Chapter 18 The Genetics of Viruses and Bacteria

Chapter 18: The Genetics of Viruses and Bacteria

What is Microbiology? q Microbiology is the science that studies microorganisms q Microorganisms, roughly, are those living things that are too small to be seen with the naked eye q Microorganisms cannot be distinguished phylogenetically from “Macroorganisms”, e. g. , includes fungi as well as bacteria, etc. (that is, they are not, as a whole, a closely related group of organisms) q Microbiology is more a collection of techniques: Aseptic technique, Pure culture technique, Microscopic observation of whole organisms, etc. q A microbiologist usually first isolates a specific microorganism from a population and then cultures it

Importance of Microbes q Microbes are producers—they provide energy to ecosystems q Microbes are fixers—they make nutrients available from inorganic sources, e. g. , nitrogen q Microbes are decomposers—they free up nutrients from no longer living sources q Microbes form symbioses (such as mycorrhizal fungi associated with plant roots—though these are somewhat macroscopic; also the bacteria found in legume root nodules, etc. ) q Microbes serve as endosymbionts (e. g. , chloroplasts and mitochondria) q Microbes make fermentation products (ethanol!), food (beer! Cheese! Yogurt! Half-sour pickles!), Biotech products (e. g. , recombinant insulin), etc. q Germ theory of disease; Normal flora

Relative Microbe Sizes

Examples of Types of Viruses

What is a Virus? q Viruses consist of protein capsids and nucleic acid (DNA or RNA) plus some viruses (virions) have a lipid envelope (enveloped viruses) q Viruses are… “. . . infectious agents of small size and simple composition that can multiply only in living cells of animals, plants and bacteria [plus fungi & protozoa]. q Viruses are obligate parasites that are metabolically inert when they are outside their hosts. They all rely, to varying extents, on the metabolic processes of their hosts to reproduce themselves. q The viral diseases we see are due to the effects of this interaction between the virus and its host cell (and/or the host’s response to this interaction). ” Encyclopedia Britannica

Virus (Virion Particle) q The Virion is what defines a virus as a virus q A Virion is the extracellular state of a virus q The job of Virions is to find new cells to infect q As such, Virions are a durable state that is “designed” to attach to susceptible cells q The Virion is then responsible for translocation of the virus genome into the cell q The Virion consists of a DNA (or RNA) genome surrounded by Protein that, in turn, may be surrounded by a Lipid Bilayer q The Protein layer is called a Capsid q The Lipid Bilayer is called an Envelope

Steps of Virus Replication 1. Adsorption (attachment) 2. Penetration (nucleic-acid release) 3. Synthesis (of RNA and proteins, as well as DNA if DNA genome) 4. Maturation (assembly of virion) 5. Release (lysis or chronic release, e. g. , budding, with the latter coinciding with release for various enveloped viruses) Caveat: It is important to realize that variation among viruses is between virus strains/species; any one kind of virus cannot replicate in multiple ways, have more than one virion morphology, or vary in genome type, etc.

DNA Virus Life Cycle Lysis

Bacteriophage Lytic Cycle Lysis

Lysogenic Cycle (Temperate Phage) Lysis Only temperate phage are able to display lysogeny

Enveloped RNA Virus An example of an animal virus Budding Acquisition of plasma membrane as envelope

HIV Life Cycle

Budding HIV Life Cycle

Bacteria Sex q Viruses move genetic material from cell to cell q Mostly this material is their own genomes, i. e. , genes that collectively code for the production of new viruses q Bacteria DNA also can move from cell to cell q Once received by a cell, this DNA may be incorporated into the bacterial genome via recombination q This idea of DNA sourced from different parents recombining into a single chromosome is equivalent to eukaryotic sex (i. e. , fertilization followed by recombination) q Transformation, Transduction, Conjugation

Why study bacterial genetics? • Its an easy place to start – history – we know more about it • systems better understood – simpler genome – good model for control of genes • build concepts from there to eukaryotes – bacterial genetic systems are exploited in biotechnology

Bacteria • Bacteria review – one-celled organisms – prokaryotes – reproduce by binary fission – rapid growth • generation every ~20 minutes • 108 (100 million) colony overnight! – dominant form of life on Earth – incredibly diverse

Bacterial genome • Single circular chromosome – haploid – naked DNA • no histone proteins – ~4 million base pairs • ~4300 genes • 1/1000 DNA in eukaryote Intro to Bacteria video

No nucleus! • No nuclear membrane – chromosome in cytoplasm – transcription & translation are coupled together • no processing of m. RNA – no introns – but Central Dogma still applies • use same genetic code

Binary fission • Replication of bacterial chromosome • Asexual reproduction – offspring genetically identical to parent – where does variation come from?

Variation in bacteria • Sources of variation – spontaneous mutation – transformation • plasmids • DNA fragments – transduction – conjugation – transposons bacteria shedding DNA

Transformation: DNA picked up directly from the medium and recombined into the genome Competent cell: capable of picking up DNA

Generalized Transduction

Plasmids

Conjugation Moves plasmid more so than chromosomal DNA

Bacterial Genetics Regulation of Gene Expression

Bacterial metabolism • Bacteria need to respond quickly to changes in their environment – if have enough of a product, need to stop production • why? waste of energy to produce more • how? stop production of synthesis enzymes – if find new food/energy source, need to utilize it quickly • why? metabolism, growth, reproduction • how? start production of digestive enzymes

Regulation of Metabolism e. g. , transcription

Reminder: Regulation of metabolism • Feedback inhibition – product acts as an allosteric inhibitor of 1 st enzyme in tryptophan pathway - = inhibition

Another way to Regulate metabolism • Gene regulation – block transcription of genes for all enzymes in tryptophan pathway • saves energy by not wasting it on unnecessary protein synthesis - = inhibition

Gene regulation in bacteria • Control of gene expression enables individual bacteria to adjust their metabolism to environmental change • Cells vary amount of specific enzymes by regulating gene transcription – turn genes on or turn genes off • ex. if you have enough tryptophan in your cell then you don’t need to make enzymes used to build tryptophan – waste of energy – turn off genes which codes for enzymes

Control of Gene Expression q Operons- sequence of DNA that directs particular biosynthetic pathways q 4 Major Components of an operon q. Regulatory gene- produces a repressor protein that prevents gene expression by blocking DNA polymerase q. Promotor region- sequence of DNA where RNA Polymerase attaches for transcription q. Operator region- can block action of RNA Polymerase if region is occupied by repressor protein q. Structural gene- contain DNA sequence that code for several related enzymes that direct production of an end product.

Control of Gene Expression q It makes energetic sense to make or use proteins responsible for certain metabolic processes only when those processes are needed. q Trp Operon- enzymes make needed tryptophan q. Repressor inactivated in response to presence of tryptophan q. Tryptophan acts as Corepressor q“Repressable enzymes”- Usually turned on and has to be turned off. q Lac Operon q. Controls breakdown of lactose q. Lactose presence needed to turn on Operon q“inducible enzymes”- Usually turned off and needs to be turned on.

So how can genes be turned off? • First step in protein production? – transcription – stop RNA polymerase! • Repressor protein – binds to DNA near promoter region blocking RNA polymerase • binds to operator site on DNA • blocks transcription

Genes grouped together • Operon – genes grouped together with related functions • ex. enzymes in a synthesis pathway – promoter = RNA polymerase binding site • single promoter controls transcription of all genes in operon • transcribed as 1 unit & a single m. RNA is made – operator = DNA binding site of regulator protein

Trp Operon (low trp densities) Recall that the promoter is the site of RNA polymerase binding Don’t worry about the names of these genes and products

Trp Operon (higher trp densities) Corepression Negative regulation Equilibrium: Likelihood of being in bound state depends on trp density

Repressor protein model Operon: operator, promoter & genes they control serve as a model for gene regulation RNA polymerase RNA repressor TATA polymerase promoter operator gene 1 gene 2 gene 3 gene 4 DNA Repressor protein turns off gene by blocking RNA polymerase binding site. repressor protein

Repressible operon: tryptophan Synthesis pathway model RNA polymerase When excess tryptophan is present, binds to tryp repressor protein & triggers repressor to bind to DNA RNA repressor TATA polymerase gene 1 – blocks (represses) transcription gene 2 gene 3 gene 4 repressor promoter operator DNA repressor protein tryptophan repressor tryptophan – repressor protein complex conformational change in repressor protein!

Tryptophan operon What happens when tryptophan is present? Don’t need to make tryptophan-building enzymes Tryptophan binds allosterically to regulatory protein

Inducible operon: lactose Digestive pathway model RNA polymerase When lactose is present, binds to lac repressor protein & triggers repressor to release DNA RNA repressor TATA polymerase gene 1 – induces transcription gene 2 gene 3 repressor promoter operator gene 4 DNA repressor protein lactose repressor lactose – repressor protein complex conformational change in repressor protein!

Lactose operon What happens when lactose is present? Need to make lactose-digesting enzymes Lactose binds allosterically to regulatory protein