effect of the crowded cell-like environment and PTMs on protein folding. In addition, the stability/flexibility of proteins is regulated by temperature. CONCLUSION This paper concludes that the cellular environment could directly intervene in protein folding. The long-term interactions of the cellular environment and sequence evolution may enable proteins to fold efficiently. Therefore, to correctly understand the folding mechanism of proteins, the effect of the cellular environment on protein folding should be considered.
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Affiliation(s)
- Juan Zeng
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, Guangdong 523808, China.,Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Zunnan Huang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, Guangdong 523808, China
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Raymond-Bouchard I, Goordial J, Zolotarov Y, Ronholm J, Stromvik M, Bakermans C, Whyte LG. Conserved genomic and amino acid traits of cold adaptation in subzero-growing Arctic permafrost bacteria. FEMS Microbiol Ecol 2018. [DOI: 10.1093/femsec/fiy023] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Isabelle Raymond-Bouchard
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Jacqueline Goordial
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
- Bigelow laboratory for Ocean Sciences, 60 Bigelow Dr, East Boothbay, ME, 04544, USA
| | - Yevgen Zolotarov
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Jennifer Ronholm
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Martina Stromvik
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Corien Bakermans
- Altoona College, Pennsylvania State University, 3000 Ivyside Park, Altoona, PA, 16601, USA
| | - Lyle G Whyte
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
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Zhu C, Sun B, Liu T, Zheng H, Gu W, He W, Sun F, Wang Y, Yang M, Bei W, Peng X, She Q, Xie L, Chen L. Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival. BMC Genomics 2017; 18:436. [PMID: 28583064 PMCID: PMC5460551 DOI: 10.1186/s12864-017-3784-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 05/10/2017] [Indexed: 11/24/2022] Open
Abstract
Background Vibrio parahaemolyticus causes serious seafood-borne gastroenteritis and death in humans. Raw seafood is often subjected to post-harvest processing and low-temperature storage. To date, very little information is available regarding the biological functions of cold shock proteins (CSPs) in the low-temperature survival of the bacterium. In this study, we determined the complete genome sequence of V. parahaemolyticus CHN25 (serotype: O5:KUT). The two main CSP-encoding genes (VpacspA and VpacspD) were deleted from the bacterial genome, and comparative transcriptomic analysis between the mutant and wild-type strains was performed to dissect the possible molecular mechanisms that underlie low-temperature adaptation by V. parahaemolyticus. Results The 5,443,401-bp V. parahaemolyticus CHN25 genome (45.2% G + C) consisted of two circular chromosomes and three plasmids with 4,724 predicted protein-encoding genes. One dual-gene and two single-gene deletion mutants were generated for VpacspA and VpacspD by homologous recombination. The growth of the ΔVpacspA mutant was strongly inhibited at 10 °C, whereas the VpacspD gene deletion strongly stimulated bacterial growth at this low temperature compared with the wild-type strain. The complementary phenotypes were observed in the reverse mutants (ΔVpacspA-com, and ΔVpacspD-com). The transcriptome data revealed that 12.4% of the expressed genes in V. parahaemolyticus CHN25 were significantly altered in the ΔVpacspA mutant when it was grown at 10 °C. These included genes that were involved in amino acid degradation, secretion systems, sulphur metabolism and glycerophospholipid metabolism along with ATP-binding cassette transporters. However, a low temperature elicited significant expression changes for 10.0% of the genes in the ΔVpacspD mutant, including those involved in the phosphotransferase system and in the metabolism of nitrogen and amino acids. The major metabolic pathways that were altered by the dual-gene deletion mutant (ΔVpacspAD) radically differed from those that were altered by single-gene mutants. Comparison of the transcriptome profiles further revealed numerous differentially expressed genes that were shared among the three mutants and regulators that were specifically, coordinately or antagonistically modulated by VpaCspA and VpaCspD. Our data also revealed several possible molecular coping strategies for low-temperature adaptation by the bacterium. Conclusions This study is the first to describe the complete genome sequence of V. parahaemolyticus (serotype: O5:KUT). The gene deletions, complementary insertions, and comparative transcriptomics demonstrate that VpaCspA is a primary CSP in the bacterium, while VpaCspD functions as a growth inhibitor at 10 °C. These results have improved our understanding of the genetic basis for low-temperature survival by the most common seafood-borne pathogen worldwide. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3784-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chunhua Zhu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China
| | - Boyi Sun
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China
| | - Taigang Liu
- College of Information Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Centre at Shanghai, Shanghai, 201203, People's Republic of China
| | - Wenyi Gu
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Centre at Shanghai, Shanghai, 201203, People's Republic of China
| | - Wei He
- Shanghai Hanyu Bio-lab, 151 Ke Yuan Road, Shanghai, 201203, People's Republic of China
| | - Fengjiao Sun
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China
| | - Yaping Wang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China
| | - Meicheng Yang
- Shanghai Institute for Food and Drug Control, 1500 Zhang Heng Road, Shanghai, 201203, People's Republic of China
| | - Weicheng Bei
- State Key Laboratory of Agricultural Microbiology, Laboratory of Animal Infectious Diseases, College of Animal Science & Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200, Copenhagen N, Denmark
| | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200, Copenhagen N, Denmark
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China.
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Baraúna RA, Freitas DY, Pinheiro JC, Folador ARC, Silva A. A Proteomic Perspective on the Bacterial Adaptation to Cold: Integrating OMICs Data of the Psychrotrophic Bacterium Exiguobacterium antarcticum B7. Proteomes 2017; 5:proteomes5010009. [PMID: 28248259 PMCID: PMC5372230 DOI: 10.3390/proteomes5010009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/24/2016] [Accepted: 12/05/2016] [Indexed: 11/30/2022] Open
Abstract
Since the publication of one of the first studies using 2D gel electrophoresis by Patrick H. O’Farrell in 1975, several other studies have used that method to evaluate cellular responses to different physicochemical variations. In environmental microbiology, bacterial adaptation to cold environments is a “hot topic” because of its application in biotechnological processes. As in other fields, gel-based and gel-free proteomic methods have been used to determine the molecular mechanisms of adaptation to cold of several psychrotrophic and psychrophilic bacterial species. In this review, we aim to describe and discuss these main molecular mechanisms of cold adaptation, referencing proteomic studies that have made significant contributions to our current knowledge in the area. Furthermore, we use Exiguobacterium antarcticum B7 as a model organism to present the importance of integrating genomic, transcriptomic, and proteomic data. This species has been isolated in Antarctica and previously studied at all three omic levels. The integration of these data permitted more robust conclusions about the mechanisms of bacterial adaptation to cold.
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Affiliation(s)
- Rafael A Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Dhara Y Freitas
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Juliana C Pinheiro
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Adriana R C Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
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Vullo D, De Luca V, Del Prete S, Carginale V, Scozzafava A, Capasso C, Supuran CT. Sulfonamide inhibition studies of the γ-carbonic anhydrase from the Antarctic bacterium Pseudoalteromonas haloplanktis. Bioorg Med Chem Lett 2015; 25:3550-5. [PMID: 26174556 DOI: 10.1016/j.bmcl.2015.06.079] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 12/18/2022]
Abstract
The Antarctic bacterium Pseudoalteromonas haloplanktis encodes for a γ-class carbonic anhydrase (CA, EC 4.2.1.1), which was cloned, purified and characterized. The enzyme (PhaCAγ) has a good catalytic activity for the physiologic reaction of CO2 hydration to bicarbonate and protons, with a k(cat) of 1.4×10(5) s(-1) and a k(cat)/K(m) of 1.9×10(6) M(-1)×s(-1). A series of sulfonamides and a sulfamate were investigated as inhibitors of the new enzyme. Methazolamide and indisulam showed the best inhibitory properties (K(I)s of 86.7-94.7 nM). This contribution shed new light on γ-CAs inhibition profiles with a relevant class of pharmacologic agents.
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Affiliation(s)
- Daniela Vullo
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Viviana De Luca
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Sonia Del Prete
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy; Università degli Studi di Firenze, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Vincenzo Carginale
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Andrea Scozzafava
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy.
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy; Università degli Studi di Firenze, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
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10
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De Luca V, Vullo D, Del Prete S, Carginale V, Scozzafava A, Osman SM, AlOthman Z, Supuran CT, Capasso C. Cloning, characterization and anion inhibition studies of a new γ-carbonic anhydrase from the Antarctic bacterium Pseudoalteromonas haloplanktis. Bioorg Med Chem 2015; 23:4405-4409. [PMID: 26145820 DOI: 10.1016/j.bmc.2015.06.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
A new γ-class carbonic anhydrase (CA, EC 4.2.1.1) was cloned, purified and characterized from the Antarctic bacterium Pseudoalteromonas haloplanktis, PhaCAγ. The enzyme has a medium-low catalytic activity for the physiologic reaction of CO2 hydration to bicarbonate and protons, with a kcat of 1.4×10(5)s(-1) and a kcat/Km of 1.9×10(6)M(-1)s(-1). An anion inhibition study of PhaCAγ with inorganic anions and small molecule inhibitors is also reported. Many anions present in sea water, such as chloride, fluoride, sulfate, iodide, but also others such as azide, perchlorate and tetrafluoroborate did not inhibit this enzyme. Pseudohalides such as cyanate, thiocyanate, cyanide, selenocyanide, and also bicarbonate, nitrate, nitrite and many complex inorganic anions showed inhibition in the millimolar range (KI in the range of 1.7-9.3mM). The best PhaCAγ inhibitors detected in this study were diethyldithiocarbamate (KI of 0.96 mM) as well as sulfamide, sulfamate, phenylboronic acid and phenylarsonic acid (KI in the range of 82-91 μM). Since γ-CAs are poorly understood at this moment, being present in carboxysomes and thus involved in photosynthesis, this study may be relevant for a better understanding of these processes in Antarctic bacteria/cyanobacteria.
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Affiliation(s)
- Viviana De Luca
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Daniela Vullo
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Sonia Del Prete
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy; Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Vincenzo Carginale
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Andrea Scozzafava
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Sameh M Osman
- Department of Chemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Zeid AlOthman
- Department of Chemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy; Università degli Studi di Firenze, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Polo Scientifico, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy.
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Yang J, Li J, Mai Z, Tian X, Zhang S. Purification, characterization, and gene cloning of a cold-adapted thermolysin-like protease from Halobacillus sp. SCSIO 20089. J Biosci Bioeng 2013; 115:628-32. [DOI: 10.1016/j.jbiosc.2012.12.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/04/2012] [Accepted: 12/13/2012] [Indexed: 10/27/2022]
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Feller G. Psychrophilic enzymes: from folding to function and biotechnology. SCIENTIFICA 2013; 2013:512840. [PMID: 24278781 PMCID: PMC3820357 DOI: 10.1155/2013/512840] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/06/2012] [Indexed: 05/10/2023]
Abstract
Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
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Perera E, Rodríguez-Casariego J, Rodríguez-Viera L, Calero J, Perdomo-Morales R, Mancera JM. Lobster (Panulirus argus) hepatopancreatic trypsin isoforms and their digestion efficiency. THE BIOLOGICAL BULLETIN 2012; 222:158-170. [PMID: 22589406 DOI: 10.1086/bblv222n2p158] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
It is well known that crustaceans exhibit several isoforms of trypsin in their digestive system. Although the number of known crustacean trypsin isoforms continues increasing, especially those derived from cDNA sequences, the role of particular isoenzymes in digestion remains unknown. Among invertebrates, significant advances in the understanding of the role of multiple trypsins have been made only in insects. Since it has been demonstrated that trypsin isoenzyme patterns (phenotypes) in lobster differ in digestion efficiency, we used this crustacean as a model for assessing the biochemical basis of such differences. We demonstrated that the trypsin isoform known to be present in all individuals of Panulirus argus has a high catalytic efficiency (k(cat)/K(m) ) and is the most reactive toward native proteinaceous substrates, whereas one of the isoforms present in less efficient individuals has a lower k(cat) and a lower k(cat)/K(m), and it is less competent at digesting native proteins. A fundamental question in biology is how genetic differences produce different physiological performances. This work is the first to demonstrate that trypsin phenotypic variation in crustacean protein digestion relies on the biochemical properties of the different isoforms. Results are relevant for understanding trypsin polymorphism and protein digestion in lobster.
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Affiliation(s)
- Erick Perera
- Center for Marine Research, University of Havana, Cuba.
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Mereghetti P, Riccardi L, Brandsdal BO, Fantucci P, De Gioia L, Papaleo E. Near native-state conformational landscape of psychrophilic and mesophilic enzymes: probing the folding funnel model. J Phys Chem B 2010; 114:7609-19. [PMID: 20518574 DOI: 10.1021/jp911523h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In recent years, increased interest has been directed to the study of enzyme adaptation to low temperatures. In particular, a peculiar folding funnel model was proposed for the free energy landscape of a psychrophilic alpha-amylase and other cold-adapted enzymes. In the present contribution, the comparison between the near native-state dynamics and conformational landscape in the essential subspace of different cold-adapted enzymes with their mesophilic counterparts, as obtained by more than 0.1 micros molecular dynamics simulations at different temperatures, allows the folding funnel model to be probed. Common characteristics were highlighted in the near native-state dynamics of psychrophilic enzymes belonging to different enzymatic families when compared to the mesophilic counterparts. According to the model, a cold-adapted enzyme in its native-state consists of a large population of conformations which can easily interconvert and result in high structural flexibility.
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Affiliation(s)
- Paolo Mereghetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milan, Italy
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The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl Environ Microbiol 2010; 76:2304-12. [PMID: 20154119 DOI: 10.1128/aem.02101-09] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Psychrobacter arcticus strain 273-4, which grows at temperatures as low as -10 degrees C, is the first cold-adapted bacterium from a terrestrial environment whose genome was sequenced. Analysis of the 2.65-Mb genome suggested that some of the strategies employed by P. arcticus 273-4 for survival under cold and stress conditions are changes in membrane composition, synthesis of cold shock proteins, and the use of acetate as an energy source. Comparative genome analysis indicated that in a significant portion of the P. arcticus proteome there is reduced use of the acidic amino acids and proline and arginine, which is consistent with increased protein flexibility at low temperatures. Differential amino acid usage occurred in all gene categories, but it was more common in gene categories essential for cell growth and reproduction, suggesting that P. arcticus evolved to grow at low temperatures. Amino acid adaptations and the gene content likely evolved in response to the long-term freezing temperatures (-10 degrees C to -12 degrees C) of the Kolyma (Siberia) permafrost soil from which this strain was isolated. Intracellular water likely does not freeze at these in situ temperatures, which allows P. arcticus to live at subzero temperatures.
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Alimenti C, Vallesi A, Pedrini B, Wüthrich K, Luporini P. Molecular cold-adaptation: Comparative analysis of two homologous families of psychrophilic and mesophilic signal proteins of the protozoan ciliate,Euplotes. IUBMB Life 2009; 61:838-45. [DOI: 10.1002/iub.228] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Xie BB, Bian F, Chen XL, He HL, Guo J, Gao X, Zeng YX, Chen B, Zhou BC, Zhang YZ. Cold adaptation of zinc metalloproteases in the thermolysin family from deep sea and arctic sea ice bacteria revealed by catalytic and structural properties and molecular dynamics: new insights into relationship between conformational flexibility and hydrogen bonding. J Biol Chem 2009; 284:9257-69. [PMID: 19181663 DOI: 10.1074/jbc.m808421200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Increased conformational flexibility is the prevailing explanation for the high catalytic efficiency of cold-adapted enzymes at low temperatures. However, less is known about the structural determinants of flexibility. We reported two novel cold-adapted zinc metalloproteases in the thermolysin family, vibriolysin MCP-02 from a deep sea bacterium and vibriolysin E495 from an Arctic sea ice bacterium, and compared them with their mesophilic homolog, pseudolysin from a terrestrial bacterium. Their catalytic efficiencies, k(cat)/K(m) (10-40 degrees C), followed the order pseudolysin < MCP-02 < E495 with a ratio of approximately 1:2:4. MCP-02 and E495 have the same optimal temperature (T(opt), 57 degrees C, 5 degrees C lower than pseudolysin) and apparent melting temperature (T(m) = 64 degrees C, approximately 10 degrees C lower than pseudolysin). Structural analysis showed that the slightly lower stabilities resulted from a decrease in the number of salt bridges. Fluorescence quenching experiments and molecular dynamics simulations showed that the flexibilities of the proteins were pseudolysin < MCP-02 < E495, suggesting that optimization of flexibility is a strategy for cold adaptation. Molecular dynamics results showed that the ordinal increase in flexibility from pseudolysin to MCP-02 and E495, especially the increase from MCP-02 to E495, mainly resulted from the decrease of hydrogen-bond stability in the dynamic structure, which was due to the increase in asparagine, serine, and threonine residues. Finally, a model for the cold adaptation of MCP-02 and E495 was proposed. This is the first report of the optimization of hydrogen-bonding dynamics as a strategy for cold adaptation and provides new insights into the structural basis underlying conformational flexibility.
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Affiliation(s)
- Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
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Adekoya OA, Sylte I. The Thermolysin Family (M4) of Enzymes: Therapeutic and Biotechnological Potential. Chem Biol Drug Des 2009; 73:7-16. [DOI: 10.1111/j.1747-0285.2008.00757.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Marziale F, Pucciarelli S, Ballarini P, Melki R, Uzun A, Ilyin VA, Detrich HW, Miceli C. Different roles of two gamma-tubulin isotypes in the cytoskeleton of the Antarctic ciliate Euplotes focardii: remodelling of interaction surfaces may enhance microtubule nucleation at low temperature. FEBS J 2008; 275:5367-82. [PMID: 18959762 DOI: 10.1111/j.1742-4658.2008.06666.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Gamma-tubulin belongs to the tubulin superfamily and plays an essential role in the nucleation of cellular microtubules. In the present study, we report the characterization of gamma-tubulin from the psychrophilic Antarctic ciliate Euplotes focardii. In this organism, gamma-tubulin is encoded by two genes, gamma-T1 and gamma-T2, that produce distinct isotypes. Comparison of the gamma-T1 and gamma-T2 primary sequences to a Euplotesgamma-tubulin consensus, derived from mesophilic (i.e. temperate) congeneric species, revealed the presence of numerous unique amino acid substitutions, particularly in gamma-T2. Structural models of gamma-T1 and gamma-T2, obtained using the 3D structure of human gamma-tubulin as a template, suggest that these substitutions are responsible for conformational and/or polarity differences located: (a) in the regions involved in longitudinal 'plus end' contacts; (b) in the T3 loop that participates in binding GTP; and (c) in the M loop that forms lateral interactions. Relative to gamma-T1, the gamma-T2 gene is amplified by approximately 18-fold in the macronuclear genome and is very strongly transcribed. Using confocal immunofluorescence microscopy, we found that the gamma-tubulins of E. focardii associate throughout the cell cycle with basal bodies of the non-motile dorsal cilia and of all of the cirri of the ventral surface (i.e. adoral membranelles, paraoral membrane, and frontoventral transverse, caudal and marginal cirri). By contrast, only gamma-T2 interacts with the centrosomes of the spindle during micronuclear mitosis. We also established that the gamma-T1 isotype associates only with basal bodies. Our results suggest that gamma-T1 and gamma-T2 perform different functions in the organization of the microtubule cytoskeleton of this protist and are consistent with the hypothesis that gamma-T1 and gamma-T2 have evolved sequence-based structural alterations that facilitate template nucleation of microtubules by the gamma-tubulin ring complex at cold temperatures.
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Affiliation(s)
- Francesca Marziale
- Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Italy
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Effects of introducing negative charges into the molecular surface of thermolysin by site-directed mutagenesis on its activity and stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:481-8. [DOI: 10.1016/j.bbapap.2007.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 11/12/2007] [Accepted: 12/10/2007] [Indexed: 11/22/2022]
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Prieto J, Epinat JC, Redondo P, Ramos E, Padró D, Cédrone F, Montoya G, Pâques F, Blanco FJ. Generation and analysis of mesophilic variants of the thermostable archaeal I-DmoI homing endonuclease. J Biol Chem 2007; 283:4364-74. [PMID: 17999959 DOI: 10.1074/jbc.m706323200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hyperthermophilic archaeon Desulfurococcus mobilis I-DmoI protein belongs to the family of proteins known as homing endonucleases (HEs). HEs are highly specific DNA-cleaving enzymes that recognize long stretches of DNA and are powerful tools for genome engineering. Because of its monomeric nature, I-DmoI is an ideal scaffold for generating mutant enzymes with novel DNA specificities, similarly reported for homodimeric HEs, but providing single chain endonucleases instead of dimers. However, this would require the use of a mesophilic variant cleaving its substrate at temperatures of 37 degrees C and below. We have generated mesophilic mutants of I-DmoI, using a single round of directed evolution that relies on a functional assay in yeast. The effect of mutations identified in the novel proteins has been investigated. These mutations are located distant to the DNA-binding site and cause changes in the size and polarity of buried residues, suggesting that they act by destabilizing the protein. Two of the novel proteins have been produced and analyzed in vitro. Their overall structures are similar to that of the parent protein, but they are destabilized against thermal and chemical denaturation. The temperature-dependent activity profiles for the mutants shifted toward lower temperatures with respect to the wild-type activity profile. However, the most destabilized mutant was not the most active at low temperatures, suggesting that other effects, like local structural distortions and/or changes in the protein dynamics, also influence their activity. These mesophilic I-DmoI mutants form the basis for generating new variants with tailored DNA specificities.
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Affiliation(s)
- Jesús Prieto
- Structural Biology and Biocomputing Programme, NMR Group and Macromolecular Crystallography Group, Spanish National Cancer Center, c/Melchor Fernández Almagro 3, 28029-Madrid, Spain
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