69341 - Molecular Biology of Prokaryotes

Learning outcomes

The student will gain in depth knowledge of the most important regulatory strategies adopted by bacteria to control gene expression with a particular focus on the mechanisms governing transcriptional regulation and post-transcriptional control exerted by non-coding (regulatory) RNAs. In particular, at the end of the course, the student will be able to:  1) analyse and discuss the main topics about regulation of gene expression; 2) understand, analyse and discuss research papers; 3) plan experimental approaches to study a biological problem.

Course contents

Introduction. Components, structure and mechanisms of bacterial RNA polymerase. Structure and function of bacterial promoters and interactions between RNA polymerase and promoter DNA. Regulation of transcription in bacteria. Interaction between transcriptional regulators and DNA operators: origins of specificity in protein-DNA recognition, recognition of chemical signature of the DNA bases (base readout), recognition of sequence dependent DNA shape (shape readout).

Regulatory non-coding RNAs. Post-transcriptional regulation mediated by non-coding RNAs: biological roles and mechanisms of action. Major classes of trans-acting ncRNAs: cis-encoded (antisense) ncRNAs, trans-encoded ncRNAs. trans-acting ncRNA: 5'-UTR sequences of mRNAs, riboswitches, RNA thermometers and Ribozymes. Protein-interacting ncRNA. Multifunctional ncRNAs.

CRISPR/Cas immunity in bacteria. Interaction bacteriophage/host: detailed analysis of CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated), a prokaryotic adaptive immune system. Different stages of CRISPR immunity: Immunization, Expression and Processing, Interference. Detailed analysis of Type 2 CRISPR/Cas system of Streptococcus pyogenes: focus on tracrRNA, RNAse III and Cas9. Major applications of CRISPR/Cas9 in genome editing and gene expression modulation: comparison with other tools currently used for genome editing like Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). 

Readings/Bibliography

Reviews and seminal papers.

Teaching methods

Lessons, analysis and in class discussion of seminal research papers. Summarizing PowerPoint presentations.

Assessment methods

The final exam will verifiy the acquisition of the main learning outcomes. In particular the student will be able to:

1) analyse and discuss in details the main topics about regulation of gene expression;

2) understand, analyse and discuss research papers;

3) plan experimental approaches to study a biological problem.

The final exam is made of two parts. Part one: analysis and presentation of a seminal research paper (learning outcome 2); part two: oral exam (assessment of learning outcomes 1 and 3).

Teaching tools

Reviews and seminal research papers. PowerPoint presentations.

Office hours

See the website of Davide Roncarati