Download Gene expression control by selective RNA processing and

MINIREVIEW
Gene expression control by selective RNA processing and
stabilization in bacteria
Tatiana Rochat1, Philippe Bouloc2 & Francis Repoila3,4
ne
tique et Microbiologie, Universit
INRA, UR892, Virologie et Immunologie Moleculaires, Jouy-en-Josas, France; 2Institut de Ge
e Paris-Sud, CNRS,
UMR8621, Orsay, France; 3INRA, UMR1319 Micalis, Jouy-en-Josas, France; and 4AgroParisTech, UMR Micalis, Jouy-en-Josas, France
1
Correspondence: Francis Repoila, INRA,
UMR1319 Micalis, F78350 Jouy-en-Josas,
France. Tel.: +(33) 134 65 20 69;
fax: +(33) 134 65 20 65;
e-mail: [email protected]
Received 18 April 2013; accepted 22 April
2013. Final version published online 13 May
2013.
Abstract
RNA maturation is a key event regulating genes at post-transcriptional level. In
bacteria, it is employed to adjust the amounts of proteins and functional
RNAs, often in response to environmental constraints. During the process of
RNA maturation, enzymes and factors that would otherwise promote
RNA degradation convert a labile RNA into a stable and biologically functional
molecule.
DOI: 10.1111/1574-6968.12162
Editor: Andre Klier
MICROBIOLOGY LETTERS
Keywords
RNA maturation; RNA degradation;
RNA stability; RNase; translation;
post-transcriptional regulation.
Introduction
The expression of genetic information operates through
consecutive steps ranging from transcription to posttranscriptional events, generally ending in protein
synthesis. Each of these steps is regulated to adjust the
expression of each gene to physiological needs imposed
by the environment and the organism development. In
bacteria, in contrast to eukaryotes, these steps are coupled
in space and time, and their direct input, that is, RNA, is
less stable; the average half-life of a bacterial messenger
RNA (mRNA) is in a range of minutes vs. hours in
eukaryotes (Belasco, 2010; Silva et al., 2011). Although
the importance of post-transcriptional regulatory processes affecting RNA has been established for a few decades, they have been rather overlooked in bacteria.
Nevertheless, several investigations in the mid-80s provided an essential base. For example, studies on the processing of T4 phage gene, 32 mRNA were instrumental in
the identification of RNase E as the major endoribonuclease (Gorski et al., 1985; Mudd et al., 1988), and
inverted repeats within repetitive extragenic palindromic
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sequences (REPs) were demonstrated to play an active
role in RNA stability and affect the differential expression
occurring in polycistronic operons (Newbury et al.,
1987a, b). In recent years, a series of discoveries has
underlined the significance of the phenomenon. For
instance, (1) many small RNAs (sRNAs) mediate regulations via imperfect RNA–RNA pairing and affect mRNA
processing and stability (Repoila & Darfeuille, 2009; Wagner, 2009; Caron et al., 2010); (2) many genes express
antisense transcripts (asRNAs) and may be subject to
their effect via modulation of the mRNA stability and
translational efficacy (Lasa et al., 2011); and (3) players in
mRNA turnover can be targeted by antimicrobial agents
highlighting the vital character of RNA processing and
stability (Olson et al., 2011).
In bacteria, RNA processing cleaves RNA molecules
into shorter fragments, and RNA degradation leads to
oligonucleotides and ribonucleotides monomers. RNA
degradation is a constitutive phenomenon affecting each
transcript. It involves specific interplays of endo- and
exoribonucleases and results in shutting off gene activity.
However, under precise circumstances and with the
FEMS Microbiol Lett 344 (2013) 104–113
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RNA maturation and regulation
involvement of specific regulatory actors (RNAs and
proteins), RNA processing stabilizes RNA and becomes a
crucial element controlling gene expression by modulating the fate, the abundance and the activity of transcripts
(Arraiano et al., 2010; Caron et al., 2010; Condon
& Bechhofer, 2011). To avoid confusion, we will employ
the term (1) ‘RNA maturation’ to refer to a specific regulatory cleavage, which usually occurs within the 5′ transcript region and changes a transcript to a biologically
active RNA molecule, and (2) ‘RNA degradation’ for a
cleavage triggering RNA decay. For example, it is wellknown that ribosomal and transfer RNAs (rRNAs and
tRNAs) are synthesized as prefunctional transcripts and
acquire their biological activity through maturation.
Although these molecules are quite stable, they are also
degraded (Deutscher, 2009).
Remarkably, distantly related bacteria such as Escherichia coli and Bacillus subtilis have converged on a similar
macromolecular complex, named ‘degradosome’, for
much of their RNA processing. However, the components of the degradosome may differ between species,
and even be absent in some bacteria (Carpousis, 2007;
Gorna et al., 2012; Lehnik-Habrink et al., 2012). The
fate of each piece of a cleaved RNA molecule does not
depend on a specific processing enzyme, a particular
cleavage site or in the cleavage process, but rather in
each end product. In addition, regulators such as
proteins, metabolites, and sRNAs can guide endoribonuclease complexes to their targeted RNA sequences
stimulating a regulatory cleavage rather than RNA
degradation (Fig. 1; see below).
In this review, we report recent and significant examples
of RNA maturation processes turning a silent or weakly
active RNA molecule into a fully functional transcript by
highlighting the mechanisms and regulators involved.
Common and crucial actors to RNA
maturation and degradation
One of the major modes initiating RNA maturation and
RNA decay is accomplished by the degradosome, a multiprotein complex centered on an endoribonuclease enzyme
that cleaves single-stranded RNA (ssRNAs) substrates. To
date, degradosomes have been characterized only in a few
bacteria. In addition to the endoribonuclease, the
degradosome usually consists of three other major components providing it with (1) a processive exoribonuclease activity, (2) a RNA helicase function, (3) an activity
most likely coordinated with the carbon metabolism via a
glycolytic (enolase, phosphofructokinase) or a Krebs cycle
enzyme (aconitase) (Carpousis, 2007; Gorna et al., 2012;
Lehnik-Habrink et al., 2012). Moreover, degradosomes
seem to be membrane associated (Khemici et al., 2008;
Lehnik-Habrink et al., 2011a, b). Evolutionarily unrelated
proteins can ensure analogous functions rendering RNA
processes slightly different in various species (Morita
et al., 2005; Commichau et al., 2009; Ikeda et al., 2011;
Prevost et al., 2011; Roux et al., 2011). In Enterobacteriaceae (e.g. E. coli) and related Gram-negative species,
RNase E is the endoribonuclease of the degradosome;
however, in the Gram-positive phylum of Firmicutes
(e.g. B. subtilis, Staphylococcus aureus) where RNase E is
absent, the unrelated endoribonuclease RNase Y replaces
it (Fig. 2) (Lehnik-Habrink et al., 2011a, b; Roux et al.,
2011). Although RNase E and RNase Y can degrade
native and processed transcripts, they are sensitive to the
Fig. 1. Factors governing the fate of a
messenger RNA. The behavior of primary
transcripts relies on the action of ribonucleases
(violet) and other regulatory factors that guide
RNAs to degradation or to maturation into
functional RNA products according to the
individual case. Blue lines symbolize RNAs;
Pacman cartoons and scissors symbolize
endoribonucleolytic and exoribonucleolytic
activities, respectively. sRNA, small RNA;
mRNA, messenger RNA; RBS, ribosome
binding site; AUG, translation initiation codon.
FEMS Microbiol Lett 344 (2013) 104–113
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106
T. Rochat et al.
Fig. 2. RNA decay pathways in Escherichia
coli and Bacillus subtilis. Pyrophosphate
removal from the 5′ end of primary transcripts
is catalyzed by the pyrophosphohydrolase
RppH. This first step of RNA decay and the
double-stranded-dependent internal cleavage
catalyzed by RNAse III are common to E. coli
and B. subtilis. Endoribonucleolytic cleavage of
mRNA is performed by 5′ monophosphatedependent endoribonucleases (RNase E in
E. coli; RNase Y in B. subtilis), and the decay
of cleaved RNAs is mediated exclusively by
3′ to 5′ exoribonucleases in E. coli (PNPase,
RNase R, and RNase II) or by both 3′ to 5′
exoribonucleases and the 5′ to 3′ exo- and
endoribonucleolytic activities of RNase J in
B. subtilis. Oligoribonucleotides are finally
processed to mononucleotides by
oligoribonucleases.
phosphorylation status of the 5′ RNA end (Mackie, 1998;
Shahbabian et al., 2009). Their action is rather limited on
primary transcripts that bear a 5′ triphosphate group and
is greatly enhanced once the RNA pyrophosphohydrolase,
RppH, has converted the 5′ triphosphate RNA end into a
5′ monophosphate (Celesnik et al., 2007; Richards et al.,
2011). Nevertheless, endoribonucleolytic cleavages often
take place within the 5′ mRNA regions generating new
5′-P extremities which (1) stimulate further cleavage by
RNase E and RNase Y, and (2) break apart the ribosome
binding site (RBS) from the remaining mRNA, exposing
the latter to further endoribonucleolytic degradation after
clearing of translating ribosomes.
In Gram-negative bacteria, PNPase (polynucleotide phosphorylase) ensures the processive exoribonuclease activity
from 3′ to 5′ to degrade transcripts, yet external enzymes
to the degradosome may assist PNPase (e.g. RNase R,
RNase II, and Poly(A) polymerase) for a complete degradation (for detailed review see Arraiano et al., 2010). In
Firmicutes, PNPase is present, but RNase J (made up of
two paralogous enzymes, J1 and J2) is also a component of
the degradosome (Commichau et al., 2009). RNase J,
which has also a ssRNA endoribonuclease activity, accom-
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plishes a processive RNA 5′ to 3′ degradation, a unique feature reported to date in bacteria and supposed previously
to be restricted to eukaryotes (Britton et al., 2007; Mathy
et al., 2007; Li de la Sierra-Gallay et al., 2008). Because of
this capacity for 5′ to 3′ RNA hydrolysis, degradation in
Firmicutes could be initiated from the 5′ end via RNase J,
or from the 3′ end of the original transcript via PNPase
action (a pathway common with Gram-negative bacteria),
depending on the mode of initiation of the decay (Fig. 2)
(Condon, 2007).
The ribonuclease III (RNase III) is another major
nuclease that belongs to a universally conserved endoribonuclease family. RNase III specifically binds to doublestranded RNAs (dsRNAs) and cleaves at specific locations
(MacRae & Doudna, 2007). In bacteria, RNase III generates 5′ monophosphate and 3′ hydroxyl termini, each
strand of the dsRNA having two nucleotides 3′ overhanging due to a staggered cleavage. In addition to RNase E
and RNase J, RNase III is an essential player in rRNA
maturation, and in certain bacterial species, the three
nucleases coexist and participate together in specific and
coordinated RNA maturations without functional redundancy (MacRae & Doudna, 2007; Taverniti et al., 2011).
FEMS Microbiol Lett 344 (2013) 104–113
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RNA maturation and regulation
Several other bacterial endoribonucleases have been
discovered. These nucleases are encoded by the chromosome (e.g. RNase G, RNase P, RNase Z) (Arraiano et al.,
2010), toxin–antitoxin (TA) modules (e.g. RnlB, RelE,
MqsR, MazF, VapC) (Yamaguchi & Inouye, 2009), or
phages (e.g. RegB) (Sanson & Uzan, 1995). Although
their active role in gene expression control and cell physiology has been well established, they do not appear to be
involved in the recent examples selected for this review
(excepted MazF; see below); therefore, they will not be
presented in further detail.
Factors governing the fate of cleaved
RNAs
Although not totally understood, the fate of each RNA
molecule produced by cleavage follows from the
concerted or the independent action of intrinsic features
of the RNA substrate and trans regulatory factors
(e.g. proteins, translating ribosomes, metabolites, and
sRNAs; Fig. 1). Intrinsic features mainly rely on local
sequences and/or the folding of the RNA substrate. Endoribonucleases act on ss- or dsRNAs, by recognizing
sequences and/or secondary structures, but environmental
modifications can induce local structural changes in the
RNA folding, and these novel conformations are no
longer recognized as substrate. For instance, RNase E is a
ssRNA-specific enzyme cutting preferentially A/U-rich
regions near a hairpin structure; conversions from ss- to
dsRNA of the cleavage site region or modifications of the
hairpin can abolish the RNase E activity (Mackie, 2013).
Similarly, PNPase and RNase J process ssRNAs but are
blocked by hairpin-loop structures. Thus, under specific
physiological conditions, a local switch from ss- to
dsRNA turns off degradation (RNA processing) and
provides a stable RNA (RNA maturation) (Condon, 2003,
2010). Most generally, trans acting factors appear to guide
the action of endoribonucleases to their targets or in
contrast to ‘hide’ the latter from cleavage (Marujo et al.,
2003; Prevost et al., 2011; Stazic et al., 2011; Bandyra
et al., 2012). For example, in E. coli, the degradosome
interacts with transcription and translation machineries,
as well as with two key players of the bacterial posttranscriptional regulation, Hfq and sRNAs (Morita et al.,
2005; Vogel & Luisi, 2011; Tsai et al., 2012). Hfq is a
RNA chaperone providing favorable environments for
RNA/RNA interactions and protects partners from degradation or, in contrast, induces their degradation (Vogel &
Luisi, 2011; Sobrero & Valverde, 2012). Many sRNAs act
by pairing to mRNAs, and RNA duplexes formed increase
or decrease the translation efficacy and/or the stability of
the mRNA. In Gram-negative bacteria, numerous cases
of sRNA/mRNA duplexes associated with Hfq are
FEMS Microbiol Lett 344 (2013) 104–113
substrate for RNase E and RNase III leading to RNA
decay (Repoila & Darfeuille, 2009; Waters & Storz, 2009).
Nonetheless, besides the 5′-, 3′-rRNA maturation
(Deutscher, 2009), several examples have been described
where the cleavage process does not trigger RNA decay but
instead stabilizes the transcript that becomes fully functional.
RNA maturation and gene activation
The genetic information in bacteria is generally organized
in operon structures that generate polycistronic transcripts containing different open reading frames (ORFs)
that encode various proteins. To match specific physiological requirements, the level of each protein needs to be
adjusted. Among possible mechanisms, RNA cleavage
permits the separation of ORFs and confers different fates
to each RNA portion (upstream and downstream of the
cleavage site). In E. coli for instance, the dnaG operon
expresses constitutively the rpsU-dnaG-rpoD polycistronic
mRNA that encodes the S21 ribosomal protein, the primase and the vegetative sigma factor r70, respectively. This
mRNA is cleaved by RNase E between dnaG and rpoD,
resulting in the selective increase in decay rate of the
primase part and in a significant difference in protein
levels expressed in the cell; ~ 50–100 copies of DnaG and
~ 3000 copies of r70 (Burton et al., 1983; Yajnik & Godson, 1993). Similarly in B. subtilis, the gapA operon is
mainly transcribed under a bicistronic mRNA encoding
the negative regulator of its own transcription, CggR, and
GapA, the glycolytic enzyme glyceraldehyde-3-phosphate
dehydrogenase, respectively. The differential needs for
each protein are adjusted by an RNase Y-dependent
cleavage occurring upstream of the gapA encoding
sequence. The gapA transcript is relatively stable
(> 3 min) as its 5′ end bears a stem-loop structure
protecting it from RNase J degradation; in contrast, the
cggR RNA is very unstable (< 30 s) (Ludwig et al., 2001;
Condon, 2003).
In bacteria, glmS encodes the glucosamine-6-phosphate
synthase, an essential enzyme of amino sugar metabolism.
The glmS RNA is expressed from an operon structure,
and its 5′ untranslated region (5′UTR) undergoes a cleavage that leads to an activation in E. coli and closely
related species (activation by RNA maturation) (Urban &
Vogel, 2008). In contrast, the sequence found in B. subtilis and relatives provokes RNA degradation (repression by
an autocatalytic cleavage) (Winkler et al., 2004). In
E. coli, glmS is transcribed on a bicistronic mRNA, downstream glmU that encodes an essential uridyltransferase.
RNase E cleaves at the translation stop codon of glmU
mRNA generating two mRNAs, glmU and glmS. glmU
mRNA is rapidly degraded, and glmS mRNA is stabilized
and efficiently translated (Fig. 3a). Indeed, the 161ª 2013 Federation of European Microbiological Societies
Published by John Wiley & Sons Ltd. All rights reserved
108
T. Rochat et al.
(a)
(b)
nucleotide-long 5′ UTR of glmS mRNA folds in a stem
loop that sequesters the ribosome binding site (RBS) and
hampers translation. In the presence of Hfq, the sRNA
GlmZ pairs to the 5′ portion of the glmS stem loop. The
formation of GlmZ/glmS mRNA duplex releases the RBS
and enables ribosomes to translate glmS mRNA. As a
consequence, glmS mRNA is stabilized due to the formation of the ribonucleoprotein complex Hfq/GlmZ/glmS
mRNA and the presence of translating ribosomes covering the mRNA (Kalamorz et al., 2007; Urban & Vogel,
2008). In this example, the RNA maturation process and
its activator effect on glmS mRNA relies on the folding of
the 5′UTR and the formation of a duplex GlmZ/glmS
mRNA, both protecting the glmS transcript from further
degradation after the RNase E–dependent cleavage.
A similar regulatory system based on RNA maturation
sRNA-dependent has also been described in Clostridium
perfringens, a Firmicute. In this species, the expression of
the collagenase, a major virulence factor, is enhanced by
the pairing of its encoding mRNA, colA, with the sRNA
VR-RNA (Obana et al., 2010). The 5′UTR of colA mRNA
folds in a hairpin that occludes the RBS and impairs
translation. This secondary structure is targeted by
VR-RNA that pairs to the sequence of colA involved in
the sequestration of the RBS (Fig. 3b). Remarkably, and
in addition to rendering the colA 5′UTR efficient for
translation, the formation of the VR-RNA/colA duplex
exposes a ssRNA cleavage site on colA mRNA between
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Fig. 3. Gene activation by RNA maturation.
(a) Maturation of glmU-glmS bicistronic
operon in Escherichia coli. The cleavage by
RNase E initiates the decay of glmU and the
formation of a stabilizing complex between
the 5′-UTR of glmS and the GlmZ sRNA
allowing efficient synthesis of the
glucosamine-6-phosphate synthase. (b)
Maturation of the collagenase colA mRNA in
Clostridium perfringens. The
endoribonucleolytic cleavage of colA mRNA
results in the formation of a structured 5′ end
that protects colA from subsequent
degradation and ensures a high level of
collagenase synthesis. Green or blue lines
symbolized sRNA and mRNA, respectively. The
RNA chaperone Hfq is in violet.
the RBS and the duplex formed with VR-RNA. When the
RNA cleavage occurs, it generates a novel and translatable
form of colA mRNA that bears a 5′ terminal hairpin loop
protecting the transcript from further degradation and
renders accessible to ribosomes the Shine-Dalgarno
sequence (SD) recognized by the 16S rRNA (Fig. 3b).
The processed colA mRNA is significantly more stable
than the uncut version due to the absence of the 5′ RNA
portion cleaved on the primary form. Data on this regulatory system indicate that another source of stabilization
is provided by initiating ribosomes but not the translation
process per se (Obana et al., 2010).
Regulatory RNA-mediated protection
against RNA cleavage
Several sRNAs activate gene expression by pairing to an
otherwise translation inhibitory stem loop on their
cognate target mRNAs; a mechanism termed ‘antiantisense’. For example, in Staphylococcus aureus, the regulatory RNA RNAIII pairs to and activates translation of
the hla mRNA encoding the alpha-hemolysin; in E. coli,
the sRNA RhyB activates the expression of shiA, that
encodes the shikimate transport system (Frohlich &
Vogel, 2009). This sRNA-dependent activation primarily
affects the folding of the mRNA translation initiation
region that enables translation. However, in a few cases,
an additional role has been shown for the sRNA: it also
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RNA maturation and regulation
blinds the degradosome, prevents the cleavage, and stabilizes its target. Thus, the sRNA-mediated protection
results in the functional activation of targets similarly to
the examples described in the previous section, and may
be considered as an alternative to the RNA maturationmediated activation of genes. For example, in E. coli,
DsrA, RprA, and ArcZ sRNAs pair to and allow rpoS
mRNA translation encoding rS, a major stress sigma factor. The degradation of the rpoS mRNA occurs via RNase
E- and RNase III-mediated processes (Resch et al., 2008;
McCullen et al., 2010; Vecerek et al., 2010). It was shown
that the formation of the rpoS/DsrA or the rpoS/RprA
duplexes not only renders the rpoS mRNA efficient for
translation but also protects it against the RNase E-mediated degradation (McCullen et al., 2010). In a similar
manner, the lysC riboswitch in E. coli controls the expression of the lysine-sensitive aspartokinase III, LysC, at
translational level by adopting two exclusive conformations. In the absence of lysine, the lysC riboswitch folds
in a structure where the RBS is accessible to ribosome
and translation can proceed. This folding hides a RNase
E cleavage site in the dsRNA stem. In contrast, when
lysine is present, the riboswitch and the amino acid form
a complex hiding the RBS (translation stops) and exposing the RNase E site allowing the entry of the degradasome and the subsequent RNA degradation. Thereby, the
complex riboswitch/lysine shuts off lysC expression by
blocking translation and turning the native mRNA into a
substrate for the degradosome (Fig. 4a) (Caron et al.,
2012).
A peculiar example of sRNA-mediated protection has
been reported in Streptococcus pyogenes (Ramirez-Pena
et al., 2010). The streptokinase (Ska) is a secreted key
virulence factor of S. pyogenes under control of the sRNA
FasX (Kreikemeyer et al., 2001). In absence of FasX, the
abundance of ska mRNA encoding the streptokinase is
extremely low, and its half-life is less than a minute.
When FasX is present, the half-life of ska is increased to
more than 7 min, due to the sRNA-mediated stabilization
of the mRNA. A molecular analysis demonstrated that
FasX pairs to the very 5′ end of ska mRNA, and this
dsRNA protects the mRNA against degradation (Fig. 4b).
Experimental evidences converge to suggest that the
FasX-mediated stabilization is due to the absence of
unpaired nucleotides at the very 5′ end of ska mRNA,
possibly restricting the access of RppH, RNase Y, and
RNase J (Ramirez-Pena et al., 2010).
Selective mRNA and rRNA maturation
for specialized translation
Protein synthesis is initiated by a multistep process
involving disassembled ribosomal subunits (30S and 50S),
initiation factors (IFs, i.e. IF1, IF2, and IF3), the initiator
tRNA (fMet-tRNAfMet) and mRNAs (Laursen et al., 2005;
Malys & McCarthy, 2011). For a canonical mRNA, that
(a)
(b)
Fig. 4. Regulatory RNA-mediated protection
against RNA cleavage. (a) Lysine-dependent
regulation of lysC mRNA by a riboswitch in
Escherichia coli. Two conformations of the
riboswitch exist depending on the availability
of lysine in the cytoplasm and mediate
translation (ON) or decay (OFF) of lysC mRNA.
(b) Post-transcriptional regulation of the
streptokinase mRNA by FasX sRNA in
Streptococcus pyogenes.
FEMS Microbiol Lett 344 (2013) 104–113
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Published by John Wiley & Sons Ltd. All rights reserved
110
is, an mRNA carrying a 5′UTR, the first step consists of
the formation of a binary complex made up by the 30S
ribosomal subunit associated with the RBS of the mRNA,
where the SD sequence base pairs with the anti-SD
sequence at the 3′ tail of the 16S rRNA gene. In a second
step, the 50S ribosomal subunit associates with the complex 30S mRNA, resulting in the 70S translation initiation
complex. Besides this ‘classical’ view, a substantial number of leaderless mRNAs (lmRNAs) efficiently translated
have been discovered in the three domains of life (Moll
et al., 2002; Laursen et al., 2005; Malys & McCarthy,
2011). The translation initiation process is not yet totally
elucidated, but lmRNAs are preferentially bound by 70S
ribosomes without prior disassembly compared with the
30S subunit, and once formed, the 70S–lmRNA initiation
complex is able to engage the elongation process without
requiring IFs (Udagawa et al., 2004; Brock et al., 2008).
Although certainly not dominant in bacterial species, in
silico predictions and primary transcriptomes show that
at least 15% of the genes would be transcribed as leaderless in certain genera; for example, Actinobacteria, Helicobacter, Xanthomonas, Deinococcus (Sharma et al., 2010;
Zheng et al., 2011; Schmidtke et al., 2012). The significance of the coexistence of mRNAs and lmRNAs is
currently not understood, but under certain circumstances, it may be used to respond to environmental
changes. In E. coli, in response to environmental conditions triggering the toxic effect of MazF, an endoribonuclease belonging to the mazEF TA module family, certain
T. Rochat et al.
mRNAs are specifically processed into lmRNAs and are
selectively translated by specialized ribosomes (Amitai
et al., 2009; Vesper et al., 2011). The MazF induction
shuts off synthesis of most of proteins, and only 10% are
specifically produced, including proteins provoking death
in the majority of cells within a population and survival
in a subpopulation (Amitai et al., 2009). MazF cleaves
ssRNA at specific sequences (5′-ACA-3′) located very
close upstream of the translation initiation codon, converting mRNAs with 5′ UTRs into lmRNAs (Fig. 5)
(Zhang et al., 2003; Vesper et al., 2011). Within the bulk
of RNAs targeted by MazF, the 16S rRNA is also processed in 30S subunits and 70S ribosomes. MazF cleaves
at the 3′ terminus of the rRNA and removes the anti-SD
sequence. This action of the endoribonuclease MazF generates a subpopulation of ‘stress ribosomes’ that no
longer recognize mRNAs but instead specifically translate
lmRNAs (Vesper et al., 2011). Thus, the MazF-mediated
maturation, that switches RNAs to lmRNAs and 70S ribosomes to stress ribosomes, appears as a RNA maturation
process dedicated to the translation of specific proteins in
response to harmful conditions.
Concluding remarks
RNA cleavages are crucial processes to up- or downregulate gene expression. Usually, the same enzymatic
set is involved in either RNA degradation or maturation, and the transcript fates lie in their structures
Fig. 5. MazF-mediated specialized translation.
MazF toxin is sequestered by MazE antitoxin
into a protein complex. Under stress
conditions, MazE is proteolyzed, and the
endoribonuclease MazF is released on its
active form. Its action on specific mRNAs and
on 16S rRNA genes results in the translation
of leaderless mRNAs by specialized ribosomes
lacking the anti-SD sequence (16S*).
ª 2013 Federation of European Microbiological Societies
Published by John Wiley & Sons Ltd. All rights reserved
FEMS Microbiol Lett 344 (2013) 104–113
RNA maturation and regulation
which can hide or unmask RBSs and ribonuclease sites.
The bacteria have astutely exploited the relationship
between ribonuclease and RNA structure to adapt and
survive particular growth conditions; it is likely that
many other ingenious regulations remain to be uncovered. At present, the prediction of transcript fates based
on primary sequence is not possible; genome-wide studies of transcript stability and cleavage sites, possibly
using a RNA tagging methodology (Fouquier d’Herouel
et al., 2011), will be instrumental to establish the RNA
degradation/RNA maturation relationship in bacterial
adaptation processes.
Acknowledgements
Work in the authors’ laboratories was supported by a grant
from the Agence Nationale pour la Recherche (ANR-12BSV6-0008-ReadRNA) and French governmental institutions CNRS and INRA. F.R. thanks Stephane Aymerich for
his support. We are grateful to Colin Tinsley for his help
with the English language. We apologize to colleagues whose
work has not been mentioned due to space limitations.
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