Lecture Notes

This course is a discussion-based seminar. The lecture summaries below describe the topics discussed during class.

1 Introduction to bacterial stress response In our first meeting, we will have an introduction by students and the instructor participating in course and review of details in syllabus. There will also be a brief review in microbial physiology and genetics topics that will be discussed throughout the literature in later lectures, such as the regulation of gene expression and genetics methods for investigating bacteria.
2 Bleaching in cyanobacteria Cyanobacteria are the only known photosynthetic prokaryotes that use two photosystems in oxygenic photosynthesis and are credited for creating an oxygenic atmosphere on Earth. Since cyanobacteria are primary producers, they are extremely important in carbon and nitrogen cycling in freshwater and marine systems. During high-light stress and nutrient deprivation, cyanobacteria that are incapable of fixing nitrogen (nondiazotrophic) must degrade their light harvesting apparatus to reduce light and acquire nutrients for survival. Freshwater cyanobacteria cultures that undergo this bleaching, or chlorosis, such as Synechococcus elongatus and Synechocystis, change their color from a green-blue to yellow. The bleaching process can be reversed once nutrients are reintroduced into the environment or light intensity is reduced to favorable levels for cyanobacterial growth. In this lecture, major regulators involved in controlling the bleaching process under nutrient deprivation and high-light stress will be discussed.
3 Down in the deep blue: thriving in deep-sea vents Deep-sea vents offer molten rock and bursts of hot water that support an array of bacteria that are able to use inorganic nutrients in an environment completely void of light. It has been suggested that these 'geysers' located 7000 feet below sea level and the unique species of bacteria that reside near them provide a clue of how microorganism lived on a primitive Earth. The first paper will focus on the isolation of a photosynthetic bacteria isolated from deep-sea vents and offers clues for how photosynthesis is carried out in an environment void of light. In the second paper, we will read about how genes involved in supporting the metabolism of epsilon-proteobacteria from deep sea vents offer clues on the survival of bacteria in this environment.
4 Cleaning up the Earth: bacteria and toxic chromium pollutants Hexavalent chromium (Cr(VI)) is a readily absorbed genotoxic carginogen that is used as a corrosion inhibitor in stainless steel production and other industrial processes. Chromate toxicity due to the reduction of CrVI in cells activates of an immune system response and can produce minor skin irritations. Persistent exposure to chromate has been linked to lung, kidney and stomach cancer. Therefore, alternatives to chromate have been sought in industrial applications. Chromate pollution by factories that have used the compounds has spawned efforts to discover bacteria and bacterial enzymes that can become possible candidates for chromate bioremediation. Understanding the how bacteria modulate their gene expression and morphology to combat chromate toxicity offers the first step in developing a bioremediation strategy. Shewanella oneidesis and Escherichia coli survival under chromate toxicity will be the focus of this lecture.
5 Plants as pals in survival In many cases, plants and bacteria rely on each other for survival under adverse conditions. Sinorhizobium meliloti will invade the nodules on the roots of Medicago sativa, or alfalfa, and convert atmospheric nitrogen to ammonia for a more usable form of nitrogen for the plant. For aerial plants, the colonization of Methylobacteria bacteria assists in the regulation of plant hormone production. This relationship is beneficial to the bacteria because the plants provide relief from nutrient deprivation for these microorganisms. The regulation of stress response genes in the case of both Methylobacteria and S. meliloti is vital for their colonization and symbiosis; respectively, with plants.
6 What's for dinner? Stress responses and food

The pathogen Escherichia coli O157:H7 is capable of producing the Shiga-toxin, which can lead to severe diarrhea and kidney failure, especially for children, immunocompromised individuals and elderly. The contaminant is commonly found in undercooked beef, unpasteurized milk and apple cider. Under conditions deemed harshly acidic for other bacteria, E. coli O157:H7's ability to survive low pH environments, such as the gastrointestinal tract of cattle and apple cider, demonstrates its robust mechanism for survival under acid stress conditions.

Lactobacillus sakei plays an important role in the production of cured sausage, cheese and other lactic acid-fermented food products. Bacteriocins produced by L. sakei during meat fermentation inhibit the growth of pathogenic bacteria and other microorganisms that can cause food spoilage. Due to its high tolerance under low temperature and pH, L. sakei makes a great candidate for examining the acclimation of bacteria to shifts in nutritional and environmental conditions during food production.

7 Sticking together: biofilms

Biofilms are aggregates of microorganisms protected by an exopolysaccaride matrix. The formation of biofilms by opportunistic pathogens is of great concern because of the increase in antibiotic resistance developed by these pathogens once they are in a biofilm structure. In the first paper, we will look at the role of nutrient-limitation and its link to quorum sensing (intercellular communication) and cell motility during biofilm development in the pathogen Pseudomonas aeruginosa.

The role of a major gene expression regulator in Myxococcus xanthus, a soil bacterium that obtains its organic nutrients from primarily decaying organisms, undergoes biofilm formation under carbon-limited conditions and is a premiere model organism in the study of bacterial 'social behavior'. Similar to P. aeruginosa, M. xanthus biofilm formation is regulated by nutrient-stress and, here, we will look at the role of transcriptional regulation of genes involved in its biofilm formation.

8 Combating reactive oxygen species and establishing infection Immune cells respond to bacterial infection by generating respiratory bursts, which are comprised of oxygen radials, to degrade bacteria and foreign elements by damaging their DNA, lipids and enzymes. To infect cells successfully, bacterial cells must be able to alter gene expression to combat superoxide, peroxynitrite and other reactive oxygen radical species (ROS). The mechanisms for how pathogens Salmonella and Helicobacter pylori use of superoxide dismutase and NapA (neutrophil-activation protein), respectively; during cell infection and survival during oxidative stress will be discussed in the following papers.
9 When viruses attack: phage shock response The discovery of the first phage shock protein (Psp) in Escherichia coli in the late 1980's has increased our understanding of how this microorganism modulates its gene expression during viral infection. First, we will discuss the classic paper detailing the upregulation of the first Psp in response to infection by filamentous viruses and the protein's link to E. coli protection in other stress response conditions. In the second paper, an array study twenty years later after discovery of the first Psp is used to create a model for examining the regulation of psp operon in E. coli.
10 Tug-of-war for Iron: bacterial mechanisms for evading host innate immunity and other bacterial species in order to acquire iron In a battle for survival, bacteria have evolved different mechanisms to acquire iron, an essential element. Due to the insolubility of iron hydroxides, the concentration of iron in several environments, including a host's blood serum, are considerably lower than the concentration needed for bacterial growth and survival. In order to obtain iron, many microbes expend a substantial amount of energy making molecules with strong binding affinity to iron called siderophores. To counteract these molecules, part of the host innate immunity consists of proteins called siderocalcins which sequester the iron-binding siderophores. Cleverly, pathogenic bacteria have evolved methods to evade the host's siderocalcins by modifying its siderophores thereby disguising them. In addition, other modifications of bacterial siderophores can attack cohabitant bacteria species limiting the competition for iron. In this class, we will investigate how certain bacteria species respond to the stress of iron scarcity.
11 Living well in freezing weather Survival in cold temperatures and in the presence of ice requires that enzymes and other process are capable of supporting metabolic processes. Bacteria in arctic environments must be able to produce enzymes that will function at subzero temperatures or counter the damaging effects of ice crystals to survive. Both of these papers offer an example of both processes that bacteria utilize to thrive in freezing temperatures.
12 Raman spectroscopy for evaluation of bacterial survival Raman spectroscopy is a powerful, universal tool for measuring bacterial stress response. High-quality UV resonance Raman spectroscopy of E. coli is selective for bacterial nucleic acids, while Raman spectroscopy at other laser wavelengths provides a comprehensive probe for bacteria thriving in extreme environments. The lecture will discuss the experimental tools and theory relevant to Raman spectroscopy. Models will be described that can simulate Raman spectra in order to evaluate the viability of bacteria exposed to stress conditions and investigate the survival activity of novel extremophilic microorganisms.
13 Various stress responses of Deinococcus Deinococcus are a genus of bacteria with extreme resistance to ionizing radiation, ultraviolet light, and desiccation; conditions which cause DNA damage and kill most bacteria. This pair of papers seek to investigate the mechanisms behind their ability to repair DNA using both wet biology and bioinformatic approaches. This work will also be put into the context of Astrobiology and the controversy over whether this bacteria can survive interplanetary travel or even if its radiation resistance mechanisms are of extraterrestrial origin.
14 Oral presentations