Abbott IJ, Slavin MA, Turnidge JD, Thursky KA, Worth LJ (2011) Stenotrophomonas maltophilia: emerging disease patterns and challenges for treatment. Expert Rev Anti Infect Ther 9:471-488
Avison MB, Higgins CS, Ford PJ, von Heldreich CJ, Walsh TR, Bennett PM (2002) Differential regulation of L1 and L2 ß-lactamase expression in Stenotrophomonas maltophilia. J Antimicrob Chemother 49:387-389
Bandow JE, Brötz H, Leichert LIO, Labischinski H, Hecker M (2003) Proteomic approach to understanding antibiotic action. Antimicrob Agents Chemother 47:948-955
Bebrone C, Moali C, Mahy F, Rival S, Docquier JD, Rossolini GM, Fastrez J, Pratt RF, Frére JM, Galleni M (2001) CENTA as a chromogenic substrate for studying ß-lactamases. Antimicrob Agents Chemother 45:1868-1871
Brötz-Oesterhelt H, Bandow JE, Labischinski H (2005) Bacterial proteomics and its role in antibacterial drug discovery. Mass Spectrom Rev 24:549-565
Camberg JL, Hoskins JR, Wickner S (2011) The interplay of ClpXP with the cell division machinery in Escherichia coli. J Bacteriol 193:1911-1918
Chattoraj P, Banerjee A, Biswas S, Biswas I (2010) ClpP of Streptococcus mutans differentially regulates expression of genomic islands, mutacin production, and antibiotic tolerance. J Bacteriol 192:1312-1323
Cirz RT, Chin JK, Andes DR, de Crécy-Lagard V, Craig WA, Romesberg FE (2005) Inhibition of mutation and combating the evolution of antibiotic resistance. PLoS Biol 3:e176
Crossman LC, Gould VC, Dow JM, Vernikos GS, Okazaki A, Sebaihia M, Saunders D, Arrowsmith C, Carver T, Peters N, Adlem E, Kerhornou A, Lord A, Murphy L, Seeger K, Squares R, Rutter S, Quail MA, Rajandream MA, Harris D, Churcher C, Bentley SD, Parkhill J, Thomson NR, Avison MB (2008) The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biol 9:R74
Crowley DJ, Hanawalt PC (1998) Induction of the SOS response increases the efficiency of global nucleotide excision repair of cyclobutane pyrimidine dimers, but not 6-4 photoproducts, in UV-irradiated Escherichia coli. J Bacteriol 180:3345-3352
De Carolis E, Posteraro B, Florio AR, Colonna B, Prosseda G, Bugli F, Lorenzetti SR, Fiscarelli E, Inzitari R, Iavarone F, Castagnola M, Fadda G, Sanguinetti M (2010) Analysis of heat-induced changes in protein expression of Stenotrophomonas maltophilia K279a reveals a role for GroEL in the host-temperature adaptation. Int J Med Microbiol 301:273-281
de Oliveira-Garcia D, Dall'Agnol M, Rosales M, Azzuz ACGS, Martinez MB, Girón JA (2002) Characterization of flagella produced by clinical strains of Stenotrophomonas maltophilia. Emerg Infect Dis 8:918-923
Fournier PE, Raoult D (2011) Prospects for the future using genomics and proteomics in clinical microbiology. Annu Rev Microbiol 65:169-188
Frydman J (2001) Folding of the newly translated proteins in vivo: the role of molecular chaperones. Annu Rev Biochem 70:603-647
Gilar M, Olivova P, Daly AE, Gebler JC (2005) Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions. J Sep Sci 28:1694-1703
Gould VC, Okazaki A, Avison MB (2006) ß-Lactam resistance and ß-lactamase expression in clinical Stenotrophomonas maltophilia isolates having defined phylogenetic relationships. J Antimicrob Chemother 57:199-203
Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R (2002) Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics 1:323-333
Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720-1730
Hale CA, de Boer PA (1997) Direct binding of FtsZ to ZipA, an essential component of the septal ring structure that mediates cell division in E. coli. Cell 88:175-185
Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 8:R19
Hoch JA (2000) Two-component and phosphorelay signal transduction. Curr Opin Microbiol 3:165-170
Howe RA, Wilson MP, Walsh TR, Millar MR (1997) Susceptibility testing of Stenotrophomonas maltophilia to carbapenems. J Antimicrob Chemother 40:13-17
Hu RM, Chiang KH, Lin CW, Yang TC (2008a) Modified nitrocefin-EDTA method to differentially quantify the induced L1 and L2 ß-lactamases in Stenotrophomonas maltophilia. Lett Appl Microbiol 47:457-461
Hu RM, Huang KJ, Wu LT, Hsiao YJ, Yang TC (2008b) Induction of L1 and L2 ß-lactamases of Stenotrophomonas maltophilia. Antimicrob Agents Chemother 52:1198-1200
Huang YW, Lin CW, Hu RM, Lin YT, Chung TC, Yang TC (2010) AmpN-AmpG operon is essential for expression of L1 and L2 ß-lactamases in Stenotrophomonas maltophilia Antimicrob Agents Chemother 54 2583-2589
Kihara A, Akiyama Y, Ito K (1996) A protease complex in the Escherichia coli plasma membrane: HflKC (HflA) forms a complex with FtsH (HflB), regulating its proteolytic activity against SecY. EMBO J 15:6122-6131
Koebnik R (2005) TonB-dependent trans-envelope signalling: the exception or the rule? Trends Microbiol 13:343-347
Kvint K, Nachin L, Diez A, Nyström T (2003) The bacterial universal stress protein: function and regulation. Curr Opin Microbiol 6:140-145
Li XZ, Zhang L, Poole K (2002) SmeC, an outer membrane multidrug efflux protein of Stenotrophomonas maltophilia. Antimicrob Agents Chemother 46:333-343
Lin CW, Huang YW, Hu RM, Chiang KH, Yang TC (2009) The role of AmpR in regulation of L1 and L2 ß-lactamases in Stenotrophomonas maltophilia. Res Microbiol 160:152-158
Lin XM, Yang JN, Peng XX, Li H (2010) A novel negative regulation mechanism of bacterial outer membrane proteins in response to antibiotic resistance. J Proteome Res 9:5952-5959
Lin CW, Lin HC, Huang YW, Chung TC, Yang TC (2011) Inactivation of mrcA gene derepresses the basal-level expression of L1 and L2 ß-lactamases in Stenotrophomonas maltophilia J Antimicrob Chemother 66 2033-2037
Livermore DM (2009) Has the era of untreatable infections arrived? J Antimicrob Chemother 64:29-36
Looney WJ, Narita M, Mühlemann K (2009) Stenotrophomonas maltophilia: an emerging opportunist human pathogen. Lancet Infect Dis 9:312-323
McGowan JE (2006) Resistance in nonfermenting gram-negative bacteria: multidrug resistance to the maximum. Am J Infect Control 34:S29-S37, S64-73
Mercuri PS, Ishii Y, Ma L, Rossolini GM, Luzzaro F, Amicosante G, Franceschini N, Frére JM, Galleni M (2002) Clonal diversity and metallo-ß-lactamase production in clinical isolates of Stenotrophomonas maltophilia. Microb Drug Resist 8:193-200
Molloy MP (2008) Isolation of bacterial cell membranes proteins using carbonate extraction. Methods Mol Biol 424:397-401
Morán-Barrio J, Limansky AS, Viale AM (2009) Secretion of GOB metallo-ß-lactamase in Escherichia coli depends strictly on the cooperation between the cytoplasmic DnaK chaperone system and the Sec machinery: completion of folding and Zn(II) ion acquisition occur in the bacterial periplasm. Antimicrob Agents Chemother 53:2908-2917
Moya B, Dötsch A, Juan C, Blázquez J, Zamorano L, Haussler S, Oliver A (2009) ß-lactam resistance response triggered by inactivation of a nonessential penicillin-binding protein. PLoS Pathog 5:e1000353. doi:10.1371/journal.ppat.1000353
Okazaki A, Avison MB (2008) Induction of L1 and L2 ß-lactamase production in Stenotrophomonas maltophilia is dependent on an AmpR-type regulator. Antimicrob Agents Chemother 52:1525-1528
Paez JIG, Costa SF (2008) Risk factors associated with mortality of infections caused by Stenotrophomonas maltophilia: a systematic review. J Hosp Infect 70:101-108
Pessione E, Giuffrida MG, Prunotto L, Barello C, Mazzoli R, Fortunato D, Conti A, Giunta C (2003) Membrane proteome of Acinetobacter radioresistens S13 during aromatic exposure. Proteomics 3:1070-1076
Poetsch A, Wolters D (2008) Bacterial membrane proteomics. Proteomics 8:4100-4122
Pradel N, Delmas J,Wu LF, Santini CL, Bonnet R (2009) Sec-and Tatdependent translocation of ß-lactamases across the Escherichia coli inner membrane. Antimicrob Agents Chemother 53:242-248
Rajendar B, Lucius AL (2010) Molecular mechanism of polypeptide translocation catalyzed by the Escherichia coli ClpA protein translocase. J Mol Biol 399:665-679
Reidegeld KA, Eisenacher M, Kohl M, Chamrad D, Körting G, Blüggel M, Meyer HE, Stephan C (2008) An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications. Proteomics 8:1129-1137
Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3:1154-1169
Ryan RP, Monchy S, Cardinale M, Taghavi S, Crossman L, Avison MB, Berg G, van der Lelie D, Dow JM (2009) The versatility and adaptation of bacteria from the genus Stenotrophomonas. Nat Rev Microbiol 7:514-525
Sader HS, Jones RN (2005) Antimicrobial susceptibility of uncommonly isolated non-enteric Gram-negative bacilli. Int J Antimicrob Agents 25:95-109
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, vol 1, second edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp 7.6-7.9
Sanchez MB, Hernandez A, Martinez JL (2009) Stenotrophomonas maltophilia drug resistance. Future Microbiol 4:655-660
Senol E (2004) Stenotrophomonas maltophilia: the significance and role as a nosocomial pathogen. J Hosp Infect 57:1-7
Sherman M, Goldberg AL (1992) Heat shock in Escherichia coli alters the protein-binding properties of the chaperonin groEL by inducing its phosphorylation. Nature 357:167-169
Shilov IV, Seymour SL, Patel AA, Loboda A, Tang WH, Keating SP, Hunter CL, Nuwaysir LM, Schaeffer DA (2007) The paragon algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol Cell Proteomics 6:1638-1655
Tayler AE, Ayala JA, Niumsup P, Westphal K, Baker JA, Zhang L, Walsh TR, Wiedemann B, Bennett PM, Avison MB (2010) Induction of ß-lactamase production in Aeromonas hydrophila is responsive to ß-lactam-mediated changes in peptidoglycan composition. Microbiology 156:2327-2335
Thein M, Sauer G, Paramasivam N, Grin I, Linke D (2010) Efficient subfractionation of Gram-negative bacteria for proteomics studies. J Proteome Res 9:6135-6147
Typas A, Banzhaf M, Gross CA, Vollmer W (2012) From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat Rev Microbiol 10:123-136
Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JAM (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35:W71-W74
Van Mulders SE, Stassen C, Daenen L, Devreese B, Siewers V, van Eijsden RG, Nielsen J, Delvaux FR, Willaert R (2011) The influence of microgravity on invasive growth in Saccharomyces cerevisiae. Astrobiology 11:45-55
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3:research 0034.1-0034.11
Vashist J, Tiwari V, Kapil A, Rajeswari MR (2010) Quantitative profiling and identification of outer membrane proteins of ß-lactam resistant strain of Acinetobacter baumannii. J Proteome Res 9:1121-1128
Walsh TR, McGowan AP, Bennett PM (1997) Sequence analysis and enzyme kinetics of the L2 serine ß-lactamase from Stenotrophomonas maltophilia. Antimicrob Agents Chemother 41:1460-1464
Wecke T, Mascher T (2011) Antibiotic research in the age of omics: from expression profiles to interspecies communication. J Antimicrob Chemother 66:2689-2704
Wenzel M, Bandow JE (2011) Proteomic signatures in antibiotic research. Proteomics 11:3256-3268
Wenzel M, Patra M, Albrecht D, Chen DY, Nicolaou KC, Metzler-Nolte N, Bandow JE (2011) Proteomic signature of fatty acid biosynthesis inhibition available for in vivo mechanism of action studies. Antimicrob Agents Chemother 55:2590-2596
Werbrouck H, Grijspeerdt K, Botteldoorn N, Van Pamel E, Rijpens N, Van Damme J, Uyttendaele M, Herman L, Van Coillie E (2006) Differential inlA and inlB expression and interaction with human intestinal and liver cells by Listeria monocytogenes strains of different origins. Appl Environ Microbiol 72:3862-3871
Yang TC, Huang YW, Hu RM, Huang SC, Lin YT (2009) AmpD(I) is involved in expression of the chromosomal L1 and L2 ß-lactamases of Stenotrophomonas maltophilia Antimicrob Agents Chemother 53 2902-2907
Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FSL (2010) PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26:1608-1615
Yun SH, Choi CW, Kwon SO, Park GW, Cho K, Kwon KH, Kim JY, Yoo JS, Lee JC, Choi JS, Kim S, Kim SI (2011) Quantitative proteomic analysis of cell wall and plasma membrane fractions from multidrug-resistant Acinetobacter baumannii. J Proteome Res 10:459-469
Zhou Y, Chen WN (2011) iTRAQ-coupled 2-D LC-MS/MS analysis of membrane protein profile in Escherichia coli incubated with apidaecin IB. PLoS One 6:e20442. doi:10.1371/journal. pone.0020442
