Zonula occludens toxins and their prophages in Campylobacter species

Liu, Fang; Lee, Hoyul; Lan, Ruiting; Zhang, Li

doi:10.1186/s13099-016-0125-1

Gut Pathogens

Table 2 The attachment sites of zot-containing Campylobacter prophages

From: Zonula occludens toxins and their prophages in Campylobacter species

Prophage	Start^a	End^a	Attachment gene sequence^b	tRNA (locus_tag)
CON_phi1, CON_phi2 and CON_phi3 (C. concisus 13826)^c	1582286	1582311	TTCAAATCCCTCTCTGTCCGCCACCA	tRNA-Ser (CCC13826_RS07905)
	1587508	1587533	TTCAAATCCCTCTCTGTCCGCCACCA
	1597113	1597138	TTCAAATCCCTCTCTGTCCGCCACCA
	1606718	1606743	TTCAAATCCCTCTCTGTCCGCCACCA
	1616160	1616185	TTCAAATCCCTCTCTGTCCGCCACCA
CON_phi4 (C. concisus 13826)	946941	946993	CTCATAACCCGAAGGTCGGCGGTTCAA ATCCGTCCTCCGCAACCAAATACCGA	tRNA-Met (CCC13826_RS04780)
CON_phi4 (C. concisus 13826)	937290	937342	CTCATAACCCGAAGGTCGGCGGTTCAA ATCCGTCCTCCGCAACCAAATACCGA
URE_phiZA (C. ureolyticus DSM 20703)	68067	68122	ATAACCCGAAGGTCGGAGGTTCAAGTCCT TCCTCTGCAACCAAATCACCATTTTAC	tRNA-Met (C512_RS0103965)
URE_phiZA (C. ureolyticus DSM 20703)	57811	57866	ATAACCCGAAGGTCGGAGGTTCAAGTCCT TCCTCTGCAACCAAATCACCATTTTAC
URE_phiZB (C. ureolyticus DSM 20703)	139564	139610	GTTCAAGTCTCGCTGATCGCACCATTA AAGAAAAAATTAAGAATACT	tRNA-Leu (C512_RS0100765)
URE_phiZB (C. ureolyticus DSM 20703)	130103	130149	GTTCAAGTCTCGCTGATCGCACCATTA AAGAAAAAATTAAGAATACT
COR_phiZA (C. corcagiensis CIT045)	254051	254088	CGAAGGTCAGGGGTTCAAGTCCCTTCT CTGCAACCAAA	tRNA-Met (SA94_RS06290)
COR_phiZA (C. corcagiensis CIT045)	265302	265339	CGAAGGTCAGGGGTTCAAGTCCCTTCT CTGCAACCAAA
COR_phiZB (C. corcagiensis CIT045)	257240	257264	GTTCAAATCCCTCTCTGTCCGCCAC	tRNA-Ser (SA94_RS04510)
COR_phiZB (C. corcagiensis CIT045)	247319	247343	GTTCAAATCCCTCTCTGTCCGCCAC
GRACI_phiZ (C. gracilis RM3268)	112826	112871	CTCATAACCCGAAGGTCGGTGGTTCAA ATCCACCCTCTGCAACCAA	tRNA-Met (CAMGR0001_2931)
GRACI_phiZ (C. gracilis RM3268)	102518	102563	CTCATAACCCGAAGGTCGGTGGTTCAA ATCCACCCTCTGCAACCAA
DOYLEI_phiZ (C. jejuni subsp. doylei 269.97)	303215	303241	AGGGTTCAAATCCCTCTCTGTCCGCCA	tRNA-Ser (JJD26997_RS01570)
DOYLEI_phiZ (C. jejuni subsp. doylei 269.97)	313165	313191	AGGGTTCAAATCCCTCTCTGTCCGCCA
HYO_phiZ (C. hyointestinalis subsp. hyointestinalis DSM 19053)	360409	360446	CTCATAACCCGAAGGTCGGAGGTTCAA GTCCTTCTCTC	tRNA-Met (CR67_RS01810)
	369716	369753	CTCATAACCCGAAGGTCGGAGGTTCAA GTCCTTCTCTC
HYO_phiZ (C. hyointestinalis subsp. lawsonii CCUG 27631)	1283134	1283238	CTCATAACCCGAAGGTCGGAGGTTCAAGT CCTTCTCTCGCAACCAAATAAGCATAAAA TCATCTTTTAAAGCACATTGTTTTAAAGCT TAAAATAATCTTACTTT	tRNA-Met (CHL_RS06785)
	1273720	1273824	CTCATAACCCGAAGGTCGGAGGTTCAAGT CCTTCTCTCGCAACCAAATAAGCATAAAA TCATCTTTTAAAGCACATTGTTTTAAAGCT TAAAATAATCTTACTTT

^aThe start and end positions for the attachment sites refer to the nucleotide position within the contig containing the prophage genomes, except for C. concisus strains 13826, C. jejuni subsp. doylei 269.97 and C. hyointestinalis subsp. lawsonii CCUG 27631 which refer to the nucleotide position in the full genome
^bAttachment sites overlapped with 3′ end of tRNA, the overlapped sequences were italic
^cMultiple insertion sites for CON_phi prophages in C. concisus 13826 in which only the first attachment site (for CON_phi1) overlapped with tRNA. In NCBI database, the contig encoding JEJUNI_phiZ did not cover the full prophage genome; therefore it was unable to locate the attachment sites. No attachment site was identified in IGUA_phiZ

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