Lecture Summaries

1IntroductionIntroduction and overview of the class. We will introduce ourselves, discuss the syllabus and outline the course expectations. We will also go over how to find the primary literature (PubMed and ISI Web of knowledge) and how to read and analyze the primary scientific literature. The last part of this class will be an introductory lecture on the theme "What are microbes, and where do they live?"
2The general stress response and sporulationWe will introduce the stress-response driven changes in gene expression that allow bacteria to survive a multitude of different stresses. What are the key features of a general stress response; and what are the factors that enact the gene expression programs? We will talk about how the general stress response differs from a specific stress responses and when it would be advantageous to mount a general stress response. Sporulation by the bacterium B. subtilis provides even greater protection against the environment than the E. coli general stress response; and B. subtilis spores have been found from the bottom of the sea to the Nambid desert. In the second paper we will read about the transcriptional cascades characterizing sporulation by B. subtilis.
3Evolution of the general stress response and sporulationWhat is the optimal strategy to survive environmental fluctuations? Long-term existence in a dormant state can have cause severe fitness penalties. The first paper addresses how E. coli evolves a cheater population that turns off its stress response under long-term starvation conditions and cannibalizes its related neighbors. Alternatively, some organisms like B. subtilis bet-hedge so that some cells stochastically enter and exit their general stress response in anticipation of changing conditions.
4Protein-protein interactions: Two-component systemsThe most common mechanisms by which bacteria sense and respond to their surroundings are two-component signaling systems. These typically comprise histidine kinases (HK) that respond to environmental stimuli and their cognate response regulators (RR) that enact the appropriate response in the cell. The first paper addresses how the physical arrangement of the two-component sensors leads to signal amplification. Since there are hundreds of these signaling systems in a single cell, bacteria have evolved specific HK-RR interactions to ensure faithful transmission of the signaling information. The second paper takes a systematic approach to identifying the core amino acids necessary for the specificity of the two-component signaling pathways.
5sRNAs: Regulating translation mRNA of RpoS (the general stress response activator)Small RNAs that do not encode polypeptides can still have regulatory roles, for example controlling the level of the general stress response activator RpoS in E. coli. The first sRNA discovered to target the RpoS mRNA, DsrA, is induced in response to a shift to low temperatures, and positively regulates translation of RpoS. The first paper shows how DsrA was discovered, while the second paper describes how DsrA is induced at low temperatures.
6Small molecules: The stringent responseSmall molecules can also be used in signaling processes to sense stress and enact the appropriate response. The small molecule guanosine tetraphosphate (ppGpp) is induced during nutrient starvation to enact what is known as the 'stringent response.' The first paper suggests that the enzyme RelA induces ppGpp synthesis during nutrient starvation by sensing the ratio of free tRNA to aminoacylated tRNA in stalled ribosomes. The second paper shows how ppGpp binds RNA polymerase and directs gene expression.
7Field trip to the Laub laboratoryWritten assignments are due this week. In lieu of reading and discussing papers, we will visit a microbiology laboratory (the Laub laboratory). There we will observe the behavior of several types of bacteria under the microscope, with an eye to how their morphology changes upon stress conditions. We will also examine the colony morphologies and other phenotypes of different microbes on Petri plates under stress conditions.
8Pumping out toxins: AntibioticsOne of the most common ways in which microbes deal with toxic substrates (including most classes of clinically relevant antibiotics) is to pump them out through efflux pumps. The first paper identifies the role of efflux pumps, as opposed to reduced membrane permeability, in antibiotic resistant Pseudomonas aeruginosa -- the bacterium causing many of the cystic fibrosis symptoms. The second paper concerns the structure of the pump and how it manages to pump toxins across the two membranes of the cell and the periplasm (the space between the two membranes). This paper shows that the AcrAB adaptor, which binds toxins in the cytoplasm, also directly binds the channel protein, thus opening a direct tunnel from the cytoplasm to the outer membranes of the cell.
9Scavenging toxins: Reactive oxidative speciesOxidative stress is common under aerobic conditions and can cause dramatic damage to DNA, protein and lipids. It can be so toxic that many hosts use oxidative stress as a strategy to fight pathogens. Since reactive oxygen species are not compounds that can be easily selected and pumped out, microbes have evolved superoxide dimutases to scavenge the reactive species. These enzymes catalyze the conversion of superoxide (the reactive O2 anion that is a byproduct of cellular respiration and produced by host phagocytes) into oxygen and hydrogen peroxide. The first paper shows how the effects of superoxide are diminished in the presence of superoxide dimutases enzymes. The second paper shows how the regulator of this antioxidant response was discovered.
10Promoting tolerance: Extreme heat and coldPhysical stresses such as heat shock are impossible to contain via pumping and sequestering. One option for bacteria is to make heat-sensitive processes — like protein folding — more tolerant by inducing chaperones that help proteins fold and proteases that degrade misfolded proteins. The first paper discusses how a certain subset of proteins starts to aggregate during heat shock and how chaperones can help mediate the aggregations. The second paper covers how the activity of sigma H (the activator of the heat shock response) is negatively regulated by the presence of the chaperones.
11Final oral presentations 
12Repair calls: Single-stranded DNA damageLike that of many organisms, the DNA of microbes is under constant bombardment by UV light and radiation, causing both single-stranded and double-stranded damage. Thus the cell must have repair mechanisms to restore the damaged DNA to its original state. For this class, we will focus on single-stranded damage, in which the other strand can be used as a template for the correction. The first paper shows that a nucleotide excision repair complex cuts on either side of the damaged region, while the second paper illustrates a specialized form of this repair, in which the repair enzymes are targeted to genes that are most actively being transcribed.