Protists Flashcards
(12 cards)
Eukaryotic origins and evolution
Euk origins: based on Woese’s rRNA seq, 3 domains of life. Euk arose in Archaea, acquired organelled/mt etc. 1st ID in Lokiarchaeota of Asgard superfam, also incl Odinarchaeota, thoarchaeota, etc.
1st lab grown rep/euk= P syntrophicum strain MK-D1.
Euk RNA pol similar to archaea- RPB 1-3, 6, 11 homologues in bacteria and archaea, 4,5,7,8,10,12 in archaea only.
Branching order in euk tree uncertain, but common model orgs not widely distributed. LECA= Last euk common ancestor.
Ciliate main genome and sexual cycle
DNA as information repository and 1 nucleus: ciliates has MAC (~800n, transcriptionally active) and MIC (small, diploid, silent in veg growth, may be 2+). Ciliate, e.g Paramecium sexual cycle: MIC of 2 cells-> meiosis, MACs destroyed. Haploid nuclei of each partner fuse, gen new diploid MIC. MAC dev from new MIC.
Ciliate asexual cycle
Asexual cycle: nuclei divide by mitosis, cells by binary fission. MAC creation involves elimination of some (repeated) seqs- tandem repeats, transposons, excision of Internal eliminated seqs (~60k- flanked by TAs- not enough for accurate recognition and excision) and amplification of others; adding telomeres and fragmenting genome.
Modifications directed by RNA derived from MAC: d48 strain expts-> strain doesn’t exp a surface antigen. Gene present in MIC, but elim from MAC- if restored (transformation), retained bu MIC for future rounds of sexual reproduction. Inactivate specific RNAs-> stop corresponding DNA retention by MAC.
RNA involvement and regulation of MICs and MACs
RNA binding proteins and chromatin remodelling protein RNAi knockdown-> decrease in excision. RNA transcripts from MAC direct DNA deletions from MIC to next gen’s MAC- can argue RNA is the genetic repository.
Some ciliates have diff rearrangements in MIC. Oxytricha eliminates seqs and ‘unscrambles’ them, changing order in which located- also RNA dependent.
MAC v polyploid, each chr has telomeres, so the ciliate Tetrahymena was v important in Blackburn’s early telomere studies (2009 Nobel prize for getting telomeres from rRNA genes in MAC). Many cloning vectors in euk also have telomeres from tetrahymena.
Dinoflagellate nuclei (3 key features)
Dinoflagellate nuclei unusual- referred to as ‘dinokaryon’, described as mesokaryotic. Remain condensed, fibrillar appearance (‘liquid crystalline’), high 5-hydroxymethyl uracil content, v high DNA content (~ 70x more than humans), high associated cation conc, largely dispensed w/ conventional histones. Hematodinium doesn’t show nucleosome patterning on nuclease digestion, histones not seen in westerns (ctrl was Perkinsus). Instead, have
1) Proteins w/ similar seq to bacterial histone-like proteins (HU proteins) coat DNA in proks (histone-like basic proteins (HLPs)). Absent from early branching dinoflagellates, present in core species like Symbiodinium. Perhaps acquired by lateral transfer.
2) Dinoflagellate/viral nucleoprotein (DVNP)- similar seq to DNA binding protein from viruses w/ v large genomes (100s/kbp) that infect algae- Phycodnaviridae. Exp of DVNP in Saccharomyces inhibits growth (esp if conjugated to nuclear localisation signal) and leads to reduction of histone levels. Mutations reducing histone levels help restore viability when DVNP exp, suggesting events leading to displacement of histones by DVNP.
3) Histone genes divergent but retain recognisable features. Transcribed @ low level (1/25th of typical). PolyA tail- unusual for histone mRNAs.
Histone-like proteins across bacteria, viruses, archaea, etc
Histone-like proteins in archaea- probably genuine relatives.
Proteins w/ apparent common ancestry w/ histones in large euk viruses (Marseillevirus) and some bacteria (Gram negative Bdellovibrio- proteins w/ histone folds and some seq similarity, bind DNA non-specifically- unlikely to be just convergent evolution)- arrangement v different from typical nucleosomes. Evidence for histone proteins in viruses unclear but good for archaea. Hard to distinguish ‘real’ histones from convergent evolution.
Challenging monocistronic transcripts
Euk ribosome scanning from cap-> transcripts monocistronic unless have internal ribosome entry site (IRES)- as in Picornavirus poly transcripts allowing cap-independent translation, initiation.
Trypanosome primary transcripts poly, genome has long arrays/ co-transcribed genes/ORFs w/ occasional sites. Trans-splicing w/ capped transcripts (capped leader seq gen by transcription elsewhere in genome)- spliced leader (SL) RNA transcribed from single locus of >100 tandem genes, RNA fragmented; polyA added. Mech largely same as conventional splicing.
Other isolated e.g.s of trans-splicing (plant/algal chloroplasts, metazoan) but not systematic way to gen monocistronic transcripts from poly ones. E.g, 3 separate exons for psaA in Chlamydomonas cp.
Also systematically seen in Euglena and dinoflagellates.
Alternative mitochondria
Mt: Wide variation in genome size, even among model organisms. Human 17kbp, encodes pts of CI, III, IV, ATP synthase, RNA etc. Not everything has CI-IV of ETC and ATPS. Anaerobic protists have lost some/all bioE role.
Hydrogenosomes (alternative mt): no C III/IV, ATPS but still have bioenergetic role.
1) Nyctotherus- anaerobic ciliate- remnant of mt genome, encode some pts/ complex I. Organelle has CI+II, possibly runs II backward
2) Blastocystis- stramenopile- CI+II+ alt oxidase, mt encodes CI subunits+ some ribosomal proteins.
3) Trichomonas- parabasalid has CI, probably no mt genome
Mitosomes (alterative mt)- no bioE role, still function in Fe-S cluster biogenesis, e.g., Giardia. Range of function in aerobic and anaerobic E and biosynth.
Alternative chloroplasts
Cp (biosynth and photo) genomes broadly similar among photo and non-photo org. Dinoflagellates cp genome unusual: highly reduced (just key proteins of photo ETC+ some ORFs, some of which w/out clear function). All other genes incl most tRNAs-> nucleus. Fragmented into plasmid-like ‘minicircles’ w/ ‘core’ of minicircle involved in rep, exp. Mvmt/ genes to nucleus may reduce burden of transfer to daughters. Transcripts polyU’s- unclear why. Event X-> fragmentation/genome->more chr to partition in mitosis->selective advantage to move genes to nucleus.
Mt/cp of Apicomplexa: pattern w/ inverted repeats recognisable even in Apicomplexa like Plasmodium+ Toxoplasma. Some mt no longer ox Pi, some orgs don’t photo but have cp. Usually have remnant cp genome too. Plasmodium cp genome encodes ClpC (chaperone), SufB (Fe-S cluster biogen), proteins for their exp (RNA pol, rib. Proteins). Target of protein synth inhibitors (doxycycline), isoprenoid biosynth inhibitors (fosmidomycin). Loss of photo w/ cp retention occurs in parasitic plants like Epifagus and Monotropa too. Cp w/ photo loss retain biosynth role
4 genomes per cell (secondary endosymbioses)
Cp origins in red/green algal lineage, then lateral transfer, probably by endosymbiotic acquisition of photo euk-> explain 4th genome- secondary endosymbioses, exact # unclear.
4th genome ‘nucleomorph’ in chlorarachniophytes and cryptophytes- nucleus of intermediate euk engulfed (red alga for cryptophytes, green for chlorarchniophytes). Simplified in some lineages- loss of nucleomorph or reduction of membranes. Dinoflagellates have 4/3 mem w/ no nucleomorph.
Protein targeting with secondary endosymbioses
Protein targeting and secondary endosymbioses: cp w/ 2 mem have tic and tocs+ set of pathways for passage into thylakoid if needed- equivalent to export into bacterial periplasm. Extra mems solved w/ pre-existing systems, e.g cp w/ 4 mem- mem 3 and 4 equiv to green cp envelope, like entering thylakoid of cyano/cp, TIC/TOC system (or similar) reused. Mem 1 continuous w/ ER- ERAD system (ER-assoc degrad) equivalent SELMA (symbiont-specific ER-like machinery) used. Where no mem1 (dinoflagellates), probably deliver to mem 2 w/vesicles, no SELMA.
Independent cp origin and beyond 4 genomes per cell
Cp separate origin: Paulinella chromatophora (Rhizaria clade, except for 3 Paulinella genus members, non-photo)= independent primary endosymbiosis. 2 mem around chromatophore+ 2 novel import pathways (100s of proteins inported): proteins under 90aa don’t have NTD targeting seq, proteins over 270 do.
Beyong secondary cps: some dinoflagellates lost cp, replaced w/ one acquired from haptophyte/green alga. Others replaced it w/ diatom (organism on its own)-> dinotom. Dinotoms have 2 nuclei, 2 mt, 1 cp-> 5 genomes.
Ciliate Mesodinium rubrum eats cryptophytes (alga)+ maintain their nucleus, nucleomorph, cp and mt alongside own mt, MAC, MIC-> 7 genomes.
