Gene Regulation in E.coli

	Positive Regulation	Negative Regulation
Function	Decisions about utilizing the best sources of C, N, electron donor, electron acceptor, etc.	Decisions about whether to synthesize something that might currently be available from the environment.
Regulatory protein	activator	repressor
Effectors: small signaling molecules	Inducer binds and activates the activator protein.	a. Co-repressors - some repressors may not function unless they are first bound to a small co-repressor molecule. b. Inducer - repression may be relieved when a small inducer binds and inactivates the repressor.
Relevant DNA sequences	Specific activator binding sites are recognized by activator proteins.	Specific operator sites are recognized by repressors.
Examples	a. The activator protein CAP (Catabolite Activator Protein) of E. coli interacts with the inducer cAMP. The protein subsequently binds CAP binding sites in DNA and stimulates transcription of downstream genes. This system is involved in the use of alternate carbon sources when the primary source, glucose, is in short supply. b. The activator protein virG of Agrobacterium tumefaciens is activated by phosphorylation in response to substances released from wounded plants, rather than being activated by the binding of an inducer. It subsequently directs the tryptophan and represses the transcription of genes encoding enzymes involved in tryptophan biosynthesis if glucose is not available.

modified from here.

Biological variation

Increase variability	Reduce variability
Epigenetic mechanisms Alternative splicing
Recombination
Add alleles	Reduce alleles
Horizontal Gene Transfer Endosymbiotic Gene Transfer
Natural selection	Natural selection
Gene flow	Genetic drift Bottleneck Founder effect
Mutation : Gene: substitutions, insertions and deletions (indels), re-arrangement: point-mutations (SNPs) or multiple bases Chromosome: translocation, inversion, deletion, duplication, non-disjunction

Regulatory Proteins Sequences

Gene regulation ensures that the genes of differentiated, somatic cell lines are normally repressed, and are only expressed when their products are required. Gene induction permits gene expression (derepression), and gene induction mechanisms ultimately involve molecules that bind to a DNA gene locus to induce gene expression. Some control of gene expression is tissue-specific and other control mechanisms are pleiotropic because they affect varied tissues.[a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z]. Defective RNAs are removed by nonsense-mediated decay and nonstop decay. Apoptosis is essential, programmed cell death. Sublethal stressors cause repression of housekeeping genes and activation of stress genes [t] that code for stress proteins and molecular chaperones. 'Heat shock response is an important homeostatic mechanism that enables cells to survive a variety of environmental stresses. These heat shock proteins function in multi-protein complexes as molecular chaperones and assist in the proper protein folding of stress damaged proteins, and stabilization of other cellular proteins [15-18]' [s]. Proto-oncogenes promote cell proliferation – these are genes coding for growth factors, transcription factors, and trans-membrane receptors for signal transduction by growth factors, and estrogens. Regulatory proteins bind to segments of DNA and bring about gene regulation. Most gene regulation proteins are single proteins, often homodimers or homotetramers, which bind to two ligands: a. a metabolic intermediate, and b. a cis-acting gene regulation element. Trans-acting factors are usually protein factors control gene expression by binding to cis-acting sequences, DNA sequences in the vicinity of the structural portion of a gene, which are required for gene expression. Regulatory proteins are targetted for early degradation at the proteasome by the ubiquitin-mediated protein degradation pathway. Regulation of metabolism is primarily determined by separation of enzymes and metabolites in separate compartments, by feedback control of activity (allosteric) or synthesis of inducible/repressible enzymes. Chemical cofactors are non-proteinaceous substances that assist enzymes in performing catalytic actions. Molecular genetic cofactors are activators or repressors.

trans-acting regulatory proteins

Protein	Function
activator	Regulates one or more genes by increasing the rate of transcription
autoinducers	Signaling molecules in bacterial quorum sensing that regulate mRNA production for specific genes in response to population density. Ex. homoserine lactones
catabolite gene activator protein (CAP)	Up-regulates gene expression by binding the polymerase at or near the DNA to be transcribed. Ex. cAMP dependent RNA polymerase
cofactor, coenzyme	Non-proteinaceous substances that assist enzymes in performing catalytic actions. In molecular genetics, cofactors are regulatory proteins (activators or repressors) that interact with transcription machinery, transducing regulatory information between core RNA polymerase machinery and gene-specific transcription factors. Organic, loosely bound cofactors are called coenzymes: Ex.: ATP, NAD+
prokaryotic operator	Operator proteins alter the activity (positively=activators, negatively=repressors) of RNA polymerase at a given promoter by affecting the ability of RNA-p to recognize start-sites. The operator region is adjacent to the promoter elements in most operons, and in most cases the sequences of the operator bind a repressor protein. However, E. coli possesses several operons that contain overlapping sequence elements, one that binds a repressor and one that binds an activator
repressor	Bind to the operator to permit proteins to bind on top of the promoter sequence, physically blocking promoters and preventing transcription. the repressor protein is removed, transcription may occur. Both repression and induction are examples of negative control since the repressor proteins turn off transcription. Within bacterial operons, regulator genes code for repressor proteins that bind to the operator, thus obstructing the promoters (transcription) of the structural genes.
transcription factors	Bind to DNA at specific promoter or enhancer or response element sequences or sites, at which they regulate transcription. General transcription factors (GTF's) are proteins that are important in the transcription of class II genes to mRNA templates. Ex.: basal TF, inducible TF, upstream TF

cis-acting sequences with distinct regulatory functions

Sequence	Function
enhancer	Exonic or intronic sequence that up-regulates transcription of genes within the regulated gene-cluster when bound by trans-acting transcription factors. The enhancer segment may be situated upstream or downstream of the enhanced gene, and its orientation is not fixed. ¨ ESE ¨ ISE
exon	Codes for a specific portion of the complete protein and is not spliced out from the transcribed precursor mRNA, so exits the nucleus as part of a messenger RNA molecule. For many genes, each exon contains part of the open reading frame (ORF) that codes for a specific portion of the complete protein.
insulator	DNA sequence (40 bp or more) located between the enhancer(s) and the promoter(s), or between the silencer(s) and the promoter(s) of adjacent genes or clusters of adjacent genes.
intron	DNA segments that lie between exons in the genome of eukaryotes. Some introns code for micro RNAs and represent a source of epigenetic coding; some posses translatable nucleotide sequences that, in the absence of splicing, can generate production of novel peptides (maturases) fused to the peptide encoded by the N-terminal exons, and others code for RNA products (Group I and Group II ribozymes capable of self-splicing), and are thus not "junk" DNA.
operon	Protein-encoding gene clusters in prokaryotic genes, which lack introns. RNA transcribed from prokaryotic operons is polycistronic – multiple proteins are encoded in a single transcript. Control of prokaryotic gene expression is brought about by control of the rate of transcriptional initiation by two DNA promoter sequence elements approximately 35 bases and 10 bases upstream of the site of transcriptional initiation that promote recognition of transcriptional start sites by RNA polymerase
pseudoexons	Located within intronic regions
response-elements	Recognition sites of certain transcription factors that coordinate the regulation of genes and ensure that different genes are expressed in a coordinated fashion or simultaneously. Short consensus sequences that are usually within 200 bp upstream of the transcription start site. For example, the cAMP response element (CRE) – sequence TGACGTCA – interacts with the transcription factor CREB (CRE-binding protein). Receptors for steroid hormones act as transcription factors for hormone response elements (HREs): ERE : GRE : HSE : SRE : TRE : T3RE
silencer	Control sections of exonic or intronic DNA that, like enhancers, may be located thousands of base pairs away from the gene whose transcription they suppress or downregulate. ¨ ESS ¨ ISS