Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales

Table 2 Comparison of different members of the Rhizobiales

	Re	NGR	Bj	R7A	Ml	Sm	At	Bm
Genome
Upper strand matches*					82	43	31	12
RpoN controlled gene products					184	62	69	24
Size (Mb)					7.59	6.69	5.67	3.29
Matches/Mb					10.80	6.43	5.47	3.65
GC content (%)					62.4	62.1	58.1	57
Symbiotic region^†
Upper strand matches*	24	23	31	25	24	15
RpoN controlled gene products	52	60	87	55	58	30
Size (Mb)	0.37	0.54	0.41	0.50	0.61	1.35
Matches/Mb	64.86	42.59	75.61	50.00	39.34	11.11
GC content (%)	57.3	58.5	59.1	59.3	59.7	60.4
Intergenic GC content (%)^‡	55.0	55.9	57.3	58.0	57.0	56.4	52.0	49.9
Lower strand matches*	7	11	21	16	67^¥	32^¥	23^¥	12^¥
-12 (C) distance to start codon (bp)^§	91 (231)	88 (149)	156 (214)	156 (288)	102 (209)	97 (210)	74 142)	123 (345)
Possible EBPs^¶	1	2	2	3	8	7	6	3

*Matches (possible RpoN-binding sites or -24/-12-type promoters) were predicted using PATSER (see Materials and methods). ^†p42d (Re); pNGR234a (NGR); 410 kb region on chromosome (Bj); 502 kb symbiotic island on chromosome (R7A); 610 kb symbiotic island on chromosome (Ml); pSymA (Sm). ^‡The GC-content of the intergenic (non-coding) sequences was calculated with FramePlot 2.3.2 [68]. ^§The distribution of the -12 (C) position on the intergenic sequences is biased towards the corresponding downstream CDS (this distribution is visualized by means of a boxplot in the Additional data files, page 29). Therefore the median and third quartile (between brackets) were used as indicative parameters for these distances. ^¶Possible EBPs were predicted using HMMER 2.2 g (see Materials and methods) (see also Table 3). ^¥The upstream intergenic region of the rpoN gene is included. At, Agrobacterium tumefaciens C58; Bm, Brucella melitensis 16 M; Bj, Bradyrhizobium japonicum USDA110; Ml, Mesorhizobium loti MAFF303099; NGR, Rhizobium sp. NGR234; R7A, M. loti R7A; Re, Rhizobium etli CFN42; Sm, Sinorhizobium meliloti 1021.

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