1
|
Jin J, Xiao L, Wu Y, Sun Z, Xiong Z, Li Y, Zhao Y, Yao W, Shen L, Cui Y, Tan Y, Han Y, Du Z, Cui Y, Yang R, Song K, Song Y. Characterization of an aspartate aminotransferase encoded by YPO0623 with frequent nonsense mutations in Yersinia pestis. Front Cell Infect Microbiol 2023; 13:1288371. [PMID: 38089818 PMCID: PMC10713766 DOI: 10.3389/fcimb.2023.1288371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Yersinia pestis, the causative agent of plague, is a genetically monomorphic bacterial pathogen that evolved from Yersinia pseudotuberculosis approximately 7,400 years ago. We observed unusually frequent mutations in Y. pestis YPO0623, mostly resulting in protein translation termination, which implies a strong natural selection. These mutations were found in all phylogenetic lineages of Y. pestis, and there was no apparent pattern in the spatial distribution of the mutant strains. Based on these findings, we aimed to investigate the biological function of YPO0623 and the reasons for its frequent mutation in Y. pestis. Our in vitro and in vivo assays revealed that the deletion of YPO0623 enhanced the growth of Y. pestis in nutrient-rich environments and led to increased tolerance to heat and cold shocks. With RNA-seq analysis, we also discovered that the deletion of YPO0623 resulted in the upregulation of genes associated with the type VI secretion system (T6SS) at 26°C, which probably plays a crucial role in the response of Y. pestis to environment fluctuations. Furthermore, bioinformatic analysis showed that YPO0623 has high homology with a PLP-dependent aspartate aminotransferase in Salmonella enterica, and the enzyme activity assays confirmed its aspartate aminotransferase activity. However, the enzyme activity of YPO0623 was significantly lower than that in other bacteria. These observations provide some insights into the underlying reasons for the high-frequency nonsense mutations in YPO0623, and further investigations are needed to determine the exact mechanism.
Collapse
Affiliation(s)
- Junyan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Liting Xiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhulin Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ziyao Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanbing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Department of Laboratory Medicine, Xiangya Hospital of Central South University, Changsha, China
| | - Yanting Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Wenwu Yao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Department of Microbiology and Department of Infectious Diseases, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Leiming Shen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yiming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| |
Collapse
|
2
|
Butler MI, Bastiaanssen TFS, Long-Smith C, Morkl S, Berding K, Ritz NL, Strain C, Patangia D, Patel S, Stanton C, O'Mahony SM, Cryan JF, Clarke G, Dinan TG. The gut microbiome in social anxiety disorder: evidence of altered composition and function. Transl Psychiatry 2023; 13:95. [PMID: 36941248 PMCID: PMC10027687 DOI: 10.1038/s41398-023-02325-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/05/2023] [Accepted: 01/18/2023] [Indexed: 03/23/2023] Open
Abstract
The microbiome-gut-brain axis plays a role in anxiety, the stress response and social development, and is of growing interest in neuropsychiatric conditions. The gut microbiota shows compositional alterations in a variety of psychiatric disorders including depression, generalised anxiety disorder (GAD), autism spectrum disorder (ASD) and schizophrenia but studies investigating the gut microbiome in social anxiety disorder (SAD) are very limited. Using whole-genome shotgun analysis of 49 faecal samples (31 cases and 18 sex- and age-matched controls), we analysed compositional and functional differences in the gut microbiome of patients with SAD in comparison to healthy controls. Overall microbiota composition, as measured by beta-diversity, was found to be different between the SAD and control groups and several taxonomic differences were seen at a genus- and species-level. The relative abundance of the genera Anaeromassillibacillus and Gordonibacter were elevated in SAD, while Parasuterella was enriched in healthy controls. At a species-level, Anaeromassilibacillus sp An250 was found to be more abundant in SAD patients while Parasutterella excrementihominis was higher in controls. No differences were seen in alpha diversity. In relation to functional differences, the gut metabolic module 'aspartate degradation I' was elevated in SAD patients. In conclusion, the gut microbiome of patients with SAD differs in composition and function to that of healthy controls. Larger, longitudinal studies are warranted to validate these preliminary results and explore the clinical implications of these microbiome changes.
Collapse
Affiliation(s)
- Mary I Butler
- Department of Psychiatry & Neurobehavioral Science, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | | | - Sabrina Morkl
- Department of Psychiatry & Neurobehavioral Science, University College Cork, Cork, Ireland
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Graz, Austria
| | - Kirsten Berding
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Conall Strain
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Programme, Moorepark, Fermoy, Co, Cork, T12 YN60, Ireland
| | - Dhrati Patangia
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Programme, Moorepark, Fermoy, Co, Cork, T12 YN60, Ireland
| | - Shriram Patel
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Siobhain M O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Gerard Clarke
- Department of Psychiatry & Neurobehavioral Science, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- Department of Psychiatry & Neurobehavioral Science, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| |
Collapse
|
3
|
Metabolic Robustness to Growth Temperature of a Cold- Adapted Marine Bacterium. mSystems 2023; 8:e0112422. [PMID: 36847563 PMCID: PMC10134870 DOI: 10.1128/msystems.01124-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Microbial communities experience continuous environmental changes, with temperature fluctuations being the most impacting. This is particularly important considering the ongoing global warming but also in the "simpler" context of seasonal variability of sea-surface temperature. Understanding how microorganisms react at the cellular level can improve our understanding of their possible adaptations to a changing environment. In this work, we investigated the mechanisms through which metabolic homeostasis is maintained in a cold-adapted marine bacterium during growth at temperatures that differ widely (15 and 0°C). We have quantified its intracellular and extracellular central metabolomes together with changes occurring at the transcriptomic level in the same growth conditions. This information was then used to contextualize a genome-scale metabolic reconstruction, and to provide a systemic understanding of cellular adaptation to growth at 2 different temperatures. Our findings indicate a strong metabolic robustness at the level of the main central metabolites, counteracted by a relatively deep transcriptomic reprogramming that includes changes in gene expression of hundreds of metabolic genes. We interpret this as a transcriptomic buffering of cellular metabolism, able to produce overlapping metabolic phenotypes, despite the wide temperature gap. Moreover, we show that metabolic adaptation seems to be mostly played at the level of few key intermediates (e.g., phosphoenolpyruvate) and in the cross talk between the main central metabolic pathways. Overall, our findings reveal a complex interplay at gene expression level that contributes to the robustness/resilience of core metabolism, also promoting the leveraging of state-of-the-art multi-disciplinary approaches to fully comprehend molecular adaptations to environmental fluctuations. IMPORTANCE This manuscript addresses a central and broad interest topic in environmental microbiology, i.e. the effect of growth temperature on microbial cell physiology. We investigated if and how metabolic homeostasis is maintained in a cold-adapted bacterium during growth at temperatures that differ widely and that match measured changes on the field. Our integrative approach revealed an extraordinary robustness of the central metabolome to growth temperature. However, this was counteracted by deep changes at the transcriptional level, and especially in the metabolic part of the transcriptome. This conflictual scenario was interpreted as a transcriptomic buffering of cellular metabolism, and was investigated using genome-scale metabolic modeling. Overall, our findings reveal a complex interplay at gene expression level that contributes to the robustness/resilience of core metabolism, also promoting the use of state-of-the-art multi-disciplinary approaches to fully comprehend molecular adaptations to environmental fluctuations.
Collapse
|
4
|
Calvanese M, Colarusso A, Lauro C, Parrilli E, Tutino ML. Soluble Recombinant Protein Production in Pseudoalteromonas haloplanktis TAC125: The Case Study of the Full-Length Human CDKL5 Protein. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2406:219-232. [PMID: 35089560 DOI: 10.1007/978-1-0716-1859-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 is an unconventional protein production host displaying a notable proficiency in the soluble production of difficult proteins, especially of human origin. Furthermore, the accumulation of recombinant products in insoluble aggregates has never been observed in this bacterium, indicating that its cellular physicochemical conditions and/or folding processes are rather different from those observed in mesophilic bacteria. The ability of this cell factory was challenged by producing a human protein, the cyclin-dependent kinase-like 5 (hCDKL5) in the bacterium cytoplasm at 0 °C. Human CDKL5 is a serine/threonine protein kinase characterized by the absence of a defined structure for the last two/third of its sequence, one of the largest intrinsically disordered regions so far observed in a human protein. This large unstructured domain makes difficult its production in most of the conventional hosts since the recombinant product accumulates as insoluble aggregates and/or is heavily proteolyzed. As the full-length hCDKL5 production is of great interest both for basic science and as protein drug for an enzyme replacement therapy, its production in the Antarctic bacterium was tested by combining the use of a regulated psychrophilic gene expression system with the use of a defined growth medium optimized for the host growth at subzero temperature. This is the first report of soluble and full-length recombinant production of hCDKL5 protein in a bacterium.
Collapse
Affiliation(s)
- Marzia Calvanese
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
| | - Andrea Colarusso
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
| | - Concetta Lauro
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy.
| |
Collapse
|
5
|
LIMA IGORG, BISPO JAMESR, AGOSTINHO ADSONY, QUEIROZ ALINECDE, MOREIRA MAGNASUZANAA, PASSARINI MICHELRODRIGOZ, OLIVEIRA VALÉRIAMDE, SETTE LARAD, ROSA LUIZHENRIQUE, DUARTE ALYSSONWAGNERF. Antarctic environments as a source of bacterial and fungal therapeutic enzymes. AN ACAD BRAS CIENC 2022; 94:e20210452. [DOI: 10.1590/0001-3765202220210452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/20/2021] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | - LARA D. SETTE
- Universidade Estadual Paulista Júlio de Mesquita Filho, Brazil
| | | | | |
Collapse
|
6
|
Ferrer-Miralles N, Saccardo P, Corchero JL, Garcia-Fruitós E. Recombinant Protein Production and Purification of Insoluble Proteins. Methods Mol Biol 2022; 2406:1-31. [PMID: 35089548 DOI: 10.1007/978-1-0716-1859-2_1] [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] [Indexed: 06/14/2023]
Abstract
Proteins are synthesized in heterologous systems because of the impossibility to obtain satisfactory yields from natural sources. The efficient production of soluble and functional recombinant proteins is among the main goals in the biotechnological field. In this context, it is important to point out that under stress conditions, protein folding machinery is saturated and this promotes protein misfolding and, consequently, protein aggregation. Thus, the selection of the optimal expression organism and its growth conditions to minimize the formation of insoluble protein aggregates should be done according to the protein characteristics and downstream requirements. Escherichia coli is the most popular recombinant protein expression system despite the great development achieved so far by eukaryotic expression systems. Besides, other prokaryotic expression systems, such as lactic acid bacteria and psychrophilic bacteria, are gaining interest in this field. However, it is worth mentioning that prokaryotic expression system poses, in many cases, severe restrictions for a successful heterologous protein production. Thus, eukaryotic systems such as mammalian cells, insect cells, yeast, filamentous fungus, and microalgae are an interesting alternative for the production of these difficult-to-express proteins.
Collapse
Affiliation(s)
- Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Cerdanyola del Vallès, Spain
| | - Paolo Saccardo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Cerdanyola del Vallès, Spain
| | - José Luis Corchero
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Cerdanyola del Vallès, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, Spain.
| |
Collapse
|
7
|
Soluble Recombinant Protein Production in Pseudoalteromonas haloplanktis TAC125: The Case Study of the Full-Length Human CDKL5 Protein. Methods Mol Biol 2022. [PMID: 35089560 DOI: 10.1007/978-1-0716-1859-2_132406:219-232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 is an unconventional protein production host displaying a notable proficiency in the soluble production of difficult proteins, especially of human origin. Furthermore, the accumulation of recombinant products in insoluble aggregates has never been observed in this bacterium, indicating that its cellular physicochemical conditions and/or folding processes are rather different from those observed in mesophilic bacteria. The ability of this cell factory was challenged by producing a human protein, the cyclin-dependent kinase-like 5 (hCDKL5) in the bacterium cytoplasm at 0 °C. Human CDKL5 is a serine/threonine protein kinase characterized by the absence of a defined structure for the last two/third of its sequence, one of the largest intrinsically disordered regions so far observed in a human protein. This large unstructured domain makes difficult its production in most of the conventional hosts since the recombinant product accumulates as insoluble aggregates and/or is heavily proteolyzed. As the full-length hCDKL5 production is of great interest both for basic science and as protein drug for an enzyme replacement therapy, its production in the Antarctic bacterium was tested by combining the use of a regulated psychrophilic gene expression system with the use of a defined growth medium optimized for the host growth at subzero temperature. This is the first report of soluble and full-length recombinant production of hCDKL5 protein in a bacterium.
Collapse
|
8
|
Pinney MM, Mokhtari DA, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, Herschlag D. Parallel molecular mechanisms for enzyme temperature adaptation. Science 2021; 371:371/6533/eaay2784. [PMID: 33674467 DOI: 10.1126/science.aay2784] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/23/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.
Collapse
Affiliation(s)
- Margaux M Pinney
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
| | - Daniel A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
| | - David M Sanchez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruibin Liang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Todd J Martinez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
9
|
Fongaro G, Maia GA, Rogovski P, Cadamuro RD, Lopes JC, Moreira RS, Camargo AF, Scapini T, Stefanski FS, Bonatto C, Marques Souza DS, Stoco PH, Duarte RTD, Cabral da Cruz AC, Wagner G, Treichel H. Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools. Curr Genomics 2020; 21:240-252. [PMID: 33071618 PMCID: PMC7521039 DOI: 10.2174/1389202921999200601144137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/02/2020] [Accepted: 04/20/2020] [Indexed: 12/03/2022] Open
Abstract
Abstract: Genomic and proteomic advances in extremophile microorganism studies are increasingly demonstrating their ability to produce a variety of enzymes capable of converting biomass into bioenergy. Such microorganisms are found in environments with nutritional restrictions, anaerobic environments, high salinity, varying pH conditions and extreme natural environments such as hydrothermal vents, soda lakes, and Antarctic sediments. As extremophile microorganisms and their enzymes are found in widely disparate locations, they generate new possibilities and opportunities to explore biotechnological prospecting, including biofuels (biogas, hydrogen and ethanol) with an aim toward using multi-omics tools that shed light on biotechnological breakthroughs.
Collapse
Affiliation(s)
- Gislaine Fongaro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Guilherme Augusto Maia
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Paula Rogovski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rafael Dorighello Cadamuro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Joana Camila Lopes
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Renato Simões Moreira
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Aline Frumi Camargo
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Thamarys Scapini
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Fábio Spitza Stefanski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Charline Bonatto
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Doris Sobral Marques Souza
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Patrícia Hermes Stoco
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Tadeu Delgado Duarte
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Ariadne Cristiane Cabral da Cruz
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Glauber Wagner
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Helen Treichel
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| |
Collapse
|
10
|
Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments. Nat Commun 2020; 11:3135. [PMID: 32561713 PMCID: PMC7305145 DOI: 10.1038/s41467-020-16872-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
It is commonly thought that when multiple carbon sources are available, bacteria metabolize them either sequentially (diauxic growth) or simultaneously (co-utilization). However, this view is mainly based on analyses in relatively simple laboratory settings. Here we show that a heterotrophic marine bacterium, Pseudoalteromonas haloplanktis, can use both strategies simultaneously when multiple possible nutrients are provided in the same growth experiment. The order of nutrient uptake is partially determined by the biomass yield that can be achieved when the same compounds are provided as single carbon sources. Using transcriptomics and time-resolved intracellular 1H-13C NMR, we reveal specific pathways for utilization of various amino acids. Finally, theoretical modelling indicates that this metabolic phenotype, combining diauxie and co-utilization of substrates, is compatible with a tight regulation that allows the modulation of assimilatory pathways. It is thought that when multiple carbon sources are available, bacteria metabolize them either sequentially or simultaneously. Here, the authors show that a marine bacterium can use a mixed strategy when multiple possible nutrients are provided, and analyse the metabolic pathways involved.
Collapse
|
11
|
Asymmetric biosynthesis of L-phosphinothricin by a novel transaminase from Pseudomonas fluorescens ZJB09-108. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
12
|
Enzymes from Marine Polar Regions and Their Biotechnological Applications. Mar Drugs 2019; 17:md17100544. [PMID: 31547548 PMCID: PMC6835263 DOI: 10.3390/md17100544] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
The microorganisms that evolved at low temperatures express cold-adapted enzymes endowed with unique catalytic properties in comparison to their mesophilic homologues, i.e., higher catalytic efficiency, improved flexibility, and lower thermal stability. Cold environments are therefore an attractive research area for the discovery of enzymes to be used for investigational and industrial applications in which such properties are desirable. In this work, we will review the literature on cold-adapted enzymes specifically focusing on those discovered in the bioprospecting of polar marine environments, so far largely neglected because of their limited accessibility. We will discuss their existing or proposed biotechnological applications within the framework of the more general applications of cold-adapted enzymes.
Collapse
|
13
|
Casillo A, Parrilli E, Tutino ML, Corsaro MM. The outer membrane glycolipids of bacteria from cold environments: isolation, characterization, and biological activity. FEMS Microbiol Ecol 2019; 95:5519854. [DOI: 10.1093/femsec/fiz094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/14/2019] [Indexed: 01/18/2023] Open
Abstract
ABSTRACTLipopolysaccharides (LPSs) are the main components of the external leaflet of the outer membrane of Gram-negative bacteria. Microorganisms that colonize permanently or transiently cold habitats have evolved an array of structural adaptations, some of which involve components of bacterial membranes. These adaptations assure the perfect functionality of the membrane even at freezing or sub-freezing growth temperatures. This review summarizes the state-of-the-art information concerning the structural features of the LPSs produced by cold-adapted bacteria. The LPS structure has recently been elucidated from species mainly belonging to Gammaproteobacteria and Flavobacteriaceae. Although the reported structural heterogeneity may arise from the phylogenetic diversity of the analyzed source strains, some generalized trends can be deduced. For instance, it is clear that only a small portion of LPSs displays the O-chain. In addition, the biological activity of the lipid A portion from several cold-adapted strains is reported.
Collapse
Affiliation(s)
- Angela Casillo
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy
| | - Maria Michela Corsaro
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, via Cintia, 80126 Naples, Italy
| |
Collapse
|
14
|
Parrilli E, Tedesco P, Fondi M, Tutino ML, Lo Giudice A, de Pascale D, Fani R. The art of adapting to extreme environments: The model system Pseudoalteromonas. Phys Life Rev 2019; 36:137-161. [PMID: 31072789 DOI: 10.1016/j.plrev.2019.04.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/10/2023]
Abstract
Extremophilic microbes have adapted to thrive in ecological niches characterized by harsh chemical/physical conditions such as, for example, very low/high temperature. Living organisms inhabiting these environments have developed peculiar mechanisms to cope with extreme conditions, in such a way that they mark the chemical-physical boundaries of life on Earth. Studying such mechanisms is stimulating from a basic research viewpoint and because of biotechnological applications. Pseudoalteromonas species are a group of marine gamma-proteobacteria frequently isolated from a range of extreme environments, including cold habitats and deep-sea sediments. Since deep-sea floors constitute almost 60% of the Earth's surface and cold temperatures represent the most common of the extreme conditions, the genus Pseudoalteromonas can be considered one of the most important model systems for studying microbial adaptation. Particularly, among all Pseudoalteromonas representatives, P. haloplanktis TAC125 has recently gained a central role. This bacterium was isolated from seawater sampled along the Antarctic ice-shell and is considered one of the model organisms of cold-adapted bacteria. It is capable of thriving in a wide temperature range and it has been suggested as an alternative host for the soluble overproduction of heterologous proteins, given its ability to rapidly multiply at low temperatures. In this review, we will present an overview of the recent advances in the characterization of Pseudoalteromonas strains and, more importantly, in the understanding of their evolutionary and chemical-physical strategies to face such a broad array of extreme conditions. A particular attention will be given to systems-biology approaches in the study of the above-mentioned topics, as genome-scale datasets (e.g. genomics, proteomics, phenomics) are beginning to expand for this group of organisms. In this context, a specific section dedicated to P. haloplanktis TAC125 will be presented to address the recent efforts in the elucidation of the metabolic rewiring of the organisms in its natural environment (Antarctica).
Collapse
Affiliation(s)
- Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Pietro Tedesco
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | | | - Donatella de Pascale
- Institute of Protein Biochemistry, CNR, Napoli, Italy, Stazione Zoologica "Anthon Dorn", Villa Comunale, I-80121 Napoli, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy.
| |
Collapse
|
15
|
Hamzaoğlu F, Türkyılmaz M, Özkan M. Amino acid profile and content of dried apricots containing SO 2at different concentrations during storage. QUALITY ASSURANCE AND SAFETY OF CROPS & FOODS 2018. [DOI: 10.3920/qas2018.1284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- F. Hamzaoğlu
- Department of Food Engineering, Faculty of Engineering, Ankara University, 50. Yıl YCampus, Bahçelievler Street 35, 06830 Gölbaşı, Ankara, Türkey
| | - M. Türkyılmaz
- Institute of Food Safety, Ankara University, Campus, Şehit Ömer Halisdemir Street, 06110 Diskapi, Ankara, Turkey
| | - M. Özkan
- Department of Food Engineering, Faculty of Engineering, Ankara University, 50. Yıl YCampus, Bahçelievler Street 35, 06830 Gölbaşı, Ankara, Türkey
| |
Collapse
|
16
|
Di Lorenzo F, Billod JM, Martín-Santamaría S, Silipo A, Molinaro A. Gram-Negative Extremophile Lipopolysaccharides: Promising Source of Inspiration for a New Generation of Endotoxin Antagonists. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences; University of Naples Federico II; via Cinthia 480126 80126 Naples Italy
| | - Jean-Marc Billod
- Department of Chemical and Physical Biology; CIB Centro de Investigaciones Biológicas; Ramiro de Maeztu 9 28040 Madrid Spain
| | - Sonsoles Martín-Santamaría
- Department of Chemical and Physical Biology; CIB Centro de Investigaciones Biológicas; Ramiro de Maeztu 9 28040 Madrid Spain
| | - Alba Silipo
- Department of Chemical Sciences; University of Naples Federico II; via Cinthia 480126 80126 Naples Italy
| | - Antonio Molinaro
- Department of Chemical Sciences; University of Naples Federico II; via Cinthia 480126 80126 Naples Italy
| |
Collapse
|
17
|
Mocali S, Chiellini C, Fabiani A, Decuzzi S, de Pascale D, Parrilli E, Tutino ML, Perrin E, Bosi E, Fondi M, Lo Giudice A, Fani R. Ecology of cold environments: new insights of bacterial metabolic adaptation through an integrated genomic-phenomic approach. Sci Rep 2017; 7:839. [PMID: 28404986 PMCID: PMC5429795 DOI: 10.1038/s41598-017-00876-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/01/2017] [Indexed: 12/26/2022] Open
Abstract
Cold environments dominate Earth's biosphere, hosting complex microbial communities with the ability to thrive at low temperatures. However, the underlying molecular mechanisms and the metabolic pathways involved in bacterial cold-adaptation mechanisms are still not fully understood. Herein, we assessed the metabolic features of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125), a model organism for cold-adaptation, at both 4 °C and 15 °C, by integrating genomic and phenomic (high-throughput phenotyping) data and comparing the obtained results to the taxonomically related Antarctic bacterium Pseudoalteromonas sp. TB41 (PspTB41). Although the genome size of PspTB41 is considerably larger than PhTAC125, the higher number of genes did not reflect any higher metabolic versatility at 4 °C as compared to PhTAC125. Remarkably, protein S-thiolation regulated by glutathione and glutathionylspermidine appeared to be a new possible mechanism for cold adaptation in PhTAC125. More in general, this study represents an example of how 'multi-omic' information might potentially contribute in filling the gap between genotypic and phenotypic features related to cold-adaptation mechanisms in bacteria.
Collapse
Affiliation(s)
- Stefano Mocali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.
| | - Carolina Chiellini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.,Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Arturo Fabiani
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy
| | - Silvia Decuzzi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.,Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Donatella de Pascale
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario, Monte Sant'Angelo, Via Cinthia 4, 80126, Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario, Monte Sant'Angelo, Via Cinthia 4, 80126, Naples, Italy
| | - Elena Perrin
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Emanuele Bosi
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Marco Fondi
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Angelina Lo Giudice
- Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Spianata San Raineri 86, 98122, Messina, Italy.,Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontrès 31, 98166, Messina, Italy
| | - Renato Fani
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| |
Collapse
|
18
|
Hu S, Zhang X, Lu Y, Lin YC, Xie DF, Fang H, Huang J, Mei LH. Cloning, expression and characterization of an aspartate aminotransferase gene from Lactobacillus brevis CGMCC 1306. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1304181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Sheng Hu
- School of Biological and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo, P.R. China
| | - Xiang Zhang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Yi Lu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Yue-Cheng Lin
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Dong-Fang Xie
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Hui Fang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Jun Huang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Le-He Mei
- School of Biological and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo, P.R. China
| |
Collapse
|
19
|
Tools to cope with difficult-to-express proteins. Appl Microbiol Biotechnol 2016; 100:4347-55. [DOI: 10.1007/s00253-016-7514-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 12/26/2022]
|
20
|
Wang R, Zhang M, Liu H, Xu J, Yu J, He F, Zhang X, Dong S, Dou D. PsAAT3, an oomycete-specific aspartate aminotransferase, is required for full pathogenicity of the oomycete pathogen Phytophthora sojae. Fungal Biol 2016; 120:620-630. [PMID: 27020161 DOI: 10.1016/j.funbio.2016.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/02/2016] [Accepted: 01/06/2016] [Indexed: 12/29/2022]
Abstract
Pathogen nutrient acquisition and metabolism are critical for successful infection and colonization. However, the nutrient requirements and metabolic pathways related to pathogenesis in oomycete pathogens are unknown. In this study, we bioinformatically identified Phytophthora sojae aspartate aminotransferases (AATs), which are key enzymes that coordinate carbon and nitrogen metabolism. We demonstrated that P. sojae encodes more AATs than the analysed fungi. Some of the AATs contained additional prephenate dehydratase and/or prephenate dehydrogenase domains in their N-termini, which are unique to oomycetes. Silencing of PsAAT3, an infection-inducible expression gene, reduced P. sojae pathogenicity on soybean plants and affected the growth under N-starving condition, suggesting that PsAAT3 is involved in pathogen pathogenicity and nitrogen utilisation during infection. Our results suggest that P. sojae and other oomycete pathogens may have distinct amino acid metabolism pathways and that PsAAT3 is important for its full pathogenicity.
Collapse
Affiliation(s)
- Rongbo Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Hong Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jing Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jia Yu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Feng He
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiong Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
| |
Collapse
|
21
|
Nanotechnology based activation-immobilization of psychrophilic pectate lyase: A novel approach towards enzyme stabilization and enhanced activity. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
22
|
Mukhopadhyay A, Dasgupta AK, Chakrabarti K. Enhanced functionality and stabilization of a cold active laccase using nanotechnology based activation-immobilization. BIORESOURCE TECHNOLOGY 2015; 179:573-584. [PMID: 25590281 DOI: 10.1016/j.biortech.2014.12.070] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 06/04/2023]
Abstract
A simple nanotechnology based immobilization technique for imparting psychrostability and enhanced activity to a psychrophilic laccase has been described here. Laccase from a psychrophile was supplemented with Copper oxide nanoparticles (NP) corresponding to copper (NP-laccase), the cationic activator of this enzyme and entrapped in single walled nanotube (SWNT). The activity and stability of laccase was enhanced both at temperatures as low as 4°C and as high as 80°C in presence of NP and SWNT. The enzyme could be released and re-trapped (in SWNT) multiple times while retaining significant activity. Laccase, immobilized in SWNT, retained its activity after repeated freezing and thawing. This unique capability of SWNT to activate and stabilize cold active enzymes at temperatures much lower or higher than their optimal range may be utilized for processes that require bio-conversion at low temperatures while allowing for shifts to higher temperature if so required.
Collapse
Affiliation(s)
- Arka Mukhopadhyay
- Department of Biochemistry, University of Calcutta, West Bengal, India
| | - Anjan Kr Dasgupta
- Department of Biochemistry, University of Calcutta, West Bengal, India
| | | |
Collapse
|
23
|
Bujacz A, Rutkiewicz-Krotewicz M, Nowakowska-Sapota K, Turkiewicz M. Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6. ACTA ACUST UNITED AC 2015; 71:632-45. [PMID: 25760611 DOI: 10.1107/s1399004714028016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 12/23/2014] [Indexed: 12/20/2022]
Abstract
Aminotransferases (ATs) are enzymes that are commonly used in the chemical and pharmaceutical industries for the synthesis of natural and non-natural amino acids by transamination reactions. Currently, the easily accessible enzymes from mesophilic organisms are most commonly used; however, for economical and ecological reasons the utilization of aminotransferases from psychrophiles would be more advantageous, as their optimum reaction temperature is usually significantly lower than for the mesophilic ATs. Here, gene isolation, protein expression, purification, enzymatic properties and structural studies are reported for the cold-active aromatic amino-acid aminotransferase (PsyArAT) from Psychrobacter sp. B6, a psychrotrophic, Gram-negative strain from Antarctic soil. Preliminary computational analysis indicated dual functionality of the enzyme through the ability to utilize both aromatic amino acids and aspartate as substrates. This postulation was confirmed by enzymatic activity tests, which showed that it belonged to the class EC 2.6.1.57. The first crystal structures of a psychrophilic aromatic amino-acid aminotransferase have been determined at resolutions of 2.19 Å for the native enzyme (PsyArAT) and 2.76 Å for its complex with aspartic acid (PsyArAT/D). Both types of crystals grew in the monoclinic space group P21 under slightly different crystallization conditions. The PsyArAT crystals contained a dimer (90 kDa) in the asymmetric unit, which corresponds to the active form of this enzyme, whereas the crystals of the PsyArAT/D complex included four dimers showing different stages of the transamination reaction.
Collapse
Affiliation(s)
- Anna Bujacz
- Institute of Technical Biochemistry, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Maria Rutkiewicz-Krotewicz
- Institute of Technical Biochemistry, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Karolina Nowakowska-Sapota
- Institute of Technical Biochemistry, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Marianna Turkiewicz
- Institute of Technical Biochemistry, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland
| |
Collapse
|
24
|
Ferrer-Miralles N, Saccardo P, Corchero JL, Xu Z, García-Fruitós E. General introduction: recombinant protein production and purification of insoluble proteins. Methods Mol Biol 2015; 1258:1-24. [PMID: 25447856 DOI: 10.1007/978-1-4939-2205-5_1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Proteins are synthesized in heterologous systems because of the impossibility to obtain satisfactory yields from natural sources. The production of soluble and functional recombinant proteins is among the main goals in the biotechnological field. In this context, it is important to point out that under stress conditions, protein folding machinery is saturated and this promotes protein misfolding and, consequently, protein aggregation. Thus, the selection of the optimal expression organism and the most appropriate growth conditions to minimize the formation of insoluble proteins should be done according to the protein characteristics and downstream requirements. Escherichia coli is the most popular recombinant protein expression system despite the great development achieved so far by eukaryotic expression systems. Besides, other prokaryotic expression systems, such as lactic acid bacteria and psychrophilic bacteria, are gaining interest in this field. However, it is worth mentioning that prokaryotic expression system poses, in many cases, severe restrictions for a successful heterologous protein production. Thus, eukaryotic systems such as mammalian cells, insect cells, yeast, filamentous fungus, and microalgae are an interesting alternative for the production of these difficult-to-express proteins.
Collapse
Affiliation(s)
- Neus Ferrer-Miralles
- Departament de Genètica i de Microbiologia, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | | | | | | | | |
Collapse
|
25
|
Rummel JD, Beaty DW, Jones MA, Bakermans C, Barlow NG, Boston PJ, Chevrier VF, Clark BC, de Vera JPP, Gough RV, Hallsworth JE, Head JW, Hipkin VJ, Kieft TL, McEwen AS, Mellon MT, Mikucki JA, Nicholson WL, Omelon CR, Peterson R, Roden EE, Sherwood Lollar B, Tanaka KL, Viola D, Wray JJ. A new analysis of Mars "Special Regions": findings of the second MEPAG Special Regions Science Analysis Group (SR-SAG2). ASTROBIOLOGY 2014; 14:887-968. [PMID: 25401393 DOI: 10.1089/ast.2014.1227] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A committee of the Mars Exploration Program Analysis Group (MEPAG) has reviewed and updated the description of Special Regions on Mars as places where terrestrial organisms might replicate (per the COSPAR Planetary Protection Policy). This review and update was conducted by an international team (SR-SAG2) drawn from both the biological science and Mars exploration communities, focused on understanding when and where Special Regions could occur. The study applied recently available data about martian environments and about terrestrial organisms, building on a previous analysis of Mars Special Regions (2006) undertaken by a similar team. Since then, a new body of highly relevant information has been generated from the Mars Reconnaissance Orbiter (launched in 2005) and Phoenix (2007) and data from Mars Express and the twin Mars Exploration Rovers (all 2003). Results have also been gleaned from the Mars Science Laboratory (launched in 2011). In addition to Mars data, there is a considerable body of new data regarding the known environmental limits to life on Earth-including the potential for terrestrial microbial life to survive and replicate under martian environmental conditions. The SR-SAG2 analysis has included an examination of new Mars models relevant to natural environmental variation in water activity and temperature; a review and reconsideration of the current parameters used to define Special Regions; and updated maps and descriptions of the martian environments recommended for treatment as "Uncertain" or "Special" as natural features or those potentially formed by the influence of future landed spacecraft. Significant changes in our knowledge of the capabilities of terrestrial organisms and the existence of possibly habitable martian environments have led to a new appreciation of where Mars Special Regions may be identified and protected. The SR-SAG also considered the impact of Special Regions on potential future human missions to Mars, both as locations of potential resources and as places that should not be inadvertently contaminated by human activity.
Collapse
Affiliation(s)
- John D Rummel
- 1 Department of Biology, East Carolina University , Greenville, North Carolina, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Cold Adaptation: Structural and Functional Characterizations of Psychrophilic and Mesophilic Acetate Kinase. Protein J 2014; 33:313-22. [DOI: 10.1007/s10930-014-9562-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
27
|
Giuliani M, Parrilli E, Sannino F, Apuzzo GA, Marino G, Tutino ML. Recombinant production of a single-chain antibody fragment in Pseudoalteromonas haloplanktis TAC125. Appl Microbiol Biotechnol 2014; 98:4887-95. [DOI: 10.1007/s00253-014-5582-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/24/2014] [Accepted: 01/28/2014] [Indexed: 11/28/2022]
|
28
|
Psychrophily and catalysis. BIOLOGY 2013; 2:719-41. [PMID: 24832805 PMCID: PMC3960892 DOI: 10.3390/biology2020719] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 11/24/2022]
Abstract
Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. Since the discovery that these ecosystems, contrary to what was initially expected, sustain a rather high density and broad diversity of living organisms, increasing efforts have been dedicated to the understanding of the molecular mechanisms involved in their successful adaptation to apparently unfavorable physical conditions. The first question that comes to mind is: How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered? As most of the chemical reactions that occur in living organisms are catalyzed by enzymes, the kinetic and thermodynamic properties of cold-adapted enzymes have been investigated. Presently, many crystallographic structures of these enzymes have been elucidated and allowed for a rather clear view of their adaptation to cold. They are characterized by a high specific activity at low and moderate temperatures and a rather low thermal stability, which induces a high flexibility that prevents the freezing effect of low temperatures on structure dynamics. These enzymes also display a low activation enthalpy that renders them less dependent on temperature fluctuations. This is accompanied by a larger negative value of the activation entropy, thus giving evidence of a more disordered ground state. Appropriate folding kinetics is apparently secured through a large expression of trigger factors and peptidyl–prolyl cis/trans-isomerases.
Collapse
|
29
|
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: 159] [Impact Index Per Article: 14.5] [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.
Collapse
Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
| |
Collapse
|
30
|
Optimization to low temperature activity in psychrophilic enzymes. Int J Mol Sci 2012; 13:11643-11665. [PMID: 23109875 PMCID: PMC3472767 DOI: 10.3390/ijms130911643] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 01/20/2023] Open
Abstract
Psychrophiles, i.e., organisms thriving permanently at near-zero temperatures, synthesize cold-active enzymes to sustain their cell cycle. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. 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. Considering the subtle structural adjustments required for low temperature activity, directed evolution appears to be the most suitable methodology to engineer cold activity in biological catalysts.
Collapse
|
31
|
Corchero JL, Gasser B, Resina D, Smith W, Parrilli E, Vázquez F, Abasolo I, Giuliani M, Jäntti J, Ferrer P, Saloheimo M, Mattanovich D, Schwartz S, Tutino ML, Villaverde A. Unconventional microbial systems for the cost-efficient production of high-quality protein therapeutics. Biotechnol Adv 2012; 31:140-53. [PMID: 22985698 DOI: 10.1016/j.biotechadv.2012.09.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 09/04/2012] [Accepted: 09/07/2012] [Indexed: 12/18/2022]
Abstract
Both conventional and innovative biomedical approaches require cost-effective protein drugs with high therapeutic potency, improved bioavailability, biocompatibility, stability and pharmacokinetics. The growing longevity of the human population, the increasing incidence and prevalence of age-related diseases and the better comprehension of genetic-linked disorders prompt to develop natural and engineered drugs addressed to fulfill emerging therapeutic demands. Conventional microbial systems have been for long time exploited to produce biotherapeutics, competing with animal cells due to easier operation and lower process costs. However, both biological platforms exhibit important drawbacks (mainly associated to intracellular retention of the product, lack of post-translational modifications and conformational stresses), that cannot be overcome through further strain optimization merely due to physiological constraints. The metabolic diversity among microorganisms offers a spectrum of unconventional hosts, that, being able to bypass some of these weaknesses, are under progressive incorporation into production pipelines. In this review we describe the main biological traits and potentials of emerging bacterial, yeast, fungal and microalgae systems, by comparing selected leading species with well established conventional organisms with a long run in protein drug production.
Collapse
|
32
|
Falasca P, Evangelista G, Cotugno R, Marco S, Masullo M, De Vendittis E, Raimo G. Properties of the endogenous components of the thioredoxin system in the psychrophilic eubacterium Pseudoalteromonas haloplanktis TAC 125. Extremophiles 2012; 16:539-52. [PMID: 22527046 DOI: 10.1007/s00792-012-0453-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 04/02/2012] [Indexed: 11/30/2022]
Abstract
The endogenous components of the thioredoxin system in the Antarctic eubacterium Pseudoalteromonas haloplanktis have been purified and characterised. The temperature dependence of the activities sustained by thioredoxin (PhTrx) and thioredoxin reductase (PhTrxR) pointed to their adaptation in the cold growth environment. PhTrxR was purified as a flavoenzyme and its activity was significantly enhanced in the presence of molar concentration of monovalent cations. The energetics of the partial reactions leading to the whole electron transfer from NADPH to the target protein substrate in the reconstituted thioredoxin system was also investigated. While the initial electron transfer from NADPH to PhTrxR was energetically favoured, the final passage to the heterologous protein substrate enhanced the energetic barrier of the whole process. The energy of activation of the heat inactivation process essentially reflected the psychrophilic origin of PhTrxR. Vice versa, PhTrx possessed an exceptional heat resistance (half-life, 4.4 h at 95 °C), ranking this protein among the most thermostable enzymes reported so far in psychrophiles. PhTrxR was covalently modified by glutathione, mainly by its oxidised or nitrosylated forms. A mutagenic analysis realised on three non catalytic cysteines of the flavoenzyme allowed the identification of C(303) as the target for the S-glutathionylation reaction.
Collapse
Affiliation(s)
- Patrizia Falasca
- Dipartimento di Scienze e Tecnologie dell'Ambiente e del Territorio, Università del Molise, Contrada Fonte Lappone, 86090, Pesche, IS, Italy
| | | | | | | | | | | | | |
Collapse
|
33
|
Karan R, Capes MD, DasSarma S. Function and biotechnology of extremophilic enzymes in low water activity. AQUATIC BIOSYSTEMS 2012; 8:4. [PMID: 22480329 PMCID: PMC3310334 DOI: 10.1186/2046-9063-8-4] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 02/02/2012] [Indexed: 05/31/2023]
Abstract
Enzymes from extremophilic microorganisms usually catalyze chemical reactions in non-standard conditions. Such conditions promote aggregation, precipitation, and denaturation, reducing the activity of most non-extremophilic enzymes, frequently due to the absence of sufficient hydration. Some extremophilic enzymes maintain a tight hydration shell and remain active in solution even when liquid water is limiting, e.g. in the presence of high ionic concentrations, or at cold temperature when water is close to the freezing point. Extremophilic enzymes are able to compete for hydration via alterations especially to their surface through greater surface charges and increased molecular motion. These properties have enabled some extremophilic enzymes to function in the presence of non-aqueous organic solvents, with potential for design of useful catalysts. In this review, we summarize the current state of knowledge of extremophilic enzymes functioning in high salinity and cold temperatures, focusing on their strategy for function at low water activity. We discuss how the understanding of extremophilic enzyme function is leading to the design of a new generation of enzyme catalysts and their applications to biotechnology.
Collapse
Affiliation(s)
- Ram Karan
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute of Marine and Environmental Technology, University System of Maryland, Baltimore, MD, USA
| | - Melinda D Capes
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute of Marine and Environmental Technology, University System of Maryland, Baltimore, MD, USA
| | - Shiladitya DasSarma
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute of Marine and Environmental Technology, University System of Maryland, Baltimore, MD, USA
| |
Collapse
|
34
|
Serine hydroxymethyltransferase from the cold adapted microorganism Psychromonas ingrahamii: a low temperature active enzyme with broad substrate specificity. Int J Mol Sci 2012; 13:1314-1326. [PMID: 22408393 PMCID: PMC3291962 DOI: 10.3390/ijms13021314] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/12/2012] [Accepted: 01/12/2012] [Indexed: 11/17/2022] Open
Abstract
Serine hydroxymethyltransferase from the psychrophilic microorganism Psychromonas ingrahamii was expressed in Escherichia coli and purified as a His-tag fusion protein. The enzyme was characterized with respect to its spectroscopic, catalytic, and thermodynamic properties. The properties of the psychrophilic enzyme have been contrasted with the characteristics of the homologous counterpart from E. coli, which has been structurally and functionally characterized in depth and with which it shares 75% sequence identity. Spectroscopic measures confirmed that the psychrophilic enzyme displays structural properties almost identical to those of the mesophilic counterpart. At variance, the P. ingrahamii enzyme showed decreased thermostability and high specific activity at low temperature, both of which are typical features of cold adapted enzymes. Furthermore, it was a more efficient biocatalyst compared to E. coli serine hydroxymethyltransferase (SHMT) particularly for side reactions. Many β-hydroxy-α-amino acids are SHMT substrates and represent important compounds in the synthesis of pharmaceuticals, agrochemicals and food additives. Thanks to these attractive properties, this enzyme could have a significant potential for biotechnological applications.
Collapse
|
35
|
Romoli R, Papaleo MC, de Pascale D, Tutino ML, Michaud L, LoGiudice A, Fani R, Bartolucci G. Characterization of the volatile profile of Antarctic bacteria by using solid-phase microextraction-gas chromatography-mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:1051-9. [PMID: 22012672 DOI: 10.1002/jms.1987] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Bacteria belonging to the Burkholderia cepacia complex (Bcc) are significant pathogens in Cystic Fibrosis (CF) patients and are resistant to a plethora of antibiotics. In this context, microorganisms from Antarctica are interesting because they produce antimicrobial compounds inhibiting the growth of other bacteria. This is particularly true for bacteria isolated from Antarctic sponges. The aim of this work was to characterize a set of Antarctic bacteria for their ability to produce new natural drugs that could be exploited in the control of infections in CF patients by Bcc bacteria. Hence, 11 bacterial strains allocated to different genera (e.g., Pseudoalteromonas, Arthrobacter and Psychrobacter) were tested for their ability to inhibit the growth of 21 Bcc strains and some other human pathogens. All these bacteria completely inhibited the growth of most, if not all, Bcc strains, suggesting a highly specific activity toward Bcc strains. Experimental evidences showed that the antimicrobial compounds are small volatile organic compounds, and are constitutively produced via an unknown pathway. The microbial volatile profile was obtained by SPME-GC-MS within the m/z interval of 40-450. Solid phase micro extraction technique affords the possibility to extract the volatile compounds in head space with a minimal sample perturbation. Principal component analysis and successive cluster discriminant analysis was applied to evaluate the relationships among the volatile organic compounds with the aim of classifying the microorganisms by their volatile profile. These data highlight the potentiality of Antarctic bacteria as novel sources of antibacterial substances to face Bcc infections in CF patients.
Collapse
Affiliation(s)
- Riccardo Romoli
- Dipartimento di Produzioni Vegetali, del Suolo e dell'Ambiente Agroforestale (DIPSA), Firenze, Italy.
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Wilmes B, Kock H, Glagla S, Albrecht D, Voigt B, Markert S, Gardebrecht A, Bode R, Danchin A, Feller G, Hecker M, Schweder T. Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125. Appl Environ Microbiol 2011; 77:1276-83. [PMID: 21183643 PMCID: PMC3067249 DOI: 10.1128/aem.01750-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/13/2010] [Indexed: 11/20/2022] Open
Abstract
The psychrophilic model bacterium Pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, of P. haloplanktis strain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacterium P. haloplanktis in its natural environments.
Collapse
Affiliation(s)
- Boris Wilmes
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Holger Kock
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Susanne Glagla
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Dirk Albrecht
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Birgit Voigt
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Stephanie Markert
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Antje Gardebrecht
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Rüdiger Bode
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Antoine Danchin
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Georges Feller
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Michael Hecker
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Thomas Schweder
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| |
Collapse
|
37
|
Wilmes B, Hartung A, Lalk M, Liebeke M, Schweder T, Neubauer P. Fed-batch process for the psychrotolerant marine bacterium Pseudoalteromonas haloplanktis. Microb Cell Fact 2010; 9:72. [PMID: 20858251 PMCID: PMC2954877 DOI: 10.1186/1475-2859-9-72] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 09/21/2010] [Indexed: 11/30/2022] Open
Abstract
Background Pseudoalteromonas haloplanktis is a cold-adapted γ-proteobacterium isolated from Antarctic sea ice. It is characterized by remarkably high growth rates at low temperatures. P. haloplanktis is one of the model organisms of cold-adapted bacteria and has been suggested as an alternative host for the soluble overproduction of heterologous proteins which tend to form inclusion bodies in established expression hosts. Despite the progress in establishing P. haloplanktis as an alternative expression host the cell densities obtained with this organism, which is unable to use glucose as a carbon source, are still low. Here we present the first fed-batch cultivation strategy for this auspicious alternative expression host. Results The key for the fed-batch cultivation of P. haloplanktis was the replacement of peptone by casamino acids, which have a much higher solubility and allow a better growth control. In contrast to the peptone medium, on which P. haloplanktis showed different growth phases, on a casamino acids-containing, phosphate-buffered medium P. haloplanktis grew exponentially with a constant growth rate until the stationary phase. A fed-batch process was established by feeding of casamino acids with a constant rate resulting in a cell dry weight of about 11 g l-1 (OD540 = 28) which is a twofold increase of the highest densities which have been obtained with P. haloplanktis so far and an eightfold increase of the density obtained in standard shake flask cultures. The cell density was limited in the fed-batch cultivation by the relatively low solubility of casamino acids (about 100 g l-1), which was proven by pulse addition of casamino acid powder which increased the cell density to about 20 g l-1 (OD540 = 55). Conclusion The growth of P. haloplanktis to higher cell densities on complex medium is possible. A first fed-batch fermentation strategy could be established which is feasible to be used in lab-scale or for industrial purposes. The substrate concentration of the feeding solution was found to influence the maximal biomass yield considerably. The bottleneck for growing P. haloplanktis to high cell densities still remains the availability of a highly concentrated substrate and the reduction of the substrate complexity. However, our results indicate glutamic acid as a major carbon source, which provides a good basis for further improvement of the fed-batch process.
Collapse
Affiliation(s)
- Boris Wilmes
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49, D-17489 Greifswald, Germany
| | | | | | | | | | | |
Collapse
|
38
|
Characterization of the RNA degradosome of Pseudoalteromonas haloplanktis: conservation of the RNase E-RhlB interaction in the gammaproteobacteria. J Bacteriol 2010; 192:5413-23. [PMID: 20729366 DOI: 10.1128/jb.00592-10] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The degradosome is a multienzyme complex involved in mRNA degradation in Escherichia coli. The essential endoribonuclease RNase E contains a large noncatalytic region necessary for protein-protein interactions with other components of the RNA degradosome. Interacting proteins include the DEAD-box RNA helicase RhlB, the glycolytic enzyme enolase, and the exoribonuclease PNPase. Pseudoalteromonas haloplanktis, a psychrotolerant gammaproteobacterium distantly related to E. coli, encodes homologs of each component of the RNA degradosome. In P. haloplanktis, RNase E associates with RhlB and PNPase but not enolase. Plasmids expressing P. haloplanktis RNase E (Ph-RNase E) can complement E. coli strains lacking E. coli RNase E (Ec-RNase E). Ph-RNase E, however, does not confer a growth advantage to E. coli at low temperature. Ph-RNase E has a heterologous protein-protein interaction with Ec-RhlB but not with Ec-enolase or Ec-PNPase. The Ph-RNase E binding sites for RhlB and PNPase were mapped by deletion analysis. The PNPase binding site is located at the C-terminal end of Ph-RNase E at the same position as that in Ec-RNase E, but the sequence of the site is not conserved. The sequence of the RhlB binding site in Ph-RNase E is related to the sequence in Ec-RNase E. Together with the heterologous interaction between Ph-RNase E and Ec-RhlB, our results suggest that the underlying structural motif for the RNase E-RhlB interaction is conserved. Since the activity of Ec-RhlB requires its physical interaction with Ec-RNase E, conservation of the underlying structural motif over a large evolutionary distance could be due to constraints involved in the control of RhlB activity.
Collapse
|
39
|
Sundareswaran VR, Singh AK, Dube S, Shivaji S. Aspartate aminotransferase is involved in cold adaptation in psychrophilic Pseudomonas syringae. Arch Microbiol 2010; 192:663-72. [DOI: 10.1007/s00203-010-0591-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 05/19/2010] [Accepted: 05/21/2010] [Indexed: 11/28/2022]
|
40
|
Papa R, Rippa V, Duilio A. Identification of the transcription factor responsible for L-malate-dependent regulation in the marine Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. FEMS Microbiol Lett 2009; 295:177-86. [PMID: 19646180 DOI: 10.1111/j.1574-6968.2009.01589.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Two-component systems are widespread in nature and constitute the most common mechanism of transmembrane signal transduction in bacteria. Recently, a functionally active two-component system consisting of malS and malR genes possibly involved in the expression of a C4-dicarboxylate transporter system (dctAB operon) was identified in the marine Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. In this paper, we performed a functional analysis of the two-component system and demonstrated its involvement in the regulation of the expression of C4-dicarboxylate transporter genes. The expression of the C4-dicarboxylate transporter genes was induced by l-malate with the promoter element located upstream of the dctA gene being active only in the presence of the inducer. A sigma(54) promoter responsible for the l-malate dependent transcription regulation was identified and functionally characterized. The molecular mechanism involves an inverted repeat sequence located upstream the sigma(54) promoter that was shown to bind regulatory proteins only in the presence of l-malate. The protein factor responsible for the induction of the dctAB operon expression was eventually identified as the transcriptional regulatory protein MalR. MalR is the first transcriptional factor identified in P. haloplanktis TAC125 and one of the few transcriptional modulators reported so far in cold adapted bacteria.
Collapse
Affiliation(s)
- Rosanna Papa
- Department of Public Health Sciences, La Sapienza University, Rome, Italy
| | | | | |
Collapse
|
41
|
Papa R, Parrilli E, Sannia G. Engineered marine Antarctic bacteriumPseudoalteromonas haloplanktisTAC125: a promising micro-organism for the bioremediation of aromatic compounds. J Appl Microbiol 2009; 106:49-56. [DOI: 10.1111/j.1365-2672.2008.03971.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
42
|
Guaragna A, Amoresano A, Pinto V, Monti G, Mastrobuoni G, Marino G. Synthesis and Proteomic Activity Evaluation of a new Isotope-Coded Affinity Tagging (ICAT) Reagent. Bioconjug Chem 2008; 19:1095-104. [DOI: 10.1021/bc800010b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Annalisa Guaragna
- Dipartimento di Chimica Organica e Biochimica Università di Napoli Federico II Via Cinthia, 4 I-80126 Napoli, Italy
| | - Angela Amoresano
- Dipartimento di Chimica Organica e Biochimica Università di Napoli Federico II Via Cinthia, 4 I-80126 Napoli, Italy
| | - Vittoria Pinto
- Dipartimento di Chimica Organica e Biochimica Università di Napoli Federico II Via Cinthia, 4 I-80126 Napoli, Italy
| | - Gianluca Monti
- Dipartimento di Chimica Organica e Biochimica Università di Napoli Federico II Via Cinthia, 4 I-80126 Napoli, Italy
| | - Guido Mastrobuoni
- Dipartimento di Chimica Organica e Biochimica Università di Napoli Federico II Via Cinthia, 4 I-80126 Napoli, Italy
| | - Gennaro Marino
- Dipartimento di Chimica Organica e Biochimica Università di Napoli Federico II Via Cinthia, 4 I-80126 Napoli, Italy
| |
Collapse
|
43
|
Ruggiero I, Raimo G, Palma M, Arcari P, Masullo M. Molecular and functional properties of the psychrophilic elongation factor G from the Antarctic Eubacterium Pseudoalteromonas haloplanktis TAC 125. Extremophiles 2007; 11:699-709. [PMID: 17541754 DOI: 10.1007/s00792-007-0088-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 04/17/2007] [Indexed: 11/25/2022]
Abstract
The molecular and functional properties of the elongation factor (EF) G from the psychrophilic Antarctic eubacterium Pseudoalteromonas haloplanktis (Ph) were studied. PhEF-G catalyzed protein synthesis in vitro that was inhibited by fusidic acid, an antibiotic specifically acting on EF-G. The EF interacted with GDP only in the presence of P. haloplanktis ribosome and fusidic acid with an affinity similar to that displayed by Escherichia coli EF-G. The psychrophilic translocase elicited a ribosome-dependent GTPase that was competitively inhibited by GDP, the slowly hydrolyzable GTP analog GppNHp, and the protein synthesis inhibitor ppGDP. The temperature dependence of the activity of PhEF-G reached its maximum at least 26 degrees C beyond the growth temperature of P. haloplanktis (4-20 degrees C). The heat inactivation profile of the ribosome-dependent GTPase of PhEF-G gave a temperature for half inactivation (46 degrees C), significantly lower than that for half denaturation measured by either UV- (57 degrees C) or fluorescence-melting (62 degrees C). This finding was attributed to a different effect of the temperature on the catalytic domain with respect to that elicited on the other domains constituting the EF, thus confirming the differential molecular flexibility present in psychrophilic enzymes. A molecular model, based on the 3D coordinates of a thermophilic EF-G, showed differences only in connecting loops.
Collapse
Affiliation(s)
- Immacolata Ruggiero
- Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | | | | | | | | |
Collapse
|
44
|
Abstract
By far the largest proportion of the Earth's biosphere is comprised of organisms that thrive in cold environments (psychrophiles). Their ability to proliferate in the cold is predicated on a capacity to synthesize cold-adapted enzymes. These enzymes have evolved a range of structural features that confer a high level of flexibility compared to thermostable homologs. High flexibility, particularly around the active site, is translated into low-activation enthalpy, low-substrate affinity, and high specific activity at low temperatures. High flexibility is also accompanied by a trade-off in stability, resulting in heat lability and, in the few cases studied, cold lability. This review addresses the structure, function, and stability of cold-adapted enzymes, highlighting the challenges for immediate and future consideration. Because of the unique properties of cold-adapted enzymes, they are not only an important focus in extremophile biology, but also represent a valuable model for fundamental research into protein folding and catalysis.
Collapse
Affiliation(s)
- Khawar Sohail Siddiqui
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
| | | |
Collapse
|
45
|
Papa R, Rippa V, Sannia G, Marino G, Duilio A. An effective cold inducible expression system developed in Pseudoalteromonas haloplanktis TAC125. J Biotechnol 2007; 127:199-210. [PMID: 16959351 DOI: 10.1016/j.jbiotec.2006.07.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 05/18/2006] [Accepted: 07/02/2006] [Indexed: 11/23/2022]
Abstract
A regulative two-component system previously identified in Pseudoalteromonas haloplanktis TAC125 was used to construct a cold inducible expression system that is under the control of l-malate. Performances of the inducible system were tested for both psychrophilic and mesophilic protein production using two "difficult" proteins as control. The results obtained demonstrated that both psychrophilic beta-galactosidase and yeast alpha-glucosidase are produced in a fully soluble and catalytically competent form. Optimal conditions for protein production, including growth temperature, growth medium and l-malate concentration were also investigated. Under optimized conditions yields of 620 and 27 mg/l were obtained for beta-galactosidase and alpha-glucosidase, respectively.
Collapse
Affiliation(s)
- Rosanna Papa
- Department of Organic Chemistry and Biochemistry, Federico II University of Naples, Napoli, Italy
| | | | | | | | | |
Collapse
|
46
|
Vigentini I, Merico A, Tutino ML, Compagno C, Marino G. Optimization of recombinant human nerve growth factor production in the psychrophilic Pseudoalteromonas haloplanktis. J Biotechnol 2006; 127:141-50. [PMID: 16859797 DOI: 10.1016/j.jbiotec.2006.05.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Revised: 04/26/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
The optimization of production strategy is a very useful tool to attain high level of recombinant protein at a low cost. A promising biotechnological application of psychrophilic bacteria is their use as non-conventional host for the recombinant production of useful proteins. The lowering of the expression temperature can in fact facilitate the correct folding of heterologous proteins that accumulate in insoluble form as inclusion bodies when produced in Escherichia coli. An example of such "difficult" proteins is the human nerve growth factor (hNGF). The gene encoding the mature form of hNGF was expressed in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 at 4 degrees C. Western blotting experiments demonstrated that the protein was produced in soluble form and translocated in the periplasmic space. Furthermore, an analytical gel filtration chromatography confirmed that the recombinant protein was largely in dimeric form. For a more efficient recombinant rhNGF production, the influence of cultivation operational strategies and growth conditions (medium composition, temperature, specific growth rate) on biomass yield and recombinant protein production was investigated in batch and chemostat cultivations. The highest product yield of soluble rhNGF (7.5mg(NGF)g(dryweight)(-1)) has been achieved in batch culture at 4 degrees C on Schatz medium with addition of tryptone and vitamins.
Collapse
Affiliation(s)
- Ileana Vigentini
- Università degli Studi di Milano, Dipartimento di Scienze Biomolecolari e Biotecnologie, Via Celoria, 26 20133 Milano, Italy
| | | | | | | | | |
Collapse
|
47
|
Papa R, Rippa V, Sannia G, Marino G, Duilio A. Recombinant protein expression system in cold loving microorganisms. Microb Cell Fact 2006. [DOI: 10.1186/1475-2859-5-s1-s37] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
48
|
Castellano I, Di Maro A, Ruocco MR, Chambery A, Parente A, Di Martino MT, Parlato G, Masullo M, De Vendittis E. Psychrophilic superoxide dismutase from Pseudoalteromonas haloplanktis: biochemical characterization and identification of a highly reactive cysteine residue. Biochimie 2006; 88:1377-89. [PMID: 16713057 DOI: 10.1016/j.biochi.2006.04.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Accepted: 04/03/2006] [Indexed: 01/19/2023]
Abstract
A psychrophilic superoxide dismutase (SOD) has been characterized from the Antarctic eubacterium Pseudoalteromonas haloplanktis (Ph). PhSOD is a homodimeric iron-containing enzyme and displays a high specific activity, even at low temperature. The enzyme is inhibited by sodium azide and inactivated by hydrogen peroxide; it is also very sensitive to peroxynitrite, a physiological inactivator of the human mitochondrial Mn-SOD. Even though PhSOD is isolated from a cold-adapted micro-organism, its heat stability is well above the maximum growth temperature of P. haloplanktis, a feature common to other Fe- and Mn-SODs. The primary structure of PhSOD was determined by a combination of mass spectrometry and automated Edman degradation. The polypeptide chain is made of 192 amino acid residues, corresponding to a molecular mass of 21251 Da. The alignment with other Fe- and Mn-SODs showed a high amino acid identity with Fe-SOD from Vibrio cholerae (79%) and Escherichia coli (70%). A significant similarity is also shared with human mitochondrial Mn-SOD. PhSOD has the unique and highly reactive Cys57 residue, located in a variable region of the protein. The three-dimensional model of the PhSOD monomer indicates that Cys57 is included in a region, whose structural organization apparently discriminates between dimeric and tetrameric SODs. This residue forms a disulfide adduct with beta-mercaptoethanol, when this reducing agent is added in the purification procedure. The reactivity of Cys57 leads also to the formation of a disulfide bridge between two PhSOD subunits in specific denaturing conditions. The possible modification of Cys57 by physiological thiols, eventually regulating the PhSOD functioning, is discussed.
Collapse
Affiliation(s)
- I Castellano
- Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Via S. Pansini 5, 80131 Napoli, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Pálsdóttir HM, Gudmundsdóttir A. Expression and purification of a cold-adapted group III trypsin in Escherichia coli. Protein Expr Purif 2006; 51:243-52. [PMID: 16879980 DOI: 10.1016/j.pep.2006.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 06/12/2006] [Indexed: 10/24/2022]
Abstract
The recently classified group III trypsins include members like Atlantic cod (Gadus morhua) trypsin Y as well as seven analogues from other cold-adapted fish species. The eight group III trypsins have been characterized from their cDNAs and deduced amino acid sequences but none of the enzymes have been isolated from their native sources. This study describes the successful expression and purification of a recombinant HP-thioredoxin-trypsin Y fusion protein in the His-Patch ThioFusion Escherichia coli expression system and its purification by chromatographic methods. The recombinant form of trypsin Y was previously expressed in Pichia pastoris making it the first biochemically characterized group III trypsin. It has dual substrate specificity towards trypsin and chymotrypsin substrates and demonstrates an increasing activity at temperatures between 2 and 21 degrees C with a complete inactivation at 30 degrees C. The aim of the study was to facilitate further studies of recombinant trypsin Y by finding an expression system yielding higher amounts of the enzyme than possible in our hands in the P. pastoris system. Also, commercial production of trypsin Y will require an efficient and inexpensive expression system like the His-Patch ThioFusion E. coli expression system described here as the enzyme is produced in very low amounts in the Atlantic cod.
Collapse
Affiliation(s)
- Helga Margrét Pálsdóttir
- Science Institute, University of Iceland, Laeknagardi, Vatnsmýrarvegi 16, Reykjavík IS-101, Iceland
| | | |
Collapse
|
50
|
Papa R, Glagla S, Danchin A, Schweder T, Marino G, Duilio A. Proteomic identification of a two-component regulatory system in Pseudoalteromonas haloplanktis TAC125. Extremophiles 2006; 10:483-91. [PMID: 16791470 DOI: 10.1007/s00792-006-0525-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
The capability of microorganisms to utilize different carbohydrates as energy source reflects the availability of these substrates in their habitat. Investigation of the proteins involved in carbohydrate usage, in parallel with analysis of their expression, is then likely to provide information on the interaction between microorganisms and their ecosystem. We analysed the growth behaviour of the marine Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 in the presence and in the absence of different carbon source. A marked increase in the optical density was detected when L: -malate was added to the growth medium. Bacterial proteins differently expressed in the presence of L: -malate were identified by proteomic profiling experiments. On the basis of their relative increase, six proteins were selected for further analyses. Among these, the expression of a putative outer membrane porin was demonstrated to be heavily induced by L: -malate. The presence of a functionally active two-component regulatory system very likely controlled by L: -malate was found in the upstream region of the porin gene. A non functional genomic porin mutant was then constructed showing a direct involvement of the protein in the uptake of L: -malate. To the best of our knowledge, the occurrence of such a regulatory system has never been reported in Pseudoalteromonads so far and might constitute a key step in the development of an effective inducible cold expression system.
Collapse
Affiliation(s)
- Rosanna Papa
- Department of Organic Chemistry and Biochemistry, Federico II University of Naples, Napoli, Italy
| | | | | | | | | | | |
Collapse
|