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. 2012 Apr 5;205(11):1677–1687. doi: 10.1093/infdis/jis252

Table 2.

Mutations Observed Between Isogenic Staphylococcus aureus Strain Pairs or Series Exposed to Vancomycin

Mutationsc
ORF IDa Gene Product Function Protein Sizeb Type Change Truncated Sizec
Clinically derived pairs
 1. A5937/A5940
  SA1062 stp1 Serine/threonine phosphatase Signal transduction 247 Deletion Frameshift 113
  SA1844 agrA Accessory gene regulator A Transcription 238 Insertion Glu162Stop 161
  SA0500 rpoB RNA polymerase subunit β Transcription 1183 SNP His481Tyr
  SA1505 lysP Lysine-specific permease Amino acid metabolism/transport 315 SNP Leu290Phe
  SA2093 ssaA2 Staphylococcal secretory antigen Immune interaction 267 Insertion Frameshift 190
  SA0022 5′-nucleotidase Nucleic acid metabolism/transport 773 SNP Asp537Asp
 2. A6224/A6226
  SA0793 dltA d-alanine-poly(phosphoribitol) ligase, subunit 1 Cell wall/outer membrane metabolism 485 SNP Ser38Arg
  SA0020 yycI Regulatory protein, WalKR operon Cell wall/outer membrane metabolism 262 Deletion Frameshift 51
  SA0905 atl Bifunctional autolysin Cell wall/outer membrane metabolism 1255 SNP Ser752Ser
  SA1246 arlS Histidine-kinase Signal transduction 451 Insertion Frameshift 38
  SA1022 mraW S-adenosyl-methyltransferase Amino acid metabolism/transport 311 Deletion Frameshift 143
  SA1721 pcrA ATP-dependent helicase DNA replication and repair 730 SNP Glu455Glu
  SA0467 tilS tRNA(ile)-lysidine synthetase Nucleic acid metabolism/transport 431 SNP Met128Ile
  SA0587 PsaA adhesin homologue Inorganic ion transport/metabolism 309 Deletion Frameshift 225
  SA1528 Universal stress protein Stress response 137 SNP Leu105Leu
  SA0837 2-isopropylmalate synthase Amino acid metabolism/transport 381 Insertion Frameshift 296
  SA1778 Hypothetical protein Unknown 114 Deletion Frameshift 76
  SA0349 Hypothetical protein Unknown 495 SNP Pro474Ser
  SA0668 Hypothetical protein Unknown 157 SNP Val41Ile
 3. A6300/A6298
  SA2024 rpsK 30S ribosomal protein S11 Translation 129 SNP Arg127Gly
  SA1404 rpsU 30S ribosomal protein S21 Translation 67 Deletion Frameshift 51
  SA0926 purD Phosphorybosylamine-glycine ligase Nucleotide metabolism/transport 415 SNP Val389Ala
  SA1491 hemL Glutamate-1-semialdehyde-2,1-aminomutase Secondary metabolism biosynthesis 425 SNP Gly48Asp
  SA2480 drp35 Lactonase Carbohydrate metabolism and transport 324 SNP Asn83Ser
  SA1398 Diacylglycerol kinase, putative Lipid metabolism 114 SNP Glu66Lys
  SA0949 Hypothetical protein Unknown 179 Deletion No start codon
  SA0556 Hypothetical protein Unknown 210 SNP Phe147Phe
Clinically derived series
 A9635/A9636
  SA1438 greA Transcription elongation factor Transcription 158 1. SNP 2. Insertion Arg29Pro, 30Ser, 31Cys 160
 A9637
  SA1404 rpsU 30S ribosomal protein S21 Translation 67 Deletion Frameshift 53
  SA1478 Hypothetical protein Unknown 94 SNP Glu24Lys
 A9638
  SA0617 vraG ABC transporter permease ABC transporter, defense 633 SNP Ala580Val
  SA1702 yvqF Protein of the VraSR operon Cell wall/outer membrane metabolism 233 SNP Asn74Asp
  SA2047 rplC 50S ribosomal protein L3 Translation 220 SNP Gly7Val
  SA1404 rpsU 30S ribosomal protein S21 Translation 67 Deletion Frameshift 53
  SA1861 ilvC Ketol-acid reductoisomerase Amino acid metabolism and transport 334 Deletion 30Gln/31Gly 332
 A9639
  SA1067 vraG ABC transporter permease ABC transporter, defense 633 SNP Ala580Val
  SA1870 rsbW Ser-protein kinase, anti-σ β factor Transcriptional regulation 159 Deletion 88Ser/89Phe 157
  SA1404 rpsU Ribosomal protein S21 Translation 67 Deletion Frameshift 53
  SA1861 ilvC Ketol-acid reductoisomerase Amino acid metabolism/transport 334 Deletion 30Gln/31Gly 332
Laboratory-derived series
 A8117/A8118
  SA0018 walK Sensor protein kinase Cell wall/outer membrane metabolism 608 1. SNP, 2. SNP Arg263Cys, Ser273Asn
  SA2147 tcaR Teichoplanin-resistance associated HTH-type transcriptional regulator Transcription 151 SNP-1, SNP-2 Ile69Ser, Lys95Asn
  SA1936 luxS S-ribosylhomocysteinase Amino acid metabolism/transport, quorum sensing 156 SNP Lys15Glu
 A8392
  SA0018 walK Sensor protein kinase Cell wall/outer membrane metabolism 608 Deletion 371Gln 607
  SA1702 yvqF Protein of the VraSR operon Cell wall/outer membrane metabolism 233 SNP Leu57Phe
  SA0500 rpoB RNA polymerase subunit β Transcription 1183 SNP Ser1052Leu
  SA2147 tcaR Teicoplanin resistance associated HTH-type transcriptional regulator Transcription 151 1. SNP, 2. SNP Ile69Ser, Lys95Asn
  SA0375 guaB Inosine-5-monophosphate dehydrogenase Nucleotide metabolism/transport 488 SNP Glu417Glu

Abbreviations: ABC, ATP binding casette; ATP, adenosine triphosphate; ID, identification; ORF, open reading frame; SNP, single-nucleotide polymorphism.

a ORF ID derived from N315 genome annotation.

b Sizes of the gene or protein based on the susceptible strain of S. aureus.

c Size of the truncated/extended protein in the nonsusceptible strain of S. aureus.