Bacteria, Archaea, Eukaryote, Virus Phylogeny Groups, SARS CoV-2, and Infectious Spread Flashcards
What are the 8 bacterial phylogeny groups?
- Cyanobacteria
- Gram (+)
- Deep branching thermophiles
- Deep branching gram (-)
- PVC
- Spirochetes
- Proteobacteria
- CPR (candidate phyla radiation)
Cyanobacteria characteristics
- oxygenic photosynthesis
- ancestors of chloroplasts
- many also fix nitrogen
- may be filamentous/multicellular
- found in communities with other organisms
Gram (+) characteristics
- Firmicutes & actninoycetes
- tough skin
- commonly form endospores
- models for bacterial development
What are examples of gram (+) bacteria
- bacillus subtilis
- bacillus thuringiensis - insecticide
- clostridim botulinum - botox
Proteobacteria/Gram (-) characteristics
- largest and most diverse group in structure and metabolism
- commonly endosymbionts
- ancestors of mitochondrion
What are examples of proteobacteria/gram (-) bacteria
- e.coli
- rickettsia
Deep-branching gram (-) characteristics
- gram -, but diverged early from proteobacteria
What are examples of deep-branching gram (-)
- Fusobacteria - virulent pathogens, dental plaque
- Chorobi - green sulfur bacteria, chlorosomes (efficient photosynthesis)
Spriochetes
- spiral cell
- endoflagellum
- agent of lyme disease
PVC
- compartmentalized cells
- many have no peptidoglycan
What are examples of PVC bacteria
- planctomycetes = internal double-membrane around DNA
- verrucomicrobia
- chlamydiae
Deep branching thermophiles
- extreme environments
- diverse and highly mosaic genomes - many share genes and traits with archaea
What are the 5 groups of Archaeal diversity?
- Euryarchaeota
- Crenarchaeota
- TACK (proteoarchaeota) - includes crenarchaeota
- Asgard
- DPANN
Asgard/Lokiarchaeota
- have several genes previously through to be unique to eukaryotes
- many models indicate that eukaryotes branch from lokiarchaeota
Euryarchaeota
- includes methanogens
Crenarchaeota
- includes many hyperthermophiles
TACK (proteoarchaeota)
- includes crenarchaeota
DPANN
- loss of many genes
- typical of obligate symbionts
What is cultured bacteria and archaea versus not cultured
- cultured - known about bacteria
- not cultured - not known about organisms
What is metagenomics
- the study of community genomes (recover organisms and DNA from environmental samples and then sequence the entire sample)
- example: human microbiome, sargasso sea, deepwater horizon oil spill
Why use metagenomics
- helps to discover new organisms, metabolic capabilities, and phylogenetic relationships
- better awareness of microbial communities
What is FISH
- Fluorescence In Situ Hybridization
- Tag signature sequences on specific microbes (archaea, bacteria, or eukaryotes) with fluorescence - helps identify them in large mixed sample
What are 8 major clades of eukaryote diversity
- Opisthokonta
- Amoebozoa
- Plantae (Archaeplastida)
- Rhizaria
- Alveolata
- Stramenopiles (Heterokonta)
- Discoba
- Metamonada
What are 2 supergroups of eukaryote diversity
- SAR (supergroup) - includes rhizaria, alveolata, stramenopiles
- Excavata (supergroup) - includes discoba and metamonada
Opsithokonta characteristics
- animals
- true fungi (yeast)
- microsporidians
Amoebozoa characteristics
- amebas
- slime molds
- includes human & agricultural pathogens
Plantae (archaeplastida) characteristics
- land plants - secondary endosymbiosis
- red algae
Rhizaria characteristics
- amebas with filamentous pseudopods
- part of SAR supergroup
Alveolata characteristics
- protists with cortical alveoli
- includes human & agricultural pathogens
- part of SAR supergroup
Stramenopiles (heterokonta) characteristics
- protists with hairy flagella
- includes human & agricultural pathogens
- brown algae
- part of SAR supergroup
Discoba characteristics
- protists with mitochondria with discoid cristae
- part of excavata supergroup
Metamonada characteristics
- protists lacking mitochondria
- part of excavata supergroup
What is the cause of malaria
- alveolata phylogeny group
- organism: plasmodium (parasite)
What is the cause of epidemic diarrhea
- metamonada phylogeny group
- organism: giardia
What is the cause of sleeping sickness
- euglenozoa (discoba) phylogeny group
- organism: trypanosoma
What is the cause of red tides
- alveolata phylogeny group
- organism: dinoflagellates
What is the cause of the great irish potato famine
- heterokonta phylogeny group
- organism: phytopthora
Fungi characteristics
- very close to animals
- multicellular and unicellular (yeast) forms
- mycelia = networks of filaments (hypahae) for nutrient absorption and communication
Algae characteristics
- primary producers
- evolved from englufing phototrophs
Excavata supergroup characteristics
- many devastating human pathogens: giardia (diarrhea), t.brucei(sleeping sickness)
- no introns
- polysistronic gene expression
- two nuclei
What are the 7 virus classifications (Baltimore Classification)?
- dsDNA
- ssDNA
- dsRNA
- (+) sense ssRNA
- (-) sense ssRNA
- Retrovirus
- ParaRetrovirus
Characteristics of dsDNA and examples
- must enter host nucleus before replication
- host cell polymerases replicate DNA, transcribe into + sense mRNA for ribosome to read
- phage lambda: bacteriphage lambda (e.coli), chloroviruses (algae), herpeseviruses (chickenpox), human papillomavirus
Characteristics of ssDNA and examples
- (+) ssDNA
- complimentary - strand DNA is synthesized, allows for transcription of + mRNA
- Geminivirus: bacteriophage M13 (e.coli), parvovirus (cat, dog, animals)
Characteristics of dsRNA and examples
- needs RNA dependent RNA polymerase and doesn’t require host machinery for duplication
- RdRP duplicates existing dsRNA and + sense mRNA is transcribed
- Rotavirus: birnavirus (fish) cystovirus (bacteria), reoviruse (infants)
Characteristics of + sense ssRNA and examples
- need RNA dependent RNA polymerase
- RdRp encodes - sense strand so + sense strand can continue replication
- ribosome can directy access the mRNA and turn into protein
- rhinovirus: coronavirus, flaviviruse (zika fever, yellow fever, hepatitis C), poliovirus, tobacco mosaic virus
Characteristics of - ssRNA and examples
- need RNA dependent RNA polymerase
- RdRp transcribes - sense RNA into + sense mRNA for ribosomes to read
- Rabies: filovirus (ebola), orthomyxoviruse (influenza), paramyxoviruses (measels and mumps), rhabdovirus (rabies)
Characteristics of retroviruses and examples
- needs reverse transcriptase
- + sense RNA is converted by RT into DNA -> DNA is incorperated into host genome -> makes + mRNA
- Human immunodeficiency virus: HIV (AIDS), FeLV, RSV, ALV
- difficult to treat since viral DNA is embedded in host DNA and you must kill the cell in order to kill the virus
Characteristics of pararetrovirus and examples
- needs reverse transcriptase
- dsDNA is transcribed into + sense mRNA
- RT turns mRNA into DNA and used to make more DNA by RT
- Caulimorvirus: hepadanvirus (hepatitis B)
What are the three bacteriophage cycles?
- Lytic cycle - progeny phage are packaged in capsids and release by cell lyses
- Lysogenic Cycle - phage integrates with host genome and bacteria duplicates
- Slow release: phages assemble without capsid and exit host cell without lysis -> cell continues to reproduce slowly
Explain the lytic and lysogenic cycle how do they relate
- Lytic: bacteriophage insert DNA -> host cell creates capsids and replicates DNA -> host cell packages progeny phages -> cell lyses to release phages
- Lysogenic cycle: bacteriophage insert DNA -> DNA integrates with host genome by site specific recombination -> bacteria reproduces with host and viral DNA
- Lysogenic can switch into lytic if there is environmental stress: viral DNA is excised out of host genome
How do animal viruses attach and enter the cell?
- membrane fusion by viral RNA with membrane: attaches to host cell receptor proteins, viral membrane fuses with host membrane, and coated RNA enters cytoplasm.
- Endocytosis by viral RNA: attached to receptor proteins and is endocytosed with host cell membrane (endosome), lysosome fuses and acidifies endosome, releasing uncoated RNA into cytoplasm
- Endocytosis by viral DNA: attached to receptor proteins and is endocytosed with host cell membrane (endosome), endosome docks onto nuclear membrane and releases uncoated dsDNA into nucleus
Four types of receptor proteins for viruses to attach to
- LPS
- OmpF
- TolC
- Flagellar motor
- receptor specificity drives host range specificity and tissue topism
How do you monitor virus growth?
Batch culture: culture medium + host cells + virons → count # free virons at different points in time
How to count viral particles?
Plaque assay
* bacteriophage: add free virons into solution to make phage stock → add e.coli in rich browth culture → add phage-infected bacteria into liquid agar and pour mixture onto agar plate → incubate overnight
* animal cells: Animal cells: grow monolayer of animal cells first → on top add liquid medium with virus mixed in → after infection, removing viral medium → add gelatin medium and identify plaques
* Results:
- if there are plaques (zones of clearance in an other wise smooth bacteria lawn = sign of viral infection) → count number of plaques ($10^6$ phages per one bacteria)
- if the plaques are far apart → low MOI (multiplicity of infection)
Cyopathic Effects (CPE)
- Structural changes to animal cells by viral infection
- culture human cells on plate → infect with poliobirus → imaged by phase conrast microscopy at different times post infection → compare to uninfected control culture
- Results: Uninfected cells have an oblong shape and are attached → after infection, circular and detached → after lysing, dead cells cump together and plaques form
How to visualize viral infection of animal cells?
- Cyopathic Effects (CPE)
- GFP - tagged viral capsid protein: infect lawn of host cells → visualize by fluorescence microscoppy
Bacteriophage Growth Curve
Animal Virus Growth Curve
What are specific virus steps antiviral can target?
- block binding/invasion
- block RT
- block integration
- block capsid maturation
AZT (azidothymidine) - what mechanisms does it inhibit as an anti-retroviral?
- azt binds to RT and blocks DNA synthesis
- inhibit protease cleavage (necessary enzyme for capsid assembly)
Cryo Electron Microscopy
- Virus is preserved at cold temp and then frozen
- allows us to see the viruses 3D space as well as the native structure
Transmission Electron Microscopy
- beam of electrons is shot at virus
- allows us to see their 2D shape
Mechanism of transformation: Gram (+) bacteria
- transforming double strand DNA binds to Transformasome (DNA binding protein and pore) → DNA is cut into a single strand DNA and taken in by competence specific sssDNA binding proteins → RecA protein recombines DNA into bacterial plasmid
Mechanism of transformation: Gram (-) bacteria
pilus binds to dsDNA and retracts → dsDNA unwinds and becomes ssDNA when entering cytoplasm → RecA integrates ssDNA to homologous site
Transposable elements
- Barbara McClintock: Mobile DNA fragments within the genome
Modes of disease transmission
- contact transmission
- vehicle transmission
- vector transmission
Contact transmission
- Direct contact
- indirect contact by fomites
- droplets
Vehicle Transmission
- Waterborne
- Airborne, including dust particles
- Foodborne
Vector Transmission
- Mechanical (on insect bodies)
- Biological (microbes multiply inside of living vector body)
What are the stages of infection?
- incubation: time between acquisition of the pathogen and onset of symptoms (can still be contagious here)
- prodome stage: nonspecific symptoms (fever or tiredness)
- period of invasion: disease-specific symptoms increase and height of viral load
- convalescent: ultimate recovery and symtoms disappear, usually take 10 days.
Signs versus Symptoms
- Sign: objective markers (classic signs of inflammation: redness, warmth, loss of function, swelling)
- Symptoms: subjective indicator (experienced by the person)
SARS CoV-2 Characteristics
- enveloped, (+) ss RNA virus
- E, S, and M
- S-protein is how they attach to host cells and are potential antigens for therapies
SARS CoV-2 Transmission
- Contact transmission (direct contact, droplet, fomites)
SARS CoV-2 Viral Cycle
- SARS-CoV-2 uses spike proteins to attach to ACE2 (angiotensen converting enzyme 2) on host membrane and enters
- Genome is released and ribosome translates + sense RNA
- RdRp also transcribes the negative sense strand
- replicated + sense RNA is then assembled and released
SARS CoV-2 Viral Load and Antibodies
SARS CoV-2 Diagnostic Tests
- PCR - amplifies and detects RNA from host secretion sample
- Antigen test - newer test that detects for viral proteins
- Antibody tests - determines if individual has had past infection
SARS CoV-2 Therapeutic Strategies
- dexamethasone: inhibits inflammatory cytokines and neutrophil infiltration
- chloroquine or hydroxychloroquin: prevents virus from entry and encoding
- remdesivir, ribavarin, or favipiravir: inhibits RdRp (most success)
- monoclonal antibody: neutralizes the virus
SARS CoV-2 Vaccines Strategies
- Pfizer (mRNA)
- Moderna (mRNA)
- J&J (adenovirus)
- Novavax (protein)
- Pfizer and moderna are most effective
Differences between Archaea, Eukarya, and Bacteria
- Cell membrane: Archaea have an entirely different cell membrane structure (ether linkage) than bacteria and eukarya (ester linkage). Archaea also have monolayer or bilayer membranes.
- Inhibitors that affect translation: Archaea sensitivity to inhibitors is more similar to eukaryotes
- RNA polyemerase: SDS page shows that archaea RNA polymerase is a mixture of bacteria and eukaryote RNA polymerase
