SUPPLEMENTARY INFORMATION. A comparative study of outer membrane proteome between a paired colistinsusceptible
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1 SUPPLEMENTARY INFORMATION A comparative study of outer membrane proteome between a paired colistinsusceptible and extremely colistin-resistant Klebsiella pneumoniae strains Raad Jasim, Mark A. Baker, 2 Yan Zhu, 3 Meiling Han, 3 Elena K. Schneider- Futschik, 4 Maytham Hussein, 4 Daniel Hoyer, 4,5,6 Jian Li, 3* Tony Velkov 4* Drug Development and Innovation, Drug Delivery, Disposition and Dynamics. Monash Institute of Pharmaceutical Sciences, Monash University, 38 Royal Parade, Parkville 3052, Victoria, Australia. 2 Priority Research Centre in Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia. 3 Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia. 4 Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria 300, Australia. 5 The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia. 6 Department of Molecular Medicine, The Scripps Research Institute, 0550 N. Torrey Pines Road, La Jolla, CA 92037, USA. Correspondence: Tony Velkov, Phone: Fax: E- mail: colistin.polymyxin@gmail.com or Tony.Velkov@unimelb.edu.au * Corresponding authors S
2 Content: -Supplementary Tables: 8 -Supplementary Figures: 3 -Total pages: 0 S2
3 Table S8. OMP proteome differences between paired colistin-susceptible and extremely colistin-resistant K. pneumoniae ATCC 3883 strains. Sensitive K. pneumoniae ATCC 3883 Resistant K. pneumoniae ATCC 3883 Protein name Number of peptides detected Protein name Number of peptides detected Cobyric acid synthase 4-aminobutyraldehyde Phosphoheptose isomerase (EC ) Purine nucleoside phosphorylase (EC ) FIG004088: inner membrane protein YebE Selenocysteine-specific translation elongation factor Sulfur carrier protein adenylyltransferase ThiF Maltose/maltodextrin transport ATPbinding protein MalK (EC ) ATP-dependent protease La (EC ) Type I Glycoprotein-polysaccharide metabolism DNA-binding protein H-NS PTS system, mannose-specific IIA component (EC ) / PTS system, mannose-specific IIB component (EC ) Glycerol-3-phosphate acyltransferase (EC ) LPS-assembly lipoprotein RlpB precursor (Rare lipoprotein B) dehydrogenase (EC.2..9) Galactose/methyl galactoside ABC transport system, permease protein MglC (TC 3.A..2.3) LSU ribosomal protein L3p (L3e) Galactose/methyl galactoside ABC transport system, ATP-binding protein MglA (EC ) SSU ribosomal protein S2p (SAe) Myo-inositol 2-dehydrogenase (EC...8) Glutathione S-transferase (EC ) LSU ribosomal protein L5p (Le) Threonyl-tRNA synthetase (EC 6...3) Purine nucleoside phosphorylase (EC ) Osmotically inducible lipoprotein B precursor Nucleoside permease NupC NADH-ubiquinone oxidoreductase chain M (EC.6.5.3) Cell division protein FtsA LSU ribosomal protein L3p (L3Ae) Adenylate cyclase (EC 4.6..) Serine hydroxymethyltransferase (EC 2..2.) PTS system, N-acetylglucosaminespecific IIA component (EC ) / PTS system, N-acetylglucosaminespecific IIB component (EC ) / PTS system, N-acetylglucosamine- Phage shock protein A S3
4 specific IIC component (EC ) Hypothetical lipoprotein YajG precursor FIG : hypothetical protein Small heat shock protein Alcohol dehydrogenase (EC...) Lysyl-tRNA synthetase (class II) (EC 6...6) Sulfur carrier protein adenylyltransferase ThiF Putative outer membrane protein LSU ribosomal protein L22p (L7e) Putative phosphosugar isomerase Putative lipoprotein Cysteine synthase (EC ) 2 kda hemolysin precursor Threonyl-tRNA synthetase (EC 6...3) Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A..3.2) Transcriptional activator of maltose Universal stress protein E regulon, MalT 4-aminobutyraldehyde dehydrogenase (EC.2..9) Tail-specific protease precursor (EC ) Acetaldehyde dehydrogenase, ethanolamine utilization cluster FIG : hypothetical protein Chromosome partition protein MukB Maltoporin (maltose/maltodextrin high-affinity receptor, phage lambda receptor protein) UDP-N-acetylmuramoylalanyl-Dglutamate--2,6-diaminopimelate ligase (EC ) SSU ribosomal protein Sp Osmotically inducible lipoprotein B precursor 6-phosphofructokinase class II (EC 2.7..) ATP synthase A chain (EC ) LSU ribosomal protein L5p (L27Ae) Alkyl hydroperoxide reductase protein C (EC.6.4.-) Cobalt-precorrin-2 C20- methyltransferase (EC ) Pyruvate formate-lyase (EC ) Lipoprotein Galactose/methyl galactoside ABC transport system, permease protein MglC (TC 3.A..2.3) LSU ribosomal protein Lp (L0Ae) Cell division protein FtsZ (EC ) SSU ribosomal protein S5p (S2e) LSU ribosomal protein L24p (L26e) Pyruvate dehydrogenase E component (EC.2.4.) S-adenosylmethionine synthetase Entericidin B precursor (EC ) Inosine-5'-monophosphate dehydrogenase (EC...205) Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE Phosphoglycerate kinase (EC Asparagine synthetase [glutaminehydrolyzing] ) (EC ) LSU ribosomal protein L22p (L7e) Putative phosphosugar isomerase LSU ribosomal protein L3p (L3e) Chaperone protein HtpG SgrR, sugar-phosphate stress, LSU ribosomal protein L20p S4
5 transcriptional activator of SgrS small RNA LSU ribosomal protein L6p (L9e) Cysteine synthase (EC ) GTP-binding protein TypA/BipA Cytochrome d ubiquinol oxidase subunit II (EC.0.3.-) LSU ribosomal protein L5p (Le) Small heat shock protein DNA-directed RNA polymerase beta' Aspartate--ammonia ligase (EC subunit (EC ) 6.3..) Adenosine deaminase (EC ) Membrane fusion protein of RND family multidrug efflux pump NADP-dependent malic enzyme (EC Septum site-determining protein...40) MinD IncF plasmid conjugative transfer Chaperone protein DnaK surface exclusion protein TraT LSU ribosomal protein L28p LSU ribosomal protein L0p (P0) Entericidin B precursor Di/tripeptide permease DtpB UDP-N-acetylglucosamine - Carbamoyl-phosphate synthase carboxyvinyltransferase (EC ) large chain (EC ) LSU ribosomal protein Lp (L0Ae) ABC transporter, ATP-binding protein Lysine decarboxylase, inducible (EC 4...8) Uncharacterized protein YeaG Formate efflux transporter (TC 2.A.44 Uridine phosphorylase (EC ) family) Maltose-6'-phosphate glucosidase (EC ) Hexuronate transporter Preprotein translocase secy subunit (TC 3.A.5..) Septum site-determining protein MinD Maltoporin (maltose/maltodextrin high-affinity receptor, phage lambda receptor protein) SSU ribosomal protein SSU ribosomal protein S8p, zincindependent Phosphate acetyltransferase (EC ) Osmotically inducible lipoprotein E precursor LSU ribosomal protein L2p Sugar diacid utilization regulator SdaR PTS system, sucrose-specific IIB component (EC ) / PTS system, sucrose-specific IIC component (EC ) 5'-methylthioadenosine nucleosidase (EC ) / S- adenosylhomocysteine nucleosidase (EC ) S5
6 Uridine phosphorylase (EC ) Alkyl hydroperoxide reductase subunit C-like protein Translation initiation factor 2 Rod shape-determining protein MreB UDP-N-acetylglucosamine--Nacetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N- acetylglucosamine transferase (EC ) SSU ribosomal protein S5p (S2e) LSU ribosomal protein L9p 5-keto-2-deoxygluconokinase (EC ) / uncharacterized domain Aspartate aminotransferase (EC 2.6..) Glucose-6-phosphate isomerase (EC ) ATP synthase alpha chain (EC ) FIG : hypothetical protein S6
7 Figure S Figure S. Alignment of the mgrb genes of the colistin-susceptible K. pneumoniae ATCC 3883 (GenBank: JSZI ) and the paired extremely colistin-resistant K. pneumoniae ATCC S7
8 Figure S2 Figure S2. Alignment of the PhoP genes of the colistin-susceptible K. pneumoniae ATCC 3883 (GenBank: JSZI ) and the paired extremely colistin-resistant K. pneumoniae ATCC S8
9 Figure S3 S9
10 Figure S3. Alignment of the PhoQ genes of the colistin-susceptible K. pneumoniae ATCC 3883 (GenBank: JSZI ) and the paired extremely colistin-resistant K. pneumoniae ATCC S0
Table S9A: List of taurine regulated genes in Bp K96243 Chr 1 (up regulated >=2 fold) Cluster no GENE ID Start Stop Strand Function
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f(x) = x R² = RPKM (M8.MXB) f(x) = x E-014 R² = 1 RPKM (M31.
14 12 f(x) = 1.633186874x - 21.46732234 R² =.995616541 RPKM (M8.MXA) 1 8 6 4 2 2 4 6 8 1 12 14 RPKM (M8.MXB) 14 12 f(x) =.821767782x - 4.192595677497E-14 R² = 1 RPKM (M31.XA) 1 8 6 4 2 2 4 6 8 1 12 14
Supplemental Information
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Protein Class/Name. Pathways. bat00250, bat00280, bat00410, bat00640, bat bat00270, bat00330, bat00410, bat00480
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Figure S1: Abundance of Fe related proteins in oceanic Synechococcus sp. strain WH8102 in. Ferredoxin. Ferredoxin. Fe ABC transporter
0.004 SW nm 0.04 0.03 nm nm 0.16 0.1 nm nm 0.40 0.3 nm nm 0.80 0.5 nm 1.6 1 nm 16 10 nm 160 100 nm 0 nm 0.04 nm 0.16 nm 0.40 nm 0.80 nm 1.6 nm 16 nm 160 nm Spectral counts 0 nm 0.04 nm 0.16 nm 0.40 nm
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