Lecture 13: Regulation of Gene Expression Pt. 2: MICR 321

MICR 321: Advanced Microbiology Lecture 13: Chapter 11: Regulation of Gene Expression: Genes & Operons Types of Regulation Negative regulation - genes in an operon are constitutively expressed unless they are turned off by a repressor protein Positive regulation –...

MICR 321: Advanced Microbiology Lecture 13: Chapter 11: Regulation of Gene Expression: Genes & Operons Types of Regulation Negative regulation - genes in an operon are constitutively expressed unless they are turned off by a repressor protein Positive regulation – genes in an operon are not expressed unless they are turned on by an activator protein Regulation can be inducible, repressible, or both Inducers – increases gene expression activate an activator OR inactivate a repressor Co-repressor – decreases gene expression activate a repressor OR inactivate an activator Apo- v. holo-protein  Negative regulation negative inducible system negative repressible system Positive regulation positive inducible system Regulation of Gene Expression Cells express only the genes they need in a particular environment. Why? Expression of genes can occur at different levels Transcriptional regulation Posttranscriptional regulation Translational regulation Posttranslational regulation Riboswitches Riboswitch: RNA element in mRNA leaders that can sense metabolites RNA folds into 3D structure that allows ligand to bind Ligand binding leads to conformational change: – Change can lead to terminator/anti-terminator alterations – Change can change access to ribosomal binding site  Fig 11.24 T Box Mechanism: tRNA Sensing First discovered for gene expression of aminoacyl-tRNA synthetases in B. subtilis tRNA without attached amino acid leads to increased expression – Unpaired regions in leader allow for RNA base-pairing – Anti-terminator forms tRNA with attached amino acid leads to decreased expression – Terminator forms  Fig 11.25 Metabolite-binding Riboswitches Small molecules can bind directly to leader RNA Typically involved in same metabolic pathway Has been found for many types of molecules (atoms): – Some amino acids (lysine) – Some vitamins (B12) – Some nucleic acid bases (guanine) – Some cofactors (SAM) – Some metal ions (Mg) Can be through transcription attenuation or blocking the transcription initiation region  Fig 11.26 Regulation of mRNA Degradation mRNA template is required for translation Half-life: the time it takes for the amount of a particular template to be reduced by 50% of the starting amount Some transcripts last 1-5 minutes Increased half-life → increased protein production RNase E targets its own RNA Low RNase E increases message High RNase E binds transcript and triggers degradation of mRNA Ex. Autogenous regulation  Sass et al, 2017. Sci Rep Wagner et al, 2015. Adv Gen Regulation by sRNAs sRNA – small RNAs Non-protein coding RNA Involved in posttranscriptional regulation Individual bacteria may encode hundreds of sRNAs Can be encoded in intergenic regions or antisense and form secondary stem loop structures. Have been implicated in the regulation of physiology, metabolism, and virulence. Mechanisms of sRNA-interactions  Fig 11.27 Regulation of translation Initiation of translation is relatively sensitive to mRNA structure Elongation is not as sensitive Proteins and sRNAs can bind mRNA and block translation initiation regions Both prevent 30s binding and initiation Similar mechanism can lead to activation of translation Ex: bound protein or sRNA can disrupt secondary structure and expose the ribosomal binding site Thermosensor RNA thermometer Potential role for virulence?  Cook, Univ. Binghamton Posttranslational Regulation Are all polypeptides active proteins? Proteins may need to be modified for activity Common modifications include: – Phosphorylation – Methylation – Acetylation Phosphorylation is a common signal involved in transduction systems Two-component systems Posttranslational Regulation: Feedback Inhibition End products of a pathway bind to the first enzyme in the pathway to inhibit its activity Common for biosynthetic pathways More sensitive and faster for modulating the amount of end product Ex. trp operon A few important questions… 1. Why would an organism want so much regulation? 2. Why occur at different levels? 3. Why make an mRNA if you’re not going to translate it? 4. Why sRNAs instead of repressors/activators? MICR 321: Advanced Microbiology Chapter 12: Global Regulation: Regulons & Stimulons Global Regulatory Mechanisms Bacteria must be able to adapt quickly to a wide variety of conditions Nutrient availability Moisture/desiccation Temperature Global regulatory mechanisms – allow for simultaneous regulation of numerous operons to respond to environmental changes Regulon – several distinct operons controlled by a single regulatory protein. TrpR regulon – includes all the genes in the trp operon including trpR itself LexA regulon – the SOS genes induced after DNA damage AdcR regulon – zinc homeostasis system, controls import and efflux Almost all genes are part of some regulon and regulons often overlap Stimulon – a collection of all regulons that respond to the same environmental condition  Fig 12.1 Catabolite-sensitive operons Catabolites – smaller molecules resulting from the breakdown of larger molecules Energy is expended for production of enzymes involved in catabolism of carbon sources Catabolite repression – mechanism for ensuring cells preferentially use the best energy source These operons are often called catabolite sensitive glucose effect: as glucose gives most ATP and represses operons required for utilization of other carbon sources What type of growth curve is this? Stress Responses in Bacteria Many bacterial global regulons are designed to quickly cope with stress. Osmolarity, pH, temperature, metal availability, nutrient access Must be flexible to respond to more than one stress at a time → thus the overlap of global regulons E. coli Heat Shock Response 30 unique heat shock proteins (Hsps) increase after temperature increase and then slowly decline Involved in normal growth Protein folding (especially denatured proteins) Protein degradation for damaged proteins DnaK – cellular thermometer Normally binds to new proteins and helps them to fold but under heat shock conditions it binds to denatured proteins helping them to refold  Box 12.3 Signal Transduction Systems (STS) in Bacteria Some gene regulation requires that bacteria “sense” the external environment and regulate expression accordingly Sensor proteins & response proteins Two-component STS histidine kinase – sits in the membrane, senses external environment, and autophosphorylates itself response regulator – intracellular protein that transfers the phosphate to itself and performs regulatory function