Regulation of Bacterial Gene Activity
Within any cell, not all genes are active at the same time. Some gene products need to be continuously synthesized, whereas others are necessary only during certain phases of the life cycle or in particular environments. Even when genes are "turned on," the quantity of proteins they specify may need to be controlled. Therefore, the activity of virtually all genes needs to be regulated to make the most efficient use of the energy available to the cell. These mechanisms may act at one or more levels, such as at the level of the gene by controlling the timing and/or rate of transcription. Other control mechanisms may operate during or after translation.
The transcriptional activity of genes may be unregulated if their products are needed regardless of environmental conditions. Such products are said to be synthesized constitutively. The quantity of products from constitutively expressed genes can vary, however, depending upon the relative affinities of their promoters for RNA polymerase. Proteins that are required only under certain conditions, are usually governed by one or more regulatory proteins. Regulatory proteins usually do not have an enzymatic function, but instead interact with the DNA in or near the promoter of a gene to regulate transcription.
There are two basic types of regulatory proteins: repressors and activators. A repressor protein binds to a site called the operator within an operon. The attachment of a repressor protein to an operator prevents transcription of the structural genes in the same operon. A gene with this form of regulation is said to be under negative control. Proteins required for the expression of an operon are called activators. They may bind to initiator or activator sites that are located within an operon's promoter or, in the case of enhancer sites, they may bind at sequences far from the operon. When the binding of a regulatory protein to an initiator or enhancer site stimulates transcription of structural genes in the operon, a positive control mechanism is said to be at work.
The stimuli to which regulated genes respond may vary from relatively small molecules (e.g., sugars, amino acids) to relatively large substances (e.g., in eukaryotes, a complex of a steroid hormone and its protein receptor). A substance that turns on gene transcription is referred to as an inducer, whereas a substance that turns transcription off is said to be a corepressor. Inducible genes are usually involved in catabolic (degradative) reactions, as in the breakdown of a polysaccharide into simple sugars. Repressible genes are usually involved in anabolic (synthetic) reactions, as in the construction of amino acids from simpler precursors. Thus, there are two main types of transcriptional controls: (1) negative and (2) positive. Negative control can either be inducible or repressible and positive control is known only to be inducible. In addition, genes may be regulated by global controls or by posttranslational mechanisms discussed in sections 4 and 5 in the following text.
Negative, Inducible Control
The classic example of negative control by way of an inducible operon is the lactose operon of E. coli. β-galactosidase is an enzyme with dual functions. Its primary function is to catabolize lactose to glucose and galactose. Its secondary function is to convert the 1-4 linkage of glucose and galactose (in lactose) to a 1-5 linkage in allolactose. This enzyme is not normally present in high concentrations when lactose is absent from the cell's environment. Shortly after adding lactose to a medium in which glucose is absent, the enzyme begins to be produced. A transport protein called galactoside permease is required for the efficient transport of lactose across the cell membrane. This protein also appears in high concentration after lactose becomes available in the medium. The wild-type lactose operon (Fig. 10-11) consists of a regulatory gene (lacI) and an operon containing a promoter sequence (lacP), an operator locus (lacO), and three structural genes for β-galactosidase (lacZ), permease (lacY), and transacetylase (lacA; an enzyme whose function in lactose metabolism remains unresolved).
Mutations at each of these loci have been found allowing for detailed understanding of the functions of each of these genes.
Promoter Alleles
p + = wild-type promoter; normal affinity for RNA polymerase
p – = mutant promoter cannot bind RNA polymerase; none of the structural genes in the lactose operon are transcribed
p s = increased affinity for recognition by RNA polymerase; elevates the transcriptional level of the operon; s = "super promoter".
p i cr = affects the CRP-cAMP binding site to reduce the level of expression of lactose operon genes below 10% of wild type; i cr = insensitive to catabolite repression
Operator Alleles
O + = in the absence of repressor, this operator "turns on" the structural genes in its own operon; i.e., the lacZ+ and lacY+ alleles in the same segment of DNA (cis position) can produce proteins; this operator is sensitive to the repressor; i.e., repressor will "turn off" the synthetic activity of the structural genes in the lactose operon
O c = a constitutive operator that is insensitive to repressor and permanently "turns on" the structural genes in the lactose operon
Galactosidase Alleles
Z + = makes β-galactosidase if its operon is "turned on" or "open"
Z – = a missense mutation that makes a modified, enzymatically inactive product called lacCZ protein
Z –ns = results in the destruction of the polycistronic message down stream from the mutation so that there is no expression of any of the downstream lactose operon genes (a polar mutation); ns = nonsense
Permease Alleles
Y + = makes β-galactoside permease if its operon is "turned on"
Y – = no detectable permease is formed regardless of the state of the operator; probably a nonsense mutation
Regulator Alleles
I + = makes a diffusible repressor protein that inhibits synthetic activity in any o+ operon in the absence of lactose; in the presence of lactose, repressor is inactivated
I – = a defective regulator that is unable to produce active repressor due to a nonsense or missense mutation
I s = makes a "super repressor" that is insensitive to lactose and inactivates any O+ operon
There is some overlap in the promoter and operator sites of the lac system; in some other operons the operator locus may be totally embedded in the promoter. The regulatory gene constitutively produces a repressor protein at low levels because it has an inefficient promoter. Its synthesis is unaffected by the level of lactose in the cell. The normal promoter of the lac operon, by contrast, binds RNA polymerase very efficiently. In the absence of lactose (noninduced conditions), an active repressor protein (produced by lacI) binds to the operator. RNA polymerase can neither bind to the promoter nor "read through" the operator sequence because repressor protein occupies that region. Hence, transcription of all three structural genes in the lac operon is prevented.
When lactose is present (induced conditions), it is transported inefficiently into the cell because only a few molecules of permease would normally be present. Inside the cell, some of the lactose would be converted to allolactose by β-galactosidase. Allolactose is the inducer of the lac operon. It binds to the repressor protein and causes a conformational change in the protein that alters the site by which it binds to the operator. This conformational change in a protein as a consequence of binding to another molecule is called an allosteric transformation. The allolactose-repressor complex can no longer bind to the operator, and it falls off the DNA. RNA polymerase can now read through the operator to transcribe the structural genes in the operon. The increased amount of permease now transports lactose across the membrane in large quantities, and the sugar is then digested by β-galactosidase. When lactose becomes depleted from the medium, newly synthesized repressor proteins will not be coupled with allolactose, so they can bind to the operator and shut off transcription of the structural genes in the operon. Furthermore, allolactose can reversibly bind to repressor protein, so that under low levels of lactose in the cell allolactose would tend to dissociate from repressor-allolactose complexes. Even when the lac operon is repressed, occasionally the repressor protein will diffuse from the operator momentarily. RNA polymerase may then be able to "sneak" past the open operator and synthesize a molecule of polycistronic mRNA, thus accounting for the very low levels of permease and β-galactosidase that are normally present in the cell. Bacterial mRNA molecules have a very short half-life (only a few minutes), so synthesis of proteins stops very soon after a cell is repressed. Proteins, on the other hand, are much more stable, but they would be diluted out with each subsequent cell division.
EXAMPLE 10.8 Bacteria of genotype I+ O+ Z+ Y+ grown on media devoid of lactose will produce neither galactosidase nor permease because I+ makes repressor substance that inactivates the O+ operator and "turns off " the synthetic activity of structural genes Y+ and Z+in its own operon.
EXAMPLE 10.9 Partial diploids can be produced in bacteria for this region of the chromosome. Cells of the genotype I– O+ Z+ Y– / I+ Oc Z–Y+ will produce the lacCZ protein constitutively (i.e., either with or without the presence of lactose inducer) because the allele Oc permanently "turns on" the genes in its operon (i.e., those in cis position with Oc). β-Galactosidase will be produced only inductively because in the presence of lactose (inducer), the diffusible repressor substance from lacI+ will be inactivated and allow the structural gene lacZ+ in cis position with the operator O+ to produce enzyme.
The wild-type operon of the regulatory gene (lacI) in the lactose system consists of just a promoter (pi) and the structural gene for the repressor protein (I+). Its wild-type promoter is very inefficient, and only a few molecules of lac-repressor protein exist in the cell. In the operons of most regulatory genes in other systems, however, an operator locus is adjacent to its promoter, and autoregulation is possible. The repressor proteins made by these operons bind to their own operators to terminate transcription when the concentrations of their respective repressor molecules are elevated.
Negative, Repressible Control
An example of a repressible operon under negative control is the tryptophan system of E. coli (Fig. 10-12).
The amino acid tryptophan is synthesized in five steps, each step mediated by a specific enzyme. The genes responsible for these five enzymes are arranged in the trp operon in the same order as their enzymatic protein products function in the biosynthetic pathway. The regulatory gene for this system constitutively synthesizes a nonfunctional protein called aporepressor. When tryptophan is in oversupply, the excess tryptophan acts as a corepressor by binding to the aporepressor forming a functional repressor complex. The functional repressor binds to the trp operator and coordinately represses transcription of all five structural genes in the operon. The promoter and operator regions overlap significantly, and binding of active repressor and RNA polymerase are thus competitive. When tryptophan is in lowconcentration, tryptophan dissociates from the aporepressor, and the aporepressor protein falls off the operator. RNA polymerase then synthesizes the polycistronic mRNA for all five enzymes of the tryptophan pathway.
A secondary regulatory mechanism also exists in the tryptophan operon. At the 50 end of the polycistronic mRNA of this operon a 162 base pair leader sequence precedes the coding segments for the five enzymes. There are two adjacent tryptophan codons in the leader peptide. When tryptophan is present in excess, transcription of the rest of the trp operon is prevented because RNA polymerase generates a transcription termination sequence; this phenomenon is known as attenuation. A model (Fig. 10-13) that explains attenuation assumes that (when tryptophan is abundant) movement of bacterial ribosomes follows closely behind the movement of RNA polymerase as it synthesizes mRNA, and all intra molecular base pairing is prevented in the mRNA segment in contact with the ribosome. In the experimental absence of ribosomes, only the leader mRNA is transcribed and no translation occurs [Fig. 10-13(a)]. Leader segments 1 and 2 become folded into stem and loop A by complementary base pairing, whereas segments 3 and 4 fold into stem and loop C that acts as a transcription termination signal. As RNA polymerase synthesizes the seven uracils that follow segment 4, these uracils and the adjacent paired 3-4 region of mRNA (having just folded into stem and loop C) form a terminator signal that causes RNA polymerase to prematurely dissociate from the DNA before it can transcribe any of the DNA coding segments for the five enzymes of the trp operon.
When only the concentration of activated trp-tRNAs is low[Fig. 10-13(b)] ribosomes begin to translate region 1, thereby preventing pairing of regions 1 and 2. However, the ribosome tends to stall momentarily (especially at the pair of tryptophan codons), allowing pairing of regions 2 and 3 to forma B stem-and-loop structure (called an antiterminator); regions 3 and 4 are thereby prevented from forming the C termination signal, and RNA polymerase is allowed to continue transcription on into the trp operon.
If activated trp-tRNAs are abundant [Fig. 10-13(c)], ribosomes follow so closely behind RNA polymerase that the anti-terminator B structure cannot form, and therefore the terminator C structure does form. Thus, only the leader peptide (but none of the five enzymes of the operon) can be translated from the prematurely terminated mRNA.
The repressor mechanism coarsely regulates the tryptophan system, whereas the attenuation mechanism fine tunes the control over tryptophan concentrations. Attenuation of the trp operon is also sensitive to the concentrations of several amino acids other than tryptophan. Operons for the amino acids histidine and leucine, however, are thought to be regulated only by attenuation.
Positive, Inducible Control
An example of a positive, inducible regulatory mechanism is found in the arabinose operon of E. coli. Arabinose is a sugar that requires three enzymes (coded by genes araB, araA, araD) for its metabolism. Two additional genes are needed to transport arabinose across the cell membrane, but they are located at a distance from the BAD cluster coding for the catabolic enzymes. The regulatory gene araC is close to the promoter for the BAD cluster. The protein product of the araC gene (AraC) is a repressor of the BAD cluster when the substrate arabinose is absent. However, when arabinose is present, it binds to the repressor (AraC), forming an activator complex that facilitates the binding ofRNApolymerase to the promoter, thus inducing transcription of the operon. The preceding story is a gross oversimplification of the complexity that is already known about the regulation of the arabinose system. For example, cyclic adenosine monophosphate (cAMP) and catabolite activator protein (CAP; also known as cyclic AMP receptor protein, CRP) are also involved in the regulation of the arabinose system. The action of these last two molecules in the phenomenon of catabolite repression is discussed in the next section.
Global Regulation or Multiple Controls
A genetic locus may be regulated by more than one mechanism. When glucose is available, there is no need to catabolize other sugars, and the genes coding for these other sugar-catabolizing enzymes can be turned off. For example, if glucose is absent and lactose is present in the medium, the lac operon would be induced. But if glucose is present, induction of the lac operon does not occur. This phenomenon was originally termed the glucose effect; it is now known as catabolite repression. A complex of two molecules, namely, cAMP and CAP, acts as the activator in catabolite repression.Within the lac promoter (Fig. 10-11), there is a site for binding of a cAMP-CAPcomplex.RNA polymerase only binds effectively to the promoter if cAMP-CAP complex is also bound to this site. As the level of glucose increases within the cell, the amount of cAMP decreases and less cAMP-CAP complex is available to activate the lac operon. CAP is produced at low levels by its own genetic locus. The enzyme adenylate cyclase (adenylcyclase) converts adenosine triphosphate (ATP) to cyclic adenosine monophosphate (cAMP). Adenylate cyclase can become activated to first messenger status by the interaction of specific cell receptors with their target molecules; the cAMP thus produced (second messenger) can then regulate a battery of genes coordinately.
Posttranslation Control
The expression of genes can be regulated after proteins have been synthesized (posttranslation control). Feedback inhibition (or end-product inhibition) is a regulatory mechanism involving inhibition of enzymatic activity. The end product of a synthetic pathway (usually a small molecule such as an amino acid) may combine loosely (if in high concentration) with the first enzyme in the pathway. This union does not occur at the catalytic site of the enzyme, but it does modify the tertiary or quaternary structures of the enzyme and hence inactivates the catalytic site. This allosteric transformation of the enzyme blocks its catalytic activity and prevents overproduction of the end product of the pathway and its intermediate metabolites.
EXAMPLE 10.10 The end product isoleucine in E. coli, when present in high concentration, unites with the first enzyme in its synthetic pathway and thus inhibits the entire pathway until isoleucine returns to normal levels through cellular consumption. Intermediates in the biosynthetic pathway are in numbered boxes; e = enzyme; g = gene.
Practice problems for these concepts can be found at:
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