Regulation of Gene Expression

1. Regulation of Gene Expression

3. Regulatory factors 1) Gene copy number 2) Transcriptional control 2-1) Promoters 2-2) Terminators, attenuators and anti-terminators 2-3) Induction and repression : regulatory protein 2-4) Attenuation: trp operon 2-5) Two- component regulatory systems 2-6) Global regulatory systems 2-7) Feast or famine and the RpoS regulon 2-8) Quorum sensing 3) Translational control 3-1) Ribosome binding 3-2) Codon usage 3-3) Stringent response 3-4) Regulatory RNA 3-5) Phase variation

4. Gene copy number Most genes on the bacterial chromosome are present as single copies (with a few notable exceptions such as the genes for ribosomal RNA); therefore , gene copy number is not an important method of control for most of the normal metabolic activities of a bacterial cell. It does become important however when we consider plasmid-mediated characteristics, particularly with reference to the cloning and expression of heterologous DNA. Some plasmids are present within the cell in very high numbers, running into thousands of copies and this is reflected in the enhanced level of expression of the genes they carry.

5. 1) promoters

6. The principal method of control of gene expression in bacteria is by regulating the amount of mRNA produced from that gene. • The nucleotide sequences of promoters vary considerably, affecting the binding affinity of RNA polymerases and thus the frequency of transcription initiation. • Amount of mRNA is determined by the affinity of RNA polymerase for the promoter. • Mutations that result in a shift away from the consensus sequence usually decrease promoter function; conversely, mutations toward consensus usually enhance promoter function. • Promoters can be divided to two classes: • Strong promoter • Weak promoter

8. Transcription initiation is regulated by proteins that bind to or near promoters. three types of proteins regulate transcription initiation by RNA polymerase: • Specificity factors alter the specificity of RNA polymerase for a given promoter or set of promoters. • Repressors impede access of RNA polymerase to the promoter. • Activators enhance the RNA polymerase-promoter interaction.

9. Operon • The gene cluster and promoter , plus additional sequences that function together in regulation, are called an Operon. • Operon that include two to six gene transcribed as a unit are common; some operon contain 20 or more genes. • The genes in the operon are coordinately regulated. • In E. coli for example, there are 4289 genes in the genome but , many of these are organized into 578 known operons.

10. Lac operon

13. Regulon • A network of operons with a common regulator is called regulon. • Definition: A set of genes or operons, expressed from separate promoter sites but controlled by the same regulatory molecule is called a regulon.

14. Alternative promoters and ơ-factors • ơ-factor allows the polymerase to recognize specifically the two conserved nucleotide motifs in the promoter region. • Most bacterial species have several different ơ-factors.

17. Anti- ơ-factors • Proteins that bind to a specific ơ-factor and prevent it interacting with the core RNA polymerase. • Anti-ơ-factors also provide an additional layer of transcriptional regulation. • For example: flagella-specific ơ-factor ơ 28

19. Terminators, attenuators and anti terminators • Transcriptional termination can play a role in adjusting the level of expression of different genes within an operon. • . E coli, has at least two classes of termination signals: • one class relies on a protein factor called ρ (rho) • ρ-independent

20. Most p-independent terminators have two distinguishing features: • The first is a region that produces an RNA transcript with self complementary sequences permitting the formation of a hairpin structure centered 15 to 20 nucleotides before the projected end of the RNA strand. • The second feature is a highly conserved string of three A residues in the template strand that are transcribed into U residues near the 3' end of the hairpin.

21. The p-dependent terminators lack the sequence of repeated A residues in the template strand but usually include a CA-rich sequence called a rut (rho utilization) element. The ρ protein associates with the RNA at specific binding sites and migrates in the 5‘->3' direction until it reaches the transcription complex that is paused at a termination site. Here it contributes to release of the RNA transcript The ρ protein has an ATP-dependent RNA-DNA helicases activity that promotes translocation of the protein along the RNA, and ATP is hydrolyzed by p protein during the termination process.

23. Induction and repression: regulatory proteins • Gene products that increase in concentration under particular molecular circumstances are referred to as inducible; the process of increasing their expression is induction. • Gene products that decrease in concentration in response to a molecular signal are referred to as repressible, and the process is called repression.

24. The binding of the repressor protein to the operator prevents the initiation of transcription. • This repressor protein is produced by a separate gene (lac I ) that is not part of the lac operon. • Binding of the repressor to the operator prevents the RNA polymerase from obtaining access to the promoter or from initiating transcription.