Integrated transcriptomic and proteomic analysis of the bile stress response in probiotic Lactobacillus salivarius LI01
Tài liệu tham khảo
Gao, 2010, Dose-response efficacy of a proprietary probiotic formula of lactobacillus acidophilus CL1285 and lactobacillus casei LBC80R for antibiotic-associated diarrhea and Clostridium Difficile-associated diarrhea prophylaxis in adult patients, Am. J. Gastroenterol., 105, 1636, 10.1038/ajg.2010.11
Hickson, 2007, Use of probiotic lactobacillus preparation to prevent diarrhoea associated with antibiotics: randomised double blind placebo controlled trial, BMJ, 335, 80, 10.1136/bmj.39231.599815.55
Hsieh, 2012, Eradication of Helicobacter pylori infection by the probiotic strains Lactobacillus johnsonii MH-68 and L. salivarius ssp. salicinius AP-32, Helicobacter, 17, 466, 10.1111/j.1523-5378.2012.00992.x
Tsilingiri, 2012, Probiotic and postbiotic activity in health and disease: comparison on a novel polarised ex-vivo organ culture model, Gut, 61, 1007, 10.1136/gutjnl-2011-300971
Corr, 2007, Bacteriocin production as a mechanism for the antiinfective activity of lactobacillus salivarius UCC118, Proc. Natl. Acad. Sci. U. S. A., 104, 7617, 10.1073/pnas.0700440104
Riboulet-Bisson, 2012, Effect of lactobacillus salivarius bacteriocin Abp118 on the mouse and pig intestinal microbiota, PLoS One, 7, 10.1371/journal.pone.0031113
Daniel, 2006, Selecting lactic acid bacteria for their safety and functionality by use of a mouse colitis model, Appl. Environ. Microbiol., 72, 5799, 10.1128/AEM.00109-06
McCarthy, 2003, Double blind, placebo controlled trial of two probiotic strains in interleukin 10 knockout mice and mechanistic link with cytokine balance, Gut, 52, 975, 10.1136/gut.52.7.975
O'Mahony, 2001, Probiotic impact on microbial flora, inflammation and tumour development in IL-10 knockout mice, Aliment. Pharmacol. Ther., 15, 1219, 10.1046/j.1365-2036.2001.01027.x
Begley, 2005, The interaction between bacteria and bile, FEMS Microbiol. Rev., 29, 625, 10.1016/j.femsre.2004.09.003
Jacobsen, 1999, Screening of probiotic activities of forty-seven strains of Lactobacillus spp. by in vitro techniques and evaluation of the colonization ability of five selected strains in humans, Appl. Environ. Microbiol., 65, 4949, 10.1128/AEM.65.11.4949-4956.1999
Alcantara, 2012, Proteomic and transcriptomic analysis of the response to bile stress of Lactobacillus casei BL23, Microbiology, 158, 1206, 10.1099/mic.0.055657-0
Koskenniemi, 2011, Proteomics and transcriptomics characterization of bile stress response in probiotic lactobacillus rhamnosus GG, Mol. Cell. Proteomics, 10, M110, 10.1074/mcp.M110.002741
Lee, 2013, Proteomic and transcriptional analysis of lactobacillus johnsonii PF01 during bile salt exposure by iTRAQ shotgun proteomics and quantitative RT-PCR, J. Proteome Res., 12, 432, 10.1021/pr300794y
Hamon, 2012, Investigation of biomarkers of bile tolerance in lactobacillus casei using comparative proteomics, J. Proteome Res., 11, 109, 10.1021/pr200828t
Lv, 2014, Administration of Lactobacillus salivarius LI01 or Pediococcus pentosaceus LI05 improves acute liver injury induced by D-galactosamine in rats, Appl. Microbiol. Biotechnol., 98, 5619, 10.1007/s00253-014-5638-2
Xiang, 2010, Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish, BMC Genomics, 11, 472, 10.1186/1471-2164-11-472
Gan, 2007, Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ), J. Proteome Res., 6, 821, 10.1021/pr060474i
Chong, 2006, Isobaric tags for relative and absolute quantitation (iTRAQ) reproducibility: implication of multiple injections, J. Proteome Res., 5, 1232, 10.1021/pr060018u
Wang, 2010, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data, Bioinformatics, 26, 136, 10.1093/bioinformatics/btp612
Benjamini, 2001, Controlling the false discovery rate in behavior genetics research, Behav. Brain Res., 125, 279, 10.1016/S0166-4328(01)00297-2
Begley, 2006, Bile salt hydrolase activity in probiotics, Appl. Environ. Microbiol., 72, 1729, 10.1128/AEM.72.3.1729-1738.2006
Fang, 2009, Allelic variation of bile salt hydrolase genes in lactobacillus salivarius does not determine bile resistance levels, J. Bacteriol., 191, 5743, 10.1128/JB.00506-09
Stock, 2000, Two-component signal transduction, Annu. Rev. Biochem., 69, 183, 10.1146/annurev.biochem.69.1.183
Wayne, 2012, Involvement of WalK (VicK) phosphatase activity in setting WalR (VicR) response regulator phosphorylation level and limiting cross-talk in Streptococcus Pneumoniae D39 cells, Mol. Microbiol., 86, 645, 10.1111/mmi.12006
Winkler, 2008, Essentiality, bypass, and targeting of the YycFG (VicRK) two-component regulatory system in gram-positive bacteria, J. Bacteriol., 190, 2645, 10.1128/JB.01682-07
Brown, 2003, The MerR family of transcriptional regulators, FEMS Microbiol. Rev., 27, 145, 10.1016/S0168-6445(03)00051-2
Pei, 2001, Type II CAAX prenyl endopeptidases belong to a novel superfamily of putative membrane-bound metalloproteases, Trends Biochem. Sci., 26, 275, 10.1016/S0968-0004(01)01813-8
Hubscher, 2008, Phylogenetic distribution and membrane topology of the LytR-CpsA-Psr protein family, BMC Genomics, 9, 617, 10.1186/1471-2164-9-617
Chan, 2014, The capsular polysaccharide of Staphylococcus aureus is attached to peptidoglycan by the LytR-CpsA-Psr (LCP) family of enzymes, J. Biol. Chem., 289, 15680, 10.1074/jbc.M114.567669
Liszewski Zilla, 2015, LytR-CpsA-Psr enzymes as determinants of bacillus anthracis secondary cell wall polysaccharide assembly, J. Bacteriol., 197, 343, 10.1128/JB.02364-14
Wegrzyn, 2005, Molecular guardians for newborn proteins: ribosome-associated chaperones and their role in protein folding, Cell. Mol. Life Sci., 62, 2727, 10.1007/s00018-005-5292-z
Brock, 1998, Initiation factors of protein biosynthesis in bacteria and their structural relationship to elongation and termination factors, Mol. Microbiol., 29, 409, 10.1046/j.1365-2958.1998.00893.x
Aoki, 1997, The gene encoding the elongation factor P protein is essential for viability and is required for protein synthesis, J. Biol. Chem., 272, 32254, 10.1074/jbc.272.51.32254
Frydman, 2001, Folding of newly translated proteins in vivo: the role of molecular chaperones, Annu. Rev. Biochem., 70, 603, 10.1146/annurev.biochem.70.1.603
Frees, 2007, Clp ATPases and ClpP proteolytic complexes regulate vital biological processes in low GC, Gram-positive bacteria, Mol. Microbiol., 63, 1285, 10.1111/j.1365-2958.2007.05598.x
Zolkiewski, 2006, A camel passes through the eye of a needle: protein unfolding activity of clp ATPases, Mol. Microbiol., 61, 1094, 10.1111/j.1365-2958.2006.05309.x
Diez, 2000, The universal stress protein a of Escherichia coli is required for resistance to DNA damaging agents and is regulated by a RecA/FtsK-dependent regulatory pathway, Mol. Microbiol., 36, 1494, 10.1046/j.1365-2958.2000.01979.x
Seifart Gomes, 2011, Universal stress proteins are important for oxidative and acid stress resistance and growth of Listeria monocytogenes EGD-e in vitro and in vivo, PLoS One, 6, 10.1371/journal.pone.0024965
Lopez-Gomollon, 2009, New insights into the role of fur proteins: FurB (All2473) from anabaena protects DNA and increases cell survival under oxidative stress, Biochem. J., 418, 201, 10.1042/BJ20081066
Sakoh, 2005, Proteolytic activity of HtpX, a membrane-bound and stress-controlled protease from Escherichia coli, J. Biol. Chem., 280, 33305, 10.1074/jbc.M506180200
Akiyama, 2009, Quality control of cytoplasmic membrane proteins in Escherichia coli, J. Biochem., 146, 449, 10.1093/jb/mvp071
Cai, 2014, Analysis of the transcriptional regulator GlpR, promoter elements, and posttranscriptional processing involved in fructose-induced activation of the phosphoenolpyruvate-dependent sugar phosphotransferase system in Haloferax mediterranei, Appl. Environ. Microbiol., 80, 1430, 10.1128/AEM.03372-13
Escapa, 2013, The role of GlpR repressor in pseudomonas putida KT2440 growth and PHA production from glycerol, Environ. Microbiol., 15, 93, 10.1111/j.1462-2920.2012.02790.x
Sanchez, 2005, Proteomic analysis of global changes in protein expression during bile salt exposure of Bifidobacterium longum NCIMB 8809, J. Bacteriol., 187, 5799, 10.1128/JB.187.16.5799-5808.2005
Stetina, 2014, The transcriptional response of lactobacillus sanfranciscensis DSM 20451T and its tcyB mutant lacking a functional cystine transporter to diamide stress, Appl. Environ. Microbiol., 80, 4114, 10.1128/AEM.00367-14
Holecek, 2015, Ammonia and amino acid profiles in liver cirrhosis: effects of variables leading to hepatic encephalopathy, Nutrition, 31, 14, 10.1016/j.nut.2014.03.016
Hernandez, 2015, Bile-induced peptidoglycan remodelling in salmonella enterica, Environ. Microbiol., 17, 1081, 10.1111/1462-2920.12491
Weidenmaier, 2008, Teichoic acids and related cell-wall glycopolymers in gram-positive physiology and host interactions, Nat. Rev. Microbiol., 6, 276, 10.1038/nrmicro1861
Steen, 2005, Autolysis of Lactococcus lactis is increased upon D-alanine depletion of peptidoglycan and lipoteichoic acids, J. Bacteriol., 187, 114, 10.1128/JB.187.1.114-124.2005
Perea Velez, 2007, Functional analysis of D-alanylation of lipoteichoic acid in the probiotic strain lactobacillus rhamnosus GG, Appl. Environ. Microbiol., 73, 3595, 10.1128/AEM.02083-06
Kimber, 2004, The structure of (3R)-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Pseudomonas Aeruginosa, J. Biol. Chem., 279, 52593, 10.1074/jbc.M408105200
Zhu, 2013, The two functional enoyl-acyl carrier protein reductases of Enterococcus faecalis do not mediate triclosan resistance, mBio, 4, e00613, 10.1128/mBio.00613-13
Taranto, 2003, Bile salts and cholesterol induce changes in the lipid cell membrane of lactobacillus reuteri, J. Appl. Microbiol., 95, 86, 10.1046/j.1365-2672.2003.01962.x
Machado, 2004, Osmotic response in lactobacillus casei ATCC 393: biochemical and biophysical characteristics of membrane, Arch. Biochem. Biophys., 422, 61, 10.1016/j.abb.2003.11.001
Lewinson, 2004, Alkalitolerance: a biological function for a multidrug transporter in pH homeostasis, Proc. Natl. Acad. Sci. U. S. A., 101, 14073, 10.1073/pnas.0405375101
Holdsworth, 2013, Multidrug resistance protein MdtM adds to the repertoire of antiporters involved in alkaline pH homeostasis in Escherichia coli, BMC Microbiol., 13, 113, 10.1186/1471-2180-13-113
Lubelski, 2006, LmrCD is a major multidrug resistance transporter in Lactococcus lactis, Mol. Microbiol., 61, 771, 10.1111/j.1365-2958.2006.05267.x
Zaidi, 2008, The ABC-type multidrug resistance transporter LmrCD is responsible for an extrusion-based mechanism of bile acid resistance in Lactococcus lactis, J. Bacteriol., 190, 7357, 10.1128/JB.00485-08
Wu, 2010, Effect of bile salts stress on protein synthesis of lactobacillus casei Zhang revealed by 2-dimensional gel electrophoresis, J. Dairy Sci., 93, 3858, 10.3168/jds.2009-2967
Burns, 2010, Inside the adaptation process of Lactobacillus delbrueckii subsp. lactis to bile, Int. J. Food Microbiol., 142, 132, 10.1016/j.ijfoodmicro.2010.06.013
Hamon, 2011, Comparative proteomic analysis of lactobacillus plantarum for the identification of key proteins in bile tolerance, BMC Microbiol., 11, 63, 10.1186/1471-2180-11-63
Hecker, 1996, Heat-shock and general stress response in Bacillus Subtilis, Mol. Microbiol., 19, 417, 10.1046/j.1365-2958.1996.396932.x
Derre, 1999, CtsR, a novel regulator of stress and heat shock response, controls clp and molecular chaperone gene expression in gram-positive bacteria, Mol. Microbiol., 31, 117, 10.1046/j.1365-2958.1999.01152.x
Suokko, 2008, ClpL is essential for induction of thermotolerance and is potentially part of the HrcA regulon in lactobacillus gasseri, Proteomics, 8, 1029, 10.1002/pmic.200700925
Chastanet, 2003, clpP of Streptococcus salivarius is a novel member of the dually regulated class of stress response genes in gram-positive bacteria, J. Bacteriol., 185, 683, 10.1128/JB.185.2.683-687.2003
Paul, 2004, rRNA transcription in Escherichia coli, Annu. Rev. Genet., 38, 749, 10.1146/annurev.genet.38.072902.091347
Janosi, 1994, Ribosome recycling factor (ribosome releasing factor) is essential for bacterial growth, Proc. Natl. Acad. Sci. U. S. A., 91, 4249, 10.1073/pnas.91.10.4249
Achberger, 1981, The role of the delta peptide of the Bacillus Subtilis RNA polymerase in promoter selection, J. Biol. Chem., 256, 7424, 10.1016/S0021-9258(19)68980-5
Xue, 2010, The delta subunit of RNA polymerase, RpoE, is a global modulator of Streptococcus mutans environmental adaptation, J. Bacteriol., 192, 5081, 10.1128/JB.00653-10
Rabatinova, 2013, The delta subunit of RNA polymerase is required for rapid changes in gene expression and competitive fitness of the cell, J. Bacteriol., 195, 2603, 10.1128/JB.00188-13
Martin, 2006, Lactobacillus salivarius CECT 5713, a potential probiotic strain isolated from infant feces and breast milk of a mother-child pair, Int. J. Food Microbiol., 112, 35, 10.1016/j.ijfoodmicro.2006.06.011
An, 2014, Integrated transcriptomic and proteomic analysis of the bile stress response in a centenarian-originated probiotic Bifidobacterium longum BBMN68, Mol. Cell. Proteomics, 13, 2558, 10.1074/mcp.M114.039156
Greenbaum, 2003, Comparing protein abundance and mRNA expression levels on a genomic scale, Genome Biol., 4, 1, 10.1186/gb-2003-4-9-117
Maier, 2009, Correlation of mRNA and protein in complex biological samples, FEBS Lett., 583, 3966, 10.1016/j.febslet.2009.10.036
Galperin, 2001, Conserved ‘hypothetical’ proteins: new hints and new puzzles, Comp. Funct. Genomics, 2, 14, 10.1002/cfg.66