Table S1. Bacterial strains and plasmids used in this study.

Strain Genotype or description SourceEscherichia coli

DH5αF-, φ80d deoR lacZΔM15 endA1 recA1 hsdR17(rK-mK+) supE44 thi-1 gyrA96 relA1 Δ(lacZYA-argF) U169

Invitrogen.

Campylobacter jejuni

81-176 Wild type isolated from a diarrheic patient, undergone laboratory passage.

Korlath, JA et al. "A point-source outbreak of campylobacteriosis associated with consumption of raw milk." Journal of infectious diseases 152.3 (1985): 592-596.

81116

Wild type, isolated from humans during a waterborne outbreak at a school in southeast England in 1981; undergone laboratory passage.

Manning, G et al. 2001. Evidence for a genetically stable strain of Campylobacter jejuni. Appl. Environ. Microbiol. 67:1185-1189.

11168-OWild type, originally isolated from the feces of a diarrheic patient in 1977 by Martin Skirrow; minimal laboratory.

Newell, D and Skirrow, M. Veterinary Laboratories Agency.

11168-GS Wild type, genome sequenced isolate, undergone laboratory passage.

Gaynor, EC et al. "The genome-sequenced variant of Campylobacter jejuni NCTC 11168 and the original clonal clinical isolate differ markedly in colonization, gene expression, and virulence-associated phenotypes." Journal of bacteriology 186.2 (2004): 503-517.

81-176 Colony 1 aptI61T Single colony isolate, whole genome sequenced. This study.

81-176 Colony 2 purFA304G

Single colony isolate, whole genome sequenced. This study.

81-176 Colony 3 purFG292S

Single colony isolate, whole genome sequenced. This study.

81-176 Colony 4 aptI61T Single colony isolate, whole genome sequenced. This study.

81-176 Colony 5 purFG95delinsGV

Single colony isolate, whole genome sequenced. This study.

81-176 Colony 1 aptI61T + pRRH-aptREF

Mutant single colony isolate with genome-integrated copy of operon containing reference sequence of apt.

This study.

81-176 Colony 2 purFA304G + pRRH-purFT91del

Mutant single colony isolate with genome-integrated copy of operon containing purFT91del.

This study.

81-176 Colony 3 purFG292S + pRRH- purFT91del

Mutant single colony isolate with genome-integrated copy of operon containing purFT91del.

This study.

81-176 Colony 5 purFG95delinsGV + pRRH: purFT91del

Mutant single colony isolate with genome-integrated copy of operon containing purFT91del.

This study.

81-176 + pRRH-aptA133T

81-176 with genome-integrated copy of aptA133T operon. This study.

81-176 + pRRH-purFA304G

81-176 with genome-integrated copy of purFA304G operon. This study.

81-176 + pRRH-purFG292S

81-176 with genome-integrated copy of purFG292S operon. This study.

81-176 + pRRH- 81-176 with genome-integrated copy of This study.

Strain Genotype or description SourcepurFG95delinsGV purFG95delinsGV operon.

81-176 Δapt::aprR Replacement deletion of apt with apramycin resistance cassette. This study.

81-176 96 Single colony isolates

96 single colony isolates – Sanger sequenced genotypes are shown in Figure 3A.

This study.

81-176 purFG95V Single colony isolate 56, passaged 1X. This study.81-176 aptA133T Single colony isolate 95, passaged 1X. This study.81-176 purFG292S Single colony isolate 45, passaged 1X. This study.81-176 aptE154A Single colony isolate 82, passaged 1X. This study.81-176 purFV336F Single colony isolate 79, passaged 1X. This study.81-176 aptG135_136GinsGTANARVLLVDDLIATG

Single colony isolate 93, passaged 1X. This study.

81-176 purFT91del Single colony isolate 29, passaged 1X. This study.81-176 purFV93_D96del Single colony isolate 88, passaged 1X. This study.81-176 aptP93_F94insFETFSCEYDLEYGSDK

Single colony isolate 27, passaged 1X. This study.

81-176 DRH461 Strain 81-176 with an unmarked deletion of astA arylsulfatase reporter

Hendrixson DR, et al. “Transcription of σ54-dependent but not σ28-dependent flagellar genes in Campylobacter jejuni is associated with formation of the flagellar secretory apparatus.” Mol Microbiol (2013) 50: 687–702

81-176 DRH461 + pRRA-RBSastA

Arylsulfatase deletion strain with genome-integrated astA reporter fused to reference RBS.

This study.

81-176 DRH461 + pRRA-RBS*astA

Arylsulfatase deletion strain with genome-integrated astA reporter fused to apt RBS sequence in colony 15.

This study.

81-176 argH::cat Arginine auxotroph strain of C. jejuni for use in SILAC. Dmitry Apel. University of British Columbia.

81-176 purFT91del Δcj1132c::aprR

Replacement deletion of cj1132c with apramycin resistance cassette in the purFT91del single colony background.

This study.

81-176 purFT91del Δcj1132c::aprR + pRRH-cj1132c

Complementation of the replacement deletion of cj1132c with genome-integrated copy of cj1132c in the purFT91del single colony background.

This study.

Plasmids (maintained in E. coli strain)

pGEM-T Linearized cloning vector, blue-white screening; ampicillin resistance. Novagen.

pAC1A Vector containing the apramycin resistance cassette.

Cameron, A et al. "Hygromycin B and Apramycin Antibiotic Resistance Cassettes for Use in Campylobacter jejuni." PloS ONE (2014): e95084.

pRRA Genome-insertional gene delivery vehicle; apramycin resistance.

Cameron, A et al. "Hygromycin B and Apramycin Antibiotic Resistance Cassettes for Use in Campylobacter jejuni." PloS ONE (2014): e95084.

Strain Genotype or description Source

pRRH Genome-insertional gene delivery vehicle; hygromycin resistance.

Cameron, A et al. "Hygromycin B and Apramycin Antibiotic Resistance Cassettes for Use in Campylobacter jejuni." PloS ONE (2014): e95084.

pGEM-purFCloning plasmid harboring purF and flanking regions, from PCR with oligos 6409 and 6410. Ampicillin resistance.

This study.

pGEM-aptCloning plasmid harboring apt and flanking regions, from PCR with oligos 6413 and 6414. Ampicillin resistance.

This study.

pGEM-purF::aprR

Plasmid containing replacement deletion of purF coding sequence, created via inverse PCR with oligos 6411 and 6412 and ligation to apramycin cassette. Ampicllin and apramycin resistance.

This study.

pGEM-apt::aprR

Plasmid containing replacement deletion of apt coding sequence, created via inverse PCR with oligos 6415 and 6416 and ligation to apramycin cassette; Ampicillin and apramycin resistance.

This study.

pRRH-aptREF

Genome-insertional gene delivery plasmid harboring apt reference sequence operon, insert created with oligos 2775 and 2776; hygromycin resistance.

This study.

pRRH-purFT91del

Genome-insertional gene delivery plasmid harboring purFT91del operon, insert created with oligos 2777 and 2778; hygromycin resistance.

This study.

pRRH-aptA133T

Genome-insertional gene delivery plasmid harboring aptA133T operon, insert created with oligos 2775 and 2776; hygromycin resistance.

This study.

pRRH-purFA304G

Genome-insertional gene delivery plasmid harboring purFA304G operon, insert created with oligos 2777 and 2778; hygromycin resistance.

This study.

pRRH-purFG292S

Genome-insertional gene delivery plasmid harboring purFG292S operon, insert created with oligos 2777 and 2778; hygromycin resistance.

This study.

pRRH-purFG95delinsGV

Genome-insertional gene delivery plasmid harboring purFG95delinsGV operon, insert created with oligos 2777 and 2778; hygromycin resistance.

This study.

pRRA-RBSastA (CGAGGCA)

Genome-insertional gene delivery plasmid harboring astA reporter fused to apt RBS reference sequence. Insert created with oligos 3812 and 3814; apramycin resistance.

This study.

pRRA-RBS*astA (CGAAGCA)

Genome-insertional gene delivery plasmid harboring astA reporter fused to apt RBS sequence in colony 15. Insert created with oligos 3813 and 3814; apramycin resistance.

This study.

Strain Genotype or description Source

pGEM-cj1132cCloning plasmid harboring cj1132c and flanking regions, from PCR with oligos 0540 and 0541. Ampicillin resistance.

This study.

pGEM-cj1132c::aprR

Plasmid containing replacement deletion of cj1132c coding sequence, created via inverse PCR with oligos 0542 and 0543 and ligation to apramycin cassette. Ampicillin and apramycin resistance

This study.

pRRH-cj1132c

Genome-insertional gene delivery plasmid harboring cj1132c with native promoter, insert created with oligos 8168 and 8169; hygromycin resistance.

This study.