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Te Tari Moromoroiti me te Ārai Mate

MICR 335: Molecular Microbiology

First Semester - 18 points

Course prescription

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.

"One of my favourite labs of undergrad! Lecturers knew their stuff and both lecturers and lab staff were always willing to help. Good stuff" - MICR 335 student, 2019.

Course overview

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  • Prokaryotes display a wide range of metabolic diversity and the control of gene expression under different conditions is an important component of understanding and exploiting microbes. Whether it be physiological adaptation to different environments or the mechanisms by which pathogens evolve through the acquisition and regulation of virulence genes, an understanding of Molecular Microbiology is an important component of modern Microbiology.

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  • This course in Molecular Microbiology provides fundamental knowledge in gene regulation, underlying genetic regulatory mechanisms and microbial genomics and you will:

    1. become familiar with the key systems bacteria use to regulate expression from their genomes
    2. explore specific regulatory systems that respond to different stimuli and the technologies that can be used to explore gene expression.

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  • This paper provides a strong framework in molecular microbiology that is underpinned by a laboratory course that provides hand-on experience with many of the skills and techniques that are used in a microbial genetics laboratory. 

Lecture course overview

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

Lab course overview

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. 

Course prerequisites

One of MICR 221, GENE 221 


View the details of this paper on the University of Otago website


There is no recommended text for MICR 335 but you will be directed to and discuss relevant scientific papers during lectures.

Teaching staff

For more information

View the details of this paper on the University of Otago website

Students are encouraged to contact staff by email to make arrangements for a time to discuss course-related matters.