Investigating genome reduction of Bordetella pertussis using a multiplex PCR-based reverse line blot assay (mPCR/RLB)

Lam, Connie; Octavia, Sophie; Sintchenko, Vitali; Gilbert, Gwendolyn L; Lan, Ruiting

doi:10.1186/1756-0500-7-727

Table 1 Details of genes within selected regions of difference (RD) for this study and comparison to RD in other studies

From: Investigating genome reduction of Bordetella pertussis using a multiplex PCR-based reverse line blot assay (mPCR/RLB)

Genes within RDs*	Representative gene for this study	Gene function	King *et al.*(2010)[5]	Brinig *et al.*(2006)[16]	Heikkinen *et al.*(2007)[19]	Caro *et al.*(2006)[3]
BP0024- BP0030		MaoC family protein	RD1
BP0393- BP0396		Hypothetical protein	RD2
BP0502- BP0511		Hypothetical protein	RD3-RD4	RD1
BP0513- BP0516	N/A		RD3-RD4
BP0612- BP0644	N/A		RD6
BP0593	N/A		RD7
BP0712- BP0715	BP0711/BP0712	Putative phosopholipase	RD9	RD2
BP0910A- BP0934	BP0919	Putative succinate-semialdehyde dehydrogenase [NADP+]	RD13	RD3	L1	RD-1
BP0910A- BP0934	BP0930	Putative CoA ligase	RD13	RD3	L1	RD-1
BP1131-BP1141	BP1136	Heme uptake regulator	RD15-RD16	RD4-RD5	L2	RD-2
BP1158-BP1176	BP1170	Putative exported protein	RD17	RD6		RD-3
BP1225	N/A		RD19
BP1553	BP1553	Putative exported protein	RD24
BP1638-BP1639	BP1638	Hypothetical protein	RD25	RD7
BP1663-BP1674/77	BP1664	Glutathione S-transferase	RD27	RD8
BP1663-BP1674/77	BP1669	Lactate dehydrogenase	RD27	RD8
BP1676-BP1677	N/A		RD28	RD9
BP1698	N/A		RD30
BP1948-BP1966	BP1948	Branched-chain amino acid-binding protein	RD33	RD10	L3	RD-4
	BP1954	Probable oxidoreductase
	BP1962	Putative ferrisiderophore receptor
BP2088-BP2103	BP2102	lysR family transcriptional regulator	RD35		L4
BP2133-BP2134	N/A		RD37
BP2136-BP2139	N/A		RD38-RD39			RD-5
BP2167-BP2180	BP2167	Putative integral membrane protein	RD40
BP2272-BP2274	BP2273	Putative periplasmic protein	RD41	RD11		RD-6
BP2517-BP2518	BP2518	Sarcosine oxidase beta subunit	RD43	RD12
BP2519-BP2523	BP2522	FolD bifunctional protein	RD44
BP2627-BP2629	BP2627	Pseudogene	RD45	RD13		RD-7
BP2670-BP2671	BP2671	Hypothetical protein	RD46	RD14
BP2822-BP2839	BP2825	GntR family transcriptional regulator	RD48
BP2883	N/A		-			RD-8
BP2921-BP2924	BP2921	Hypothetical protein	RD50	RD15
BP3104-BP3110/3	BP3107	Putative gamma-glutamyltranspeptidase (exported protein)	RD52-RD54	RD16-RD17		RD-9
BP3104-BP3110/3	BP3113	Pseudogene	RD52-RD54	RD16-RD17		RD-9
BP3188-BP3202	N/A		RD55
BP3314-BP3322	BP3319	Putative IclR-family transcriptional regulator	RD56	RD18		RD-10
BP3314-BP3322	BP3322	Putative binding-protein-dependent transport protein	RD56	RD18		RD-10
BP3352-BP3390	BP3384	Putative phage terminase	RD57-RD59	RD19
BP3477	N/A		RD60
BP3840-BP3861	BP3842	Hypothetical protein	RD63-RD64	RD20
BP3840-BP3861	BP3853	Conserved hypothetical protein	RD63-RD64	RD20

*Gene nomenclature in this column is based on the numbering of genes in Tohama I (NC_002929).
N/A- RDs for which either primers or probes could not be selected for efficient mPCR/ RLB or which could not be amplified during mPCR and were subsequently left out of analysis.

Back to article page