Week 3 => viral genomes, Endosymbiotic, Symbiosis and Genome Reduction Flashcards
Viruses
Viruses are entities whose genomes are elements of nucleic acid that replicate inside living cells using the cellular synthetic machinery and cause the synthesis of specialized elements [virions] that can transfer the genome to other cells
Virion
a complete virus particle that consists of an RNA or DNA core with a protein coat sometimes with external envelopes and that is the extracellular infectious form of a virus
Baltimore classification
dsDNA
ssDNA
dsRNA
(+) ssRNA
(-) ssRNA
ssRNA-RT (DNA intermediate)
dsDNA-RT (RNA intermediate)
Viruses are classified according to ____
- Nature of genome and flow “information”: The Baltimore classification (1971)
- shape and capsid structure
- presence/absence of envelope
Trend of host and Baltimore class of virus
There is no trend, very uneven distribution of virus genome type to host type
Virus abundance
- 10 million viral particles per mL of seawater, all virus in ocean contain more carbon than 75 million blue whales
- viruses are by far the most abundant biological entities in the oceans, comprising of 94% of the nucleic-acid-containig particles. HOWEER, because of their small size they only comprise approximately 5% of the biomass
‘Typical’ features of viral genomes
- There are no typical features! genomes can be linear, circular, or alternate between the two (retrovirus becoming provirus)
- Gene density is high
- Compositionally biased (e.g., A/T or G/C rich)
- Fast-evolving, divergent gene sequences
- Viral genomes are extremely diverse
Provirus
Viral form when a retrovirus reverse transcribe RNA genome and incorporate DNA into host genome
‘Types’ of viral genes
- Genes with detectable homologs in cellular life forms (i.e., detectable by molecular phylogeny)
- Virus-specific genes (no detectable holomlogs)
ORFans
Open reading frames
Homologs
Biological features, such as genes or chromosomes, that are inherited from a common ancestor
Hallmark genes
The hallmarks summarize information across multiple gene sets by emphasizing genes that display coordinate expression and represent well-defined biological processes.
NOTE: there are not many viral hallmark genes, and no such genes are shared y all viruses
What are the relative frequencies of these types of genes (virus specific genes)?
It depends on the virus. The bigger the genome, the more ORFans there are (proportionately). ‘Moderate’ to ‘large’ viral genomes are often >80% ORFan genes
Family ‘giant viruses’ belong to?
Nucleo-cytoplasmic large DNA virus (NCLDV) family
What type of genome do all giant viruses have?
dsDNA
List 4 of the largest known viral genomes
1) Pandoavirus salinus (Pandoraviridae)
2) Megavirus chilensis (Mehaviridae)
3)Cotesia congreta bracovirus (polydaviridae)
4)Baccilus mageterium phage G (Caudovirales)
Mimivirus
- Giant virus in amoebae
- ‘Mimicking microbe’ (Gram-stain-positive)
- dsDNA virus
- 400 nm particle size
- 1181404 base pair genome sequence
- 1262 putative open reading frames, 10% which exhibit a similarity to proteins of known functions
- Presence of numerous genes encoding central protein-translation components including four amino-acyl transfer RNA synthases, peptide release factor 1, translation elongation factor, EF-TU, and translation initiation factor 1
- Genome exhibits 6 tRNAs
- Size and complexity of the genome challenge the established frontier between viruses and parasitic cellular organisms
Pandoraviruses
- Amoeba viruses with genomes up to 3.5 Mb reaching that of parasitic eukaryotes
- micrometer-sized ovoid particles contain DNA genomes of at least 2.5 to 1.9 megabytes
- > 93% of the 2500 genes are ORFans
- 16 genes were found to have spliceosome (i.e., eukaryotic) introns
- Some (but not all) of the translation-associated genes found in mimivirus were found in Pandora virus (And vice versa)
Example of a mimivirus gene that appears to be of host (i.e., eukaryotic) origin
Mimivirus tyrosyl-tRNA synthase gene
Three groups of giant viruses
- mimiviruses
- pithoviruses
- pandoraviruses
Key observations from investigating the genomes of the three groups of giant viruses
1) for a given viral genome, most of the genes that can be analyzed phylogenetically (which is not many) exhibit greatest similarity to eukaryotic genes, not to genes in other giant viruses
2) very few genes in giant viral genomes are most similar to those in other viruses
Virus as fourth domain of life or ‘bags of genes’? study observations/message
- translation-associated gene sin giant viruses exhibit a ‘patchy’ distribution (present in some, but not others)
- ‘Universal’ genes (i.e., those with homologs in at least two of the three domains of life) have been independently acquired by different giant viruses from their eukaryotic hosts (often Acanthamoeba, the host of mimiviruses and pandoraviruses)
- Each group of giant viruses appears to have evolved from viruses with substantially smaller gene repertoires
Yaravirus
- 80 nm amoeba virus with near-complete “ORFan genome”
- 6 tRNAs (no not match commonly used codons)
- 44924 bp dsDNA genome encoding for 74 predicted proteins
- 90% of yaravirus genes have never been described before, representing ORFans
- only 6 genes had distant homologs in public database
What are the six yaravirus genes that have distant homologs in public database?
an exonuclease/recombinase, a packaging-ATPase, a bifunctional DNA primase/polymerase and three hypothetical proteins
Virophage
- virus of viruses
- a unique parasite of the giant mimivirus
icosahedral small virus, sputnik, 50 nm in size - Considering its functional analogy with bacteriophage, we classify this virus as a virophage. The virophage could eb a vehicle mediating lateral gene transfer between giant viruses
Sputnik
- the sputnik genome is an 18.343 kb circualr dsDNA and contains genes that are linked to viruses infecting each of the three domains of life Eukarya, Archea, and Bacteria
- does not infect Acanthamoeba, it infects mimivirus
- Sputnik gene transcription and replication appears to be performed and regulated by mimivirus-encoded machinery
Mamavirus
=mimivirus (just from different type of Achanthamoaba)
The “dual hypothesis of lichens”
suggestion that lichens are not single organisms, but a compound of a fungus and an alga
Evolution by association
“the living together of unlike organisms”
The symbiotic perspective on evolution, which argues that “higher species” have evolved from a merger of two or more different kinds of organisms living together, is now clearly established with definitive molecular evidence demonstrating that mitochondria and chloroplasts have evolved from symbiotic bacteria.
Symbiogenetics
The study of the genetic systems that result from the co-evolution of organisms from different species. It’s a new research field that focuses on how nonrelated organisms integrate their genomes.
Three foundational organelles
the mitochondria, the photosythetic plasmid, and the basal bodies of flagella were themselves once free-living (prokaryotic) cells
Autogenous (classical) model
proposed that the ancestral eukaryotic ell was photosynthetic, having evolved from cyanobacterium-like prokaryote
Internal features of the eukaryotic cells evolved from within the cell, and were inherited in a vertical fashion
Xenogenous (symbiotic) model
Proposed that mitochondria and chloroplast were derived from prokaryotes by endosymbiosis (also possibility that the flagella of eukaryotes were endosymbiotic)
Genome reduction occurs from ___
deletion events
Genome reduction is common in ____
Intracellular Bactria, such as obligate intracellular pathogens and endosymbionts
What does genome reduction contribute to in bacteria?
The evolution of strictly host-dependent bacterial variants
Mutations, rearrangements is seen in ___ of bacteria
All lifestyles
Endosymbionts
- organisms that form a symbiotic relationship with another cell or organism.
- are symbionts that live within the tissues or cells of their host for part of their life cycle.
- Endosymbionts that can replicate withing hist cells are termed intracellular. Of these intracellular associates, certain highly specialized ones have lost the ability to replicate outside of host cells and are obligate intraceullar
Gene acquisition by HGT (GEI and Plasmid) is seen in ____
Extracellular bacterium, facultative pathogen, symbiont
Symbiont
- an organism that is very closely associated with another, usually larger, organism
- Any species that lives in close association with another. broadly speaking, symbiosis includes obligate and facultative relationships that are parasitic, mutualistic or commensal.
Mycoplasma and the ‘minimal genome’ concept
The minimal set of genes that can support the basic cellular processes of a FREE-LIVING organism in a ‘rich’ growth medium and in the absence of any selective pressure
Mycoplasma genitalium
a human urogenital pathogen
How do genomes get so small so so odd?
- mutational biases
- deletion biases
- Population genetics
- “how the bacteria make a living”
Aphids nutritional symbiosis
Aphids feed on plants, they suck the sap out of the phloem. this diet is rich in carbohydrates and deficient in amino acids. Some of these amino acids cannot be synthesized by the insect but are supplied by the intracellular symbionts Buchnera aphidicola.
What are Aphids intracellular symbiont?
Buchnera aphidicola
What is endosymbionts of insects characterized by?
Their occurrence in specialized host cells called bacteriocytes
What are bacteriosomes (or mycetomes)?
Bacteriocytes are sometimes grouped into organ-like called bacteriosomes that occur in the body cavity of aphids and in the anterior gut region of tsetse flies.
Obligate mutualism
Obligate mutualism is a special case of mutualism where an ecological interaction between species mutually benefits each other, and one or all species are unable to survive without the other. In some obligate relationships, only one species is dependent on the relationship.
Wigglesworthia
The bacterial endosymbiont in Tsetse flies, the bacteria provides B-complex vitamins
Blochmannia
The bacterial endosymbiont in certain ants, the bacteria may provide amino acids and fatty acids
Sitophilus oryzae
The bacterial endosymbiont of weevils, the bacterial provides vitamins and increases host mitochondrial enzymatic activity
What are gamma-proteobacteria most important for in insect nutritional symbioses?
- Cofactor, protists groups, and carriers
- Purine, pyrimidines, nucleotides and nucleosides (amino acid synthesis)
Obligate intracellular pathogens
- Cox. brun.
- Anapl. marg.
- Ehrl. rumin
- Wolb. wMel
- Rick. con
- Rick. prow.
- Rick. typhi
- Chlam. murid
- Chlam. pneum.
- Chlam. trach
- Chlam. cav.
- Phytopl. aster
- Myco. leprae
Obligate intracellular mutualists
- Block. flor
- Bloch. penn.
- Buchnera BP
- Buchnera SG
- Buchnera AP
- Wiggles. brev.
- Wolb. wBm
- Parachlamydia sp
What type of obligate intracellular mutualists contribute the most to amino acid synthesis?
Gamma-Proteobacteria
Insect nutritional symbiosis with two distinct symbionts
Both symbionts ‘definition’ in their own way but nevertheless complementary: they help the insect and each other (example sharpshooter insects)
Homalodisca coagulata (Glassy-Winged sharpshooter)
- has two distinct symbionts (Sulcia muelleri and Baumannia cicadelinicola), and have complementary metabolic capabilities
Sulcia genes associated with essential amino acid biosynthesis
- Leucine
- isoleucine
- Lysine
- Arginine
- Phenylalanine
- Tryptophan
- Threonine (and homoserine)
- valine (and 2-ketovaline)
Baumannia genes associated with essential amino acid biosynthesis
- Methionine (from homoserine)
- Histodine
Sulcia genes involved in vitamin/cofactor biosynthesis
Menaquinone (from DHNA and polysioprenoids)
Baumannia genes involved in vitamin/cofactor biosynthesis
- CoA (from k-ketovaline)
- Biotin
- heme (partial)
- glutathione
- Thiamin
- Riboflavin
- BH4 precursor
- Folate
- pyridoxal 5’-P
Between Sulcia and Baumannia which is more involve din amino acid biosynthesis and which i smore involved in Vitamin/cofactor biosynthesis?
- Sulcia = Amino acids
- Baumannia = vitamin/cofactor
Massive gene decay in the leprosy bacillus
- The Mycobacterium leprae lineage has recently discarded more than 2000 genes
- less than half of the genome contains functional genes but pseudogenes with intact counterparts in M. Tuberculosis, abound.
- Gene deletion and decay have eliminated many important metabolic activities
commensal symbiont
A symbiont that benefits from an association withing conferring a serious disadvantaged or advantage to the host
Mutualist
A symbiont that provides a benefit tot he host and, in turn, benefits from the association
Obligately intracellular
An organism that replicates exclusively within a host cell
Parasite
A symbiont that propagates by causing some degree of harm to the host
Genetic drift
This described the changes in the frequencies of alleles or genotypes as a result of chance alone. This stochastic effect plays an especially important role in small populations, in which can accelerate the fixation of slightly deleterious mutations
Reductive evolution
A conceptual framework that considers the evolutionary and molecular mechanisms that drive genome streamlining in most intracellular bacteria. Current views suggest that gene loss reflects relaxed selection in dispensable traits, elevated mutation pressure, and even the loss of beneficial function mutations as a result of genetic drift in small bacterial populations. furthermore, reduced recombination documented in some intracellular associates might prevent the recovery of lost alleles of gene regions
Extensive genome reduction can occur on a _____evolutionary time scale
Short
Serial passage procedure:
- bacteria grown on agar with repeated one-cell bottlenecks (various wild-type and mutS mutant strains)
- each day random colonies were picked and streaked onto new plates (up to 270 times, and approximately 25 generations per cycle)
- Cells at various time points were saved and frozen for future investifation
- Genomes analyzed with microarrays, DNA sequencing, Southern Hybridization and pulsed-filed gel electrophoreisis
