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Table 1 List of the ncRNAs differentially expressed in the rph-1 Δpnp double mutant vs the rph-1 control strain in stationary phase. ncRNAs were quantified with the RNAseq technology in the rph-1 Δpnp double mutant and the rph-1 control strain. FC is the fold-change of expression in the rph-1 Δpnp double mutant compared to the rph-1 control

From: PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli

ncRNA

Description

FC

rph-1 Δpnp double mutant vs rph-1 control

agrA

Inactive antisense sRNA

6.1

arcZ

sRNA positive antisense regulator of rpoS; binds Hfq

0.5

arrS

Antisense sRNA regulator of gadE and acid resistance; GadE-regulated

0.4

csrB

CsrA-binding sRNA. antagonizing CsrA regulation; blocks the CsrA binding of hundreds of mRNAs

7.0

cyaR

sRNA effector of ompX mRNA instability, cAMP-induced; hfq-dependent

2.3

dsrA

Regulatory sRNA enhances translation of rpoS; component of acid resistance regulatory circuit; also antagonist of H-NS function by decreasing H-NS levels

0.5

gadY

sRNA regulator of gadAB transcriptional activator GadX mRNA

3.2

gcvB

GcvB sRNA gene divergent from gcvA; represses oppA, dppA, gltI and livJ expression; regulated by gcvA and gcvR; this is gcvB-L, terminated at T2, 90% of gcvB RNA is from gcvB-S, encoding a 134 nt RNA terminating at T1

5.3

glmY

sRNA activator of glmS mRNA, glmZ processing antagonist

0.5

glmZ

sRNA antisense activator of glmS mRNA, Hfq-dependent

6.1

micA

sRNA regulator of ompA, lamB, ompX and phoP, Hfq-dependent

1.7

micF

Regulatory antisense sRNA affecting ompF expression; member of soxRS regulon

1.7

omrA

sRNA downregulating OM proteins and curli; positively regulated by OmpR/EnvZ; binds Hfq

0.3

omrB

sRNA downregulating OM proteins and curli; positively regulated by OmpR/EnvZ; binds Hfq

0.2

psrD

Novel sRNA, function unknown

3.7

rdlA

Antisense sRNA RdlA affects LdrA translation; proposed addiction module in LDR-A repeat, with toxic peptide LdrA

0.5

rnpB

RNase P, M1 RNA enzyme component; involved in transfer RNA and 4.5S RNA-processing

5.7

rprA

Positive regulatory antisense sRNA for rpoS translation

0.6

rybB

sRNA effector of ompC and ompW mRNA instability; requires Hfq

0.4

rydC

sRNA regulator of csgD and yejABEF

2.3

ryeA

Novel sRNA, function unknown

1.9

ryjB

Novel sRNA, function unknown

2.1

sgrS

sRNA that destabilzes ptsG mRNA; regulated by sgrR

9.8

sibA

Antisense sRNA regulator of toxic IbsA protein; in SIBa repeat

26.0

sibB

Antisense sRNA regulator of toxic IbsB protein; in SIBb repeat

3.2

sibC

Antisense sRNA regulator of toxic IbsC protein; in SIBc repeat

11.3

sibD

Antisense sRNA regulator of toxic IbsD protein; in SIBd repeat

13.0

sibE

Antisense sRNA regulator of toxic IbsE protein; in SIBe repeat

1.9

sokB

Antisense sRNA blocking mokB, and hence hokB, translation

0.5

sokX

Antisense sRNA, function unknown

3.2

ssrA

tmRNA, 10Sa RNA; acts as tRNA-Ala and mRNA template for tagging proteins resulting from premature transcription termination for degradation, a process known as trans-translation

1.4

symR

sRNA destabilizing divergent and overlapping symE mRNA

0.5