Lecture 10: Horizontal Gene Transfer and Bacterial Diversity Summer 2024 PDF

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6/30/24 0:00 Bacteria and Archaea are prokaryotic and Lecture 10: Horizontal Gene Transfer and they don’t reproduce sexually. How do Bacterial Diversity they generate genetic variability? Reading: Major way is through Horizontal Gene Transfer Horizontal Gene Transfer: – Transfer from one independent organism to Chapt. 6 Sect. 6.4, Chapt. 16 Sect. 16.6-8 another 3 mechanisms: Bacterial Diversity: Transformation Chapt. 3 Sect. 3.10 Conjugation Chapt. 20 Sects: 2-7,10 Chapt. 21 All Sects. Transduction Chapt. 22 All Sects. Horizontal Gene Transfer Competent bacteria have membrane-bound protein complexes that bring DNA into the cell. How is DNA changed during this process? Fig. 16.22 Transformation - up take of free DNA from ↓ “Doubled strand DNA → singled strand DNA” environment Competent cell uptake DNA " ability to Only a few bacterial genera known to be Nuclease [l Y naturally competent: Gram + Streptococcus, Bacillus = DNA can then be integrated into genome [ Gram - Haemophilus, Neisseria, Acinetobacter Figure 16.22 Transformation in Streptococcus pneumoniae. Upon 3 contacting DNA, the DNA uptake pilus retracts to bring it to the plasma membrane surface. Membrane-bound ComEA directs the DNA to a membrane channel (ComEC) and an endonuclease. One strand passes through the channel to the cytoplasm (ATP hydrolysis) and the other is [ Il degraded. Artificial Transformation Horizontal Gene Transfer 2 Conjugation - DNA transfer by direct cell In lab with bacteria not Electroporator naturally competent (e.g., contact E. coli) Requires pili, plasmids - Critical step in cloning Two technique: - The F (Fertility) Factor of E. - - Calcium chloride - makes cells coli is a well-studied more permeable conjugative plasmid - Electroporation - pulses high voltage, temporary holes in cell wall Some conjugative plasmids, - called R factors, encode and plasma membrane, “so DNA can resistance to antibiotics 6 enter” 1  6/30/24 30:25 Plasmid encoded Conjugation: F+ x F– Mating relaxase Horizontal Gene Transfer enzyme nicks one Donor + Recipient strand for F factor 3 Transduction - bacterial gene transfer by Single-strand F F- Conjugative phages plasmid - 1. Pilus 3. 31 5/ enters recipient Viruses that infect bacteria. Extends Abundant and diverse >10 billion/liter of sea water donor synthesizes recipient replicate strand to form double stranded Impact composition, behavior complementary to replace F-factor plasmid of microbial communities fransfer strand - ensure A new 2. 4. 2 phage types Bacteriophage T4 F-factor remain complementary double strain - Virulent-lytic cycles strand is also - Temperate - lysogenic cycles made in here A new complementary 8 strand made in here via Rolling Circle Replication 33:47 Will be degraded 36:50 ~ I Cycles Fig. 6.15 Lytic vs Lysogenic Phage Generalized Transduction During lytic cycle Any part of bacterial genomes transferred - - "cut" During phage assembly, pieces of degraded host DNA - packaged into phage - - is generated Bacterial genome degraded But transduction is the transfer of bacterial genes. How does this happen? 45:30 Specialized Transduction Phage Therapy Therapeutic use of phages to treat during lysogenic cycle pathogenic bacterial infections - specific part of genome Pros and cons must be transferred considered prophase incorrectly exercises, Approaches: Phage Cocktails, Phage-Antibiotic Combinations takes part of genome with it Link to TEDx Phage Therapy Talk Sewage Saved my Husband's Life https://www.youtube.com/watch? v=AbAZU8FqzX4 2  6/30/24 intestinal tract 30 % human feces Obligate anerobe-human , & - Well-Studied Bacterial Phyla alkaliphile Bacterial Diversity carotine - vitamin Phylogenetic Tree of Life spiruling – Deinococcus-Thermus Lanabaena- aquatic-green S ATP NADPH) – Cyanobacteria - fix CO2 (generate & 3 Domains C trachomatis – Chlamydiae STD C Pneumoniae I. - -. mediseBoreburdr i Taxonomic rank – Spirochaetes flexible , - one below ? – Bacteroidetes Domain is called a Phylum – Proteobacteria Alpha, Beta, Gamma, Delta, Epsilon – Fermicutes – Actinobacteria 57:03 59:33 Phylum Deinococcus -Thermus Phylum Cyanobacteria Primary producers in many Thermus aquaticus ecosystems – Thermophile Oxygen photosynthesis – Grows at 70-750C Water as electron donor, – Source of Taq polymerase Oxygen is Produced for PCR 2 Photosystems (PSI and PSII) Deinococcus radiodurans Generate ATP and NADPH – Not thermophilic, but used in Calvin Cycle to fix CO2 extremely resistant to Structures radiation and desiccation Thylakoids with Chlorophyll protein bouda – Rapid DNA repair 15 Carboxysomes 63;50 66:20 Phylum Cyanobacteria Phylum Cyanobacteria Genus: Anabaena Genus: Spirulina Aquatic bacterium Alkaliphile (soda lakes) High [carotene] Two processes Food additive – protein, oxygenic photosynthesis vitamin rich N fixation- reduction of atmospheric nitrogen (N2) to ammonium Problem: enzyme nitrogenase for N fixation is sensitive to 02 Solution: differentiate vegetative cells into heterocysts devoid of O2 that fix N2 heterocysts ? Definition: Specialized thick-walled cells in what is filamentous cyanobacteria. and its function ? Function: Facilitate nitrogen fixation by creating an anaerobic environment, protecting the enzyme nitrogenase from oxygen. 3  6/30/24 76 : 07 Phylum Chlamydiae Chlamydia Reproduction is Unique Genus: Chlamydia Begins with attachment of an Gram – , obligate intracellular infections, dormant Elementary Body bacteria (EB) to host cell surface Human and animal pathogens Inside cell, EB developed into In humans, two important reproductive, non-infectious Reticulate species: Body (RB) – C. pneumoniae – C. trachomatis RBs differentiate back into EBs that Human cells (red) infected with – Causes #1 reported are released by host cell lysis. Chlamydia (green) bacterial STD in U.S. 86:13 Phylum Spirochaetes Phylum Bacteroidetes Flexible, helical shape Genus: Bacteroides Flagella within periplasm Obligate anaerobes – Axial filament live without 02 – Rotation turns whole cell Important bacteria of the human intestinal tract Pathogens Treponema pallidum-syphillis About 30% of the bacteria cultured from Borrelia burdoferi - Lyme Disease (ticks) human feces are Bacteroides - - Erythema Migrans (bulls eye rash) Function : 21 Degrade complex, dietary polysaccharides Syphillis Treponema Pallidum = disease (ticks) Borrelia burduteri Lyme - rash bull eye - Erythema Migrans Phylum Proteobacteria (Gram Negatives) Alpha Proteobacteria Gall = Some are Photoheterotrophs Largest group Anoxygenic photosynthesis – Rhodospirillum – Five major classes (Alpha, Beta, Other Gamma, Delta, and Epsilon) - Rhizobium - root nodules, fix N2 - Argobacterium. Diverse cell forms and metabolism Plant pathogen – Heterotrophs - Transfer DNA into plant cells causing – Phototrophs tumors (galls). – Lithotrophs Rickettsia in animal - obligate intracellular bacteria 24 - Rocky Mountain spotted Fever (tick) 4  6/30/24 Alpha Proteobacteria tip Caulobacter Life Cycle (See Fig. 21.7) Swarmer Cell: Motile, cannot replicate DNA, responsible for dispersal. genus: caulobacter stalk ↑ Stalked Cell: Non-motile, can replicate DNA, anchored to surfaces, Gram -, aquatic X undergoes asymmetric division to produce a new swarmer cell. Can’t Can dimorphic replicate its replicate its Cell division generates: single DNA DNA - Motile swarmer cell flagellum - supportwim - Non-motile stalked cell S - why stalk? → allow cell to attach to surface in aquatic environment, Using gradient centrifugation, pure populations of efficient nutrient uptake swarmer cells can be isolated from Caulobacter cultures. 26 25 : 38 Beta Proteobacteria Gamma Proteobacteria live in intestine of human and animal Some are chemolithotrophs Includes “Enterics” Facultative NOz- Nitrate, sulfur, iron oxidizers anaerobes Ex: Nitrosomonas Escherichia coli - some strains normal inhabitants intestine, Oxidizes ammonia to nitrite NUz others pathogenic (0157:H7) 1st step of Nitrification Salmonella – food poisoning Also "non-enterics”: Some are human pathogens Pseudomonas aeruginosa- pathogen in Cystic Fibrous ↓ Neisseria meningitidis and (CF) and burn wound patients gonorrhoeae pigment pyoverdin - a Siderophore & Burkholderia cepcia Vibrio cholerae- cholera plant pathogen Shewanella - non-pathogen, aquatic and soil, Also human respiratory pathogen extracellular electron transport Mudwatts are microbial fuel cells that harness the Some bacteria can transfer electrons electrogenic potential of soil microbes to produce extracellularly, to acceptors outside the cell. electrical power. The gram-negative Cathode bacterium Shewanella (high O2) can transfer electrons extracellularly onto e- certain metals. “Shewy the Electric Bacterium” Anode (low O2) This bacterium “breathes” metals, much like humans breathe oxygen. 5  6/30/24 Delta Proteobacteria Fig. 20.19 Myxococcus Fruiting Body Formation Gliding motility Genus: Myxococcus Stress, starvation Extension, attachment, Signal aggregation retraction of type IV pills Gram - , social, soil bacteria Myxospores Attack other bacteria at top to swarm on the surface Gliding motility (no flagella) Nutrient limiting, cells assemble Vegetative cells into fruiting bodies Germination – with dormant myxospores Myxospore 50 : 43 51 : 04 + Cytosine content Guanin Epsilon Proteobacteria Phylum Firmicutes (Low G+C Gram+) Also called phylum Includes Pathogens Campylobacterota Staphylococcus (MRSA) - ↓ Streptococcus Methicillin-Resistant - Only 2 genus of bacteria staphylococcus aureus What are they? Also “Good” bacteria Campylobacter & Helicobacter Lactobacillus, What diseases do they Lactococcus cause? enteritis , Guillain-Barré syndrome (GBS) Lactic acid fermentation Campylobacter - Helicobacter - gastric cancer , gastritis , peptic ulcer disease Cheese, yogurt See page 451 Phylum Firmicutes: Spore Formers What’s in this bottle? Two major genera: Clostridium and Bacillus Bacillus thuringiensis - C. tetani Produces insecticidal toxin C. botulinum – botulism, produces neurotoxin (Bt corn) (Botox) Toxin forms holes in insect C. difficile – colitis, Inflammation of colon gut · B. subtilis – non pathogenic soil bacterium B. anthracis - anthrax 6  6/30/24 Bacillus Sporulation: A Tale of Two Cells Triggered by lack of nutrients Like people, cells usually deliberate Survival mechanism, produces spore that can survive very carefully before committing to Spore inside dramatic changes in Spore forms inside mother cell mother cell that will lyse, releasing mature their lifestyle spore C. Stephens, Current Biology 1998 Spore is dormant, heat and stress resistant, but can germinate and become an How does Bacillus sense stress to initiate sporulation? & actively growing cell through nutrient limitation. Phylum Actinobacteria (High G+C Gram +) Genus: Mycobacterium Human pathogens M. tuberculosis M. leprae Acid-fast cell walls Waxy lipids Genus: streptomyces Form hyphae and mycelia Source of many antibiotics makes chemical Geosmin - Odor of moist soil 39 7