These three protein-binding sRNAs have intrinsic activity such as

These bacterial RNA regulatory elements are sequences located at the 5′ end ofmRNAs that can
adopt different conformations in response to environmental signals, including stalled ribosomes, uncharged tRNAs, elevated temperatures, or small molecule ligands. They usually consist of two parts including the aptamer region, which binds the ligand, and the
so-called expression platform, which regulates gene expression through alternative RNA structures that affect transcription or
translation. It has been shown that
upon binding of
the ligand,
the riboswitch changes conformation. These changes usually involve
alternative hairpin structures that form or disrupt
transcriptional terminators or antiterminators or
that occlude or
expose ribosome-binding sites. However, in
general, most riboswitches repress transcription or translation in the presence of the metabolite ligand; only
a few riboswitches
that activate gene expression have been characterized. Furthermore, due to the modular nature of
riboswitches, the same aptamer
domain can mediate different regulatory outcomes or operate through distinct mechanisms in different
contexts. For instance, the cobalamin riboswitch, which binds the coenzyme form of vitamin
B12, operates by
transcription termination for the btuB genes in Gram-positive bacteria but modulates translation initiation for the cob operons of Gram-negative bacteria.

 

Reports have shown that three protein-binding
sRNAs have
intrinsic activity such as RNase P or contribute essential functions
to a ribonucleoprotein particle such as 4.58 and tmRNA. On the other hand, three other protein-binding
sRNAs,
CsrB, 6S, and Glm Y, act in a regulatory fashion to antagonize
the activities of their cognate proteins by mimicking
the structures of other nucleic acids.  More specifically, the CsrB and CsrC RNAs of E. coli modulate the activity
of CsrA, an RNA-binding protein that regulates carbon usage and bacterial motility upon entry into
stationary phase and other nutrient-poor conditions. Moreover, E. coli 6S RNA
mimics an open promoter to bind to and sequester the cr70-containing RNA
polymerase. When 6S is abundant, especially in stationary phase, it is able to complex with much
ofthe cr70-bound, housekeeping form of RNA polymerase but is not
associated with the crs-bound, stationary phase form of RNA polymerase. As a result, the
interaction between 6S and cr70holoenzyme inhibits transcription
from certain cr70 promoters and increases transcription from some a s-regulated promoters, in part by
altering the competition between cr70 and crs holoenzyme
binding to promoters. In addition sRNA, Glm Y, has
recently been proposed to have a protein-binding mode of
action and is thought to function by titrating an RNA-processing factor away from a
homologous sRNA, GlmZ. Both GlmZ and GlmY
promote accumulation of the GlmS glucosamine-6- phosphate
synthase;
however, they do so by
distinct mechanisms. GlmY expression basically inhibits a GlmZ-processing event that
renders GlmZ unable to activate glmS translation.

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These sRNAs are encoded in cis on the DNA strand opposite
the target RNA and share extended regions of complete complementarity
with
their
target, often 75 nucleotides or more. It appears
that
the
initial
interaction between the sRNA and target RNA involves only limited
pairing, though the duplex can, subsequently, be extended. Furthermore,
the
well-studied
examples of cis-encoded antisense sRNAs reside on plasmids or other mobile genetic elements;
however, chromosomal versions of these sRNAs increasingly
are
being
found. It has been shown that most of the cis-encoded antisense sRNAs expressed from
bacteriophage, plasmids, and transposons function to
maintain the appropriate copy number of the mobile
element.

They
achieve
this
through a variety of mechanisms, including inhibition of
replication primer formation and transposase translation. Another common
group acts as antitoxins to repress the translation of toxic proteins
that kill cells from which the mobile element has been lost.

For
instance, in E. coli, there are also two sRNAs, OhsC and IstR, that are encoded directly adjacent to genes
encoding potentially toxic proteins. Although these sRNAs
are not true antisense RNAs, they do contain extended regions of perfect complementarity (19 and 23 nucleotides) with the toxin
mRNAs.  Moreover, another
group of cis-encoded antisense sRNAs modulates the expression of genes in an operon. Some of these sRNAs are
encoded in regions complementary to intervening sequences between ORFs. For example, in E. coli, base pairing
between the stationary phase-induced GadY antisense
sRNA and the gadXW mRNA leads to cleavage of the duplex between the gadX and gadW genes and increased levels of a
gadX
transcript.

 

Contrarily to the cis-encoded antisense sRNAs, trans-encoded
base
pairing sRNAs share only limited complementarity with their
target mRNAs. These sRNAs regulate the translation and/or stability
of target mRNAs. In fact, the majority of the regulation by
the known trans-encoded sRNAs is negative.  Base pairing between the sRNA and its target mRNA usually leads to
repression of protein levels through translational
inhibition, mRNA degradation, or both. To date, the bacterial sRNAs characterized
primarily
bind to the 5’UTR of mRNAs and most often occlude the
ribosome-binding
site,
though some sRNAs such as GcvB and RyhB inhibit translation
through base pairing far upstream of the AUG of the repressed gene. The
sRNA-mRNA duplex is then frequently subject to degradation by RNase E.

Furthermore, theoretically, base pairing between a
trans-encoded sRNA and its target could promote transcription termination or anti termination. Also, most
of the trans-encoded sRNAs are synthesized under very
specific growth conditions. For instance, In E. coli, for
example, these regulatory RNAs are induced by low iron, oxidative stress, outer
membrane stress, elevated glycine, changes in glucose concentration, and elevated glucose-phosphate levels.

Even
more
importantly, it appears that a given base
pairing sRNA often regulates multiple targets which
implies that a single sRNA can globally modulate a particular
physiological response. In fact, a well-characterized regulatory effects of these sRNAs include the downregulation
of iron-sulfur cluster-containing enzymes under conditions
of low iron (E. coli RyhB), repression of outer membrane porin proteins
under conditions of membrane stress (E. coli MicA
and RybB), and repression of quorum sensing at low cell density (Vibrio Qrr).

 

CRISPR sequences are highly variable DNA regions that consist of a -550
bp leader sequence followed by a series of repeat-spacer units. The CRISPR
repeats are
regularly interspersed with unique spacers of 26 to 72 base pairs; these spacers are not typically repeated in a given
CRISPR array.  Although
the repeats can be similar between species, the spacers between the repeats are not conserved
at all, often varying even between strains. Adjacent to the CRISPR DNA array are
several CRISPR-associated (CAS) genes. The molecular functions of
the CAS proteins are still mostly obscure,
but they often contain RNA- or DNA-binding domains, helicase motifs, and endo- or exonuclease
domains. Overall, CRISPR RNAs have been shown to provide resistance
to
bacteriophage and prevent plasmid conjugation.

 

These essentially are other sRNAs that not only
encode small proteins, but also have additional roles as sRNA regulators.

These
dual
function RNAs include a few of the trans-encoded base pairing
sRNAs that encode proteins in addition to base pairing
with
target
mRNAs.

For instance, the S. aureus RNAIII has been shown to base
pair with mRNAs encoding virulence factors and a transcription factor but also encodes a 26 amino acid
8-hemolysin
peptide.