Kostas — NUMTs — mtDNA sequences integrated into nuclear DNA. Ongoing research around which nuclear regions are most susceptible to NUMT invasion. Role for AT, including TAT motif? Variability in NUMT size — larger NUMT probably implies more recent inclusion. Nuc Acids Res paper “Mammalian NUMT insertion is non-random”. https://pubmed.ncbi.nlm.nih.gov/22761406/ Debate around whether there is a link between placement of NUMTs and action of retrotransposons. NAR says that NUMT insertion regions have predicted high DNA curvature, open chromatin, often next to A+T. Flanking regions rich in transposons — do NUMTs insert into transposons or do transposons come afterwards? Is this good, bad, or neutral for nDNA? Can we learn this from the distributions of NUMT content across species?
Fewer in parasites, lots in eusocial? Artefacts?
How do we lose these things after we’ve gotten them? Just through recombination?
(Also NUPTs)s
Belén — transposons. Do exist in bacteria, carrying genes for e.g. AMR. Curcubita mtDNA have transposons from nDNA insertions. Nice article https://academic.oup.com/mbe/article/27/6/1436/1116867?login=true 6.4% and 2.1% nDNA sequences, mostly retrotransposons. How are these controlled? Coding vs noncoding features?
Question 1.
Why might different genome structural choices (high/low GC content, intergenic spacing, lots/few introns, etc) be good or bad for different organisms?
Sophie– GC Content. Extremophiles having high GC content- there are some that don’t have a high GC content.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1360284
-experimental work, hope binding behaves across temperature/salt content
https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.0c07670- theoretical content on binding behaviours
Increased GC content leads to stacking structures, making it more stable. Theoretical work shows hydrogen bonds between double strands offers stability. GC content important for stability under extreme conditions. Euks don’t have such a big struggle with how tight their binding is in their DNA, as they have well-packed DNA anyway.
https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.0c07670- GC content in plants. GC content scales with size of plant genome, lacking on detail for reason for it. Fig3. shows GC content varies with habitat of the plant (thermodynamic stability, based on environ. conditions). Increased GC content, more stress resistant.
https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.0c07670 GC bindings are more sensitive to mutation, more likely to mutate to AT. Seems counter intuitive?
Iain– Systematic pressure for C->U->T. This is just an asymmetrical bias.
Metabolism building these bases are not the same, some of the bases are harder to build than others.
Back to Sophie–Bacteria have 25-75% difference in GC content, hypothesis based on difficulty of generating AT compared to GC. https://www.sciencedirect.com/science/article/pii/S0168952502026902
Robert– GC content + Flexibility/robustness of genome. https://www.sciencedirect.com/science/article/abs/pii/S2214540021000505 Optimising gene expression in heterologous systems. Gene transfer in the cell-> proteins of interest. mRNA stability has to be examined to maximise expression. Looks at synonymous codons across species. Codon usage affected by availability of tRNA. In optimising protein expression, you can replace the wobble base with G or C from A or T to optimise protein expression. So there is selective pressure on the wobble base (the third base in a codon). This has also been seen here: https://pubmed.ncbi.nlm.nih.gov/18289875/ But this is human gene expression in bacteria. So selective pressure, but on synthetic genes- to make more of the protein that you want from that system.
https://pubmed.ncbi.nlm.nih.gov/21535357/ (also synthetic bio)
GC content can be increased if you want to increase gene expression of your gene of interest, https://www.embopress.org/doi/full/10.15252/embr.201948220
Increase GC content at 5’ end of the gene can increase your mRNA stability, and consequent expression. https://www.cell.com/cell-systems/fulltext/S2405-4712(20)30080-6
Iain reinstates on getting to grips with the major terms/dogma of mol bio. And that GC favouring of organelles ins an epiphenomenol, and actually want to increase amount of hydrophobic AAs, of which GC are increased in the coding sequence of hydrophobic proteins.
Kostas– Helicosporidium (non-photosynthetic parasite, lives in the gut of insects) ncbi.nlm.nih.gov/pmc/articles/PMC3162594/pdf/pone.0023624.pdf Nince examples in Table 1 of GC count of plastid DNA of different species, esp helico. Has the smallest Plastid genome in viridiplantae. Some species with small gene counts (like parasites) have reduced GC content (as seen in kostas dataset). But helico is an exception to that, has a lower GC content than expected. Main genes can have higher GC count, and this is related to extromophility of the species.
Iain–
Codon bias
GC-rich codons happen to encode hydrophobic amino acids
Mutational pressure C -> T favours LOW GC contents
“This is most likely due to the strong asymmetric mutational pressure
arising from the hydrolytic deamination of cytosine into uracil,
which is converted into thymine (Reyes et al., 1998)”
(Longevity and) thermodynamic stability
“GC content has been hypothesized to modulate
longevity through its influence on the thermodynamic stability of
the mtDNA molecule (Samuels, 2005)”
Availability of nucleotides
“Also, adenine depletion has sometimes been
observed during oxidative stress (Aalto and Raivio, 1993; Ott
et al., 2007). mtDNA could thus preferentially utilize GC-rich co-
dons to optimize chemical stability of nucleic acids in the mito-
chondrion and to avoid depleting these redox-linked pools under
stress, resulting in selection for increased GC content.”
[references and quotes are given from Johnston & Williams Cell Systems paper]
GC content influences ageing, because GC content confers stability.
Bookmarked Introns for next week. Also intergenic regions and repeats
Jo–
Introns originated from selfish elements- genetic sequences that can enchange their own transmission. There is great diversity in the way they do this. Can be transposable elements, self-promoting plasmids etc. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001126#sec008 In this paper they talk about a selfish element getting horizontally transferred from bacteria ( flavorbacteria) to mitochondria of a marine heterotrophic katablepharid (https://en.wikipedia.org/wiki/Katablepharid) protist. This selfish element provides the mito with a type II restriction modification (RM) system, which provides bacteria defense against foreign DNA . Type 2 means the methyltransferase (protects DNA, anti-toxin) and endonuclease (cuts DNA, toxin) of this system are encoded as two separate proteins . (https://en.wikipedia.org/wiki/Restriction_modification_system)
If found within an organellar genome, a functional RM system could simply act to protect the genome from invasion by viruses/phages, plasmids, or other sources of foreign DNA.
This RM element could act to bias spread of the host mtDNA within the katablepharid population, and so act a gene driven in organelle genes, esp in cases of mitochondrial fusion. RM+ mtDNA could lead to digestion of unprotected RM- mtDNA, biasing inheritance of RM+.
This prediction sets out that selfish genetic elements will take up important roles in inter-organellar genome conflict.
Kostas–
https://davislab.oeb.harvard.edu/files/davislab/files/l_cai_et_al_current_bio_2021.pdf?m=1616100585 Sapria Parasitic (holoparasite, no PS) plant, large genome size. Most of the none-coding genes are ‘jumping genes’ . Shows a direct relationship to prokaryotes, and how they permit HGT (how bacteria get genes from viruses and antibiotic resistance etc). Parasitic plants also share this, by having large numbers of jumping genes- so we see ‘fossils’ of HGT in the plant genome. So can track the history and evolution by looking at the genome and these transposable elements- even looking at the parasitic relationship.
Maize has loads of transposons, and are very active in maizeHumans have around 44% of genome as transposons ( but completely inactive in humans).
Fig1 in paper, shows 60% of this parasites genome is jumping genes (transposons). Fig3, massive gene loss in ABA genes in this species. Parasitic plants have lost many genes related to the same process (stress response, PS, energetics). The more parasitic you are (ie the more on another you rely on for energy), the bigger this gene loss will be.
Sapria had biggest gene loss from across plants, 45%, and has many introns in its genome. Has no chloroplast genome, very reduced mt genome too.
Fig4. Short intron density is high for all parasitic plants shown (with high GC count), but Sapria has the most long introns. These are made up of many repeat sequences. Maybe Sapria retains many jumping genes to allow high level of HGT between it and its host?
Q to the team: Are there transposons in organelles?
Thoughts: In mammals whole mtDNA is transcribed at once, does this challenge transposon dynamics? Plant mtDNA is full of junk- are transposons part of that? What about methylation- is oDNA methylated as much as nuclear DNA? Is transposon presence on organelles linked to evolutionary stage/ lifestyle? Are there different rates of uptake of transposons, does this depend on environment i.e. environments with greater population density/multispecies mixes?
Iain– Protist machinery (as in the paper Jo linked above) can control its own oDNA mutations, as can Msh1 in corals and plants. Is there anything that organelles can do to control/have transposons etc?
Patrick Chinnery, Mark Stoneking, James Stewart (mutator mouse, so mice accumulate proofreading errors as they age)
And cross-taxa structure of plastid DNA.
Robert- homing endonucleases. Endonucleases are splicing tools for DNA, to cut DNA strands. Eg. Restriction enzymes (a subset of endonucleases) can be specific for a specific sequence of DNA. Bacteria use this against viruses, which is where we get the powerful CRISPR-Cas9 system (https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1337&context=honorstheses)
Question 2.
a. Why might the cell want organelles to proliferate with their oDNA intact?
Kostas–
https://www.nature.com/articles/s41477-019-0575-9
https://www.tandfonline.com/doi/full/10.1080/07352689.2017.1327762
oDNA mutations contribute to CMS (cytoplasmic male sterility). Happens to plants when they lose the option to produce male reproductive parts. We take advantage of it when it comes to crops, CMS plants have increased yield and can be used in breeding. Nucleus can take advantage of CMS. Mitos are involved in CMS (Jo- as is Msh1). Nucleus can express restorer-of-fertility genes, to restore fertility. So still most of the power here lies with the nucleus.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163470/ MTPTs – mtDNA genes, derived from/relation to plastids. Cells with many plastids have these sort of genes, as well as a large variety of size of plastid genes, increases the number of MTPTs. MTPTs are mainly see in land plants. Hard to do mito->plastid transfer, easier to do plastid->mito transfer
Iain– you want to maintain your existing genome to keep the tried-and-tested way of living. So organisms want an intermediate mutation rate. All of our replication machinery is under selection pressure. 1/genome length mutation rate is common across organisms.
Jo- mutations are just bad news generally. We know alot of specific mtDNA mutations that directly cause human disease. These genes are really dense ie most regions in mtDNA directly code for very important genes and all important for normal function.
Belen– https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013395 Somatic cell mutations are generated over lifetime. Iain adds that different mitochondria subtypes are found differentially over the lifetime of mice.
b. Why might organelles want the cell to proliferate with its nDNA intact?
Belen– https://febs.onlinelibrary.wiley.com/doi/full/10.1111/j.1742-4658.2009.06874.x
Intuitively, makes sense if protein import is efficient for the chloroplast (and/or mitochondria), and the set-up is working well for those organelles, it would be happy without the nDNA mutating.
c. Why might the cell want organelles to proliferate with new oDNA mutations?
Kostas– Mitochondria act like a dumping-ground of genes. Mitochondria can act to proliferate mutations., and can be a garbage- collector for genes from elsewhere in the cell (plastids, nucleus).
Belen– https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013395 Somatic mutations in mtDNA control regions, Some human pops may have evolved to keep somatic mutations in these regions to benefit from them. mtDNA sites critical for replication or transcription, mutations an these regions are found more in older pops, and is genetically controlled, correlated in parent/offspring paris. Tissue-specific Somatic point mutations in mtDNA are associated with healthy ageing, and it is genetically influenced. Degenerative ageing is caused by drastic forms of mtDNA damage, not point mutations. In this paper, correlation between mtDNA heteroplasmy and healthy ageing. Each population is specific though. The organism might want to replace mtDNA every few decades to be able to keep it without damage. https://www.fightaging.org/archives/2010/10/the-possibility-of-beneficial-mitochondrial-dna-mutations/
Mouse ageing paper– Rose, Giuseppina, et al. “Somatic point mutations in mtDNA control region are influenced by genetic background and associated with healthy aging: a GEHA study.” PLoS One 5.10 (2010): e13395.
Also another paper that shows that these somatic mutations are not harmful in mice– XXX
d. Why might organelles want the cell to proliferate with new nDNA mutations?
Tree of Life
Warnowiaceae (plankton with an organelle eye)
Octocorallia (corals with MutS) incl Corallium rubrum
Sequoiadendron giganteum
Ginkgo biloba
Monocercomonoides (mt-lacking flagellate; Cytosolic Fe-S cluster assembly system LGT from bacteria)
Reclinomonas americana
Rattus norvegicus + Bartonella
Uroderma bilobatum (tent-making bats)
Francisella tularensis (rabbit fever bacterium)
Ancoracysta twista (mt-rich flagellate)
Codariocalyx motorius (telegraph plant)- angiosperms, distributed in SE Asia, lateral leaflets move elliptically and periodically (probably to scan light intensities, or to deter predators), terminal leaves open during sunlight, movement regulated in pulvini. electric and osmotic mechanisms participate in the oscillating system.
– Neocallistamastigomycota (phylum of anaerobic funghi; symbionts (dig.tract) of larger herbivores; hydrogenosomes
– Marchantia polymorpha (cosmopolitan species; weird reproduction)
– Mixotricha paradoxa (protist, parasite, one endosymbiont: spherical bacteria functions as mitochondria; three ectosymbionts: cilia
– Striga hermonthica (hemiparasitic; LGT from sorghum; ShContig9438 is most like Sorghum bicolor; also contains genes from Oryza sativa; causes chlorosis, stunting in maize, rice, millet, sugarcane, and cowpea; grows towards hormones (strigloactones) from host root; haustorium)
– Parasitaxus ustas (conifer, family Podocarpaceae; sole species of genus Parasitaxus; only know parasitic gymnosperm; lacks roots, always found attached to Falcatifolium taxoides; photosynthetic genes lack from plastid genome; not haustorial; considered myco-heterotroph)
Marchantiophyta- (liverworts, big mt genomes)
Ectomicorrhiza- (symbiotic plant root fungi)
Amanita bisporigera– Angel of death mushroom, will inhibit your RNA polymerase and melt your liver
Anastatica hierochuntica- desert angiosperm with ability to dry out
Acantharia- Radiolaria with strontium sulphate skeleton, also an example of tertiary endosymbiosis.
Schizochytrium – a stramenopile, used to be considered a fungi, commercial use as produces DHA.
Skeletonema- chain-forming colonial genus, cosmopolitan centric Diatoms, 2 chloroplasts per cell, asexual reproduction decreases their size (due to silica based walls) up until a sexual mechanism takes over to form auxospores (whose cell wall is only lightly silicified) that help increase again their size, auxospores assist in getting them in resting stage (up to years),mutualism with bacteria
Blepharisma- genus of unicellular ciliates, pink pigmentation,photophobic, both sexual and asexual reproduction through conjugation of opposite mating types
Chondrocladia lyra (harp sponge)- carnivorous deep-sea, uses a rhizoid to anchor itself to seafloor, efficient net-like skeleton with velcro-like hooks and spines to catch prey, this skeleton is optimized to grab spermatophores from other individuals (released from terminal balls), fertilization occurs in the middle of filaments
Crithidia fasciculata (Kinetoplast, single mito- forms a tubular network)
Rhodella reticulata (red alga, single mito)
Tistrella mobilis (gram negative alphaproteobacteria that produces didemnins)
Candidatus Desulforudis audaxviator- found 2.8km inside S. African mine- gets food from inorganic sources (such as calcite)
Pelargonium sp. – Angiosperm. Biparental inheritance of both chloroplast and mitochondrial genomes, nuclear incomparability of one chloroplast genome leads to variegation, mtDNA from the parents recombine in the hybrid.
Acidianus infernus- Lithotrophic growth- facultative aerobe, either aerobic by S0 oxidation or anaerobically via S0 reduction with H2.
Ideonella sakaiensis- Digests PET plastic.
Antechinus- small marsupial, breeds once a year for two weeks before mass male die out
Sulfolobus Islandicus- Archaea, chosen for ‘organism with a dormant period’- virus-induced dormancy.
Rafflesia arnoldii — holoparasitic angiosperm living its life inside Tetrastigma leucostaphyum budding only to reproduce — has no roots, stems or leaves; cannot photosynthesize
Snowflake yeast — Saccharomyces cerevisiae on the cusp of multicellularity displaying high degrees of evolvability due to ACE2 KO.
Leishmania donovani obligate endosymbiont with biphasic lifestyle — maintains monoclonal “template” displaying high aneuploidy turnover and haplotype selection
Amborella trichopoda — ancestor to all modern angiosperms — underwent polyploidization
Plains viscacha — possibly first described tetraploid mammal species
Epiphanes senta — species complex of rotifer. Interesting in terms of studying genetic distance and speciation processes (cox1 drift of about 10%). Dwarf males without stomatogastric nervous systems with larger females
Sphaerotecum destruens — mtDNA at the “fungal-animal boundary” — salmon parasite, the spore stage of which can apparently only replicate in salmonid cell lines
Halomonas titanicae eats rust. Isolated from samples taken from The Titanic.
Stanieria — possibly indicators of ancient planktonic blooms (attaches only to larger colonies of algae, sinking to the bottom, thus deposited)
Magnetococcus marinus — first evidence of a magnetosome, later also found many places (also our brains)
Midichloria mitochondria — gram-negative, nonspore-forming bacteria — symbiont of Ixodes ricinus (a tick) — sets up shop inside mitochondria and eats them!
Panagrolaimus davidi — doubly uniparental mtDNA inheritance (father → son; mother → daughter+soma?)
Methanobrevibacter smithii — most prevalent archaeon in human gut biomes (at least in Korea ~5-15% of total gut biome). In this ToL, we found a study with (presumably) a guy who had archaea in his belly button
Sciaphila thaidanica and densiflora — small flowery and mycoheterotrophic plants in the family Triuridaceae, highly reduced (and compact) plastome size and gene count, no photosynthesis
Ambystoma (mole salamander) — all-female populations, steal sperm from co-occuring, related species but also perform kleptogenesis, polyploids with odd number of genome
Selaginella lepidophylla — resurrection plant, extreme drought tolerance (by synthesizing trehalose), cool curling mechanisms for the inner and the outer stems
Buxbaumia viridis — a rare epixylic bryophyte, extremely short gametophyte, much larger and obvious sporophyte, cool spore’s waxy cuticle responds to the raindrops when mature enough, performs bad when competition is around
Drakaea – orchids that use a hinge-based stem to swing thynnid wasps for pollination. They deceive male wasps by having a leafy part that looks (shape and colour) and smells like a female wasp (which are flightless). Scent is probably the dominant deceiving factor.
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