General info about viruses
- Acellular, cannot replicate alone, hijacks host cellular machinery to replicate
- Displays tropism-interacts with specific hosts/host ranges
-Specificity of interaction determines host range
-genomes have wide range, varies from innocuous to lethal
-can impact gene expression
general structure of viruses
○ Protein coat (capsid) surrounds nucleic acid
○ Enclosed in protein-containing membrane (enveloped) or not (naked)
§ Tegument: cluster of proteins that lines space between capsid and viral envelope
○ Nucleic acid either RNA or DNA
how are viruses classified?
Nature of genome: All cells + viruses need to make mRNA to make protein, viral mRNA produced from viral genome inside host
Relationship between genome and mRNA produced is central to Baltimore Virus Classification System
* Viral structure ○ Filamentous, helical capsid symmetry ○ Genome is coiled, can very in size ○ Icosahedral capsid * Presence/Absence of envelope
Size of viral particle
group of viruses to know
Group 1. Double stranded DNA viruses
§ Bacteriophage lambda: infects E coli § Chloroviruses: infect algae, controlling algae blooms § Herpes Viruses: causes chickenpox, genital infections, and birth defects § Papillomavirus: strains cause warts and tumours
Group 4: (+) sense single-stranded RNA viruses
§ Coronavirus such as SARS-CoV-2 cause severe respiratory disease
§ Flaviviruses: cause hepatitis C, Zika fever, West Nile disease, yellow and dengue fever
Group 5: (-) sense single-stranded RNA viruses
§ Filoviruses: Ebola virus cause severe hemorrhagic disease
§ Orthomyxoviruses: causes influenzas
Group 6: Retroviruses (RNA reverse-transcribing viruses)
§ Lentiviruses include human immunodeficiency virus (HIV_: cause of aids
Viral infection and reproduction of influenza
-Attachment: virus attached to target cell
-Penetration: cell engulfs by endocytosis
-Uncoating: viral contents released
-Biosynthesis (complicated by presence of an envelope): viral RNA enters nucleus, replicated by viral RNA polymerase
-Assembly: new phage particles assembled
-Release (mechanism determines what kind of virus: viral particles released, cell continues to make new virus
Life cycle: the tailed phage
- Attachment to specific host cell receptors (that play role in normal cell function)
- Phage genome is injected through the cell wall and membrane and capsid is shed
- Undergoes two different types of life cycles
- Lytic cycle
○ rapid phage replication and host cell lyses, ex T2, T4, ebola - Lysogenic cycle
○ phage infects and inserts its DNA into host chromosome as prophage (copy of genetic material)
○ Activated to excise and follow lytic life cycle by triggers
○ Ex: phage lambda - Can either go through lytic or side track into lysogenic and wait to be released and back into lytic cycle
Mutualism, what is it and example
Example: Lichen
* Formation consists of fungus, algae, and bacteria (cyanobacterium in this case)
* Fungus provides minerals and protection from UV
* Bacterium and/or alga provides photosynthetic nutrition
* Checklist:
○ Removal of one partner=death or reduced growth of other
○ Interdependent of each other
○ Genomes of each species show advanced degeneration
○ Products produced by one partner is utilized by the other
Synergism, what is it and example
both species benefit through growth, but partners easily separated, can grow independently
Example: cow rumen microbiome
* Rumen bacteria ferment complex polysaccharides from grass, making H2 and CO2, methanogens convert these gases to methane Cow benefits because it can eat and digest hay and grass, rumen benefits from being provided an anaerobic atmosphere and is taken care of living in the cow
Commensalism, what is it and example
one species benefits, partner nether benefits or is harmed
Example: Beggiatoa and other sulfur spring microbes
In ecosystems with high concentrations of toxic H2S, microbial mats containing sulfur oxidizers reduce the toxicity and allow growth of other species
Amensalism, what is it and example
one species benefits, other is harmed, interaction is non-specific (will kill anything in its way)
Example: Streptomyces and other soil bacteria
* Streptomyces are prolific producers of natural antibiotics, use molecules to kill and lyse other bacteria in the soil, releasing their nutrients for consumption by the Streptomyces
Parasitism, what is it and example
one species benefits, other is harmed, interaction is specific and usually obligatory for the parasite
Example: Legionella pneumophila, ameba’s and human lung macrophages
* Causative agent of Legionnaire's disease, usually infects freshwater amoebas, can affect lung macrophages * Infection source- usually contaminated air conditioning
endosymbiosis
- Many insect species infected by intracellular bacteria-endosymbionts
- Wolbachia occur naturally in almost 50% of insect species, have evolved where it provides nutrients for some insects
○ Useful to fight against malaria
○ Reduces lifespan of mosquito and disease
Can see each other’s genomes in the other
- Wolbachia occur naturally in almost 50% of insect species, have evolved where it provides nutrients for some insects
general info of microbiomes, what are they, where are they found, how are they formed?
- Microbes form foundation of all earth’s ecosystems
○ Soil, water, air, bodies of plants and animals- In nature, microbes never found as single species ecosystem, they form microbial ecosystems or microbiomes
○ Are microbial collectives
Can contain bacteria archaea, fungi, protists and viruses
- In nature, microbes never found as single species ecosystem, they form microbial ecosystems or microbiomes
What is the ‘omics revolution?
The use of high-throughput (multiple of the same reaction at same time) methods to look at molecular signatures of microbes
3 Main Questions of the ecosystems-microbiomes-that are studied
- Who is there?
- What are they doing?
- How do they respond to different conditions? (in response to each other and environment)
- What molecules can be used to figure this out?
○ RNA DNA proteins etc.
DNA sequencing
Ecosystem is sampled, gDNA extracted and subjected to either:
A. Amplicon sequencing -Target gene amplified, barcoded, sequenced
B. Metagenomic (shotgun) sequencing
-Extracted gDNA broken into bits, barcoded, directly sequenced
-Computer is used to pull out signature genes from sequenced pool
Both reveal alpha diversity or species richness, evenness and dominance,
used as screening technique
Who is there/methods
Culture
-The Great Plate Count Anomaly”
-Culture techniques not supportive of many bacterial species, they find lab conditions too alien to survive
-Some are oligotrophs (can only survive in environment with low amounts of nutrients)
-Some depend directly on/are inhibited by other species
-Some are non-viable, or viable but not culturalable
-high-throughput culture or culturomics
-Reduces labour intensity (use AI + robots)
-Allows culture under many different conditions
-Allows picking of thousands of colonies into multi-well plates
RNA sequencing
-Extract the RNA from a community
-Transcribe to DNA (using a viral reverse transcriptase enzyme)
-Barcode and sequence
-Match transcripts to known genomes
Benefits: who’s there and who’s alive to transcribe at the moment
how to know what
microbiomes doing?
Predictive
○ Look at metagones, use powerful computer to match MAGs (metagenome-associated genomes) to predict possible functions
○ Pros: lots of info, seeing proteins that are transcribed/made
Direct
○ Proteomics
§ Extract all proteins in sample, sequence peptide fragments using mass-spectrometry § Computer to match peptides to proteins and proteins to genes
○ Metabolomics (metabonomics)
§ Extract all molecules in sample § Subject directly to mass-spectrometry or NMR spectroscopy § Use powerful computer to match compound signatures from obtained spectra to standards
○ Metatranscriptomics (RNA-Seq)
mRNA content reflects active transcription-what the cells are doing/making in response to the environment
Secretome
the collection of proteins and other biological factors that are released by a cell, tissue, or organism into the extracellular space
Lipidome
the collection of all lipids in a cell, organ, or part of a cell
Resistome
a collection of antibiotic resistance genes (ARGs) in a microbiome
Multi-omics integration
- Carry out multiple ‘omics studies on given sample, longitudinally
- Integrate metadata into analysis
Metadata: all info of nutrition, environment, etc.
- Integrate metadata into analysis
Phenome
he collection of observable characteristics of an organism, including the physical and chemical results of how genes interact with an individual’s environment
