EFB325 Cell Physiology

Regulation of gene expression

Cells do not express all of the genes in the genome all of the time

There are some fundamental reasons why a cell does not express all of the genes in its genome all of the time. Gene expression is the process of producing the final, active product of a particular gene-it may be a protein or an RNA (like rRNA or tRNA).

• gene expression to produce protein uses a lot of energy-cells (and organisms) will best survive if they make most efficient use of energy
• some genes are involved in the process of cell differentiation and organism development-those gene products are functional only at a particular point in the developmental process
• some genes are involved in responding to special circumstances or signals-those gene products are needed only in those special situations
• in a multicellular organism, different cells perform different functions, they use different sets of proteins-yet nearly all cells contain a complete copy of the genome-only a fraction of the genes are used by any particular cell type

Some genes are active nearly all the time=constitutive expression

• some gene products are needed by nearly all cells, at almost every stage of development, no matter what the situation; so those genes are always active=housekeeping genes
• for example: the genes for the enzymes of glycolysis and other basic metabolism, proteins of the cytoskeleton and chromosomes, proteins of the ER, Golgi, nuclear envelope

The expression of many genes is regulated

they may be active in coordination with or in response to:

• stage of development
• cellular differentiation
• environmental signal (light, temperature, gravity)
• nutritional/chemical environment (sugar, amino acid, hormone signal)
• time of day (circadian clock)
• cell cycle

Production of the active gene product can be regulated at many different stages of expression

The best form of gene regulation is a system that is rapidly turned on when that function is needed and turned off when it is no longer needed

1) changes to the chromosome (generally not reversible)

• gene amplification: some cells undergo chromosome replication without cell division, which results in exponential increases in gene copy number and much higher levels of gene expression; example: amphibian oocytes require many ribosomes, so the regions of the chromosomes containing the rRNA genes are amplified to allow greater synthesis of rRNA
• DNA rearrangement: there are examples of rearrangement of genes in a chromosome to change the position of the coding region of a gene next to a promoter; involves breakage and re-connection of the strands of DNA
• DNA methylation: a methyl group can be added to C (cytosine) bases in DNA, which does not affect their base-pairing properties, but does result in lower levels of transcription in that region; there are enzymes to add or to remove the methyl groups; the methylation of a C can be transmitted to progeny: the daughter chromosomes will have the original strand methylated, which is recognized by an enzyme that methylates a C on the new strand

2) initiation of transcription

• chromatin packing: the region to be transcribed must undergo decondensation to allow the transcription factors and RNA polymerase to bind to the promoter; this includes disruption of the binding of DNA to the histones in the nucleosomes
• binding of RNA polymerase to the promoter and initiation (a major point of regulation, discussed in detail below)

3) RNA processing=splicing & translocation to cytoplasm (a modulation step)

• alternative splicing: splicing in/out different combinations of introns can lead to the synthesis of slightly different proteins from a single gene

4) RNA turnover=stability of RNA (effective method of turning off expression)

• once an mRNA is synthesized, it can be translated until it is degraded
• the length of the poly(A) tail can determine how long a mRNA lasts

5) initiation and rate of translation

6) trafficking to proper cellular compartment

7) protein activation (by folding, cleavage, modification, assembly of polypeptides)

• regulation of enzyme activity

8) protein turnover=protein stability (another way of turning a function off)

• protein degradation by proteases

Initiation of transcription is a major point of gene regulation

• the rate at which transcription is initiated varies dramatically among different genes and can be regulated by the cell

Regulation of transcription in prokaryotes

For the most part, there is little or no differentiation of different cell types for a particular prokaryote (although some bacteria produce spores or other cysts). Also, conservation of energy/resources can be particularly important for a bacterial cell in terms of competitive ability. Therefore, in bacteria genes are regulated to allow most efficient use of available resources for growth and survival.

• in prokaryotes, enzymes that work in a single physiological function and thus need to be produced simultaneously and in equal proportions are arranged in an operon
• in an operon, multiple genes (coding for protein) are transcribed together as a single mRNA; thus transcription of more than one gene is regulated by a single promoter

Promoters

• the RNA polymerase can bind to the promoter and initiate transcription by itself, although different promoters have stronger or weaker affinity for binding RNA polymerase=strong or weak promoters
• binding of the RNA polymerase can be prevented or assisted by other regulatory proteins which bind to a region of DNA with a particular DNA sequence, adjacent to or within the promoter
• the ability of these regulatory proteins to bind to the DNA is often dependent upon whether they are bound or not to some other molecule, which is called an effector
• regulatory proteins may control the transcription of more than one promoter, thus serving in the broad control of several different functions in the cell simultaneously

for example:

• the lac operon of E. coli includes genes for enzymes involved in the utilization of lactose
• when E. coli has glucose (its preferred sugar) available and no lactose, a repressor protein binds to a region of the DNA (called the operator) overlapping the promoter and prevents binding of RNA polymerase; therefore these enzymes are not synthesized in the absence of lactose
• when lactose is present, lactose binds to the repressor protein, causing it to release from the operator (lactose is the effector molecule); now the RNA polymerase can bind to the promoter and the genes for lactose utilization are expressed

example 2:

• transcription of a weak promoter can be increased by an activator protein
• activator proteins help the binding of the RNA polymerase to the promoter

Specificity of the RNA polymerase for different promoters can be switched by changing the sigma factor protein present in the cell

• since the sigma factor subunit of RNA polymerase is responsible for recognizing the promoter in prokaryotes, by switching expression of one sigma factor for another, broad changes in the types of genes transcribed can occur

for example:

• a new type of sigma factor is produced when cells experience heat shock, which causes the transcription of the "normal" set of genes to stop, and a different set of genes are now transcribed (to produce the heat shock proteins)
• when Bacillus cells are triggered to develop into spores, a new sigma factor is produced that is specific for the sporulation genes

In prokaryotes, translation of an mRNA is simultaneous with transcription producing that mRNA

• as the mRNA is released from the RNA polymerase, it can immediately be translated as soon as ribosomes bind
• in some cases, the activity of translation by the ribosomes can affect the process of transcription=attentuation
• for example: in some genes, if the ribosomes stall during translation, this has an effect on the activity of RNA polymerase performing transcription (usually occurs in genes related to amino acid biosynthesis)

Regulation of transcription in eukaryotes

Regulation in eukaryotes in much more complex and allows for many more points of regulation.

• there are three types of RNA polymerase, which utilize different types of promoters
• each gene (for protein) is transcribed separately (one transcript=one gene); so transcription of every gene is regulated by its own promoter
• transcription is independent of translation (no attenuation in eukaryotes)
• RNA polymerase requires other proteins (transcription factors) in order to bind to the promoter and initiate transcription

Initiation of transcription can be activated or repressed by protein factors binding to DNA

in eukaryotes, RNA polymerase requires transcription factors to bind to the promoter and initiate transcription

• in eukaryotes, regulatory proteins can bind to regions of DNA distant from the startpoint of transcription (as many as thousands of base-pairs away); this allows for the combination of many different regulatory factors in controlling transcription of a single gene
• regulatory DNA sequences within 100 bases of the core promoter are called proximal control elements, and the transcription factor proteins that bind to these regions of DNA probably interact locally with the basal transcription complex
• regulatory DNA sequences much farther away (thousands of base-pairs) can also activate or repress transcription upon the binding of transcription factor proteins to those regions of DNA: DNA elements that bind activator proteins are called enhancers, DNA elements that bind repressor proteins are called silencers
• these regulatory elements can act over long distance of DNA, because they loop back and interact with the core promoter elements
• transcription factor proteins usually have two functional domains: one for binding to the control element in the DNA and the other (the activation domain) for interaction with other transcription factors or the RNA polymerase

Regulation of transcription by multiple types of regulatory proteins allows for complexity and specificity

• one regulatory protein can regulate a number of different genes, as long as they have the control elements in the DNA adjacent to the promoter to which the regulatory protein will bind
• a regulatory protein can be present in a certain tissue type, another is present under hormone stimulation, another is present only at a certain developmental stage allowing a combinatorial system of gene regulation
• in most cases, we don't know what it is that turns on expression of the genes, which encode the transcription factors

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