First Semester - 18 points
The bacterial nucleoid and its influence on gene expression. Molecular mechanisms by which bacteria adapt to environmental change. Regulation of gene expression by proteins and small RNAs. Riboswitches. Bacterial RNA maturation.
MICR335 provides fundamental knowledge of gene regulation in bacteria through analysis of the physiological adaptations of bacteria to their environment and the underlying genetic regulatory mechanisms. Throughout the course, general principles are emphasized and their application illustrated through the use of topical examples. Course readings are selected chapters from advanced texts, and reviews and original papers from the literature. PDFs of these will be placed on Blackboard when available.
Section A: General overview of genetic regulatory mechanisms (Lectures 1-9, Professor Clive Ronson)
1. The E. coli chromosome: physical and genetic structure; role of DNA supercoiling and chromosome-organising proteins. H-NS and FIS as transcriptional regulators.
2. Organisation and structure of regulatory elements; transcriptional versus translational control; promoter structure; RNA polymerase; Sigma factors; mechanism of transcriptional initiation; how regulatory proteins may affect transcriptional initiation.
3. Regulation via Sigma factors – motility and heat shock.
4. ppGpp and the stringent response
5. Regulation by extracellular stimuli; overview of two-component regulatory systems; critical control points; the Dct system.
Section B: Global regulation of respiration and molecular responses to oxidative stress (Lectures 10-16, Professor Greg Cook, Dr Matt McNeill and Dr Rachel Darnell)
6. Sensing the absence of oxygen using ArcBA and Fnr.
7. Anaerobic respiration: hierarchal control of electron acceptor utilisation in E. coli.
8. Response to oxidative stress: Oxygen, friend or foe?
Section C: Regulatory RNAs and CRISPR-Cas (Lectures 17-22, Associate Professor Peter Fineran)
9. Gene regulation by regulatory RNAs and riboswitches
10. Small RNA-mediated CRISPR-Cas adaptive immunity
Section D: Gene regulation by toxin-antitoxin modules and stationary phase adaptation (Lectures 23-16, Dr Jennifer Robson)
11. The regulation and role of bacterial TA systems: Molecular switches that lead to persistence.
12. Stationary phase adaptation - regulation at all levels
The objectives of the lab course are to provide hands-on experience with many of the skills and techniques that are used in a microbial genetics laboratory, and to develop skills in scientific record-keeping and reporting. The lab course is in the form of a research project that runs for two periods per week for four weeks, for a nominal total of 36 hours, but small amounts of work will also be required on additional days. The opportunity is provided for you to learn from your mistakes and repeat steps as required. You are required to maintain careful laboratory records and to write your experiment up in the form of a short scientific paper for assessment.
1. Weekly Laboratory Quizzes: 10%
2. Written Laboratory Report: 20%
3. A written three-hour final examination comprising four either/or essay questions: 70%
To pass the paper, you must achieve a minimum of 50% overall.
One of MICR 221, GENE 221
There is no recommended text for MICR 335 but you will be directed to and discuss relevant scientific papers during lectures.
Students are encouraged to contact staff by email to make arrangements for a time to discuss course-related matters.
For more information on this course, please contact Sesquicentennial Distinguished Professor Greg Cook.