TABLE 1.

csRNAs predicted in streptococcal species.

Species	Strain	csRNA	Screening method	Confirmed by	Length (nt)	Direct target	Mechanism of action	Regulatory function	References
S. pneumoniae	R6 D39	csRNA1	PredictRegulon server	Northern blot	93	comC, spr0081, spr0159, brnQ, and spr1097	Translational repression by base pairing	Autolysis and competence modulation	Halfmann et al., 2007; Marx et al., 2010; Tsui et al., 2010; Schnorpfeil et al., 2013
		csRNA2			96
		csRNA3			98
		csRNA4			92
		csRNA4			148
		csRNA5
S. agalactiae	NEM316	csRNA10	Non-coding RNA gene finder	RNA-seq, Northern blot	145	ND	ND	ND	Marx et al., 2010; Pichon et al., 2012; Rosinski-Chupin et al., 2015
		csRNA11			96
		csRNA12			118
		csRNA13			218
S. mitis	B6	csRNA1	Non-coding RNA gene finder	Northern blot	94	ND	ND	ND	Marx et al., 2010
		csRNA2			97
		csRNA3			99
		csRNA4			96
		csRNA5			146
S. mitis	SF100	csRNA2	Non-coding	NC	98	ND	ND	ND	Marx et al., 2010
		csRNA6	RNA gene finder		200
S. oralis	Uo5	csRNA1	Non-coding RNA gene finder	Northern blot	95	ND	ND	ND	Marx et al., 2010
		csRNA2			98
		csRNA3			100
		csRNA4			93
		csRNA6			200
S. sanguinis	SK36	csRNA1-1	Non-coding RNA gene finder	Northern blot	89	pilT	Putative translational repression by base pairing	Inhibition of biofilm formation	Marx et al., 2010; Ota et al., 2017
		csRNA1-2	Non-coding		93	ND	ND	ND	Marx et al., 2010
		csRNA1-3	RNA gene	Northern blot	87
		csRNA2	finder		96
		csRNA7			85
		csRNA8			176
S. pyogenes	MGAS315	csRNA14	Non-coding	RNA seq	68	ND	ND	ND	Marx et al., 2010;
		csRNA15	RNA gene finder		142				Le Rhun et al., 2016
		csRNA25			129
S. gordonii	str. Challis substr. CH1	csRNA1	Non-coding RNA gene finder	NC	87	ND	ND	ND	Marx et al., 2010
		csRNA2-1			96
		csRNA2-2			94
		csRNA7			90
		csRNA21			58
		csRNA22			202
S. mutans	UA159	csRNA23-1	Non-coding RNA gene finder	NC	79	ND	ND	ND	Marx et al., 2010
		csRNA23-2			81
		csRNA24			152
S. gallolyticus	UCN34	csRNA9	Non-coding RNA gene finder	NC	63	ND	ND	ND	Marx et al., 2010
		csRNA18			66
		csRNA38			138
		csRNA39			118
		csRNA40-1			65
		csRNA40-2			71
S. dysgalactiae subsp. Equisimilis	GGS_124	csRNA14	Non-coding RNA gene finder	NC	68	ND	ND	ND	Marx et al., 2010
		csRNA15			141
		csRNA16			127
		csRNA17			117
S. equi subsp. equi	4047	csRNA18	Non-coding RNA gene finder	NC	50	ND	ND	ND	Marx et al., 2010
		csRNA17			105
S. equi subsp. zooepidemicus	MGCS10565	csRNA18	Non-coding RNA gene finder	NC	67	ND	ND	ND	Marx et al., 2010
		csRNA19			105
		csRNA20			108
S. suis	05ZYH33	csRNA26	Non-coding RNA gene finder	NC	172	ND	ND	ND	Marx et al., 2010
		csRNA27			73
		csRNA28			58
S. uberis	0140J	csRNA29	Non-coding RNA gene finder	NC	84	ND	ND	ND	Marx et al., 2010
		csRNA30			83
		csRNA31			67
		csRNA32			140
S. thermophilus	St0 plasmid pSt0	csRNA9	Non-coding RNA gene finder	NC	60	ND	ND	ND	Marx et al., 2010
S. thermophilus	CNRZ1066	csRNA33	Non-coding RNA gene finder	NC	66	ND	ND	ND	Marx et al., 2010
		csRNA34			85
		csRNA35			64
		csRNA36			97
		csRNA37			127
S. lutetiensis	033	csRNA9	BLAST analysis	NC	63	ND	ND	ND	Denapaite et al., 2016
		csRNA18			66
		csRNA38			137
		csRNA39			119
S. infantis	GTC849	csRNA2	BLAST analysis	NC	98	ND	ND	ND	Denapaite et al., 2016
		csRNA3			100
		csRNA4			93
		csRNA6			200

NC, Not confirmed; ND, Not determined.