Analysis of Protein Thermostability Enhancing Factors in Industrially Important Thermus Bacteria Species

Elucidation of evolutionary factors that enhance protein thermostability is a critical problem and was the focus of this work on Thermus species. Pairs of orthologous sequences of T. scotoductus SA-01 and T. thermophilus HB27, with the largest negative minimum folding energy (MFE) as predicted by the UNAFold algorithm, were statistically analyzed. Favored substitutions of amino acids residues and their properties were determined. Substitutions were analyzed in modeled protein structures to determine their locations and contribution to energy differences using PyMOL and FoldX programs respectively. Dominant trends in amino acid substitutions consistent with differences in thermostability between orthologous sequences were observed. T. thermophilus thermophilic proteins showed an increase in non-polar, tiny, and charged amino acids. An abundance of alanine substituted by serine and threonine, as well as arginine substituted by glutamine and lysine was observed in T. thermophilus HB27. Structural comparison showed that stabilizing mutations occurred on surfaces and loops in protein structures.

[1]  M. J. Baedecker,et al.  Modern marine sediments as a natural analog to the chemically stressed environment of a landfill , 1979 .

[2]  Pernilla Turner,et al.  Potential and utilization of thermophiles and thermostable enzymes in biorefining , 2007, Microbial cell factories.

[3]  A. Mills,et al.  Biogeochemical Conditions Favoring Magnetite Formation during Anaerobic Iron Reduction , 1987, Applied and environmental microbiology.

[4]  G. Haki,et al.  Developments in industrially important thermostable enzymes: a review. , 2003, Bioresource technology.

[5]  Michael Zuker,et al.  UNAFold: software for nucleic acid folding and hybridization. , 2008, Methods in molecular biology.

[6]  J. McDonald.  Temperature Adaptation at Homologous Sites in Proteins from Nine Thermophile–Mesophile Species Pairs , 2010, Genome biology and evolution.

[7]  Sandip Paul,et al.  Analysis of Nanoarchaeum equitans genome and proteome composition: indications for hyperthermophilic and parasitic adaptation , 2006, BMC Genomics.

[8]  Derek R. Lovley,et al.  Oxidation of aromatic contaminants coupled to microbial iron reduction , 1989, Nature.

[9]  R. Nussinov,et al.  Folding and binding cascades: Dynamic landscapes and population shifts , 2008, Protein science : a publication of the Protein Society.

[10]  P Argos,et al.  Protein thermal stability, hydrogen bonds, and ion pairs. , 1997, Journal of molecular biology.

[11]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[12]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[13]  G. Antranikian,et al.  Extremophiles as a source of novel enzymes for industrial application , 1999, Applied Microbiology and Biotechnology.

[14]  Rainer Merkl,et al.  The genome sequence of the extreme thermophile Thermus thermophilus , 2004, Nature Biotechnology.

[15]  S. Trivedi,et al.  Protein thermostability in Archaea and Eubacteria. , 2006, Genetics and molecular research : GMR.

[16]  N. Grishin,et al.  PROMALS3D: a tool for multiple protein sequence and structure alignments , 2008, Nucleic acids research.

[17]  P Argos,et al.  Thermal stability and protein structure. , 1979, Biochemistry.

[18]  R. Varadarajan,et al.  Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. , 2002, Biochemistry.

[19]  J. McDonald,et al.  Patterns of temperature adaptation in proteins from Methanococcus and Bacillus. , 1999, Molecular biology and evolution.

[20]  E. Brzuszkiewicz,et al.  Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01 , 2011, BMC Genomics.

[21]  M. Hoffmann,et al.  Reductive dissolution of fe(III) oxides by Pseudomonas sp. 200 , 1988, Biotechnology and bioengineering.

[22]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[23]  G. Taylor,et al.  Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium. , 1998, Structure.

[24]  I. Lasa,et al.  Thermophilic enzymes and their biotechnological potential. , 1993, Microbiologia.

[25]  A. Sali,et al.  Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.

[26]  A. Alexandre,et al.  Response to temperature stress in rhizobia , 2013, Critical reviews in microbiology.

[27]  R. Williams,et al.  DNA relatedness of Thermus strains, description of Thermus brockianus sp. nov., and proposal to reestablish Thermus thermophilus (Oshima and Imahori) , 1995, International journal of systematic bacteriology.

[28]  Carla Mattos,et al.  Protein-water interactions in a dynamic world. , 2002, Trends in biochemical sciences.

[29]  S. Capasso,et al.  Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A , 1997, Protein science : a publication of the Protein Society.

[30]  A. Sali,et al.  Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.

[31]  K. S. Yip,et al.  The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures. , 1995, Structure.

[32]  W. Delano.  The PyMOL Molecular Graphics System (2002) , 2002 .

[33]  Torsten Schwede,et al.  BIOINFORMATICS Bioinformatics Advance Access published November 12, 2005 The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling , 2022 .

[34]  Jorng-Tzong Horng,et al.  PGTdb: a database providing growth temperatures of prokaryotes , 2004, Bioinform..

[35]  R. Cicerone,et al.  Biogeochemical aspects of atmospheric methane , 1988 .

[36]  G. Antranikian,et al.  Heat-stable enzymes from extremely thermophilic and hyperthermophilic microorganisms , 1995, World journal of microbiology & biotechnology.

[37]  Maliha S. Nash,et al.  Handbook of Parametric and Nonparametric Statistical Procedures , 2001, Technometrics.

[38]  Z. Yang,et al.  Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. , 1998, Molecular biology and evolution.

[39]  M. Serra,et al.  Stability of RNA hairpins closed by wobble base pairs. , 1998, Biochemistry.

[40]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[41]  J. Rosenthal,et al.  A role for A-to-I RNA editing in temperature adaptation. , 2012, Physiology.

[42]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[43]  Bert L de Groot,et al.  Protein thermostability calculations using alchemical free energy simulations. , 2010, Biophysical journal.

[44]  Kelly P. Nevin,et al.  Dissimilatory Fe(III) and Mn(IV) reduction. , 1991, Advances in microbial physiology.

[45]  S. T. de Farias,et al.  Preferred codons and amino acid couples in hyperthermophiles , 2002, Genome Biology.

[46]  C. Gross,et al.  Identification of the sigma E subunit of Escherichia coli RNA polymerase: a second alternate sigma factor involved in high-temperature gene expression. , 1989, Genes & development.

[47]  P. Engel,et al.  Protein thermostability in extremophiles. , 1998, Biochimie.

[48]  P. Clote,et al.  Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. , 2005, RNA.

[49]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[50]  S. Kjelleberg,et al.  The role of RNA stability during bacterial stress responses and starvation. , 2000, Environmental microbiology.

[51]  S. Pack,et al.  Protein thermostability: structure-based difference of amino acid between thermophilic and mesophilic proteins. , 2004, Journal of biotechnology.

[52]  K. Dill.  Dominant forces in protein folding. , 1990, Biochemistry.

[53]  G. Antranikian,et al.  Determination of the kinetic parameters during continuous cultivation of the lipase-producing thermophile Bacillus sp. IHI-91 on olive oil , 1997, Applied Microbiology and Biotechnology.

[54]  S. Shapiro,et al.  An Analysis of Variance Test for Normality (Complete Samples) , 1965 .

[55]  E. Kimura,et al.  Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens. , 2003, Genome research.

[56]  A. Rowbotham,et al.  Chromium in the environment: an evaluation of exposure of the UK general population and possible adverse health effects. , 2000, Journal of toxicology and environmental health. Part B, Critical reviews.

[57]  J. Samuelson,et al.  Enzyme Engineering , 2013, Methods in Molecular Biology.

[58]  G. Olsen,et al.  Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[59]  L. Regan,et al.  Using loop length variants to dissect the folding pathway of a four-helix-bundle protein. , 1999, Journal of molecular biology.

[60]  D. Opperman,et al.  Aerobic Cr(VI) reduction by Thermus scotoductus strain SA‐01 , 2007, Journal of applied microbiology.

[61]  R. Sharp,et al.  Isolation and preliminary taxonomic studies of Thermus strains isolated from Yellowstone National Park, USA. , 1986, Journal of general microbiology.

[62]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[63]  Andras Fiser,et al.  Proteomic profiling of the granular cell layer from rats submitted to the experimental model of temporal lobe epilepsy , 2013 .

[64]  T. Satyanarayana,et al.  Thermophilic Moulds in Biotechnology , 1999, Springer Netherlands.

[65]  Dhanesh Ramachandram,et al.  Predicting the Minimum Free Energy RNA Secondary Structures using Harmony Search Algorithm , 2009 .

[66]  François Stricher,et al.  A graphical interface for the FoldX forcefield , 2011, Bioinform..

[67]  X.-X. Zhou,et al.  Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins , 2007, Amino Acids.

[68]  François Stricher,et al.  The FoldX web server: an online force field , 2005, Nucleic Acids Res..

[69]  I. E. Sánchez.  Protein folding transition states probed by loop extension , 2007, Protein science : a publication of the Protein Society.

[70]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[71]  S. Shapiro,et al.  An analysis of variance test for normality ( complete samp 1 es ) t , 2007 .