Small non-coding RNAs in plant-pathogenic Xanthomonas spp

Figures & data

Table 1. Rfam classification of verified sRNAs from Xanthomonadaceae.

Accession^a	ID	Members^b	Features	Ref.
RF02222	sX2	sX2	-	^22
RF02223	sX4	sX4	HrpG/HrpX-dependent accumulation	^22
RF02224	sX5	sX5	HrpX-induced	^22
		SmsR26	Hfq-dependent accumulation	^34
RF02225	sX6	sX6	-	^22
RF02226	sX7	sX7	-	^22
RF02227	sX8	sX8	HrpX-induced	^22
RF02228	sX9	sX9	-	^22
RF02230	sX11	sX11	HrpG/HrpX-repressed	^22
		SmsR35	-	^34
RF02231	sX12	sX12	HrpX-induced, contributes to virulence	^22
RF02232	sX13	sX13	Regulator of virulence, Hfq-independent accumulation	^22 ^, ^24
		SmsR39	Hfq-independent accumulation	^34
RF02233	sX14	sX14	Hfq-dependent accumulation	^22 ^, ^24
		sRNA-Xoo3	Hfq-dependent accumulation	^21
RF02234	sX15	sX15	-	^22
RF02235	asX1	asX1	HrpG/HrpX-dependent accumulation	^22
RF02236	asX2	asX2	-	^22
RF02237	asX3	asX3	-	^22
RF02238	asX4	asX4	HrpX-induced	^22
		sRNA-Xoo4	Hfq-independent accumulation	^21
RF02239	asX6	asX6	-	^22
RF02221	sRNA-Xcc1	sRNA-Xcc1	HrpX-induced	^20 ^, ^54
		sX1	-	^22
		sX10	-	^22
		sRNA-Xoo6	Hfq-independent accumulation	^21
		SmsR6	-	^34
RF02240	sRNA-Xoo1	sRNA-Xoo1	Hfq-dependent accumulation	^21
		SmsR36	Hfq-dependent accumulation	^34
RF02241	sRNA-Xoo2	sRNA-Xoo2	Hfq-dependent accumulation	^21
RF02242	sRNA-Xoo5	sRNA-Xoo5	Hfq-independent accumulation	^21
RF02243	sRNA-Xoo8	sRNA-Xoo8	Hfq-independent accumulation	^21
RF01811	PtaRNA1	PtaRNA1	Predicted type I antitoxin	^19

a Rfam release Rfam 11.0 (August 2012).^{29 b} sRNAs verified by northern blot in: Xcv 85-10 (sX/asX), Xcc 8004 (sRNA-Xcc), Xoo PXO99 (sRNA-Xoo), and Smal K279a (SmsR).

Figure 1. (A) Conservation of sX13. LocARNA prediction of the consensus secondary structure of all sX13 family members in xanthomonads listed in the Rfam database (Rfam 11.0, Aug. 2012).^29,55 Compensatory mutations that retain the sX13 structure are indicated by circles. (B) Model of potential physiological functions of sX13 in Xcv according to Schmidtke et al.²⁴ sX13 accumulates in response to extracellular stimuli and indirectly promotes HrpG activation, which is induced by unknown signaling pathways.^56,57 sX13 supposedly impacts on motility, quorum sensing (QS), and the activity of other sRNAs by repressing Hfq synthesis. Boxed arrows, wavy lines, and circles indicate genes, mRNAs, and proteins. Dashed circles mark unknown proteins or signaling pathways. Green, red, and dashed arrows denote positive, negative, and putative effects.

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