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Class 1
dsDNA genomes - Genome replication and transcription utilize the same mechanism as host cells; depending on cell types infected can often use the host's DdDp and DdRp.
Class 2
ssDNA (+ and -) genomes, most are (+)ssDNA - Transcription would yield (-)mRNA so need to form a replicative intermediate = dsDNA -> used as template for transcription and genome replication.
Class 3
dsRNA genomes - Must encode and carry RdRp for transcription and genome replication.
Class 4
(+)ssRNA genomes - Must encode RdRp for transcription and genome replication; Genome = mRNA but only 1 copy enters cell; upon entry, the RdRp gene is immediately translated -> copies genome to (-)ssRNA, then to (+)ssRNA.
Class 5
(-)ssRNA genomes - Must encode and carry RdRp for transcription and genome replication; RdRp carried in virion makes (+)ssRNA copies of genome following entry = mRNAs and used as templated to produce (-)ssRNA genomes.
Class 6
Retroviruses, (+)ssRNA genomes - Must encode and carry RdDp (reverse transcriptase) enzyme to convert genome to dsDNA following entry; dsDNA provirus integrated into the host genome; transcription and genome replication are performed using the host DdRp.
Class 7
Reverse-transcribing DNA viruses, dsDNA genomes - Transcription performed by the host DdRp; Virus encodes RdDp that synthesizes DNA genomes from genome-length transcripts.
Viruses first appearance
~4 billion years ago - after cells.
RNA world hypothesis
Where RNA was the main genetic material, and they may have played a role in the transition from RNA to DNA.
Gene transfer mechanism
Viruses could have evolved to facilitate gene transfer among organisms, enhancing genetic diversity and host fitness, mostly in prokaryotes.
Lytic and latent evolution
May have been primarily latent, evolving lytic capabilities later to spread more effectively to new hosts.
φX174 replication
Uses rolling circle replication to convert its ssDNA genome into a double-stranded form, which then serves as a template for producing more ssDNA genomes; causes lysis of the host cell through inhibition of peptidoglycan synthesis, leading to the release of new virions.
M13 replication
Also employs rolling circle replication, BUT, maintains its ssDNA form throughout the process; releases virions without lysing the host cell, allowing the infected cells to continue growing and resulting in chronic infection.
T7 replication
Utilizes rolling circle replication to form concatemeric DNA with terminal repeats; a phage-encoded nuclease cuts the concatemer into individual linear dsDNA genomes for packaging into capsids; causes cell lysis through phage-encoded holin and lysozyme, releasing new virions.
Mu replication
Can replicate via lytic or lysogenic pathways; in the lytic cycle, it causes cell lysis; in lysogeny, it integrates into the host genome; replication involved transposition, where the Mu transposase integrates the viral genome into multiple sites in the host DNA.
Pox Viruses replication
Replicate entirely in the host cell cytoplasm; they carry their machinery for DNA replication and transcription, as they cannot rely on the host's nuclear processes.
Adenoviruses replication
Replicate in the nucleus of the host cell; they utilize a unique mechanism involving leading strand synthesis on both DNA template strands.
SV40 replication
SV40 is a circular dsDNA virus that replicates in the nucleus using the host's DNA polymerase; it involved both leading and lagging strand synthesis, with early viral genes expressed first to produce proteins necessary for replication.
Herpesviruses replication
Herpesviruses are large, enveloped dsDNA viruses that also replicate in the nucleus; they utilize a rolling circle mechanism to produce concatemeric DNA.
Poliovirus replication
Entry: endocytosis after receptor binding; Replication: translated into a polyprotein in the cytoplasm; RdRp synthesizes (-)ssRNA for new (+)ssRNA genomes; Release: cell lysis.
Coronaviruses replication
Entry: endocytosis after receptor binding; Replication: similar to poliovirus; polyprotein is cleaved, and RdRp synthesizes (-)ssRNA; Release: budding from the cell membrane.
Rabies virus replication
Entry: endocytosis after receptor binding; Replication: viral RNA is transcribed into mRNA and (+)ssRNA in the cytoplasm; Release: budding.
Influenza virus replication
Entry: endocytosis after binding to sialic acid receptors; Replication: transcription occurs in the nucleus; segmented genome allows reassortment; Release: budding.
Hepadnaviruses replication
Entry: nucleocapsid enters the nucleus; Replication: the viral genome is completed and transcribed into mRNAs; RdRp synthesizes (-)ssDNA; Release: budding.
Reoviruses replication
Entry: endocytosis; Replication: transcription occurs within the viral particle; mRNA is translated, the new dsRNA is synthesized; Release: cell lysis.
Phages contribution to ocean ecology
Regulation of bacterial populations: Phages act as natural predators of bacteria, controlling their populations and maintaining microbial balance.
Nutrient cycling
When phages lyse bacterial cells, they release organic matter, which provides nutrients for other microbes, enhancing nutrient cycling.
Genetic exchange
Phages facilitate horizontal gene transfer among bacteria, increasing genetic diversity and allowing for rapid adaptation to environmental changes.
Impact on microbial food webs
By influencing bacterial abundance, phages affect the structure and dynamic of microbial food webs, which are crucial for oceanic primary production.
Biogeochemical processes
Phages contribute to biogeochemical cycles, such as carbon and nitrogen cycles, by enhancing the turnover of organic material.
Bacterial strategies against phages
Bacteria use enzymes to cut foreign phage DNA; incorporate phage DNA sequences to recognize and target phages in future infections; mutate surface receptors to prevent phage binding; create protective biofilms that shield them from phage attacks; produce a polysaccharide capsule to block phage access.
Phage strategies against bacteria
Some phages evolve proteins to inhibit bacterial CRISPR defenses; adapt their binding proteins to attach to various bacterial strains; choose to destroy the host or integrate into its genome, allowing persistence; rapidly adapt through genetic changes, enhancing their ability to infect hosts.
PAMP and DAMP
What is a PAMP and DAMP?
PAMP
Conserved molecular structures found on pathogens that are recognized by the immune system.
DAMP
Molecules released by damaged or dying cells that signal tissue injury and activate the immune response.
Bacteriophages
Viruses that infect bacteria, found in the gut and microbiome.
Adenoviruses
DNA viruses that cause respiratory infections.
Herpesviruses
DNA viruses that cause herpes.
Papillomaviruses
DNA viruses that cause skin warts and cervical cancer.
Rhinoviruses
RNA viruses that cause the common cold.
Coronaviruses
RNA viruses that cause COVID-19.
Influenza viruses
RNA viruses that cause the flu.
Animal viruses
Viruses that can be transmitted from animals to humans, known as zoonotic viruses.
Plant viruses
Viruses that infect plants and are often ingested through dietary intake.
Vibrio cholerae
A phage that is harmful to humans and is the causative agent of cholera.
Viriods
The smallest known infectious agents, consisting of a short strand of circular, single-stranded RNA without a protein coat.
Prions
Infectious agents that consist entirely of protein and cause diseases in animals and humans.
Mutation
Heritable change in a DNA sequence that can lead to a change in phenotype; can occur spontaneously or via horizontal gene transfer.
Mutant
A cell or virus derived from the wild-type strain that carries a nucleotide sequence change.
Genotype
Genetic composition of an organism (genetic blueprint).
Phenotype
Observable physical or biochemical traits of an organism (observable characteristics).
Selection
A powerful genetic tool that allows the isolation of a single mutant from a population of millions/billions of cells (selectable mutations).
Screening
Isolation of non-selectable mutants requires laborious, time-consuming screening (examining large numbers and looking for differences).
Silent mutation
Change the nucleotide sequence, but do not affect the amino acid sequence of the encoded polypeptide so do not change the phenotype.
Missense mutation
Change the sequence of amino acids in a polypeptide as a result of nucleotide changes; can affect protein structure -> change the phenotype.
Nonsense mutation
Change the nucleotide sequence to a stop codon; typically results in truncated (incomplete) proteins that lack normal activity.
Same-site revertants
Phenotype/activity-restoring mutation occurs at the same site as the original mutation.
Second-site revertants
Phenotype/activity-restoring mutation occurs at a different site in the DNA than the original mutation.
Suppressor tRNAs
tRNAs that can suppress nonsense mutations by changing the anticodon sequence to base-pair with a stop codon.
Chemical mutagens
Substances that cause mutations through nucleotide base analogs or alkylating agents, leading to DNA sequence changes.
Radiation
Energy that can cause mutations in DNA, including nonionizing (UV) and ionizing radiation (X-rays, cosmic rays, gamma rays).
Transformation
free DNA released by one cell is taken up by another cell
Transduction
DNA transfer mediated by a virus
Conjugation
DNA transfer involving cell-to-cell contact and a conjugative plasmid in the donor cell
Homologous recombination
Process that results in genetic exchange between homologous DNA sequences from two different sources
RecA
Essential protein for homologous recombination
Holliday junction
Intermediate during homologous recombination that can be resolved in either direction
Molecular Koch's postulate
The suspected causative agent must be absent from all healthy organisms but present in all diseased organisms
Transduction frequency
Used in the past to map genes on the chromosome
Phage conversion
Alteration of the phenotype of a host cell by lysogeny
Hfr strains
Strains that facilitate conjugation and DNA transfer
F plasmid
An episome that can integrate into the host chromosome
Insertion elements
Simplest transposable elements, ~1000 nucleotides long with inverted repeats
Transposons
Larger than IS elements but have the same two essential components
Conservative transposition
Transposon is excised from one location and reinserted at a second location; copy number remains constant
Replicative transposition
A new copy of the transposon is produced and inserted at a second location while the original remains
Transposon mutagenesis
Used to identify genes involved in biofilm formation
Genetic engineering
Using in vitro techniques to alter genes in the laboratory
Insulin
The first human protein produced in bacteria, crucial for treating diabetes
Human growth hormone
Used to treat growth abnormalities, cloned from mRNA and expressed in bacterial systems
Erythropoietin
Hormone that stimulates red blood cell production, produced in engineered microbes
Transgenic organisms
Genetically engineered plants or animals containing a gene or genes from other organisms
Gene mining
The process of identifying and isolating potentially useful genes from the environment
GMO biocontainment mechanism
Genetically engineered to code for synthetic amino acids which must be supplied
TAG codons
Stop codons that can be replaced to facilitate biocontainment in GMOs
Transposon insertion
Causes a change in the gene sequence leading to mutation
Biofuel production
Engineering microbes to convert cellulose to sugars and ferment them to ethanol
Antibodies in microbes
Certain antibodies can be produced in microbial systems for therapeutic purposes
Vaccines from engineered microbes
Produced using genetically engineered microbes that express specific antigens