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The basic principle of regulation in bacteria is that gene expression is
controlled by a regulator that interacts with a specific sequence orstructure in DNA or mRNA at some stage prior to the synthesis of
protein.
The stage of expression that is controlled can be transcription, when
the target for regulation is DNA, or it can be at translation, when thetarget for regulation is RNA.
When control is during transcription, it can be at initiation or at
termination. The regulator can be a protein or an RNA.
"Controlled" can mean that the regulator turns off (represses) the
target or that it turns on (activates) the target. Expression of many
genes can be coordinately controlled by a single regulator gene on the
principle that each target contains a copy of the sequence or structure
that the regulator recognizes.
Regulatory RNA
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Regulators may themselves be regulated, most typically in response to
small molecules whose supply responds to environmental conditions.
Regulators may be controlled by other regulators to make complex
circuits.
Regulation via RNA uses changes in secondary structure as the
guiding principle. The changes in structure may result from either
intramolecular or intermolecular interactions.
The most common role for intramolecular changes is for an RNA
molecule to assume alternative secondary structures by utilizing
different schemes for base pairing. The properties ofthe alternative
conformations may be different.
Secondary structure also is used to regulate the termination of
transcription, when the alternative structures differ in whether they
permit termination.
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A regulator RNA is a small RNA with a single-stranded region th at can pair with
a sing le-stranded regio n in a target RNA.
In intermolecular interactions, an RNA regulator recognizes its target by
the familiar principle of complementary base pairing
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The trp operon consists of five structural genes arranged in a contiguous
series, which code for the three enzymes (anthranilate synthetase, indol-glycerol synthetase, and tryptophan synthetase) that convert chorismic
acid to tryptophan.
The operon starts at a promoter at the left end of the cluster, trp operon
expression is controlled by two separate mechanisms:
1- Repression of expression is exercised by a represser protein (coded
by the unlinked gene trpR) that binds to an operator that is adjacent to the
promoter.
2- Attenuation controls the progress of RNA polymerase into the operon
by regulating whether termination occurs at a site preceding the first
structural gene.
The E.colitryptophan operon
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The trp operon c onsists of f ive cont iguou s s tructura l genes preceded
by a control region that includes a promoter, operator, leader peptide
cod ing region, and attenuator.
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Attenuation was first revealed by the observation that deleting a
sequence between the operator and the trpE coding region can increase
the expression of the structural genes.
This effect is independent of repression: both the basal and
derepressed levels of transcription are increased. Thus this site
influences events that occur afterRNA polymerase has set out from the
promoter (irrespective of the conditions prevailing at initiation).
An attenuator (intrinsic terminator) is located between the promoter and
the trpE gene. It provides a barrier to transcription into the structural
genes.
Termination at the attenuator respond to the level of tryptophan. In the
presence of adequate amounts of tryptophan, termination is efficient. In
the absence of tryptophan, RNA polymerase can continue into the
structural genes.
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An attenuator contro ls the
prog ression of RNAP into the
trp g enes. RNAP init iates at theprom oter and then proceeds.
In the absence of tryp toph an,the polymerase cont inue into
the stru ctural genes.
In the presence of tryp toph an,
there is ~ 90% pro babi l i ty of
Termination.
ribosome
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Eukaryotic transcription is more complex than prokaryotic transcription
and, until recently, it has seemed that every eukaryotic gene was unique
requiring its own transcription machinery.
However, it is now possible to simplify the story somewhat. The
promoters for different genes are different. Each contains a combinationof sites to which specific protein factors bind. All of these factors help
RNA polymerase to bind in the correct place and to initiate transcription.
However, the repertoire of transcription factors and transcription factor
binding sites is not unlimited.
There are three distinct RNA polymerases in a eukaryotic cell nucleus
which define the three major classes of eukaryotic transcription unit:
Transc r ipt ion in eukaryot ic cells
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Because there is no nucleus to separate the processes of transcription
and translation, when bacterial genes are transcribed, their transcripts
can immediately be translated.
Prokaryotic cells
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Transcription and translation are spatially and temporally separated ineukaryotic cells; that is, transcription occurs in the nucleus to produce a
pre-mRNA molecule.
The pre-mRNA is typically processed to produce the mature mRNA, which
exits the nucleus and is translated in the cytoplasm.
Eukaryotic cells
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mRNA in Eukaryotes
The sequence of a eukaryotic protein-coding gene is typically not
colinear with the translated mRNA; that is, the transcript of the gene is a
molecule that must be processed to remove extra sequences (introns)
before it is translated into the polypeptide.
Most eukaryotic protein-coding genes contain segments called introns,
which break up the amino acid coding sequence into segments calledexons.
The transcript of these genes is the pre-mRNA (precursor-mRNA).
The pre-mRNA is processed in the nucleus to remove the introns andsplice the exons together into a translatable mRNA. That mRNA exits the
nucleus and is translated in the cytoplasm.
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Synthesis of m ature mRNA in eukaryot ic cells
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Pre-mRNA Processing (Splicing)
The steps of pre-mRNA splicing (intron removal) are as follows:
The intron loops out as snRNPs (small nuclear ribonucleoprotein particles,
complexes of snRNAs and proteins) bind to form the spliceosome.
The intron is excised, and the exons are then spliced together.
The resulting mature mRNA may then exit the nucleus and be translated in the
cytoplasm.
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The genomic DNA contains all the information for the structure and
function of an organism.In any cell, only some of the genes are expressed,
that is, transcribed into RNA.
There are 4 types of RNA, each encoded by its own type of gene:
mRNA - Messenger RNA: Encodes amino acid sequence of a polypeptide.
tRNA - Transfer RNA: Brings amino acids to ribosomes during translation.
rRNA - Ribosomal RNA: With ribosomal proteins, makes up the
ribosomes, the organelles that translate the mRNA.
snRNA - Small nuclear RNA: With proteins, forms complexes that areused in RNA processing in eukaryotes. (Not found in prokaryotes.)
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Eukaryo t ic RNA po lymerases
polymerase location type of RNA transcribed
I nucleus/nucleolus rRNA (except for 5S rRNA)
II nucleus hnRNA (i.e. pre-mRNA)
III nucleussmall RNA such as tRNA and 5S
rRNA
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In eukaryotes there are five different RNA polymerases.
RNA polymerase Ihas become specialized for transcription of the
genes for the large ribosomal RNAs.
Eukaryotic cells need massive amounts of ribosomal RNA and they have
many copies of ribosomal RNA genes.
RNA polymerase IIis responsible for transcribing protein-encoding
genes to produce mRNA.
It has evolved some special features that allow it to be coupled to the
processing of mRNA precursors. Unlike bacteria mRNA, eukaryotic mRNA
is modified at the 5 and 3 ends and the mRNA precursor can be spliced.
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RNA polymerase II can transcribe RNA from nicked dsDNA templates
or from ssDNA templates. However, by itself, it cannot initiate
transcription at a promoter. In this respect, it resembles the core form of
bacterial RNA polymerase.
The eukaryotice enzymes also interact with a greater variety of
transcription factors. The RNAP II core enzyme is associating with
several transcription factors (TF) that are required for transcription
initiation.
RNA polymerase IIImakes transfer RNA (tRNA), small ribosoma RNA
(5S RNA) and most of the small RNAs that make up the fourth class of
RNA.
The 4th and 5th types of eukarytic RNA polymerases are the
mitochondrial and chloroplast versions.
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RNA po lymerase I prom oter region
The RNA polymerases promoters
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RNA polymerase III co re promoter
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