Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome
Tài liệu tham khảo
Checinska Sielaff, 2017, Solibacillus kalamii sp. nov., isolated from a high-efficiency particulate arrestance filter system used in the International Space Station, Int. J. Syst. Evol. Microbiol., 67, 896, 10.1099/ijsem.0.001706
Tundup, 2006, Clusters of PE and PPE genes of Mycobacterium tuberculosis are organized in operons: evidence that PE Rv2431c is co-transcribed with PPE Rv2430c and their gene products interact with each other, FEBS Lett., 580, 1285, 10.1016/j.febslet.2006.01.042
Tundup, 2014, Mycobacterium tuberculosis PE25/PPE41 protein complex induces necrosis in macrophages: role in virulence and disease reactivation?, FEBS Open Bio., 4, 822, 10.1016/j.fob.2014.09.001
Akhter, 2012, The PE/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: perhaps more?, Biochimie., 94, 110, 10.1016/j.biochi.2011.09.026
Ahmed, 2008, Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention, Nat. Rev. Microbiol., 6, 387, 10.1038/nrmicro1889
Gey van Pittius, 2006, Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions, BMC Evol. Biol., 10.1186/1471-2148-6-95
Singh, 2014, Gene cooption in Mycobacteria and search for virulence attributes: comparative proteomic analyses of Mycobacterium tuberculosis, Mycobacterium indicus pranii and other Mycobacteria, Int. J. Med. Microbiol., 304, 742, 10.1016/j.ijmm.2014.05.006
Ramage, 2009, Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution, PLoS Genet., 5, 10.1371/journal.pgen.1000767
Chaudhary, 2016, Proteome scale census of major facilitator superfamily transporters in Trichoderma reesei using protein sequence and structure based classification enhanced ranking, Gene, 585, 166, 10.1016/j.gene.2016.03.043
Rani, 2016, Functional characterization of a hexose transporter from root endophyte Piriformospora indica, Front. Microbiol., 7, 10.3389/fmicb.2016.01083
Gill, 2016, Piriformospora indica: potential and significance in plant stress tolerance, Front. Microbiol., 7, 10.3389/fmicb.2016.00332
Trivedi, 2013, Multiple abiotic stress responsive rice cyclophilin: (OsCYP-25) mediates a wide range of cellular responses, Commun. Integr. Biol., 6, e25260, 10.4161/cib.25260
Pandey, 2016, Mycobacterium tuberculosis peptidyl-prolyl isomerases also exhibit chaperone like activity in-vitro and in-vivo, PLoS One, 11, e0150288, 10.1371/journal.pone.0150288
Pandey, 2017, Mycobacterium tuberculosis peptidyl-prolyl isomerases are immunogenic, alter cytokine profile and aid in intracellular survival, Front. Cell. Infect. Microbiol., 7, 1, 10.3389/fcimb.2017.00038
Karan, 2012, Function and biotechnology of extremophilic enzymes in low water activity, Aquat. Biosyst., 8, 4, 10.1186/2046-9063-8-4
Christian, 2004, Distinct origins of tRNA(m1G37) methyltransferase, J. Mol. Biol., 339, 707, 10.1016/j.jmb.2004.04.025
Reed, 2014, Circular dichroism and fluorescence spectroscopy of cysteinyl-tRNA synthetase from Halobacterium salinarum ssp. NRC-1 demonstrates that group I cations are particularly effective in providing structure and stability to this halophilic protein, PLoS One, 9, e89452, 10.1371/journal.pone.0089452
Anderson, 2015, A novel bacterial water hypersensitivity-like protein shows in vivo protection against cold and freeze damage, FEMS Microbiol. Lett., 362, 10.1093/femsle/fnv110
Cambi, 2001, Cytidine deaminase from two extremophilic bacteria: cloning, expression and comparison of their structural stability, Protein Eng., 14, 807, 10.1093/protein/14.10.807
Frolow, 1996, Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin, Nat. Struct. Biol., 3, 452, 10.1038/nsb0596-452
Castellano, 2011, Gene cloning and protein expression of γ-glutamyltranspeptidases from Thermus thermophilus and Deinococcus radiodurans: comparison of molecular and structural properties with mesophilic counterparts, Extremophiles., 15, 259, 10.1007/s00792-011-0355-6
Kitayska, 2011, Purification and properties of a new thermostable cyclodextrin glucanotransferase from Bacillus pseudalcaliphilus 8SB, Appl. Biochem. Biotechnol., 165, 1285, 10.1007/s12010-011-9346-4
Coquelle, 2007, Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments, J. Mol. Biol., 374, 547, 10.1016/j.jmb.2007.09.049
Srivastava, 2017, Trimeric βγ-crystallin from methane-producing Thermophilic archaea, Methanosaeta thermophila, Biochemistry, 56, 1299, 10.1021/acs.biochem.6b00985
Preiss, 2013, The c-ring stoichiometry of ATP synthase is adapted to cell physiological requirements of alkaliphilic Bacillus pseudofirmus OF4, Proc. Natl. Acad. Sci., 110, 7874, 10.1073/pnas.1303333110
Babu, 2015, Survival mechanisms of extremophiles, 9
Dubnovitsky, 2009, Enzyme adaptation to alkaline pH: atomic resolution (1.08 Å) structure of phosphoserine aminotransferase from Bacillus alcalophilus, Protein Sci., 14, 97, 10.1110/ps.041029805
Guiliani, 2000, Molecular cloning, sequencing, and expression of omp-40, the gene coding for the major outer membrane protein from the acidophilic bacterium Thiobacillus ferrooxidans, Appl. Environ. Microbiol., 66, 2318, 10.1128/AEM.66.6.2318-2324.2000
Buchmeier, 2000, A parallel intraphagosomal survival strategy shared by Mycobacterium tuberculosis and Salmonella enterica, Mol. Microbiol., 35, 1375, 10.1046/j.1365-2958.2000.01797.x
Meena, 2010, Survival mechanisms of pathogenic Mycobacterium tuberculosis H 37Rv, FEBS J., 277, 2416, 10.1111/j.1742-4658.2010.07666.x
Rao, 2001, Intracellular pH regulation by Mycobacterium smegmatis and Mycobacterium bovis BCG, Microbiology, 147, 1017, 10.1099/00221287-147-4-1017
Zhang, 1999, Role of acid pH and deficient efflux of pyrazinoic acid in unique susceptibility of Mycobacterium tuberculosis to pyrazinamide, J. Bacteriol., 181, 2044, 10.1128/JB.181.7.2044-2049.1999
Metchnikoff, 1905, 182
Benjamin, 1994, Stomach NO synthesis, Nature, 368, 502, 10.1038/368502a0
Gonzalo-Asensio, 2008, PhoP: A missing piece in the intricate puzzle of Mycobacterium tuberculosis virulence, PLoS One, 3, e3496, 10.1371/journal.pone.0003496
Xu, 2003, Moritella profunda sp. nov. and Moritella abyssi sp. nov., two psychropiezophilic organisms isolated from deep Atlantic sediments, Int. J. Syst. Evol. Microbiol., 53, 533, 10.1099/ijs.0.02228-0
Xu, 2003, Metabolic enzymes from psychrophilic bacteria: challenge of adaptation to low temperatures in ornithine carbamoyltransferase from Moritella abyssi, J. Bacteriol., 185, 2161, 10.1128/JB.185.7.2161-2168.2003
Gianese, 2001, Structural adaptation of enzymes to low temperatures, Protein Eng. Des. Sel., 14, 141, 10.1093/protein/14.3.141
Yamanaka, 1998, The CspA family in Escherichia coli: multiple gene duplication for stress adaptation, Mol. Microbiol., 27, 247, 10.1046/j.1365-2958.1998.00683.x
Yamanaka, 1999, Cold shock response in Escherichia coli, J. Mol. Microbiol. Biotechnol., 1, 193
Flynn, 2010, Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians, Crit. Rev. Biochem. Mol. Biol., 45, 266, 10.3109/10409238.2010.488216
Di Giulio, 2003, The universal ancestor and the ancestor of bacteria were hyperthermophiles, J. Mol. Evol., 57, 721, 10.1007/s00239-003-2522-6
López-García, 2015, Bacterial gene import and mesophilic adaptation in archaea, Nat. Rev. Microbiol., 13, 447, 10.1038/nrmicro3485
Feller, 2010, Protein stability and enzyme activity at extreme biological temperatures, J. Phys. Condens. Matter., 22, 323101, 10.1088/0953-8984/22/32/323101
Yancey, 2015, Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms, J. Exp. Biol., 218, 1880, 10.1242/jeb.114355
Morita, 2003, Structure-based analysis of high pressure adaptation of alpha-actin, J. Biol. Chem., 278, 28060, 10.1074/jbc.M302328200
Horikoshi, 1998, Barophiles: deep-sea microorganisms adapted to an extreme environment, Curr. Opin. Microbiol., 1, 291, 10.1016/S1369-5274(98)80032-5
Ortega, 2015, Halophilic protein adaptation results from synergistic residue-ion interactions in the folded and unfolded states, Chem. Biol., 22, 1597, 10.1016/j.chembiol.2015.10.010
Nayek, 2014, Salt-bridge energetics in halophilic proteins, PLoS One, 9, 10.1371/journal.pone.0093862
Evilia, 2006, Acquisition of an insertion peptide for efficient aminoacylation by a halophile tRNA synthetase, Biochemistry, 45, 6835, 10.1021/bi0521386
Franzetti, 2001, Characterization of a novel complex from Halophilic archaebacteria, which displays chaperone-like activities in vitro, J. Biol. Chem., 276, 29906, 10.1074/jbc.M102098200
DasSarma, 2013, Amino acid substitutions in cold-adapted proteins from Halorubrum lacusprofundi, an extremely Halophilic microbe from Antarctica, PLoS One., 8, 10.1371/journal.pone.0058587
Bergqvist, 2003, Halophilic adaptation of protein-DNA interactions, Biochem. Soc. Trans., 31, 677, 10.1042/bst0310677
Singh, 2011, Extremophiles: radiation resistance microbial reserves and therapeutic implications, J. Appl. Microbiol., 110, 851, 10.1111/j.1365-2672.2011.04971.x
Zhang, 2009, Xpf and not the Fanconi anaemia proteins or Rev3 accounts for the extreme resistance to cisplatin in Dictyostelium discoideum, PLoS Genet., 5, 10.1371/journal.pgen.1000645
Hsu, 2011, DNA double-strand break repair pathway choice in Dictyostelium, J. Cell Sci., 124, 1655, 10.1242/jcs.081471
Müller-Taubenberger, 2011, The histone methyltransferase Dot1 is required for DNA damage repair and proper development in Dictyostelium, Biochem. Biophys. Res. Commun., 404, 1016, 10.1016/j.bbrc.2010.12.101
Leulliot, 2009, The family X DNA polymerase from Deinococcus radiodurans adopts a non-standard extended conformation, J. Biol. Chem., 284, 11992, 10.1074/jbc.M809342200
Daly, 2007, Protein oxidation implicated as the primary determinant of bacterial radioresistance, PLoS Biol., 5, 769, 10.1371/journal.pbio.0050092
Terato, 2011, Characterization and radio-resistant function of manganese superoxide dismutase of Rubrobacter radiotolerans, J. Radiat. Res., 52, 735, 10.1269/jrr.11105
Mojib, 2013, UV and cold tolerance of a pigment-producing Antarctic Janthinobacterium sp. Ant5-2, Extremophiles., 17, 367, 10.1007/s00792-013-0525-9
Zhang, 2007, Hymenobacter xinjiangensis sp. nov., a radiation-resistant bacterium isolated from the desert of Xinjiang, China, Int. J. Syst. Evol. Microbiol., 57, 1752, 10.1099/ijs.0.65033-0
Robinson, 2011, A major role for nonenzymatic antioxidant processes in the radioresistance of Halobacterium salinarum, J. Bacteriol., 193, 1653, 10.1128/JB.01310-10
Gerasimova, 2011, Comparative genomics of the dormancy regulons in mycobacteria, J. Bacteriol., 193, 3446, 10.1128/JB.00179-11
Chen, 2013, The Mycobacterium DosR regulon structure and diversity revealed by comparative genomic analysis, J. Cell. Biochem., 114, 1, 10.1002/jcb.24302
Honaker, 2009, Unique roles of DosT and DosS in DosR regulon induction and Mycobacterium tuberculosis dormancy, Infect. Immun., 77, 3258, 10.1128/IAI.01449-08
Miller, 2000, Evaluation of Mycobacterium tuberculosis genes involved in resistance to killing by human macrophages, Infect. Immun., 68, 387, 10.1128/IAI.68.1.387-390.2000
Gerstenmaier, 2015, The autophagic machinery ensures nonlytic transmission of mycobacteria, Proc. Natl. Acad. Sci., 112, E687, 10.1073/pnas.1423318112
Brugarolas, 2012, The oxidation-sensing regulator (MosR) is a new redoxdependent transcription factor in Mycobacterium tuberculosis, J. Biol. Chem., 287, 37703, 10.1074/jbc.M112.388611
Singh, 2007, Mycobacterium tuberculosis WhiB3 responds to O2 and nitric oxide via its [4Fe-4S] cluster and is essential for nutrient starvation survival, Proc. Natl. Acad. Sci. U. S. A., 104, 11562, 10.1073/pnas.0700490104
Singh, 2009, Mycobacterium tuberculosis WhiB3 maintains redox homeostasis by regulating virulence lipid anabolism to modulate macrophage response, PLoS Pathog., 5, 10.1371/journal.ppat.1000545
Chawla, 2012, Mycobacterium tuberculosis WhiB4 regulates oxidative stress response to modulate survival and dissemination in vivo, Mol. Microbiol., 85, 1148, 10.1111/j.1365-2958.2012.08165.x
Song, 2003, RshA, an anti-sigma factor that regulates the activity of the mycobacterial stress response sigma factor SigH, Mol. Microbiol., 50, 949, 10.1046/j.1365-2958.2003.03739.x
Cossu, 2013, Expression profiling of Mycobacterium tuberculosis H37Rv and Mycobacterium smegmatis in acid-nitrosative multi-stress displays defined regulatory networks, Microb. Pathog., 65, 89, 10.1016/j.micpath.2013.10.004
Bhaskar, 2014, Reengineering redox sensitive GFP to measure mycothiol redox potential of Mycobacterium tuberculosis during infection, PLoS Pathog., 10, 10.1371/journal.ppat.1003902
Li, 2015, Structure of ribosomal silencing factor bound to mycobacterium tuberculosis ribosome, Structure, 23, 1858, 10.1016/j.str.2015.07.014
Kumar, 2012, Mycobacterium tuberculosis DosR regulon gene Rv0079 encodes a putative, “dormancy associated translation inhibitor (DATIN), PLoS One, 7
Kumar, 2017, Commentary: modification of host responses by Mycobacteria, Front. Immunol., 8, 10.3389/fimmu.2017.00466
Manina, 2015, Stress and host immunity amplify mycobacterium tuberculosis phenotypic heterogeneity and induce nongrowing metabolically active forms, Cell Host Microbe., 17, 32, 10.1016/j.chom.2014.11.016
Grune, 2004, Decreased proteolysis caused by protein aggregates, inclusion bodies, plaques, lipofuscin, ceroid, and “aggresomes” during oxidative stress, aging, and disease, Int. J. Biochem. Cell Biol., 36, 2519, 10.1016/j.biocel.2004.04.020
Vaubourgeix, 2015, Stressed mycobacteria use the chaperone ClpB to sequester irreversibly oxidized proteins asymmetrically within and between cells, Cell Host Microbe., 17, 178, 10.1016/j.chom.2014.12.008
Raju, 2014, Post-translational regulation via Clp protease is critical for survival of Mycobacterium tuberculosis, PLoS Pathog., 10, 10.1371/journal.ppat.1003994
Grover, 2016, Analyses of methyltransferases across the pathogenicity spectrum of different mycobacterial species point to an extremophile connection, Mol. BioSyst., 10.1039/C5MB00810G
Li, 2014, Microbial communities evolve faster in extreme environments, Sci. Rep., 4, 6205, 10.1038/srep06205
Bashyam, 2004, The extracytoplasmic function sigma factors: role in bacterial pathogenesis, Infect. Genet. Evol., 4, 301, 10.1016/j.meegid.2004.04.003