. 2016 Feb 6;13(3):331–342. doi: 10.1080/15476286.2016.1144010

Table 3.

Summary of putative sRNAs in actively dividing and SSR Salmonella enterica. This table lists the following characteristics of all candidate sRNAs: strand (plus / minus / both), known sRNA similarity, structure (HS/HP), putative targets and expression patterns log-phase, 5-h C-starved and 24-h C-starved cells.

sRNA	Strand^a	Known sRNA Similarity	Structure^b	xPutative Gene Targets[Gene Products] / (Overlap)^c	Exp. In Log^d	Exp. In 5-h C-st^d	Exp. In 24-h C-st^d
sRNA176086	Plus	–	HS	• cis-pdhR [pyruvate dehydrogenase (Pyr DH) complex repressor] (3′)cis-aceE [Pyr DH decarboxylase subunit E1] (5′)	4,505	621	0
sRNA201302	Both	^E. coli* uncharacterized sRNA	HS	• cis-hpt (hypoxanthine phosphoribosyltransferase] (3′)cis- yadF [carbonic anhydrase] (3′)	230	721	0
sRNA294324	Plus	S. enterica uncharacterized sRNA	HS	• cis-rrlH [23S rRNA] (3′)cis-rrfH [5S rRNA] (5′)	16,711	3,899	0
sRNA523910	Minus	Bacterial small SRP	HP	• cis-ybaY1 (5′), cis-4.5S RNA(5′)cis- ybaZ1 (3′)	1,060	1,975	9,640
sRNA570517	Both	–	HS	• cis-STM0509 [OmpC-like outer membrane protein] (3′)cis-sfbA [Fe³⁺- / pH-inducible ABC transporter substrate-binding protein] (5′)	798	0	0
sRNA697722	Minus	–	HS	• cis-STM0636 [hypothetical protein] (5′)cis-dacA [PBP5;D-alanyl-D-alanine carboxypeptidase] (3′)	79	140	635
sRNA924744	Both	–	HS	• cis-bssR [biofilm formation regulatory protein] (3′)	115	320	0
sRNA1130547	Minus	–	HS	• cis-yccK [sulfurtransferase TusE] (5′)cis-STM1085 [YccA-like Inner membrane protein; possible modulator of FtsH protease] (3′)	42	122	5,044
sRNA1170414	Plus	–	HS	• cis-phoH [phosphate starvation-inducible ATP-binding protein PsiH] (5′)	53	383	1105
sRNA1186573	Minus	–	HS	• cis-csgD [transcriptional activator protein of curli pili production] (5′)	0	200	0
sRNA1212673	Both	E. coli uncharacterized sRNA	HS	• cis-mviN (STM1170) [putative MurJ peptidoglycan lipid II flippase] (3′)cis-flgN [FlgK/FlgL export chaperone] (3′)	1,147	51	28
sRNA1253515	Plus	Bacterial RNaseP	HS	• cis-ycfR [hypothetical outer membrane / secreted protein] (5′)	0	0	212
sRNA1288534	Plus	Campylobacter jejuni uncharacterized sRNA	HS	–	0	548	71
sRNA1289188		–	HS	–	0	548	71
sRNA1292328	Plus	–	HS	• cis-STM1250 [cytoplasmic protein] (3′)cis-STM1251 [small heat shock IbpA/B-like molecular chaperone] (5′)	0	0	429
sRNA1305985	Both	E. coli RtT	HS	• trans-SL1344_3673A [pseudogene; tdh-yibD intergenic region] cis-STM1266 [MerR-type transcriptional regulator] (3′)cis-STM1267 [YmgB-superfamily cytoplasmic protein] (3′)	111	1,720	1,440
sRNA1318601	Minus	E. coli uncharacterized sRNA	HS	• cis-STM1284 [metal ion-dependent adhesion site (MIDAS)-containing protein] (5′)cis-yeaG [PrkA-family serine protein kinase] (3′)	23	270	576
sRNA1326799	Plus	Hyperthermus butylicus uncharacterized sRNA	HS	• cis-yeaA(msrB) [peptide methionine sulfoxide reductase – oxidative stress protection] (5′)	34	114	43
sRNA1409050	Plus	–	HS	• cis-sufA [iron-sulfur cluster assembly scaffold protein] (5′)	0	253	600
sRNA1482545	Both	–	HS	• cis-pdxY [pyridoxamine / pyridoxal kinase] (3′)cis-gst [glutathionine S-transferase – detoxifiying enzyme] (3′)	0	0	143
sRNA1548865	Plus	Bacterial T-box	HS	• cis-STM1513 [putative general stress protein; GsiB] (5′)	0	221	0
sRNA1784679	Both	^*Pseudomonas aeruginosa PrrF2	HP	• cis-STM1731 [KatN-like (Mn²⁺)-catalase] (3′)cis-ompW [outer membrane (porin) protein W] (3′)	0	473	0
sRNA1799792	Plus	–	HS	• cis-adhE [bifunctional acetaldehyde-CoA / alcohol dehydrogenase] (5′)	3,307	793	128
sRNA1799950	Plus	–	HS	• cis-adhE [bifunctional acetaldehyde-CoA / alcohol dehydrogenase] (5′)	3,307	793	128
sRNA1809591	Plus	E. coli RtT	HS	• cis-tyrT [tRNA-Tyr] (3′)cis-tyrV [tRNA-Tyr] (5′)	1,535	313	238
sRNA1851877	Plus	–	HS	• cis-treA [periplasmic trehalase] (5′)• cis-STM1795 [GdhA-family glutamate dehydrogenase] (3′)	0	279	373
sRNA1888744	Plus	Hyperthermus butylicus uncharacterized sRNA	HS	• cis-manZ [mannose-specific PTS Enzyme IID component] (3′)• cis-STM1833 [putative membrane protein] (5′)	0	0	282
sRNA1897579	Minus	E. coli SsrA	HS	• cis-htpX [heat-shock Zn²⁺-dependent protease / chaperone] (CBW17867)(3′)	0	0	291
sRNA1932297	Both	–	HS	• cis-yebE [putative metal-binding inner membrane protein (tellurium resistance TerB-like] (5′)cis-STM1881 [YebF-like (putative colicin immunity) protein] (3′)	332	142	1,469
sRNA2061316	Minus	–	HS	• cis-SL1344_1952 [predicted bacteriophage protein / endonuclease] (5′)cis-SL1344_1953 [predicted bacteriophage protein] (3′)	0	27	400
sRNA2073265	Plus	–	HS	• cis-SL1344_1968 [predicted bacteriophage protein] (5′)	2,134	731	38
sRNA2176581	Both	RNaseP in multiple organisms	HP	• cis-rfbB [dTDP-glucose-4,6-dehydratase] (5′)cis-galF [UTP–glucose-1-phosphate uridylyltransferase subunit] (3′)	752	1,830	60
sRNA2285422	Both	–	HS	• cis-mglB [galactose / methyl-galactoside ABC transporter substrate-binding protein] (3′)	0	296	77
sRNA2296504	Minus	^*E. coli Leu Leader	HP	• cis-lysP [APC family lysine-specific permease] (3′)trans-cirA [(TonB-dependent) catecholate siderophore receptor] (5′)	1,013	255	76
sRNA2416394	Both	–	HS	• cis-menF [(menaquinone-specific) isochorismate synthase] (5′)cis-elaB [conserved putative inner membrane (ribosome-binding) protein] (3′)	40	430	0
sRNA2576882	Both	^*Streptococcus suis uncharacterized sRNA	HS	• cis-tnpA_1b [insertion sequence IS200 transposase] (3′)	0	0	233
sRNA2594511	Both	–	HS	• cis-acrD [RND family aminoglycoside / multidrug efflux pump] (3′)cis-ypfM [stress-induced small enterobacterial protein in E. coli; annotated as STnc250] (3′)	27	31	1,232
sRNA2759412	Minus	–	HS	• cis-gltW [tRNA-Glu] (5′)	157	1,935	67
sRNA2802132	Minus	–	HP	• cis-rrsG [16S rRNA] (5′)	11,628	1,067	0
sRNA2838164	Both	–	HS	• cis-smpB [SsrA (tmRNA)-binding protein] (3′)	47	227	3,944
sRNA3110963		^*E. coli uncharacterized sRNA	HP	–	4,438	1,451	0
sRNA3337545	Both	Bacterial Cobalamin riboswitch	HS	• cis-STM3153 [putative inner membrane protein] (5′)cis-STM3154 [putative ATP-dependent RNA helicase] (3′)	2,850	1,990	88
sRNA3378366	Plus	–	HP	• cis-dsbB [disulfide oxidoreductase; required for periplasmic disulfide bond formation] (3′)	26	0	565
sRNA3405375	Plus	–	HS	• trans-fklB [FKBP-type peptidyl-prolyl cis-trans isomerase](5′)cis-oat [putrescine aminotransferase] (5′)	0	1,022	1,536
sRNA3551252	Minus	Sulfolobus acidocaldarius uncharacterized sRNA	HP	• cis-yhcO [Barstar homolog; cytoplasmic inhibitor of extracellular RNAase (Barnase)] (5′)cis-aaeB [p-hydroxybenzoic acid (p-HBA) efflux pump subunit (YhcP)] (3′)	0	199	1,034
sRNA3554557	Both	–	HP	• cis-aaeX [membrane protein associated with p-HBA efflux pump] (5′)cis-yhcS [LysR family transcriptional regulator] (5′)	0	0	201
sRNA3943836	Minus	–	HP	• cis-STM3729 [putative Zn²⁺-binding MPN superfamily protein] (3′)cis-rpmB [50S ribosomal protein L28] (5′)	2,718	596	0
sRNA4126333	Plus	Salmonella enterica uncharacterized sRNA	HS	• cis-rrlC [23S rRNA] (5′)	2,103	436	0
sRNA4130247	Plus	–	HP	• cis-ilvX [small (stress response) protein in E. coli; not annotated in S. enterica genome] (5′)	11,226	5,800	240
sRNA4146790	Both	–	HP	• cis-trxA [thioredoxin] (3′)cis-rho [transcriptional termination factor Rho] (5′)	2,910	1,268	111
sRNA4184031	Plus	E. coli and Shigella flexneri sRNA-IS128	HP	• cis-pldA [(outer membrane) phospholipase A] (3′)cis-recQ [ATP-dependent DNA helicase] (5′)	0	70	184
sRNA4217489	Plus	–	HP	• cis-hemG [protoporphyrinogen IX dehydrogenase involved in heme biosynthesis] (3′)cis-rrsA [16S rRNA] (5′)	20,763	397	30
sRNA4236850	Minus	^*E. coli sRNA-MicC	HP	• cis-glnL [nitrogen regulation protein NR(II); sensor His-kinase in GlnLG 2-component system] (5′)cis-glnA [glutamine synthetase] (3′)	71,126	1,674	412
sRNA4250009	Plus	–	HS	–	0	31	1,242
sRNA4385784		–	HS	–	6,191	21,181	100,027
sRNA4415893	Plus	–	HP	• cis-rrsE [16S rRNA] (5′)	14,532	2,336	33
sRNA4417787	Plus	–	HS	• cis-gltV [tRNA-Glu] (3′)cis-rrlE [23S rRNA] (5′)	6085	2,357	40
sRNA4426265	Plus	E. coli uncharacterized sRNA	HP	• cis-aceA [isocitrate lyase] (3′)cis-aceK [bifunctional isocitrate dehydrogenase kinase / phosphatase] (5′)	0	445	0
sRNA4683584	Plus	E. coli sRNA-RyhB	HP	• trans- STnc2160 [64 bp noncoding RNA] (5′)cis-STM4419 (iolT2) [MFS superfamily sugar transporter] (3′)	0	59	219
sRNA4720054	Plus	Bacterial tmRNA	HS	• cis-mgtA [Mg²⁺ transporting ATPase] (5′)	2,592	1,757	78
sRNA4812322	Plus	E. coli uncharacterized sRNA	HS	• cis-tsr [methyl-accepting chemotaxis protein I] (3′)cis-STM4534 [NtrC family transcriptional regulator] (5′)	3,170	31	0
sRNA4842833	Both	E. coli SsrA	HP	• cis-deoC [deoxyribose-phosphate aldolase] (3′)cis-deoA [thymidine phosphorylase] (5′)	36	196	972

indicates that there is more than one known sRNA similar to a candidate sRNA in sequence.

Strand – Plus, positive DNA strand;Minus, negative DNA strand; Both, sRNA present on both strands.

Hairpin (HP) – simple sRNA predicted via Mfold; Highly structured (HS) – possesses more than one hairpin.

Gene Target, Gene Product and Overlap were determined from http://www.ncbi.nlm.nih.gov/pubmed Gene and Protein search databases; (5′): indicates that sRNA overlaps 5′-end of CDS; (3′): indicates that sRNA overlaps 3′-end of CDS; (AS): indicates that sRNA is transcribed internally to CDS on the opposite strand; (−) indicates that sRNA is not cis (overlapping) to any known gene and does not have an identified trans target.

Exp. in Log – transcripts count at sRNA site in non-starved logarithmically growing bacteria; Exp. in 5-h C-st – transcripts count at sRNA site in 5-h C-starved bacteria; Exp. in 24-h C-st – transcripts count at sRNA site in 24-h C-starved cells.