Primordial origin and diversification of plasmids in Lyme disease agent bacteria

Casjens, Sherwood R.; Di, Lia; Akther, Saymon; Mongodin, Emmanuel F.; Luft, Benjamin J.; Schutzer, Steven E.; Fraser, Claire M.; Qiu, Wei-Gang

doi:10.1186/s12864-018-4597-x

BMC Genomics

Table 2 Linear plasmid locations of selected NBu-Borreliella genes

From: Primordial origin and diversification of plasmids in Lyme disease agent bacteria

	Gene^a	adeC	arp/erpD	bptA	cpsZ	dbpAB^c	fnb	plzA	ospAB^c	ospC^c	ospD	pncA	res-mod1	res-mod2	sagABC DE	vlsE-like^d	vslE & vls cassettes
	PFam^b	61	163	99	92	74	none	180	53	none	none	none	1	102–167	none	170	170
B. burgdorferi	B31	lp36	lp28–1	lp25	lp28–3	lp54	lp36	–	lp54	cp26	lp38	lp25	lp25, lp28–3	lp56	–	–	lp28–1
B. bissettiae	DN127	lp28–7	–	lp25	lp28–3	lp54	lp28–7	–	lp54	cp26	–	lp25	lp25, lp28–3	–	–	–	–
B. finlandensis	SV1	–	–	lp28–2	–	lp54^h	–	lp32–6^f	lp54^h	cp26	–	lp28–2	lp32–12^f	–	–	–	lp32–6
B. mayonii	MN14–1420	lp36	–	lp25	–	lp54	–	–	lp54	cp26	lp28–3	lp25	lp25, lp28–4	–	–	–	lp28–8^e
B. mayonii	MN14–1539	lp36	–	lp25	–	lp54	–	–	lp54	cp26	lp28–3	lp25	lp25, lp28–4	–	–	–	lp28–8^e
B. afzelii	PKo	lp38	–	lp28–2	–	lp54	lp17	–	lp54	cp26	lp32–10 ^f	lp28–2	lp28–3, lp28–4	lp32–10	lp28–8	–	lp28–8
	K78	lp38	–	lp28–2	–	lp54	lp17	–	lp54	cp26	–	lp28–2	lp28–3, lp28–4	–	lp28–8	–	lp28–8
	ACA-1	lp38	–	lp28–2	–	lp54	lp17	–	lp54	cp26	lp32–10^f	lp28–2	lp28–3, lp28–4	lp32–10	lp28–8?^j	–	lp28–8?^j
	BO23^l	lp38 ⁱ	ND	ND	ND	lp54	lp17	ND	lp54^h	cp26	ND	ND	lp28–4	ND	lp28–8	ND	lp28–8
B. garinii	PBr	lp25	–	lp25	lp28–4	lp54	lp17	lp28–9	lp54	cp26	cp32–10^k	lp25	lp28–3, lp36	lp28–9 ^f	–	lp28–4, lp36 ^j	lp28–3
	Far04	lp25	–	lp25	–	lp54	lp17	–	lp54	cp26	lp32–10	lp25	lp36	lp28–9 ^f	–	–	lp28–9
	20047^l	ND	ND	ND	ND	lp54	lp17	ND	lp54	cp26	ND	ND	lp36	ND	ND	lp36 ^j	ND
B. spielmanii	A14S	lp36	–	lp38	lp28–4, lp28–8	lp54	lp17	–	lp54	cp26	–	lp38	lp28–3	–	lp28–8	–	lp28–8
B. valaisiana	VS116	right end chrm^f	–	lp25^j	lp36 ^f	lp54	–	–	lp54	cp26	lp17	lp25	lp28–3^f	cp32–7^k	lp28–8	lp28–3	lp28–8
B. japonica	HO14^l	ND	ND	lp25	ND	lp54	ND	NC	lp54	cp26	ND	lp25	ND	ND	lp28–8	ND	ND

^aThe linear plasmids that carry selected genes are indicated in the table; only apparently intact genes are indicated; hyphens (−) indicate a plasmid is absent from that completely sequenced genome. Gene names are as follows: adeC, adenine deaminase [35]; arp, arthritis related protein [134]; cpsZ, complement regulatory protein Z [86]; dbpAB, decorin binding proteins A and B [135]; fnb, fibronectin protein [136,137,138,139]; plzB, cyclic di-GMP binding protein [140, 141]; ospAB, outer surface proteins A and B [142,143,144]; ospC, outer surface protein C [103, 145], ospD, outer surface protein D [85, 146]; pncA, nicotinamidase [73]; res-mod1, restriction-modification protein PFam01 [147, 148]; res-mod2, restriction-modification protein PFam102/167 [148]; sagABCDE, synthesis of streptolysin S-like toxin [78]; vlsE-like, putative lipoproteins that are related VlsE but are encoded at a location not adjacent to vls cassette array [19]; vlsE and vls, variable outer surface protein cassettes and expression locus [149]
^bBorreliella paralogous protein family (see text)
^cThe gene contents of lp54 and cp26 gene content is very constant so only a few examples of their many important genes are shown
^dvlsE homologue not adjacent to vls cassette region
^eNamed lp28–10 in the literature but we include them as lp28–8 type plasmids (see text)
^fA relatively large, apparently truncated gene fragment whose functionality is unknown; there is no intact adeC gene in the VS116 genome
^gGene is known to have been originally present in this isolate, but its plasmid was lost from the sequenced culture [69]
^hlp54 is fused to another plasmid (see text); this gene is in the lp54 portion
ⁱlp38 is fused to lp54; this gene is in the lp38 portion
^jTwo genes of this sort are present on this plasmid
^kUnusual circular plasmid location; in B31 lp38-like indel in PBr cp32–10 and B31 lp56-like indel in VS116 cp32–7; see Additional file 1: Figure S8
^lPlasmid sequences are not complete for this isolate. ND indicates not determined; since all plasmids in this strain have not been sequenced the presence of this gene is not known

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ISSN: 1471-2164

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