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Purcarea C, Ruginescu R, Banciu RM, Vasilescu A. Extremozyme-Based Biosensors for Environmental Pollution Monitoring: Recent Developments. BIOSENSORS 2024; 14:143. [PMID: 38534250 DOI: 10.3390/bios14030143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Extremozymes combine high specificity and sensitivity with the ability to withstand extreme operational conditions. This work presents an overview of extremozymes that show potential for environmental monitoring devices and outlines the latest advances in biosensors utilizing these unique molecules. The characteristics of various extremozymes described so far are presented, underlining their stability and operational conditions that make them attractive for biosensing. The biosensor design is discussed based on the detection of photosynthesis-inhibiting herbicides as a case study. Several biosensors for the detection of pesticides, heavy metals, and phenols are presented in more detail to highlight interesting substrate specificity, applications or immobilization methods. Compared to mesophilic enzymes, the integration of extremozymes in biosensors faces additional challenges related to lower availability and high production costs. The use of extremozymes in biosensing does not parallel their success in industrial applications. In recent years, the "collection" of recognition elements was enriched by extremozymes with interesting selectivity and by thermostable chimeras. The perspectives for biosensor development are exciting, considering also the progress in genetic editing for the oriented immobilization of enzymes, efficient folding, and better electron transport. Stability, production costs and immobilization at sensing interfaces must be improved to encourage wider applications of extremozymes in biosensors.
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Affiliation(s)
- Cristina Purcarea
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Robert Ruginescu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, 060031 Bucharest, Romania
| | - Roberta Maria Banciu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania
- Department of Analytical and Physical Chemistry, University of Bucharest, 4-12 Regina Elisabeta Blvd., 030018 Bucharest, Romania
| | - Alina Vasilescu
- International Centre of Biodynamics, 1B Intrarea Portocalelor, 060101 Bucharest, Romania
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2
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Amangeldina A, Tan ZW, Berezovsky IN. Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation. Curr Res Struct Biol 2024; 7:100129. [PMID: 38327713 PMCID: PMC10847869 DOI: 10.1016/j.crstbi.2024.100129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme environmental conditions, it is possible to explore the genomic-proteomic compositional determinants of molecular mechanisms of adaptation developed by them in response to harsh environmental conditions. Using a wealth of currently available complete genomes/proteomes we were able to explore signatures of adaptation to three environmental factors, pH, salinity, and temperature, observing major trends in compositions of their nucleic acids and proteins. We derived predictors of thermostability, halophilic, and pH adaptations and complemented them by the principal components analysis. We observed a clear difference between thermophilic and salinity/pH adaptations, whereas latter invoke seemingly overlapping mechanisms. The genome-proteome compositional trade-off reveals an intricate balance between the work of base paring and base stacking in stabilization of coding DNA and r/tRNAs, and, at the same time, universal requirements for the stability and foldability of proteins regardless of the nucleotide biases. Nevertheless, we still found hidden fingerprints of ancient evolutionary connections between the nucleotide and amino acid compositions indicating their emergence, mutual evolution, and adjustment. The evolutionary perspective on the adaptation mechanisms is further studied here by means of the comparative analysis of genomic/proteomic traits of archaeal and bacterial species. The overall picture of genomic/proteomic signals of adaptation obtained here provides a foundation for future engineering and design of functional biomolecules resistant to harsh environments.
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Affiliation(s)
- Aidana Amangeldina
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
| | - Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Igor N. Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
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3
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Ashcroft E, Munoz-Munoz J. A review of the principles and biotechnological applications of glycoside hydrolases from extreme environments. Int J Biol Macromol 2024; 259:129227. [PMID: 38185295 DOI: 10.1016/j.ijbiomac.2024.129227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
It is apparent that Biocatalysts are shaping the future by providing a more sustainable approach to established chemical processes. Industrial processes rely heavily on the use of toxic compounds and high energy or pH reactions, factors that both contributes to the worsening climate crisis. Enzymes found in bacterial systems and other microorganisms, from the glaciers of the Arctic to the sandy deserts of Abu Dhabi, provide key tools and understanding as to how we can progress in the biotechnology sector. These extremophilic bacteria harness the adaptive enzymes capable of withstanding harsh reaction conditions in terms of stability and reactivity. Carbohydrate-active enzymes, including glycoside hydrolases or carbohydrate esterases, are extremely beneficial for the presence and future of biocatalysis. Their involvement in the industry spans from laundry detergents to paper and pulp treatment by degrading oligo/polysaccharides into their monomeric products in almost all detrimental environments. This includes exceedingly high temperatures, pHs or even in the absence of water. In this review, we discuss the structure and function of different glycoside hydrolases from extremophiles, and how they can be applied to industrial-scale reactions to replace the use of harsh chemicals, reduce waste, or decrease energy consumption.
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Affiliation(s)
- Ellie Ashcroft
- Microbial Enzymology Lab, Department of Applied Sciences, Ellison Building A, Northumbria University, Newcastle Upon Tyne NE1 8ST, United Kingdom.
| | - Jose Munoz-Munoz
- Microbial Enzymology Lab, Department of Applied Sciences, Ellison Building A, Northumbria University, Newcastle Upon Tyne NE1 8ST, United Kingdom.
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4
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Jang J, Chang JH. Molecular Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24065139. [PMID: 36982214 PMCID: PMC10049462 DOI: 10.3390/ijms24065139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/10/2023] Open
Abstract
Phosphoserine aminotransferase (PSAT) is a pyridoxal 5′-phosphate-dependent enzyme involved in the second step of the phosphorylated pathway of serine biosynthesis. PSAT catalyzes the transamination of 3-phosphohydroxypyruvate to 3-phosphoserine using L-glutamate as the amino donor. Although structural studies of PSAT have been performed from archaea and humans, no structural information is available from fungi. Therefore, to elucidate the structural features of fungal PSAT, we determined the crystal structure of Saccharomyces cerevisiae PSAT (ScPSAT) at a resolution of 2.8 Å. The results demonstrated that the ScPSAT protein was dimeric in its crystal structure. Moreover, the gate-keeping loop of ScPSAT exhibited a conformation similar to that of other species. Several distinct structural features in the halide-binding and active sites of ScPSAT were compared with its homologs. Overall, this study contributes to our current understanding of PSAT by identifying the structural features of fungal PSAT for the first time.
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Affiliation(s)
- Jiyeon Jang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Department of Biomedical Convergence Science and Technology, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Correspondence: ; Tel.: +82-53-950-5913; Fax: +82-53-950-6809
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5
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Marchesani F, Zangelmi E, Murtas G, Costanzi E, Ullah R, Peracchi A, Bruno S, Pollegioni L, Mozzarelli A, Storici P, Campanini B. L-Serine Biosynthesis in The Human Central Nervous System: Structure and Function of Phosphoserine Aminotransferase. Protein Sci 2023; 32:e4609. [PMID: 36851825 PMCID: PMC10031235 DOI: 10.1002/pro.4609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/12/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
Organisms from all kingdoms of life synthesize L-serine from 3-phosphoglycerate through the phosphorylated pathway, a three-step diversion of glycolysis. Phosphoserine aminotransferase (PSAT) catalyzes the intermediate step, the pyridoxal 5'-phosphate-dependent transamination of 3-phosphohydroxypyruvate and L-glutamate to O-phosphoserine and α-ketoglutarate. PSAT is particularly relevant in the central nervous system of mammals because L-serine is the metabolic precursor of D-serine, cysteine, phospholipids, and nucleotides. Several mutations in the human psat gene have been linked to serine deficiency disorders, characterized by severe neurological symptoms. Furthermore, PSAT is overexpressed in many tumors and this overexpression has been associated with poor clinical outcomes. Here, we report the detailed functional and structural characterization of the recombinant human PSAT. The reaction catalyzed by PSAT is reversible, with an equilibrium constant of about 10, and the enzyme is very efficient, with a kcat /Km of 5.9 × 106 M-1 s-1 , thus contributing in driving the pathway towards the products despite the extremely unfavorable first step catalyzed by 3-phosphoglycerate dehydrogenase. The three-dimensional X-ray crystal structure of PSAT was solved in the substrate-free as well as in the O-phosphoserine-bound forms. Both structures contain eight protein molecules in the asymmetric unit, arranged in four dimers, with a bound cofactor in each subunit. In the substrate-free form, the active site of PSAT contains a sulfate ion that, in the substrate-bound form, is replaced by the phosphate group of O-phosphoserine. Interestingly, fast crystal soaking used to produce the substrate-bound form allowed the trapping of different intermediates along the catalytic cycle. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elisa Costanzi
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Raheem Ullah
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
- Present address: Structural Biology Lab, NIBGE, Faisalabad, Pakistan
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | | | - Paola Storici
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
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Naykodi A, Patankar SC, Thorat BN. Alkaliphiles for comprehensive utilization of red mud (bauxite residue)-an alkaline waste from the alumina refinery. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:9350-9368. [PMID: 36480139 DOI: 10.1007/s11356-022-24190-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
The mining industry has powered the human endeavor to make life more innovative, flexible, and comfortable. However, it has also led to concerns due to the increasing amount of mining and associated industrial waste. Special attention is highly desired for its proper management and safe disposal in the environment. The problem has only augmented with the increase in the mining costs because of the investments needed for ecological remediation after the mining operation. It is pertinent that the targeted technologies need to be developed to utilize mining and associated industrial waste as a secondary resource to ensure sustainable mining operations. Every perceived waste is a valuable resource that is needed to be utilized to create additional value. In this review, the case of alkaline bauxite residue (red mud)-alumina refinery waste has been discussed at length. The highlight of the proposed work is to understand the importance of alkaliphile-assisted biomining-a sustainable alternative to conventional metal recovery processes. Along with the recovery of metals, pH reduction of red mud is possible through biomining, which ultimately paves the way for its complete utilization. The unique adaptation strategies of alkaliphiles make them more suitable for biomining of red mud through bioleaching, biosorption, and bioaccumulation, which have been discussed here. Furthermore, we have focused on the potential of the indigenous microflora of red mud for metal recovery in addition to its neutralization. The study of indigenous alkaliphiles from red mud, including its isolation and propagation, is crucial for the industrial-scale application of alkaliphile-based technology and has been emphasized.
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Affiliation(s)
- Ankita Naykodi
- Department of Biotechnology, Institute of Chemical Technology-IndianOil Odisha Campus, Bhubaneswar, 751013, Odisha, India
| | - Saurabh C Patankar
- Department of Chemical Engineering, Institute of Chemical Technology-IndianOil Odisha Campus, Bhubaneswar, 751013, Odisha, India
| | - Bhaskar N Thorat
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, 400019, India.
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7
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Somayaji A, Dhanjal CR, Lingamsetty R, Vinayagam R, Selvaraj R, Varadavenkatesan T, Govarthanan M. An insight into the mechanisms of homeostasis in extremophiles. Microbiol Res 2022; 263:127115. [PMID: 35868258 DOI: 10.1016/j.micres.2022.127115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023]
Abstract
The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chetan Roger Dhanjal
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rathnamegha Lingamsetty
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India.
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8
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Singh RK, Kumar D, Gourinath S. Phosphoserine aminotransferase has conserved active site from microbes to higher eukaryotes with minor deviations. Protein Pept Lett 2021; 28:996-1008. [PMID: 33588715 DOI: 10.2174/0929866528666210215140231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 11/22/2022]
Abstract
Serine is ubiquitously synthesized in all living organisms from the glycolysis intermediate 3-phosphoglycerate (PGA) by phosphoserine biosynthetic pathway, consisting of three different enzymes, namely: 3-phosphoglycerate dehydrogenase (PGDH), phosphoserine aminotransferase (PSAT), and phosphoserine phosphatase (PSP). Any functional defect or mutation in these enzymes may cause deliberating conditions, such as colon cancer progression and chemoresistance in humans. Phosphoserine aminotransferase (PSAT) is the second enzyme in this pathway that converts phosphohydroxypyruvate (PHP) to O-phospho-L-serine (OPLS). Humans encode two isoforms of this enzyme: PSAT1 and PSAT2. PSAT1 exists as a functional dimer, where each protomer has a large and a small domain; each large domain contains a Lys residue that covalently binds PLP. The PLP-binding site of human PSAT1 and most of its active site residues are highly conserved in all known PSAT structures except for Cys-80. Interestingly, Two PSAT structures from different organisms show halide binding near their active site. While the human PSAT1 shows a water molecule at this site with different interacting residues, suggesting the inability of halide binding in the human enzyme. Analysis of the human PSAT1 structure showed a big patch of positive charge around the active site, in contrast to the bacterial PSATs. Compared to human PSAT1, the PSAT2 isoform lacks 46 residues at its C-terminal tail. This tail region is present at the opening of the active site as observed in the other PSAT structures. Further structural work on human PSAT2 may reveal the functional importance of these 46 residues.
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Affiliation(s)
- Rohit Kumar Singh
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067. India
| | - Devbrat Kumar
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067. India
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067. India
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9
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A simple and reliable method for determination of optimum pH in coupled enzyme assays. Biotechniques 2020; 68:200-203. [DOI: 10.2144/btn-2019-0126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Determination of the optimum pH in a coupled enzyme assay poses significant challenges because altering the pH of the reaction mixture can affect the performance of both enzymes. Here, we demonstrate a simple and reliable method to determine the pH optimum for pyruvate kinase using the pyruvate kinase/lactate dehydrogenase coupled enzyme assay. This simple and reliable method can be broadly adapted to determine the pH optimum for various enzymes that are assayed using a coupled enzyme assay.
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10
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Liu T, Guo X, Bu Y, Zhou Y, Duan Y, Yang Q. Structural and biochemical insights into an insect gut-specific chitinase with antifungal activity. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 119:103326. [PMID: 31968227 DOI: 10.1016/j.ibmb.2020.103326] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/08/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
The antifungal activity of insect chitinase has rarely been studied. Here, we show that chitinase ChtIV, which is specifically expressed in the midgut of Asian corn borer (Ostrinia furnacalis), has antifungal activity toward phytopathogenic fungi. ChtIV exhibited high stability and mycelial hydrolytic activity in the extreme midgut environment, which has a pH of 10 and is rich in proteases. Hyper-N-glycosylation and reduced electrostatic interactions ensure the stability of ChtIV in the midgut. The structural characteristics of ChtIV are similar to two plant antifungal chitinases but distinct from an insect chitinase for cuticular chitin degradation in both the substrate-binding cleft and auxiliary binding motif. Since the phytopathogenic fungi are those that frequently invade corn, ChtIV may play a role in insect immune system and become a potential pesticide target. The crystal structures of ChtIV and its complexes with penta-N-acetylchitopentaose (a substrate) and allosamidin (an inhibitor) were obtained, which may facilitate rational design of ChtIV inhibitors as agrichemicals.
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Affiliation(s)
- Tian Liu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Xiaoguang Guo
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yunfei Bu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yong Zhou
- School of Software, Dalian University of Technology, Dalian, 116024, China
| | - Yanwei Duan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Qing Yang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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11
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Albina P, Durban N, Bertron A, Albrecht A, Robinet JC, Erable B. Influence of Hydrogen Electron Donor, Alkaline pH, and High Nitrate Concentrations on Microbial Denitrification: A Review. Int J Mol Sci 2019; 20:ijms20205163. [PMID: 31635215 PMCID: PMC6834205 DOI: 10.3390/ijms20205163] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/02/2019] [Accepted: 10/15/2019] [Indexed: 12/25/2022] Open
Abstract
Bacterial respiration of nitrate is a natural process of nitrate reduction, which has been industrialized to treat anthropic nitrate pollution. This process, also known as “microbial denitrification”, is widely documented from the fundamental and engineering points of view for the enhancement of the removal of nitrate in wastewater. For this purpose, experiments are generally conducted with heterotrophic microbial metabolism, neutral pH and moderate nitrate concentrations (<50 mM). The present review focuses on a different approach as it aims to understand the effects of hydrogenotrophy, alkaline pH and high nitrate concentration on microbial denitrification. Hydrogen has a high energy content but its low solubility, 0.74 mM (1 atm, 30 °C), in aqueous medium limits its bioavailability, putting it at a kinetic disadvantage compared to more soluble organic compounds. For most bacteria, the optimal pH varies between 7.5 and 9.5. Outside this range, denitrification is slowed down and nitrite (NO2−) accumulates. Some alkaliphilic bacteria are able to express denitrifying activity at pH levels close to 12 thanks to specific adaptation and resistance mechanisms detailed in this manuscript, and some bacterial populations support nitrate concentrations in the range of several hundred mM to 1 M. A high concentration of nitrate generally leads to an accumulation of nitrite. Nitrite accumulation can inhibit bacterial activity and may be a cause of cell death.
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Affiliation(s)
- Pierre Albina
- Laboratoire Matériaux et Durabilité des Constructions, Université de Toulouse, UPS, INSA. 135, 7 avenue de Rangueil, 31077 Toulouse CEDEX 04, France.
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 31030 Toulouse, France.
| | - Nadège Durban
- Laboratoire Matériaux et Durabilité des Constructions, Université de Toulouse, UPS, INSA. 135, 7 avenue de Rangueil, 31077 Toulouse CEDEX 04, France.
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 31030 Toulouse, France.
| | - Alexandra Bertron
- Laboratoire Matériaux et Durabilité des Constructions, Université de Toulouse, UPS, INSA. 135, 7 avenue de Rangueil, 31077 Toulouse CEDEX 04, France.
| | - Achim Albrecht
- Andra (Agence nationale pour la gestion des déchets radioactifs), 92298 Châtenay-Malabry, France.
| | - Jean-Charles Robinet
- Andra (Agence nationale pour la gestion des déchets radioactifs), 92298 Châtenay-Malabry, France.
| | - Benjamin Erable
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 31030 Toulouse, France.
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12
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Kim S, Sung J, Yeon J, Choi SH, Jin MS. Crystal Structure of a Highly Thermostable α-Carbonic Anhydrase from Persephonella marina EX-H1. Mol Cells 2019; 42:460-469. [PMID: 31250619 PMCID: PMC6602146 DOI: 10.14348/molcells.2019.0029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/23/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022] Open
Abstract
Bacterial α-type carbonic anhydrase (α-CA) is a zinc metalloenzyme that catalyzes the reversible and extremely rapid interconversion of carbon dioxide to bicarbonate. In this study, we report the first crystal structure of a hyperthermostable α-CA from Persephonella marina EXH1 (pm CA) in the absence and presence of competitive inhibitor, acetazolamide. The structure reveals a compactly folded pm CA homodimer in which each monomer consists of a 10-stranded β-sheet in the center. The catalytic zinc ion is coordinated by three highly conserved histidine residues with an exchangeable fourth ligand (a water molecule, a bicarbonate anion, or the sulfonamide group of acetazolamide). Together with an intramolecular disulfide bond, extensive interfacial networks of hydrogen bonds, ionic and hydrophobic interactions stabilize the dimeric structure and are likely responsible for the high thermal stability. We also identified novel binding sites for calcium ions at the crystallographic interface, which serve as molecular glue linking negatively charged and otherwise repulsive surfaces. Furthermore, this large negatively charged patch appears to further increase the thermostability at alkaline pH range via favorable charge-charge interactions between pm CA and solvent molecules. These findings may assist development of novel α-CAs with improved thermal and/or alkaline stability for applications such as CO2 capture and sequestration.
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Affiliation(s)
- Subin Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005,
Korea
| | - Jongmin Sung
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005,
Korea
| | - Jungyoon Yeon
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005,
Korea
| | - Seung Hun Choi
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005,
Korea
| | - Mi Sun Jin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005,
Korea
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Haque MR, Hirowatari A, Koyanagi A, Ichinose T, Abiru M, Mohri S, Furuya S, Yamamoto K. Molecular characterization and expression analysis of a phosphoserine aminotransferase involving l-serine synthesis from silkworm, Bombyx mori. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2019; 101:e21553. [PMID: 31004387 DOI: 10.1002/arch.21553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/12/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
In this study, we identified and characterized a phosphoserine aminotransferase (bmPSAT) from Bombyx mori (B. mori) that is responsible for l-serine biosynthesis. A complementary DNA that encodes bmPSAT was cloned by reverse transcriptase polymerase reaction and sequenced. The presumed amino acid sequence revealed 47-87% identity with known PSATs from insects, humans, plants, and bacteria. Through phylogenetic analysis, we found that bmPSAT is evolutionary related to insect PSATs. Recombinant bmPSAT was produced in Escherichia coli by using a cold-shock promotor and purified to homogeneity. This enzyme utilizes phosphohydroxypyruvate and glutamate for transamination. bmPSAT messenger RNA (mRNA) was expressed at higher levels in several tissues of standard strain silkworm including the silk gland, whereas a sericin-deficient silkworm strain exhibited a diminished expression of bmPSAT mRNA in the silk gland. These findings indicate that bmPSAT may play an important role in synthesizing and supplying l-serine in the larva of B. mori.
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Affiliation(s)
- Mohammad R Haque
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Aiko Hirowatari
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Ayumi Koyanagi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Takashi Ichinose
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Maiko Abiru
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Shinya Mohri
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Shigeki Furuya
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Kohji Yamamoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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N-terminal residues are crucial for quaternary structure and active site conformation for the phosphoserine aminotransferase from enteric human parasite E. histolytica. Int J Biol Macromol 2019; 132:1012-1023. [PMID: 30959130 DOI: 10.1016/j.ijbiomac.2019.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 11/24/2022]
Abstract
Phosphoserine aminotransferase (PSAT) is a pyridoxal-5'phosphate (PLP)-dependent enzyme that catalyzes the second reversible step in the phosphoserine biosynthetic pathway producing serine. The crystal structure of E. histolytica PSAT (EhPSAT) complexed with PLP was elucidated at 3.0 Å resolution and the structures of its mutants, EhPSAT_Δ45 and EhPSAT_Δ4, at 1.8 and 2.4 Å resolution respectively. Deletion of 45 N-terminal residues (EhPSAT_Δ45) resulted in an inactive protein, the structure showed a dimeric arrangement drastically different from that of the wild-type protein, with the two monomers translated and rotated by almost 180° with respect to each other; causing a rearrangement of the active site to which PLP was unable to bind. Deletion of first N-terminal 15 (EhPSAT_Δ15) and four 11th to 14th residues (EhPSAT_Δ4) yielded up to 98% and 90% decrease in the activity respectively. Absence of aldimine linkage between PLP-Lys in the crystal structure of EhPSAT_Δ4 mutant explains for such decrease in activity and describes the importance of these N-terminal residues. Furthermore, a halide-binding site was found in close proximity to the active site. A stretch of six amino acids (146-NNTIYG-151) only conserved in the Entamoeba genus, contributes to halide binding may explain that the halide inhibition could be specific to Entamoeba.
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Wang X, Li H, Gao P, Liu Y, Zeng W. Combining Support Vector Machine with Dual g-gap Dipeptides to Discriminate between Acidic and Alkaline Enzymes. LETT ORG CHEM 2019. [DOI: 10.2174/1570178615666180925125912] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The catalytic activity of the enzyme is different from that of the inorganic catalyst. In a high-temperature, over-acid or over-alkaline environment, the structure of the enzyme is destroyed and then loses its activity. Although the biochemistry experiments can measure the optimal PH environment of the enzyme, these methods are inefficient and costly. In order to solve these problems, computational model could be established to determine the optimal acidic or alkaline environment of the enzyme. Firstly, in this paper, we introduced a new feature called dual g-gap dipeptide composition to formulate enzyme samples. Subsequently, the best feature was selected by using the F value calculated from analysis of variance. Finally, support vector machine was utilized to build prediction model for distinguishing acidic from alkaline enzyme. The overall accuracy of 95.9% was achieved with Jackknife cross-validation, which indicates that our method is professional and efficient in terms of acid and alkaline enzyme predictions. The feature proposed in this paper could also be applied in other fields of bioinformatics.
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Affiliation(s)
- Xianfang Wang
- School of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China
| | - Hongfei Li
- School of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China
| | - Peng Gao
- School of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China
| | - Yifeng Liu
- School of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China
| | - Wenjing Zeng
- TianJiabing Middle School of Chengdu, Chengdu 610011, China
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Challenges and Adaptations of Life in Alkaline Habitats. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 172:85-133. [DOI: 10.1007/10_2019_97] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Wakai S. Biochemical and thermodynamic analyses of energy conversion in extremophiles. Biosci Biotechnol Biochem 2018; 83:49-64. [PMID: 30381012 DOI: 10.1080/09168451.2018.1538769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A variety of extreme environments, characterized by extreme values of various physicochemical parameters (temperature, pressure, salinity, pH, and so on), are found on Earth. Organisms that favorably live in such extreme environments are called extremophiles. All living organisms, including extremophiles, must acquire energy to maintain cellular homeostasis, including extremophiles. For energy conversion in harsh environments, thermodynamically useful reactions and stable biomolecules are essential. In this review, I briefly summarize recent studies of extreme environments and extremophiles living in these environments and describe energy conversion processes in various extremophiles based on my previous research. Furthermore, I discuss the correlation between the biological system of electrotrophy, a third biological energy acquisition system, and the mechanism underlying microbiologically influenced corrosion. These insights into energy conversion in extremophiles may improve our understanding of the "limits of life". Abbreviations: PPi: pyrophosphate; PPase: pyrophosphatase; ITC: isothermal titration microcalorimetry; SVNTase: Shewanella violacea 5'-nucleotidase; SANTase: Shewanella amazonensis 5'-nucleotidase.
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Affiliation(s)
- Satoshi Wakai
- a Graduate School of Science, Technology and Innovation , Kobe University , Kobe , Japan
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Kumar A, Alam A, Tripathi D, Rani M, Khatoon H, Pandey S, Ehtesham NZ, Hasnain SE. Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome. Semin Cell Dev Biol 2018; 84:147-157. [PMID: 29331642 DOI: 10.1016/j.semcdb.2018.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/01/2017] [Accepted: 01/09/2018] [Indexed: 02/02/2023]
Abstract
The biological paradox about how extremophiles persist at extreme ecological conditions throws a fascinating picture of the enormous potential of a single cell to adapt to homeostatic conditions in order to propagate. Unicellular organisms face challenges from both environmental factors and the ecological niche provided by the host tissue. Although the existence of extremophiles and their physiological properties were known for a long time, availability of whole genome sequence has catapulted the study on mechanisms of adaptation and the underlying principles that have enabled these unique organisms to withstand evolutionary and environmental pressures. Comparative genomics has shown that extremophiles possess the unique set of genes and proteins that empower them with biochemical machinery necessary to thrive in extreme environments. The presence of these proteins safeguards the cell against a wide array of extreme conditions such as temperature, pressure, radiations, chemicals, drugs etc. An insight into these adaptive mechanisms in extremophiles may help us to devise strategies to alter the genes and proteins that may have therapeutic potential and commercial value. Here we present an overview of the various adaptations in extremophiles. We also try to explain how mycobacterium channelizes its proteome to survive in stress conditions posed by host immune system.
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Affiliation(s)
- Ashutosh Kumar
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Anwar Alam
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Deeksha Tripathi
- Department of Microbiology, Central University of Rajasthan, Bandar Sindri, Ajmer, Rajasthan, India
| | - Mamta Rani
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, India
| | - Hafeeza Khatoon
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Saurabh Pandey
- National Institute of Pathology, Safdarjang Hospital Campus, New Delhi, India
| | - Nasreen Z Ehtesham
- National Institute of Pathology, Safdarjang Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India; JH-Institute of Molecular Medicine, Hamdard Nagar, New Delhi, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India.
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Structural adaptations of octaheme nitrite reductases from haloalkaliphilic Thioalkalivibrio bacteria to alkaline pH and high salinity. PLoS One 2017; 12:e0177392. [PMID: 28510595 PMCID: PMC5433712 DOI: 10.1371/journal.pone.0177392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 04/26/2017] [Indexed: 11/25/2022] Open
Abstract
Bacteria Tv. nitratireducens and Tv. paradoxus from soda lakes grow optimally in sodium carbonate/NaCl brines at pH range from 9.5 to 10 and salinity from 0.5 to 1.5 M Na+. Octaheme nitrite reductases (ONRs) from haloalkaliphilic bacteria of genus Thioalkalivibrio are stable and active in a wide range of pH (up to 11) and salinity (up to 1 M NaCl). To establish adaptation mechanisms of ONRs from haloalkaliphilic bacteria a comparative analysis of amino acid sequences and structures of ONRs from haloalkaliphilic bacteria and their homologues from non-halophilic neutrophilic bacteria was performed. The following adaptation strategies were observed: (1) strategies specific for halophilic and alkaliphilic proteins (an increase in the number of aspartate and glutamate residues and a decrease in the number of lysine residues on the protein surface), (2) strategies specific for halophilic proteins (an increase in the arginine content and a decrease in the number of hydrophobic residues on the solvent-accessible protein surface), (3) strategies specific for alkaliphilic proteins (an increase in the area of intersubunit hydrophobic contacts). Unique adaptation mechanism inherent in the ONRs from bacteria of genus Thioalkalivibrio was revealed (an increase in the core in the number of tryptophan and phenylalanine residues, and an increase in the number of small side chain residues, such as alanine and valine, in the core).
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Popinako AV, Tikhonova TV, Antonov MY, Shaitan KV, Popov VO. Structural adaptation of active center channels of octaheme nitrite reductases from the haloalkaliphilic bacteria Thioalkalivibrio nitratireducens to a proton deficit. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917020191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Structural investigation and inhibitory response of halide on phosphoserine aminotransferase from Trichomonas vaginalis. Biochim Biophys Acta Gen Subj 2016; 1860:1508-18. [PMID: 27102280 DOI: 10.1016/j.bbagen.2016.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 04/04/2016] [Accepted: 04/17/2016] [Indexed: 11/20/2022]
Abstract
BACKGROUND Phosphoserine aminotransferase (PSAT) catalyses the second reversible step of the phosphoserine biosynthetic pathway in Trichomonas vaginalis, which is crucial for the synthesis of serine and cysteine. METHODS PSAT from T. vaginalis (TvPSAT) was analysed using X-ray crystallography, enzyme kinetics, and molecular dynamics simulations. RESULTS The crystal structure of TvPSAT was determined to 2.15Å resolution, and is the first protozoan PSAT structure to be reported. The active site of TvPSAT structure was found to be in a closed conformation, and at the active site PLP formed an internal aldimine linkage to Lys 202. In TvPSAT, Val 340 near the active site while it is Arg in most other members of the PSAT family, might be responsible in closing the active site. Kinetic studies yielded Km values of 54 μM and 202 μM for TvPSAT with OPLS and AKG, respectively. Only iodine inhibited the TvPSAT activity while smaller halides could not inhibit. CONCLUSION Results from the structure, comparative molecular dynamics simulations, and the inhibition studies suggest that iodine is the only halide that can bind TvPSAT strongly and may thus inhibit the activity of TvPSAT. The long loop between β8 and α8 at the opening of the TvPSAT active site cleft compared to other PSATs, suggests that this loop may help control the access of substrates to the TvPSAT active site and thus influences the enzyme kinetics. GENERAL SIGNIFICANCE Our structural and functional studies have improved our understanding of how PSAT helps this organism persists in the environment.
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Boran R, Ugur A. Burkholderia multivorans SB6 Lipase as a Detergent Ingredient: Characterization and Stabilization. J SURFACTANTS DETERG 2015. [DOI: 10.1007/s11743-015-1767-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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23
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Bai W, Zhou C, Zhao Y, Wang Q, Ma Y. Structural Insight into and Mutational Analysis of Family 11 Xylanases: Implications for Mechanisms of Higher pH Catalytic Adaptation. PLoS One 2015; 10:e0132834. [PMID: 26161643 PMCID: PMC4498622 DOI: 10.1371/journal.pone.0132834] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/18/2015] [Indexed: 11/25/2022] Open
Abstract
To understand the molecular basis of higher pH catalytic adaptation of family 11 xylanases, we compared the structures of alkaline, neutral, and acidic active xylanases and analyzed mutants of xylanase Xyn11A-LC from alkalophilic Bacillus sp. SN5. It was revealed that alkaline active xylanases have increased charged residue content, an increased ratio of negatively to positively charged residues, and decreased Ser, Thr, and Tyr residue content relative to non-alkaline active counterparts. Between strands β6 and β7, alkaline xylanases substitute an α-helix for a coil or turn found in their non-alkaline counterparts. Compared with non-alkaline xylanases, alkaline active enzymes have an inserted stretch of seven amino acids rich in charged residues, which may be beneficial for xylanase function in alkaline conditions. Positively charged residues on the molecular surface and ionic bonds may play important roles in higher pH catalytic adaptation of family 11 xylanases. By structure comparison, sequence alignment and mutational analysis, six amino acids (Glu16, Trp18, Asn44, Leu46, Arg48, and Ser187, numbering based on Xyn11A-LC) adjacent to the acid/base catalyst were found to be responsible for xylanase function in higher pH conditions. Our results will contribute to understanding the molecular mechanisms of higher pH catalytic adaptation in family 11 xylanases and engineering xylanases to suit industrial applications.
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Affiliation(s)
- Wenqin Bai
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Science, Shanxi Normal University, Linfen, 041004, China
- * E-mail: (YHM); (WQB)
| | - Cheng Zhou
- National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yueju Zhao
- Institute of Agro-Products Processing Science and Technology, Chinese Academy of Agriculture Sciences, Beijing, 100193, China
| | - Qinhong Wang
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yanhe Ma
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- * E-mail: (YHM); (WQB)
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Su J, Zhang F, Sun W, Karuppiah V, Zhang G, Li Z, Jiang Q. A new alkaline lipase obtained from the metagenome of marine sponge Ircinia sp. World J Microbiol Biotechnol 2015; 31:1093-102. [PMID: 25921581 DOI: 10.1007/s11274-015-1859-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 04/23/2015] [Indexed: 11/24/2022]
Abstract
Microorganisms associated with marine sponges are potential resources for marine enzymes. In this study, culture-independent metagenomic approach was used to isolate lipases from the complex microbiome of the sponge Ircinia sp. obtained from the South China Sea. A metagenomic library was constructed, containing 6568 clones, and functional screening on 1 % tributyrin agar resulted in the identification of a positive lipase clone (35F4). Following sequence analysis 35F4 clone was found to contain a putative lipase gene lipA. Sequence analysis of the predicted amino acid sequence of LipA revealed that it is a member of subfamily I.1 of lipases, with 63 % amino acid similarity to the lactonizing lipase from Aeromonas veronii (WP_021231793). Based on the predicted secondary structure, LipA was predicted to be an alkaline enzyme by sequence/structure analysis. Heterologous expression of lipA in E. coli BL21 (DE3) was performed and the characterization of the recombinant enzyme LipA showed that it is an alkaline enzyme with high tolerance to organic solvents. The isolated lipase LipA was active in the broad alkaline range, with the highest activity at pH 9.0, and had a high level of stability over a pH range of 7.0-12.0. The activity of LipA was increased in the presence of 5 mM Ca(2+) and some organic solvents, e.g. methanol, acetone and isopropanol. The optimum temperature for the activity of LipA is 40 °C and the molecular weight of LipA was determined to be ~30 kDa by SDS-PAGE. LipA is an alkaline lipase and shows good tolerance to some organic solvents, which make it of potential utility in the detergent industry and enzyme mediated organic synthesis. The result of this study has broadened the diversity of known lipolytic genes and demonstrated that marine sponges are an important source for new enzymes.
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Affiliation(s)
- Jing Su
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic China
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Li H, Turunen O. Effect of acidic amino acids engineered into the active site cleft ofThermopolyspora flexuosaGH11 xylanase. Biotechnol Appl Biochem 2015; 62:433-40. [DOI: 10.1002/bab.1288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/02/2014] [Indexed: 11/07/2022]
Affiliation(s)
- He Li
- Department of Biotechnology and Chemical Technology; School of Chemical Technology; Aalto University; Aalto 00076 Finland
| | - Ossi Turunen
- Department of Biotechnology and Chemical Technology; School of Chemical Technology; Aalto University; Aalto 00076 Finland
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Khan ZU, Hayat M, Khan MA. Discrimination of acidic and alkaline enzyme using Chou’s pseudo amino acid composition in conjunction with probabilistic neural network model. J Theor Biol 2015; 365:197-203. [DOI: 10.1016/j.jtbi.2014.10.014] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/09/2014] [Accepted: 10/11/2014] [Indexed: 12/11/2022]
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Draft Genome Sequence of Bacillus alcalophilus AV1934, a Classic Alkaliphile Isolated from Human Feces in 1934. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01175-14. [PMID: 25395643 PMCID: PMC4241669 DOI: 10.1128/genomea.01175-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bacillus alcalophilus AV1934, isolated from human feces, was described in 1934 before microbiome studies and recent indications of novel potassium ion coupling to motility in this extremophile. Here, we report draft sequences that will facilitate an examination of whether that coupling is part of a larger cycle of potassium ion-coupled transporters.
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AcalPred: a sequence-based tool for discriminating between acidic and alkaline enzymes. PLoS One 2013; 8:e75726. [PMID: 24130738 PMCID: PMC3794003 DOI: 10.1371/journal.pone.0075726] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/16/2013] [Indexed: 11/19/2022] Open
Abstract
The structure and activity of enzymes are influenced by pH value of their surroundings. Although many enzymes work well in the pH range from 6 to 8, some specific enzymes have good efficiencies only in acidic (pH<5) or alkaline (pH>9) solution. Studies have demonstrated that the activities of enzymes correlate with their primary sequences. It is crucial to judge enzyme adaptation to acidic or alkaline environment from its amino acid sequence in molecular mechanism clarification and the design of high efficient enzymes. In this study, we developed a sequence-based method to discriminate acidic enzymes from alkaline enzymes. The analysis of variance was used to choose the optimized discriminating features derived from g-gap dipeptide compositions. And support vector machine was utilized to establish the prediction model. In the rigorous jackknife cross-validation, the overall accuracy of 96.7% was achieved. The method can correctly predict 96.3% acidic and 97.1% alkaline enzymes. Through the comparison between the proposed method and previous methods, it is demonstrated that the proposed method is more accurate. On the basis of this proposed method, we have built an online web-server called AcalPred which can be freely accessed from the website (http://lin.uestc.edu.cn/server/AcalPred). We believe that the AcalPred will become a powerful tool to study enzyme adaptation to acidic or alkaline environment.
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Battula P, Dubnovitsky AP, Papageorgiou AC. Structural basis of L-phosphoserine binding to Bacillus alcalophilus phosphoserine aminotransferase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:804-11. [PMID: 23633589 DOI: 10.1107/s0907444913002096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/21/2013] [Indexed: 11/10/2022]
Abstract
Phosphoserine aminotransferase is a vitamin B6-dependent enzyme that catalyzes the reversible conversion of 3-phosphohydroxypyruvate to L-phosphoserine using glutamate as an amine donor. In an effort to gain insight into the substrate-recognition mechanism of the enzyme, crystal structures of Bacillus alcalophilus phosphoserine aminotransferase in the presence or absence of L-phosphoserine were determined to resolutions of 1.5 and 1.6 Å, respectively. Local conformational changes induced upon substrate binding were identified. However, in contrast to other aminotransferases, no domain or subunit movements were observed. Two Arg residues (Arg42 and Arg328) and two His residues (His41 and His327) were found to form a tight binding site for the phosphate group of L-phosphoserine. Comparison with Escherichia coli phosphoserine aminotransferase in complex with the substrate analogue α-methylglutamate revealed more extensive structural changes in the case of L-phosphoserine binding. Based on the structural analysis, the flexibility of Arg328 is proposed to be critical for substrate recognition.
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Affiliation(s)
- Pradeep Battula
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, BioCity, FIN-20521 Turku, Finland
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Liszka MJ, Clark ME, Schneider E, Clark DS. Nature Versus Nurture: Developing Enzymes That Function Under Extreme Conditions. Annu Rev Chem Biomol Eng 2012; 3:77-102. [DOI: 10.1146/annurev-chembioeng-061010-114239] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Elizabeth Schneider
- Department of Chemical and Biomolecular Engineering,
- UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley, California 94720; , , ,
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Wang Y, Shi P, Luo H, Bai Y, Huang H, Yang P, Xiong H, Yao B. Cloning, over-expression and characterization of an alkali-tolerant endo-β-1,4-mannanase from Penicillium freii F63. J Biosci Bioeng 2012; 113:710-4. [DOI: 10.1016/j.jbiosc.2012.02.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 02/02/2012] [Accepted: 02/03/2012] [Indexed: 10/28/2022]
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32
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Janto B, Ahmed A, Ito M, Liu J, Hicks DB, Pagni S, Fackelmayer OJ, Smith TA, Earl J, Elbourne LDH, Hassan K, Paulsen IT, Kolstø AB, Tourasse NJ, Ehrlich GD, Boissy R, Ivey DM, Li G, Xue Y, Ma Y, Hu FZ, Krulwich TA. Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4. Environ Microbiol 2011; 13:3289-309. [PMID: 21951522 DOI: 10.1111/j.1462-2920.2011.02591.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bacillus pseudofirmus OF4 is an extreme but facultative alkaliphile that grows non-fermentatively in a pH range from 7.5 to above 11.4 and can withstand large sudden increases in external pH. It is a model organism for studies of bioenergetics at high pH, at which energy demands are higher than at neutral pH because both cytoplasmic pH homeostasis and ATP synthesis require more energy. The alkaliphile also tolerates a cytoplasmic pH > 9.0 at external pH values at which the pH homeostasis capacity is exceeded, and manages other stresses that are exacerbated at alkaline pH, e.g. sodium, oxidative and cell wall stresses. The genome of B. pseudofirmus OF4 includes two plasmids that are lost from some mutants without viability loss. The plasmids may provide a reservoir of mobile elements that promote adaptive chromosomal rearrangements under particular environmental conditions. The genome also reveals a more acidic pI profile for proteins exposed on the outer surface than found in neutralophiles. A large array of transporters and regulatory genes are predicted to protect the alkaliphile from its overlapping stresses. In addition, unanticipated metabolic versatility was observed, which could ensure requisite energy for alkaliphily under diverse conditions.
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Affiliation(s)
- Benjamin Janto
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences and Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA 15212, USA
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Deng A, Wu J, Zhang G, Wen T. Molecular and structural characterization of a surfactant-stable high-alkaline protease AprB with a novel structural feature unique to subtilisin family. Biochimie 2011; 93:783-91. [DOI: 10.1016/j.biochi.2011.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 01/20/2011] [Indexed: 10/18/2022]
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Zhao Y, Zhang Y, Cao Y, Qi J, Mao L, Xue Y, Gao F, Peng H, Wang X, Gao GF, Ma Y. Structural analysis of alkaline β-mannanase from alkaliphilic Bacillus sp. N16-5: implications for adaptation to alkaline conditions. PLoS One 2011; 6:e14608. [PMID: 21436878 PMCID: PMC3059134 DOI: 10.1371/journal.pone.0014608] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 01/04/2011] [Indexed: 11/18/2022] Open
Abstract
Significant progress has been made in isolating novel alkaline β-mannanases, however, there is a paucity of information concerning the structural basis for alkaline tolerance displayed by these β-mannanases. We report the catalytic domain structure of an industrially important β-mannanase from the alkaliphilic Bacillus sp. N16-5 (BSP165 MAN) at a resolution of 1.6 Å. This enzyme, classified into subfamily 8 in glycosyl hydrolase family 5 (GH5), has a pH optimum of enzymatic activity at pH 9.5 and folds into a classic (β/α)(8)-barrel. In order to gain insight into molecular features for alkaline adaptation, we compared BSP165 MAN with previously reported GH5 β-mannanases. It was revealed that BSP165 MAN and other subfamily 8 β-mannanases have significantly increased hydrophobic and Arg residues content and decreased polar residues, comparing to β-mannanases of subfamily 7 or 10 in GH5 which display optimum activities at lower pH. Further, extensive structural comparisons show alkaline β-mannanases possess a set of distinctive features. Position and length of some helices, strands and loops of the TIM barrel structures are changed, which contributes, to a certain degree, to the distinctly different shaped (β/α)(8)-barrels, thus affecting the catalytic environment of these enzymes. The number of negatively charged residues is increased on the molecular surface, and fewer polar residues are exposed to the solvent. Two amino acid substitutions in the vicinity of the acid/base catalyst were proposed to be possibly responsible for the variation in pH optimum of these homologous enzymes in subfamily 8 of GH5, identified by sequence homology analysis and pK(a) calculations of the active site residues. Mutational analysis has proved that Gln91 and Glu226 are important for BSP165 MAN to function at high pH. These findings are proposed to be possible factors implicated in the alkaline adaptation of GH5 β-mannanases and will help to further understanding of alkaline adaptation mechanism.
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Affiliation(s)
- Yueju Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yunhua Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yang Cao
- Graduate University, Chinese Academy of Sciences, Beijing, People's Republic of China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jianxun Qi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Liangwei Mao
- College of Life Science, Hubei University, Wuhan, People's Republic of China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Feng Gao
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Hao Peng
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiaowei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - George F. Gao
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
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Structural insights into the acidophilic pH adaptation of a novel endo-1,4-β-xylanase from Scytalidium acidophilum. Biochimie 2010; 92:1407-15. [DOI: 10.1016/j.biochi.2010.07.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 07/02/2010] [Indexed: 11/22/2022]
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Mishra V, Ali V, Nozaki T, Bhakuni V. Entamoeba histolytica Phosphoserine aminotransferase (EhPSAT): insights into the structure-function relationship. BMC Res Notes 2010; 3:52. [PMID: 20199659 PMCID: PMC2850911 DOI: 10.1186/1756-0500-3-52] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 03/03/2010] [Indexed: 11/29/2022] Open
Abstract
Background Presence of phosphorylated Serine biosynthesis pathway upstream to the de novo cysteine biosynthesis pathway makes PSAT a crucial enzyme. Besides this, phoshoserine produced by the enzyme can also be taken up directly by cysteine synthase as a substrate. PSAT is a PLP dependent enzyme where the cofactor serves as an epicenter for functional catalysis with the active site architecture playing crucial role in optimum function of the enzyme. Findings EhPSAT is a homodimer of molecular mass 86 kDa. To understand the structural modulations associated with pH dependent changes in functional activity of EhPSAT detailed biophysical studies were carried out. pH alterations had no significant effect on the secondary structure, cofactor orientation and oligomeric configuration of the enzyme however, pH dependent compaction in molecular dimensions was observed. Most interestingly, a direct correlation between pH induced modulation of functional activity and orientation of Trp 101 present in the active site of the enzyme was observed. Sodium halides nullified the pH induced global changes in the enzyme, however differential effect of these salts on the active site microenvironment and functional activity of the enzyme was observed. Conclusions The study unequivocally demonstrates that pH induced selective modification of active site microenvironment and not global change in structure or oligomeric status of the enzyme is responsible for the pH dependent change in enzymatic activity of PSAT.
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Affiliation(s)
- Vibhor Mishra
- Division of Molecular and Structural Biology, Central Drug Research Institute, Chattar Manzil Palace, Council of scientific and industrial research (CSIR), Lucknow 226001, India.
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37
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Cloning and characterization of thescoB gene encoding succinyl-CoA transferase from a moderately halophilic and alkaliphilicBacillus isolate. ANN MICROBIOL 2009. [DOI: 10.1007/bf03179209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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38
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An alkaline active xylanase: Insights into mechanisms of high pH catalytic adaptation. Biochimie 2009; 91:1187-96. [DOI: 10.1016/j.biochi.2009.06.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 06/18/2009] [Indexed: 11/21/2022]
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39
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Zhang G, Li H, Fang B. Discriminating acidic and alkaline enzymes using a random forest model with secondary structure amino acid composition. Process Biochem 2009. [DOI: 10.1016/j.procbio.2009.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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40
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Liao CJ, Chin KH, Lin CH, Tsai PSF, Lyu PC, Young CC, Wang AHJ, Chou SH. Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus. Proteins 2008; 73:362-71. [PMID: 18433062 DOI: 10.1002/prot.22071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The crystal structure of the DFA0005 protein complexed with alpha-ketoglutarate (AKG) from an alkali-tolerant bacterium Deinococcus ficus has been determined to a resolution of 1.62 A. The monomer forms an incomplete alpha7/beta8 barrel with a protruding alpha8 helix that interacts extensively with another subunit to form a stable dimer of two complete alpha8/beta8 barrels. The dimer is further stabilized by four glycerol molecules situated at the interface. One unique AKG ligand binding pocket per subunit is detected. Fold match using the DALI and SSE servers identifies DFA0005 as belonging to the isocitrate lyase/phosphoenolpyruvate mutase (ICL/PEPM) superfamily. However, further detailed structural and sequence comparison with other members in this superfamily and with other families containing AKG ligand indicate that DFA0005 protein exhibits considerable distinguishing features of its own and can be considered a novel member in this ICL/PEPM superfamily.
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Affiliation(s)
- Cheng-Jen Liao
- Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan, Republic of China
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41
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Yoshikane Y, Yokochi N, Yamasaki M, Mizutani K, Ohnishi K, Mikami B, Hayashi H, Yagi T. Crystal Structure of Pyridoxamine-Pyruvate Aminotransferase from Mesorhizobium loti MAFF303099. J Biol Chem 2008; 283:1120-7. [DOI: 10.1074/jbc.m708061200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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42
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Quesada A, Guijo MI, Merchán F, Blázquez B, Igeño MI, Blasco R. Essential role of cytochrome bd-related oxidase in cyanide resistance of Pseudomonas pseudoalcaligenes CECT5344. Appl Environ Microbiol 2007; 73:5118-24. [PMID: 17574992 PMCID: PMC1950984 DOI: 10.1128/aem.00503-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Accepted: 06/08/2007] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas pseudoalcaligenes CECT5344 grows in minimal medium containing cyanide as the sole nitrogen source. Under these conditions, an O2-dependent respiration highly resistant to cyanide was detected in cell extracts. The structural genes for the cyanide-resistant terminal oxidase, cioA and cioB, are clustered and encode the integral membrane proteins that correspond to subunits I and II of classical cytochrome bd, although the presence of heme d in the membrane could not be detected by difference spectra. The cio operon from P. pseudoalcaligenes presents a singular organization, starting upstream of cioAB by the coding sequence of a putative ferredoxin-dependent sulfite or nitrite reductase and spanning downstream two additional open reading frames that encode uncharacterized gene products. PCR amplifications of RNA (reverse transcription-PCR) indicated the cyanide-dependent up-regulation and cotranscription along the operon. The targeted disruption of cioA eliminates both the expression of the cyanide-stimulated respiratory activity and the growth with cyanide as the nitrogen source, which suggests a critical role of this cytochrome bd-related oxidase in the metabolism of cyanide by P. pseudoalcaligenes CECT5344.
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Affiliation(s)
- Alberto Quesada
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Veterinaria, Avda. de la Universidad s/n, 10071-Cáceres, España.
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Shirai T, Igarashi K, Ozawa T, Hagihara H, Kobayashi T, Ozaki K, Ito S. Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins. Proteins 2007; 66:600-10. [PMID: 17154418 DOI: 10.1002/prot.21255] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The crystal structure of alkaline liquefying alpha-amylase (AmyK) from the alkaliphilic Bacillus sp. KSM-1378 was determined at 2.1 A resolution. The AmyK structure belongs to the GH13 glycoside hydrolase family, which consists of three domains, and bound three calcium and one sodium ions. The alkaline adaptation mechanism of AmyK was investigated by the ancestral sequence evolutionary trace method and by extensive comparisons between alkaline and nonalkaline enzyme structures, including three other protein families: protease, cellulase, and phosphoserine aminotransferase. The consensus change for the alkaline adaptation process was a decrease in the Lys content. The loss of a Lys residue is associated with ion pair remodeling, which mainly consists of the loss of Lys-Asp/Glu ion pairs and the acquisition of Arg ion pairs, preferably Arg-Glu. The predicted replacements of the positively charged amino acids were often, although not always, used for ion pair remodeling.
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Affiliation(s)
- Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bio-science and Technology, Nagahama 526-0829, Japan.
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44
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Redecke L, Brehm MA, Bredehorst R. Cloning and characterization of dihydrofolate reductase from a facultative alkaliphilic and halotolerant bacillus strain. Extremophiles 2006; 11:75-83. [PMID: 17021659 DOI: 10.1007/s00792-006-0013-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Accepted: 06/30/2006] [Indexed: 10/24/2022]
Abstract
Elucidation of the molecular basis of the stability of enzymes from extremophilic organisms is of fundamental importance for various industrial applications. Due to the wealth of structural data from various species, dihydrofolate reductase (DHFR, EC 1.5.1.3) provides an excellent model for systematic investigations. In this report, DHFR from alkaliphilic Bacillus halodurans C-125 was cloned and expressed in E. coli. Functional analyses revealed that BhDHFR exhibits the most alkali-stable phenotype of DHFRs characterized so far. Optimal enzyme activity was observed in a slightly basic pH region ranging from 7.25 to 8.75. Alkali-stability is associated with a remarkable resistance to elevated temperatures (half-life of 60 min at 52.5 degrees C) and to high concentrations of urea (up to 3 M). Although the secondary structure shows distinct similarities to those of mesophilic DHFR molecules, BhDHFR exhibits molecular features contributing to its alkaliphilic properties. Interestingly, the unique phenotype is diminished by C-terminal addition of a His-tag sequence. Therefore, His-tag-derivatized BhDHFR offers the opportunity to obtain deeper insights into the specific mechanisms of alkaliphilic adaption by comparison of the three dimensional structure of both BhDHFR molecules.
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Affiliation(s)
- Lars Redecke
- Institute of Biochemistry and Food Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.
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45
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Manikandan K, Bhardwaj A, Gupta N, Lokanath NK, Ghosh A, Reddy VS, Ramakumar S. Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions. Protein Sci 2006; 15:1951-60. [PMID: 16823036 PMCID: PMC2242578 DOI: 10.1110/ps.062220206] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Crystal structures are known for several glycosyl hydrolase family 10 (GH10) xylanases. However, none of them is from an alkalophilic organism that can grow in alkaline conditions. We have determined the crystal structures at 2.2 Angstroms of a GH10 extracellular endoxylanase (BSX) from an alkalophilic Bacillus sp. NG-27, for the native and the complex enzyme with xylosaccharides. The industrially important enzyme is optimally active and stable at 343 K and at a pH of 8.4. Comparison of the structure of BSX with those of other thermostable GH10 xylanases optimally active at acidic or close to neutral pH showed that the solvent-exposed acidic amino acids, Asp and Glu, are markedly enhanced in BSX, while solvent-exposed Asn was noticeably depleted. The BSX crystal structure when compared with putative three-dimensional homology models of other extracellular alkalophilic GH10 xylanases from alkalophilic organisms suggests that a protein surface rich in acidic residues may be an important feature common to these alkali thermostable enzymes. A comparison of the surface features of BSX and of halophilic proteins allowed us to predict the activity of BSX at high salt concentrations, which we verified through experiments. This offered us important lessons in the polyextremophilicity of proteins, where understanding the structural features of a protein stable in one set of extreme conditions provided clues about the activity of the protein in other extreme conditions. The work brings to the fore the role of the nature and composition of solvent-exposed residues in the adaptation of enzymes to polyextreme conditions, as in BSX.
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Kapetaniou EG, Thanassoulas A, Dubnovitsky AP, Nounesis G, Papageorgiou AC. Effect of pH on the structure and stability of Bacillus circulans ssp. alkalophilus phosphoserine aminotransferase: Thermodynamic and crystallographic studies. Proteins 2006; 63:742-53. [PMID: 16532449 DOI: 10.1002/prot.20935] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
pH is one of the key parameters that affect the stability and function of proteins. We have studied the effect of pH on the pyridoxal-5'-phosphate-dependent enzyme phosphoserine aminotransferase produced by the facultative alkaliphile Bacillus circulans ssp. alkalophilus using thermodynamic and crystallographic analysis. Enzymatic activity assay showed that the enzyme has maximum activity at pH 9.0 and relative activity less than 10% at pH 7.0. Differential scanning calorimetry and circular dichroism experiments revealed variations in the stability and denaturation profiles of the enzyme at different pHs. Most importantly, release of pyridoxal-5'-phosphate and protein thermal denaturation were found to occur simultaneously at pH 6.0 in contrast to pH 8.5 where denaturation preceded cofactor's release by approximately 3 degrees C. To correlate the observed differences in thermal denaturation with structural features, the crystal structure of phosphoserine aminotransferase was determined at 1.2 and 1.5 A resolution at two different pHs (8.5 and 4.6, respectively). Analysis of the two structures revealed changes in the vicinity of the active site and in surface residues. A conformational change in a loop involved in substrate binding at the entrance of the active site has been identified upon pH change. Moreover, the number of intramolecular ion pairs was found reduced in the pH 4.6 structure. Taken together, the presented kinetics, thermal denaturation, and crystallographic data demonstrate a potential role of the active site in unfolding and suggest that subtle but structurally significant conformational rearrangements are involved in the stability and integrity of phosphoserine aminotransferase in response to pH changes.
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Padan E, Bibi E, Ito M, Krulwich TA. Alkaline pH homeostasis in bacteria: new insights. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1717:67-88. [PMID: 16277975 PMCID: PMC3072713 DOI: 10.1016/j.bbamem.2005.09.010] [Citation(s) in RCA: 475] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2005] [Revised: 08/19/2005] [Accepted: 09/07/2005] [Indexed: 10/25/2022]
Abstract
The capacity of bacteria to survive and grow at alkaline pH values is of widespread importance in the epidemiology of pathogenic bacteria, in remediation and industrial settings, as well as in marine, plant-associated and extremely alkaline ecological niches. Alkali-tolerance and alkaliphily, in turn, strongly depend upon mechanisms for alkaline pH homeostasis, as shown in pH shift experiments and growth experiments in chemostats at different external pH values. Transcriptome and proteome analyses have recently complemented physiological and genetic studies, revealing numerous adaptations that contribute to alkaline pH homeostasis. These include elevated levels of transporters and enzymes that promote proton capture and retention (e.g., the ATP synthase and monovalent cation/proton antiporters), metabolic changes that lead to increased acid production, and changes in the cell surface layers that contribute to cytoplasmic proton retention. Targeted studies over the past decade have followed up the long-recognized importance of monovalent cations in active pH homeostasis. These studies show the centrality of monovalent cation/proton antiporters in this process while microbial genomics provides information about the constellation of such antiporters in individual strains. A comprehensive phylogenetic analysis of both eukaryotic and prokaryotic genome databases has identified orthologs from bacteria to humans that allow better understanding of the specific functions and physiological roles of the antiporters. Detailed information about the properties of multiple antiporters in individual strains is starting to explain how specific monovalent cation/proton antiporters play dominant roles in alkaline pH homeostasis in cells that have several additional antiporters catalyzing ostensibly similar reactions. New insights into the pH-dependent Na(+)/H(+) antiporter NhaA that plays an important role in Escherichia coli have recently emerged from the determination of the structure of NhaA. This review highlights the approaches, major findings and unresolved problems in alkaline pH homeostasis, focusing on the small number of well-characterized alkali-tolerant and extremely alkaliphilic bacteria.
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Affiliation(s)
- Etana Padan
- Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel.
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48
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Dubnovitsky AP, Ravelli RBG, Popov AN, Papageorgiou AC. Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage. Protein Sci 2005; 14:1498-507. [PMID: 15883191 PMCID: PMC2253390 DOI: 10.1110/ps.051397905] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The X-ray susceptibility of the lysine-pyridoxal-5'-phosphate Schiff base in Bacillus alcalophilus phosphoserine aminotransferase has been investigated using crystallographic data collected at 100 K to 1.3 A resolution, complemented by on-line spectroscopic studies. X-rays induce deprotonation of the internal aldimine, changes in the Schiff base conformation, displacement of the cofactor molecule, and disruption of the Schiff base linkage between pyridoxal-5'-phosphate and the Lys residue. Analysis of the "undamaged" structure reveals a significant chemical strain on the internal aldimine bond that leads to a pronounced geometrical distortion of the cofactor. However, upon crystal exposure to the X-rays, the strain and distortion are relaxed and eventually diminished when the total absorbed dose has exceeded 4.7 x 10(6) Ggamma. Our data provide new insights into the enzymatic activation of pyridoxal-5'-phosphate and suggest that special care should be taken while using macromolecular crystallography to study details in strained active sites.
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