Bacterial sRNAs have a wide variety of regulatory mechanisms. Generally, sRNAs can bind to
protein targets and modify the function of the bound protein. sRNAs that interact with mRNA can also be categorized as
cis- or
trans-acting. C
is-acting sRNAs interact with genes encoded on the same
genetic locus as the sRNA. Some
cis-acting sRNAs act as
riboswitches, which have receptors for specific environmental or metabolic signals and activate or repress genes based on these signals.
Stress response Many sRNAs are involved in stress response regulation. They are expressed under stress conditions such as
cold shock,
iron depletion, onset of the
SOS response and sugar stress. The small RNA nitrogen stress-induced RNA 1 (NsiR1) is produced by
Cyanobacteria under conditions of
nitrogen deprivation. Cyanobacteria NisR8 and NsiR9 sRNAs could be related to the differentiation of nitrogen-fixing cells (
heterocysts).
Regulation of RpoS The RpoS gene in
E. coli encodes
sigma 38, a
sigma factor which regulates stress response and acts as a transcriptional regulator for many genes involved in cell adaptation. At least three sRNAs, DsrA, RprA and OxyS, regulate the translation of RpoS. DsrA and RprA both activate RpoS translation by
base pairing to a region in the leader sequence of the RpoS
mRNA and disrupting formation of a hairpin which frees up the ribosome loading site. OxyS inhibits RpoS translation. DsrA levels are increased in response to low temperatures and
osmotic stress, and RprA levels are increased in response to osmotic stress and cell-surface stress, therefore increasing RpoS levels in response to these conditions. Levels of OxyS are increased in response to
oxidative stress, therefore inhibiting RpoS under these conditions.
Regulation of outer membrane proteins The
outer membrane of
gram negative bacteria acts as a barrier to prevent the entry of
toxins into the bacterial cell, and plays a role in the survival of bacterial cells in diverse environments. Outer membrane proteins (OMPs) include
porins and
adhesins. Numerous sRNAs regulate the expression of OMPs. The porins OmpC and OmpF are responsible for the transport of
metabolites and toxins. The expression of OmpC and OmpF is regulated by the sRNAs
MicC and
MicF in response to stress conditions. The outer membrane protein
OmpA anchors the outer membrane to the
murein layer of the
periplasmic space. Its expression is downregulated in the
stationary phase of cell-growth. In
E. coli the sRNA
MicA depletes OmpA levels, in
Vibrio cholerae the sRNA
VrrA represses synthesis of OmpA in response to stress.
Virulence In some bacteria sRNAs regulate virulence genes. In
Salmonella, the
pathogenicity island encoded InvR RNA represses synthesis of the major
outer membrane protein OmpD; another co-activated DapZ sRNA from
3'-UTR represses abundant membrane Opp/Dpp transporters of oligopeptides;
Quorum sensing In
Vibrio species, the
Qrr sRNAs and the
chaperone protein
Hfq are involved in the regulation of
quorum sensing. Qrr sRNAs regulate the expression of several mRNAs including the quorum-sensing master regulators LuxR and HapR.
Biofilm Formation Biofilm is a type of bacterial growth pattern where multiple layers of bacterial cells adhere to a host surface. This mode of growth is often found in pathogenic bacteria, including
Pseudomonas aeruginosa, which can form persistent biofilm within the respiratory tract and cause chronic infection. The
P. aeruginosa sRNA SbrA was found to be necessary for full biofilm formation and pathogenicity. For example, the sRNA DsrA regulates a drug
efflux pump in
E. coli, which is a system that mechanically pumps antibiotic out of bacterial cells.
E. coli MicF also contributes to antibiotic resistance of
cephalosporins, as it regulates membrane proteins involved in uptake of these class of antibiotics. ==Target prediction==