Review articles
Regulation by transcription
attenuation in bacteria: how
RNA provides instructions for
transcription termination/
antitermination decisions
Tina M. Henkin1 and Charles Yanofsky2*
Summary
Regulation of gene expression by premature termination
of transcription, or transcription attenuation, is a common regulatory strategy in bacteria. Various mechanisms
of regulating transcription termination have been uncovered, each can be placed in either of two broad categories
of termination events. Many mechanisms involve choosing between two alternative hairpin structures in an RNA
transcript, with the decision dependent on interactions
between ribosome and transcript, tRNA and transcript, or
protein and transcript. In other examples, modification
of the transcription elongation complex is the crucial
event. This article will describe and compare several
of these regulatory strategies, and will cite specific
examples to illustrate the different mechanisms employed. BioEssays 24:700–707, 2002.
ß 2002 Wiley Periodicals, Inc.
Introduction
Studies conducted over the past forty years have established
that organisms employ numerous strategies in regulating gene
expression. The mechanisms devised modulate virtually every
event involved in transcription and translation, as well as
influencing mRNA degradation, protein stability, protein localization, protein–protein interactions, and protein function. Of
particular relevance to this report, unrelated organisms often
use completely different mechanisms to regulate expression
of the same gene. These differences sometimes reflect
variations in the use of the gene product in the respective
1
Department of Microbiology, Ohio State University.
Department of Biological Sciences, Stanford University.
Funding agency: Tina Henkin’s laboratory is supported by NIH grants ;
Grant numbers: GM47823, GM63615. Funding agency: Current
research in Charles Yanofsky’s laboratory is supported by NSF grant;
Grant number: MCB0093023.
*Correspondence to: Charles Yanofsky, Dept. Biological Sciences,
Stanford University, Stanford, CA 94305-5020.
E-mail: yanofsky@cmgm.stanford.edu
DOI 10.1002/bies.10125
Published online in Wiley InterScience (www.interscience.wiley.com).
2
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BioEssays 24.8
organisms. Thus, unlike the structural conservation that is
typical of enzymes catalyzing the same metabolic reaction in
different species, the regulatory mechanisms that are used to
modulate a specific gene’s expression often vary.
Molecular studies of gene expression have established that
transcription initiation is the principal regulated event in most
DNA-containing organisms. However, there are numerous
essential molecular processes that occur subsequent to transcription initiation. We now know that these also serve as
targets for regulatory decisions. As illustrated in this article,
transcription attenuation, which involves activation or inhibition of transcription termination at a site located between the
promoter and structural genes of an operon, is a common
regulatory strategy employed by most prokaryotes. Molecular
events relevant to the function of each operon are called into
play to determine whether or not transcription termination will
occur. Recent predictions based on known genome sequences
suggest that as many as 10% of the operons of many bacterial
species may be regulated by transcription termination.(1)
One of the principal advantages of regulating gene expression by transcription termination/antitermination is that short,
unique, RNA sequences and structures can mediate crucial
regulatory decisions. Thus a transcript sequence may have
evolved to bind a specific metabolic regulatory factor, or to
contain a unique peptide coding region. This feature could then
be exploited to allow or prevent transcription termination in
response to a specific physiological signal. The regulatory
mechanisms that are currently known to control transcription
termination are primarily RNA based and thus could have
evolved very early in the history of life, namely in the RNA
world, when RNA is believed to have served as the principal
genetic material. Several of these ‘‘early’’ RNA-dependent
regulatory processes may have been retained, in some
modified form, following adoption of DNA as the principal form
of genetic material. Alternatively, the advantages of optimizing
all the cellular events required for growth and replication may
have dictated the development of mechanisms that effectively
regulate gene expression in different ways, including transcription attenuation.
BioEssays 24:700–707, ß 2002 Wiley Periodicals, Inc.
Review articles
Most bacteria use two very different mechanisms of
transcription termination, designated intrinsic and factordependent termination.(2–4) Regulation of transcription termination in the trp operon of Escherichia coli, and in the early
region of bacteriophage lambda by the N protein, respectively,
are the paradigms for the use of these two mechanisms of
transcription termination as regulatory targets. During intrinsic
termination a segment of the transcript being synthesized by
RNA polymerase forms a stable hairpin followed by a series of
U residues. This hairpin initially serves as a transcription pause
signal, and then, upon addition of the string of U residues, the
transcribing polymerase responds by terminating transcription
and releasing both transcript and DNA template. In factordependent termination, on the other hand, Rho protein binds
as a hexamer to specific recognition sequences in an unstructured transcript segment and progresses in a 30 direction on the
transcript. If Rho contacts an RNA polymerase molecule paused
at a transcription pause site, it directs that polymerase to
release the transcript and abort transcription. Rho-dependent
termination can be modulated by controlling access of Rho
protein to the transcript or to RNA polymerase, or by altering
the sensitivity of RNA polymerase to pause signals. In mechanisms of regulation employing intrinsic termination, the
transcript often forms a preceding alternative structure, designated the antiterminator.(5,6) The antiterminator contains an
RNA sequence that is shared with the terminator helix, thus the
terminator and antiterminator structures are mutually exclusive. The use of competing alternative RNA structures allows
molecular events that regulate formation of the antiterminator
to influence terminator formation, and hence transcription termination. There are also examples where an antiantiterminator structure precedes, and has a sequence in
common with, an antiterminator. With this arrangement,
formation of the anti-antiterminator prevents formation of the
antiterminator, thereby favoring terminator formation and
termination.
In this review, we shall describe the characteristics of six
well-studied mechanisms in which transcription termination is
used to regulate gene expression. Each mechanism depends
on the unique features of specific RNA sequences or structures. These features allow a crucial, separate event to influence whether or not transcription will be terminated at a site
preceding the structural genes of an operon.
Transcription antitermination in response
to tRNA charging
Synthesis of most proteins requires all 20 amino acids in their
activated state, covalently attached to their respective tRNAs.
Availability of any specific charged tRNA is influenced by
several factors. These include the intracellular concentration
of the corresponding amino acid, the levels of the specific
tRNA and its appropriate aminoacyl-tRNA synthetase, and the
overall rate of protein synthesis. Organisms capable of
synthesizing amino acids generally attempt to overcome a
charged tRNA deficiency by increasing the rate of synthesis of
the corresponding amino acid. The logical signal to sense for
the regulatory decision would be the concentration of the
amino acid itself or the level of the corresponding charged
tRNA. Since protein synthesis is primarily dependent upon
availability of charged tRNAs, a charged or uncharged tRNA
would appear to be the most relevant signal. This signal could
be effectively monitored if there were some means of distinguishing between an uncharged and charged tRNA, such as
occurs during translation. Thus, if a transcript contained a
coding region rich in codons for a particular amino acid, this
coding region would or would not be fully translated depending
on whether the appropriate charged tRNA was plentiful.
Alternatively, if a leader RNA could be designed to directly
distinguish between charged and uncharged tRNA, the accumulation of either could then serve as the regulatory signal.
These principles, and the ability of a tRNA or a stalled ribosome
to interact with and alter the formation or stability of an RNA
hairpin structure, are common features of mechanisms used to
regulate transcription termination in the leader regions of
amino acid biosynthetic and other related operons.(5–7)
Translation-mediated transcription
attenuation
In many bacterial species, operons concerned with amino acid
synthesis and utilization are transcriptionally regulated by
ribosome-mediated transcription termination. During transcription of the leader regions of these operons a segment of
the nascent transcript can fold to form either of two competing
hairpin structures, an antiterminator or a terminator.(5) The
leader transcript also contains a short peptide coding region.
This coding region is located at a crucial position in the transcript and it generally contains codons relevant to the operon
concerned. For example, the coding region in the leader
transcript of the his operon of Salmonella typhimurium
contains 7 tandem His codons.(5) As translation of these
codons is attempted, a deficiency of charged tRNAHis leads to
stalling of the ribosome at one of these His codons. This
stalling occurs at a specific location in the nascent transcript,
allowing the antiterminator structure to form. Antiterminator
formation precludes formation of the terminator hairpin,
eliminating transcription termination. In all operons known to
be regulated by this mechanism, the terminator is an intrinsic
termination signal.
In the example shown in Fig. 1, attenuation regulation of the
trp operon of E. coli,(5) the leader RNA segment preceding the
antiterminator contains a fourteen residue coding region, trpL,
which includes two tandem tryptophan codons. When cells
have adequate levels of tryptophan-charged tRNATrp to maintain protein synthesis, the leader peptide is synthesized, the
terminator forms in the leader transcript, and transcription
is terminated. However, when cells are deficient in charged
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Figure 1. E. coli trp operon. Termination: When tryptophan is abundant, the ribosome translating trpL does not stall at the tandem Trp
codons in trpL and quickly reaches the trpL stop codon. The terminator forms in the transcript, resulting in transcription termination.
Antitermination: A deficiency in charged tRNATrp stalls the translating ribosome at one of the two tandem Trp codons in trpL. The
position of this stalling allows the antiterminator to form, which prevents terminator formation, allowing transcripton of the downstream
coding regions.
tRNATrp, the ribosome translating trpL stalls at one of these
tryptophan codons. This stalling allows the immediately adjacent downstream sequence to fold, forming an antiterminator structure. Formation of the antiterminator then prevents
formation of the competing terminator, hence termination itself
is blocked. For operons regulated in this manner, ribosome
position on a specific short peptide coding region in the transcript determines whether or not transcription will continue
into the structural genes of the operon.(5,8) Variations on this
mechanism are widely used by enteric and other bacteria.(4)
In operons regulated by this mechanism, other essential
features of the leader transcript contribute to its effectiveness.
For example, the E. coli trp operon leader transcript can form
a third hairpin structure, preceding the antiterminator. This
hairpin functions to induce transcription pausing. Formation of
this pause hairpin is crucial to attenuation, since it ensures
synchronization of transcription of the leader region with translation of the leader peptide coding region.(5) Ribosome movement then releases the paused transcription complex, allowing
transcription to resume. The NusA protein is as essential participant in most instances of transcriptional pausing.
Many operons regulated by transcription attenuation are
also regulated by a second independent mechanism. For
example, transcription initiation in the trp operon of E. coli is
controlled by a tryptophan-activated trp repressor. Activated
repressor binds to operator sites located within the trp promoter region, blocking access of RNA polymerase to the trp
promoter.(9) Tryptophan-dependent repression provides ca.
80-fold regulation of operon expression in vivo.(10) Regulation
of transcription termination, responding to charging of tRNATrp,
provides an additional 8-fold modulation in operon expression.(10) Combined, these two transcription regulatory mechanisms allow about a 600-fold range of transcription of the
structural gene region of the trp operon. Multiple regulatory
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BioEssays 24.8
mechanisms are often used to fine-tune expression of an
operon.
tRNA-mediated transcription antitermination
by the T box mechanism
Many genes participating in amino acid metabolism in Grampositive bacteria are regulated by the T box transcription termination control system. (This T box bears no relationship to
the eukaryotic T-box DNA-binding motif.) Genes in this family
have leader RNAs approximately 300 nt in length which exhibit
a highly conserved pattern of primary sequence and secondary structural elements; the system is named for the largest
conserved primary sequence element.(7,11) Each transcriptional unit responds independently to limitation for the cognate
amino acid. The response is mediated by sensing the charging
ratio of the cognate tRNA, via direct interactions between
uncharged tRNA and the leader RNA. Formation of the leader
region intrinsic terminator is controlled by a competing antiterminator of lower predicted stability.(11) The antiterminator is
stabilized by specific interactions of the leader RNA with the
cognate uncharged tRNA; regulation of transcription of the
Bacillus subtilis tyrS gene is shown as an example in Fig. 2.
The specificity of the leader RNA-tRNA interaction is primarily
mediated by pairing of a single codon, which is designated the
‘‘specifier sequence’’ and is displayed at a precise position
within the leader RNA, with the anticodon of the tRNA(11)
(Fig. 2). A second pairing of the acceptor end of the tRNA with
a bulge region of the antiterminator is responsible for the
selective response to uncharged tRNA.(12)
The T box mechanism is widely used for regulation of
aminoacyl-tRNA synthetase genes, amino acid biosynthesis
genes, and transporter genes, in Gram-positive bacteria, but is
found rarely in Gram-negative organisms.(7,13) Many genes
are regulated by this mechanism in a single organism, with
Review articles
Figure 2. B. subtilis tyrS gene. Termination: When most molecules of tRNATyr are charged with tyrosine, the tyrS leader transcript
folds to form the terminator, and transcription is terminated. Antitermination: When tRNATyr charging is low, uncharged tRNATyr
interacts with the leader transcript. This interaction stabilizes the antiterminator, which prevents terminator formation, allowing readthrough
transcription.
each transcriptional unit responding independently to the
charging ratio of the cognate tRNA. The T box mechanism is
similar to E. coli trp operon attenuation in that the regulatory
decision is mediated by assessing the lack of charging of a
specific tRNA. However, in the T box system uncharged tRNA
is monitored directly by an RNA-RNA interaction, whereas in
the trp operon of E. coli the absence of charged tRNATrp is
sensed by a translating ribosome.
The T box mechanism is used to regulate expression of the
trp operon of Lactococcus lactis.(14) This illustrates the regulatory diversity that exists in controlling expression of genes
performing the same function in different organisms. The role
of many of the elements conserved in leader RNAs in the T box
family remains to be determined, but formation of a pocket to
stabilize the tRNA–leader interaction is likely to require a complex set of structural constraints.(15) In the default state of the T
box system, transcription will terminate; readthrough is dependent on stabilization of the antiterminator by uncharged tRNA.
Protein-mediated termination or
antitermination
Organisms employ numerous regulatory proteins to control
gene expression at the level of transcription initiation. The
specificity of many of these regulatory proteins depends on
their ability to recognize and bind to specific nucleotide sequences in DNA. There are also proteins that regulate gene
expression by binding to specific RNA sequences; these often
act by altering the structure of leader RNA, to promote or prevent transcription termination. Examples are described below.
Transcription termination by the
RNA-binding protein TRAP
The transcript of the leader region of the trp operon of B. subtilis
can fold to form mutually exclusive antiterminator and
terminator structures (Fig. 3). A sequence-specific RNA
binding protein, TRAP (trp RNA-binding Attenuation Protein),
when activated by tryptophan, binds to the 50 segment of the
Figure 3. B. subtilis trp operon. Termination: Tryptophan-activated TRAP binds to the antiterminator segment of the leader RNA,
freeing the region at the base of the antiterminator to form a terminator, which causes transcription termination. Antitermination:
Tryptophan-free TRAP is inactive in RNA binding. The absence of bound TRAP allows the leader RNA to form the antiterminator structure,
preventing terminator formation and avoiding transcription termination.
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antiterminator hairpin, freeing its 30 segment to pair with the
adjacent 30 RNA segment to form a terminator helix.(16) TRAP
has eleven identical subunits and eleven tryptophan binding
sites.(17) Tryptophan-activated TRAP acts by wrapping the
antiterminator segment of the trp operon leader transcript
around its periphery.(18) The trp operon RNA sequence recognized by TRAP contains 11 UAG or GAG triplets; adjacent
triplets generally are separated by two nucleotides. The triplets
are located immediately preceding and within the 50 segment
of the antiterminator.(16) Since the stability of the antiterminator is higher than that of the terminator, TRAP binding is
required to prevent antiterminator formation. Thus, when cells
have adequate levels of tryptophan, activated TRAP binds to
the antiterminator region, the terminator forms, and transcription is terminated. Tryptophan-activated TRAP also binds to
a similar UAG/GAG repeat sequence overlapping the start
codon for trpG, the only gene required for tryptophan biosynthesis that is not in the trp operon.(16) In this instance, bound
TRAP inhibits trpG translation initiation. The TRAP regulatory
protein of B. subtilis, which directly monitors tryptophan abundance, exerts its regulatory effects at the levels of transcription
termination or translation initiation, rather than at the level of
transcription initiation as the trp repressor does in E. coli.
Like E. coli, B. subtilis also has the ability to monitor the
extent of charging of tRNATrp, and to respond to uncharged
tRNATrp accumulation by increasing expression of the genes
of tryptophan biosynthesis.(19) The uncharged tRNATrp is
sensed by the T box transcription antitermination mechanism
during transcription of the leader region of the yczA-ycbK
operon.(20) yczA encodes a protein, termed AT (Anti-TRAP),
that binds to tryptophan-activated TRAP and inhibits its ability
to bind to trp leader RNA.(21) Accumulation of uncharged
tRNATrp therefore leads to increased yczA expression and AT
production, and this results in TRAP inactivation, leading to
increased expression of all the genes required for tryptophan
biosynthesis.
A variation of the TRAP mechanism is found in the B.
subtilis pyr operon, where formation of a transcription terminator is favored by binding of a regulatory protein, PyrR, to the
leader RNA. In this case, PyrR binds to an anti-antiterminator
element that competes with a stable antiterminator; stabilization of the anti-antiterminator prevents formation of the
antiterminator, allowing formation of the terminator helix.(22)
Transcription antitermination directed
by the RNA-binding protein BglG
The bgl operon of E. coli is involved in utilization of betaglucoside sugars. This operon is regulated by transcription
termination by an RNA binding protein, BglG. BglG can bind to
the leader RNA and stabilize an antiterminator structure,
preventing formation of a competing intrinsic terminator (Fig.
4).(23) Antitermination occurs only when the substrate sugar is
available. Measurement of the sugar concentration is
mediated by the BglF protein, a phosphoenolpyruvate sugar
phosphotransferase protein that is also responsible for transport of the sugar into the cell. When the sugar substrate is
available, BglF phosphorylates the sugar and dephosphorylates BglG; when the sugar is absent, BglF phosphorylates
BglG, which prevents dimerization.(24,25) BglG cannot bind to
the leader RNA as a monomer; in the absence of BglG binding,
the leader RNA folds into the more stable terminator helix.
Expression of the downstream beta-glucosidase gene therefore occurs only when BglG is in its active state, dependent on
BglF detection of the sugar substrate. This example represents a novel dual function of a sugar transporter, which also
regulates transcription antitermination by influencing the phosphorylation state of the antiterminator protein.
Systems of this type have been identified in other sugar
utilization operons in Gram-positive organisms, including the
sucrose utilization operon in B. subtilis.(26) The bgl-type
systems are similar to the TRAP system in that binding of the
regulatory protein to the antiterminator region of the leader
Figure 4. E. coli bgl operon. Termination: When the sugar substrate is absent, BglF phosphorylates BglG, which prevents BglG
dimerization. Phosphorylated BglG cannot bind the leader RNA. Therefore the terminator forms, and transcription terminates.
Antitermination: When the sugar substrate is present, BglG is not phosphorylated and forms a dimer. The BglG dimer binds to and
stabilizes the antiterminator in the nascent transcript. Stabilization of the antiterminator prevents terminator formation, thereby preventing
transcription termination.
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RNA controls transcription termination; they differ, however, in
that BglG stabilizes the antiterminator, preventing formation of
the terminator, while TRAP destabilizes the antiterminator,
promoting termination. In addition, the RNA binding activity of
TRAP is controlled by direct binding of its effector, tryptophan,
while BglG activity is indirectly controlled by a second regulatory protein, BglF, which responds to the sugar substrate.
Factor-dependent processive
antitermination systems
A variety of transcription termination regulatory systems have
been described in which modification of the transcriptional
machinery is used to control gene expression by modulating factor-mediated premature termination of transcription.(27)
Systems of this type often use specific regulatory proteins
that bind to selected sites early in the transcriptional unit and
interact with elongating RNA polymerase to alter its response
to potential transcription termination signals. These systems
are processive in that the modified RNA polymerase will read
through multiple terminators, and in some cases is resistant to
both Rho-dependent and intrinsic termination signals.
Other systems of this general type have been identified;
these have a common requirement for specific target sequences in the 50 segment of the transcriptional unit that are
responsible for binding of an antitermination protein factor.
In addition, the elongating RNA polymerase complex is modified into a persistently terminator-resistant form that elongates
processively through multiple termination sites. For the l Q
system, NusA is the only required host factor, and Q protein
interacts with the non-template strand of the DNA of a paused
transcription complex at a site just downstream from the
promoter.(30) In contrast, the bacteriophage HK022 system is
unique in that it appears that signals in the nascent transcript are sufficient to cause processive antitermination, in the
absence of any phage-encoded protein.(31)
Direct interference with Rho function
Rho-dependent termination requires binding of the Rho hexamer to sites in a nascent transcript and its interaction with
a downstream, paused RNA polymerase complex. In the
example described below, blockage of Rho’s access to a binding site on a transcript by a stalled ribosome prevents Rhodependent transcription termination.
N protein-mediated antitermination
The classic example of this type of mechanism is found in
bacteriophage l. The transition between expression of genes
required early in infection and those required at later stages is
dependent on readthrough of a series of transcriptional terminators, to allow synthesis of transcripts encoding new sets of
gene products. Readthrough of these terminators requires
binding of the product of one of the early expressed l genes,
N protein, to sites on the nascent transcripts. N then nucleates
formation of a complex of host-encoded proteins (NusA, NusB,
NusG, ribosomal protein S10) that interact with RNA polymerase to convert it into a form resistant to the transcriptional
terminators it will encounter as it progresses along l DNA
(Fig. 5).(28) N-modified RNA polymerase can read through
either intrinsic or Rho-dependent terminators, and retains its
terminator-resistance over extended nucleotide distances.(29)
Translation-mediated antitermination
in the tna operon
The tryptophanase (tna) operon of E. coli is involved in utilization of tryptophan as a carbon and nitrogen source.
Transcription of the tna operon structural genes is subject to
Rho-mediated transcription termination (Fig. 6).(32) Initiation of
transcription of this operon is regulated by catabolite repression; continued transcription beyond its 300þ bp leader region
is regulated by tryptophan-induced transcription antitermination. This antitermination mechanism results from blockage
of Rho’s access to the nascent transcript by the ribosome
engaged in translation of a segment of the tna operon leader
RNA. The tna operon leader transcript includes a 24-residue
coding region, tnaC, which specifies a leader peptide, TnaC,
that contains a single crucial tryptophan residue. Synthesis of
Figure 5. lN. Termination: When N protein is absent, Rho binds to the transcript, interacts with a paused RNA polymerase, and
causes transcription termination. Antitermination: When N protein is present, N binds to a site in the nascent transcript and initiates the
formation of a complex containing several host proteins. The complex interacts with RNA polymerase, modifying it to a termination-resistant
form. Termination is prevented at both intrinsic and Rho-dependent terminators.
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Figure 6. E. coli tna operon. Termination: In the absence of excess tryptophan, the ribosome translating tnaC releases the leader RNA
at the tnaC stop codon. This allows Rho factor to bind to the transcript, contact a paused RNA polymerase, and terminate transcription.
Antitermination: In the presence of excess tryptophan, the newly synthesized TnaC-peptidyl-tRNA cannot be cleaved, hence the
translating ribosome remains stalled at the tnaC stop codon. The stalled ribosome blocks Rho binding and prevents transcription
termination, allowing transcription of the downstream coding regions.
TnaC in the presence of inducing levels of tryptophan results in
transcription antitermination. Cleavage of the nascent TnaCpeptidyl-tRNA is inhibited by the presence of excess tryptophan. The translating ribosome, therefore, stalls at the TnaC
stop codon.(33) Since the Rho factor binding sites in the leader
transcript are immediately adjacent to the tnaC stop codon, the
stalled TnaC-peptidyl-tRNA-ribosome complex blocks binding
of Rho to the leader transcript, thereby preventing Rho binding
and Rho-dependent termination.(33) In the absence of high
levels of tryptophan, the TnaC-peptidyl-tRNA is cleaved, the
translating ribosome dissociates at the leader peptide stop
codon, and Rho factor binds to the leader RNA, activating
transcription termination.(32,33) Some feature of TnaC-peptidyl-tRNA appears to create a specific tryptophan binding site
in the ribosome. When tryptophan is bound, it prevents the
appropriate ribosome release factor from activating cleavage of the peptidyl-tRNA. This is another example where the
sequence of the leader transcript is sufficient to direct efficient,
amino acid-specific regulation of transcription termination, in
this case by directing synthesis of the appropriate leader peptide and by placement of the Rho binding sites in the necessary
position to allow interference by the stalled ribosome.
Conclusions
There are other mechanisms of regulation by transcription
termination in bacteria that are not identical to the six examples
described above.(7) Generally attenuation mechanisms target
or sense the events that are most relevant to regulation of
the operon concerned. While this form of gene regulation has
not been analyzed in depth in eukaryotic cells, transcription
elongation is a clear target for control of gene expression,
especially in viral systems.(34) For example, pausing at a specific site in the 50 region of the HIV-1 transcript is a key element
of Tat-mediated regulation.(35) The structural conservation
of the core region of RNA polymerase in prokaryotes and
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eukaryotes provides support for the idea that many of their
basic mechanisms of transcription elongation control are
likely to be similar.(36) In addition to transcriptional regulatory
mechanisms, there are similar examples in both prokaryotes
and eukaryotes in which translation of an upstream open
reading frame (uORF) provides the basis for a regulatory
decision concerning translation of a downstream coding
region.(37–39) In eukaryotes, where ribosome binding is initiated at the 50 end of a mRNA, a short upstream coding region
can interfere with ribosome progression to a downstream
coding region. The fungal uORFs encoding the arginine
attenuator peptide, the uORF2 of the human cytomegalovirus
gpUL4, and the uORF preceding the coding region for mammalian S-adenosyldecarboxylase, are well-studied examples,
each of which is used to regulate translation of a major
downstream coding region.(39) The gpUL4 uORF-encoded
nascent peptide remains covalently attached to tRNAPro,
resembling the tna system described above. Regulation of
gene expression by RNA-RNA interactions has emerged as a
common theme in both prokaryotic and eukaryotic cells, as
exemplified recently by the discovery of multiple small
regulatory RNAs, as well as antisense and dsRNA systems.(40–42) These examples reveal how the basic features of
translation and specific RNA sequences are exploited in
regulation of gene expression.
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