Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays

Patenge, Nadja; Billion, André; Raasch, Peter; Normann, Jana; Wisniewska-Kucper, Aleksandra; Retey, Julia; Boisguérin, Valesca; Hartsch, Thomas; Hain, Torsten; Kreikemeyer, Bernd

doi:10.1186/1471-2164-13-550

Table 1 S. pyogenes M49 sRNAs, genomic location, Rfam predictions, and conservation across streptococcal genomes

From: Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays

No	ID	Left nucleotide	Right nucleotide	Size (nt)	Strand	Upstream adjacent gene	Downstream adjacent gene	Rfam and MOSES prediction	Previously published	Conservation
1	sRNASpy490131	141429	141478	49	-	ntpK	ntpE			a
2	sRNASpy490186c	194707	194791	84	+	Spy49_0186c	speG	SRP_bact	[37]	c
3	sRNASpy490206	216807^d	217021	215	+^e	fasA	rnpA	MOSES2	fasX[17]	b
4	sRNASpy490229	238850	238899	49	+	prgA	rpsL			b
5	sRNASpy490238	248530	248579	49	+	Spy49_0238	bacA			a
6	sRNASpy490241	251595	251644	49	+	rgpG	Spy49_0242			a
7	sRNASpy490305	318826	318910	84	+	Spy49_0305	Spy49_0306	23S-methyl		b
8	sRNASpy490306	319622	319776	154	+	Spy49_0306	Spy49_0307	FMN	RNA319780[20]	b
9	sRNASpy490348	362857	362906	49	+	Spy49_0348	Spy49_0349c	MOSES6		a
10	sRNASpy490366c	373806	373855	49	+	Spy49_0366c	Spy49_0367c			-
11	sRNASpy490370	376843	376892	49	+	Spy49_0370	Spy49_0371			a
12	sRNASpy490380c	385431 ^d	385526	95	+ ^e	Spy49_0380c	mtsA			b
13	sRNASpy490388	393522	393571	49	+	rplA	pyrH			a
14	sRNASpy490434	431752	431836	84	+	Spy49_0434	thrS	T-box		b
15	sRNASpy490483c	476503^d	476600	97	+ ^e	Spy49_0483c	bglG			b
16	sRNASpy490493	486133	486182	49	+	Spy49_0493	ptsK			a
17	sRNASpy490504	495351	495400	49	-	Spy49_0504	Spy49_0505c			a
18	sRNASpy490592	594852	594936	84	+	Spy49_0592	pheS			b
19	sRNASpy490727	733841	733890	49	-	Spy49_0727	Spy49_0728			a
20	sRNASpy490822	820820	820996 ^d	176	- ^e	Spy49_0822	Spy49_0823	CRISPR	RNA772970[20]	c
21	sRNASpy490827	827456	827785	329	+	Spy49_0827	Spy49_0828	CRISPR
								MOSES14		a
22	sRNASpy490845c	846977	847061	84	+	trmE	rplJ	L10_leader		c
23	sRNASpy490948c	941583	941657 ^d	74	-	Spy49_0948c	guaA			a
24	sRNASpy490957c	950434	950518	84	- ^e	Spy49_0957c	Spy49_0958c		SR914400[20]	b
25	sRNASpy491007c	1000709	1000828	119	+	pcrA	Spy49_1008	Glycine		b
26	sRNASpy491023c	1019382	1019746	364	+	Spy49_1023c	Spy49_1024	tmRNA	RNA983400[20]	b
27	sRNASpy491061c	184794	184878	84	+	Spy49_1061c	Spy49_0176			c
28	sRNASpy491095c	1092894	1092943	49	-	ptsH	nrdH			c
29	sRNASpy491122c	1117169	1117218	49	-	sodM	holA			b
30	sRNASpy491163c	1156488	1156537	49	-	Spy49_1163c	clpE			a
31	sRNASpy491167c	1163270	1163319	49	-	ileS	divIVA	T-box		-
32	sRNASpy491206c	1201615	1201734	119	-	ccdA	Spy49_1207c	MOSES16	RNA1239700[20]	a
33	sRNASpy491217c	1214010	1214059	49	-	Spy49_1217c	Spy49_1218c		SR1251900[20]	b
34	sRNASpy491243	1246370	1246419	49	+	Spy49_1243	Spy49_1244			a
35	sRNASpy491275c	1282084	1282413	329	-	Spy49_1275c	Spy49_1276c	RNaseP_bact b	RNA1320100[20]	c
36	sRNASpy491311c	1321638	1321853^d	84	- ^e	glyQ	Spy49_1312c			b
37	sRNASpy491336c	1341554	1341603	49	+	rbfA	infB			b
38	sRNASpy491340c	1346300	1346349	49	-	nusA	Spy49_1341c			b
39	sRNASpy491354	1357803	1357852	49	-	manL	manM			b
40	sRNASpy491357	1360204	1360323	119	+	Spy49_1357	serS	T-box	RNA1439100[20]	b
41	sRNASpy491409c	1413359	1413408	49	-	acpS	secA			a
42	sRNASpy491489c	1489011	1489060	49	+	Spy49_1489c	Spy49_1491c			b
43	sRNASpy491555c	1528842	1528891	49	-	Spy49_1555c	Spy49_1556c			a
44	sRNASpy491560c	1533843	1533892	49	-	Spy49_1560c	pyrG			a
45	sRNASpy491561c	1535755	1535804	49	-	pyrG	rpoE			c
46	sRNASpy491562c	1536613	1536662	49	-	rpoE	tig			a
47	sRNASpy491591	1571896	1571945	49	-	lacR2	Spy49_1592	MOSES18	SR1604140[20]	a
48	sRNASpy491596c	1574723	1574807	84	-	rplM 50S	Spy49_1597c	L13_leader		c
49	sRNASpy491671c	1654859	1654908	49	-	emm49	Spy49_1672c			a
50	sRNASpy491707c	1693440	1693489	49	-	Spy49_1707c	Spy49_1708			a
51	sRNASpy491713	1698142	1698191	49	+	Spy49_1713	Spy49_1714c		SR1719800[20]	a
52	sRNASpy491718c	1704471	1704525	54	-	ctsR	csp			a
53	sRNASpy491732c	1724321	1724370	49	+	Spy49_1732c	rpsB		SR1745900[20]	b
54	sRNASpy491738	1733300	1733433^d	133	-	Spy49_1738	Spy49_1739c		SR1754950[20]	b
55	sRNASpy491769c	1763496	1763545	49	+	hisS	rpmF			b

Coordinates and gene designations of adjacent genes are relative to the S. pyogenes NZ131 genome (NCBI accession number: NC_011375).
^a Streptococcus pyogenes.
^b Beta-haemolytic streptococci.
^c Non-beta-haemolytic streptococci.
^d Transcriptional start site determined by 5^′ RACE.
^e Strand confirmed by gene specific RT-PCR.

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