Global gene regulation and expression in bacteria

Bacterial gene

• 1000 bases

• Absence of introns

• 95% of the sequence codes for proteins

• Grouped in operons

Operons

Segment of DNA containing genes that operate under the signal of the same promoter. One mRNA → several proteins

SIgma factors

1. Interact with an RNA polymerase (RNAP) core enzyme to forme the RNAP holoenzyme and direct the complex to promoter regions

2. Facilitates the opening of the double strand DNA

3. Start of the transcription

4. Dissociation and release of the sigma factor

Initiation

Plasmid recognition

Elongation

Addition of nucleotides to the new DNA strand

Termination

• Transcript sequences that encode and RNA hairpin and terminal uridine-rich segment

• Termination by Rho enzyme (ATP dependent RNA translocase) → releases RNA by forcing uncharacterized structural changes in elongation complex

• Activity of DNA translocase Mfd and ATP

Constitutive genes

Genes continuously expressed in the cell

Regulated genes

Only expressed under certain physiological conditions or in response to stimuli

Regulation by alternative sigma factors

Activation of transcription genes under stress conditions

• Recruit core enzyme after binding to specific sequences different than the sigma factor (sigH)

Regulation by transcription factors

Proteins that bind to the DNA in cis of the promoter or to the polymerase

Regulators Helice-Turn-Helice (HTH)

• Bind to DNA via alpha helices

• 2 segments of 20 amino acids separated by 4 residues

• In dimers

Regulators ribbon helice helice (RHH)

• Antiparallel β-strands (ribbons) framed within an α helical scaffold

• Use the anti-parallel β-sheet to recognize specific nucleotide sequences and α-helices to anchor the β-sheet in the DNA major groove

Positive regulation

Direct contact with the C-terminal domain of the α subunit

Negative regulation

• Repression by steric encumbrance

• Repression by a loop in DNA

Lactose operon

The lactose operon is a set of genes in bacteria responsible for the uptake and metabolism of lactose. It consists of structural genes like lacZ, lacY, and lacA, which encode specific proteins involved in lactose utilization

Riboswitch regulations

Regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. No regulatory protein is needed to mediate the interaction

Regulations by Hfq proteins

• Hfq is an RNA-binding protein

• Facilitates the short and imperfect base-pairing interactions of regulatory small RNAs (sRNAs) with trans-encoded target mRNAs

• Permit or suppress the protein synthesis

Post-translational regulations

Control the activity, the localisation, the stability and the function of proteins after their synthesis

• Proteolytic cleavage: inactive precursors that must be cleaved to be active

• Adding a chemical group: phosphorylation, acetylation, methylation

• Formation of a disulfide bridge

Transcription factors in two-component systems

Used to perceive and adapt to environmental changes (osmolarity, chemotaxis, nutritional deficiency, antibiotic resistance, and virulence)

1. Histidine kinase: sensor, responsible for detecting external stimuli and activate by phosphorylation HTH

2. Regulatory response protein (HTH), which binds to the promoter regions of target genes to induce their expression