12&13. The microbial dimension of eukaryotic diversity Flashcards
Phylogeny
Evolutionary history of a group of organisms.
Can be inferred indirectly from nucleotide or amino acid sequence data.
Certain genes/proteins are globally distributed and allow to investigated global phylogenies.
Small subunit ribosomal RNA (SSUrRNA) gene.
Must widely used phylogenic marker.
Found in all domains of life - cellular life forms (16s rRNA in prokaryotes and 18s rRNA in eukaryotes or 12s rRNA in mitochondria and plastids).
Functionally constant (rRNA are part of the ribosome).
Sufficiently conserved, allow cloning with degenerate primers (PCR) and generate informative alignments.
Protein coding genes are increasingly used to compliment SSUrRNA genes phylogenies.
Eukaryotic cells complex endomembranes
Microfilaments Cytoplasmic membrane Nucleus Smooth ER Nucleoulus Peroxisome Golgi complex Mitochondrion Ribosomes Rough ER Nuclear pored Microtubles Flagellum Chloroplasts Lysosome Nuclear envelopes
Mitochondria from mammals
Two ribosomal RNAs (12s and 16s)
22 transfer RNAs
13 essential genes that encode subunits of the oxidative phosphorylation enzyme complexes.
However, the vast majority of mitochondria proteins (>1000 proteins) are encoded by the nuclear genome.
The Archezoa hypothesis
Tom Cavalier-Smith (1983)
The nucleus was invented before the mitochondrion was acquired.
The first eukaryotes were anaerobics.
Archezoans might provide insight into the nature of ancestral eukaryotic genomes and cell biology.
The Archezoa hypothesis would fall if we find:
- That archezoans branch among aerobic species with mitochondria (molecular phylogeny)
- Mitochondrial genes on archezoan genomes (molecular phylogeny)
- Mitochondrion-derived organelles in archezoans (cell biology)
Hydrogenosomes
Produces hydrogen.
Produce ATP through substrate level phosphorylation.
Some have a genome with mitochondrial signature.
Nuclear genomes encode reduced fractions of mitochondrial proteins set.
Mitosomes
Reduced in size - can be <100nm in diameter.
No evidence for any capacity to produce ATP.
No genome.
Nuclear genomes encoded reduced mitosomal/mitochondrial proteins set.
5 eukaryotic supergroups
Opisthokonta Amoebozoa Excavata Archaeplastida Chromalveolata
Opisthokonta
Mitochondria - Metazoa
Mitochondria - Sc
Hydrogenosome - Chytridiomycetes
Mitosome - Ec (microsporidia)
Amboebozoa
Mitosome - Eh (entamoeba)
Mitochondria - Dd
Excavata
Mitosome - Gi (Giardia) Hydrogenosome - Tv (Trichomonas) Mitochondria - Trypanosomatidae Mitochondria - Eg Mitochondria - Ra
Archaeplastida
Mitochondria - Green algae
Mitochondria - Vascular plants
Mitochondria - Red algae
Chromalveolata
Mitochondria - Tp Mitochondria - Pf Mitosome - Cp (Cryptosporidium) Hydrogenosome/mitochondria - Blastocystis RHIZARIA Mitochondria? - Radiolaria Mitochondria? - Cercozoa
Anaerobic, microaerophilic habitats
Fungi Amoebozoa Ciliates Stramenopiles Diplomonads Parabasalia
Intracellular habitats
Microsporidia
Apicomplexa
Mitochondria possess a protein machinery mediating Fe-S cluster biosynthesis
Fe-S are small co-factors.
Prosthetic groups of many proteins.
Found in all cellular life forms.
Though to represent some of the earliest catalysts.
Require complex protein machineries for biosynthesis.
Fe-S are involved in…
Electron transfers
Enzyme catalysis
Sensing - regulation
Structural; roles?
5 major eukaryotic lineages
1. Opisthokonta Animal, fungi and microsporidia, chonoflagellates. 2. Amoebozoa Slime molds, pelobionts and others 3. Excavata Euglenozoa, metamonada, parabasala and others. 4. Archarplastida Plants, red algae, glaucophytes 5. SAR Stramenopiles, alveolata and rhizania
Eukaryotic organelles with a genome (Known chloroplast genome)
Circular DNA molecules.
Typically 120-160 kbp
Contain 2 inverted repeats of 6-76 kbp
Many genes encode proteins for photosynthesis and autotrophy.
Introns common, primarily of self-splicing type.
What does SAR stand for?
The stramenopiles and alveolata
Stramenopiles
Manny free living species (diatoms - a type of algae: marine and freshwater).
Some parasitic species (Oomycetes - Phytophthora, plant pathogen (Irish potato famine) Blastocystis (animal and human gut))
Alveolates
Dinoflagellates (mostly-free living).
Ciliates (mostly free-living and some parasitic)
Apicomplexa (exclusively parasitic, most with secondary plastids)
Parasites of animals and humans.
EG Plasmodium falciparum and toxoplasma gondii
Extracellular parasites
Thrive on and in tissues without entering their host cells (mucosal surfaces).
Epithelial surfaces, interstital spaces, blood and lymph.
EG Trichomonas, Giardia
Intracellular parasites
Need to penetrate their host cells to complete life cycle.
Not killing host cells, exploits nutrients.
Cytoplasmic
Vesicular
EG Microsporidia, Cryptosporidium.
Parasitic microbial eukaryotes and their genomes
Broaden our understanding of eukaryote genomic diversity:
- Parasites are distributed across the diversity of eukaryotes.
- Genome sequences of parasites led so far to many surprising findings challenging our knowledge of the eukaryotic cells.
Important data source to discover and study traits underlying host-parasite interactions:
- Surface and secreted molecules mediating interactions with host tissues (virulence factors)
- Vaccine and diagnostic developments, identification of potential drug targets.
The opisthokonta: Animals and meazoa
Host many microbial species.
They represent very good niches for microbes in general.
EG The human microbiota
The opisthokonta: Choanoflagellates and Ichthyosporea
Mostly marine species
The opisthokonta: Fungi and microsporidia
Important decomposers of dead animals/plants.
From important symbiotic interactions with plants.
Include members of the human microbiota.
Many are pathogenic species to animals and plants.
Microsporidia found in…
Bees and many other insects including silk worms.
Humans
Microsporidia in humans
Worldwide dstribution.
Opportunistic pathogens common in AIDS - HIV +ve - patients.
The two most common microsporidia identified in humans =
>Enterocytozoon bienusi
>Encephalitozoon intestinalis
Oral-faecal route (Zoontic origins - Contacts with pets, farm animals, contaminated water, food)
Mitosomes (reduced mitochondria without a genome)
The microsporidia life cycle
Strict obligate intracellular parasites, no proliferative extracellular forms.
Depend on one or more host to proceed through host to proceed through their life cycle.
Mostly animal hosts, a few examples of protists.
Multiple examples of host switching.
Zoonotic origins for many, if not most microsporidia infecting humans.
The amoebozoa - Slime molds
Important group in soil, feed on bacteria.
Important model system for molecular cell biology and host-microbe interactions: Dictyostelium discoideum.
The amoebozoa - Entamoeba histolytica.
A common pathogen linked with poor sanitation
~50 million infections annually and ~100,000 deaths worldwide.
Ameobic dysentery and colon inflammation
Extra-intestinal abscesses (EG Hepatic, pulmonary and cerebral)
Mitosomes (without a genome)
General cellular organisation of the apicomplexa (motile and invasive form)
Microtubules Nucleus Apicoplast Mitochondria Inner membrane complex Dense granules Micronemes Polar ring +/- conoid Rhoptries
Apicomplexa actively invade their host cell
Parasite myosin and actin dependent.
The host cell is not driving the process
Plasmodium uses a similar mechanism.
Attachment -> Reorientation -> Invasion -> Replication -> Cell lysis -> Attachment
Example of Amicomplexa infecting humans - Plasmodium faliciparum
Human-anopheles mosquito life cycle, with mitochondria and apicoplast
Example of Amicomplexa infecting humans - Toxoplasma gondii
Cat-prey life cycle, dead end infections in humans - A zoonotic parasite with mitochondrion and apicoplast.
Seropsitive prevalence rates vary greatly generally (20-75%)
Thought to cause benign disease in immunocompetent adults.
Tissue cyst forming coccidia
Definative hosts - Adult forms / Sexual reproduction.
Intermediate host - Immature forms / Asexual reproduction.
Cat-prey life cycle, dead end infection - Cryptosporidium parvum, C.hominis
Only one host required, human or animal hosts.
Often a zoonotic parasite with mitosomes and no apicoplast.
Toxoplasma gondii infections in humans
Oocyst-contamination foor or water Undercooked meat Raw goats milk Congenital Organ transplant Blood transfusion
Cryptosporidium
Worldwide distribution.
Two species infection gumans:
1. C.parvum (cattle and other mammals - zoonotic origins)
2.C.homis (only in humans)
Self-limiting diarrhoea in immuno-competent people.
Profuse, water diarrhoea associated with AIDs
With reduced mitochondria and mitosomes (without a genome)
Cryptosporidium infections in humans
Small size of oocysts (diameter 3-5um). Low infective dose (1-10 oocysts). Robust oocysts (resistant to chlorine). Infectious sporulated oocysts excreted. Monoxenous development. Shared host specificity (C.parvum). Large number of oocysts excreted (up to 100 billion per calf). Proximity of domestic animals to surface water sources.
The excavata: Parabasalia
Mainly host-dependent and include parasitic forms.
Found invertebrates, birds and mammals.
Anaerobes, possess hydrogenosomes
The excavata: Diplomonads
Many are host-dependent and include parasitic forms.
Possess hydrogenosomes or mitosomes
The excavata: Euglenozoa
Free-living and parastitic forms (kinetoplastids: Trypanosoma and Leishmania)
Some possess secondary plastids (EG Euglena)
Some possess complex mitochondrial genomes - kinetoplasts ~10-20% of total DNA present in a cell.
Kinetoplastids causing human disease
African trypanosomes
Human African trypanosomiasis
Tsetse fly
Trypanosoma cruzi
Chagas’ disease
Triatomine bugs
Leishmania species
Leishmaniasis
Sand fly
Kinetoplastid: Trypanosoma cruzi
Distributed in central and south America
Chagas’ disease
Mammal-insect life cycle, zoonotic origin
Has a single mitochondria with a complex genome - kinetoplast (mini-circles, maxi-circles).
Life cycle of Trypanosoma cruzi
- Triatomine bug takes blood meal.
- Metacyclic trypomastigotes penetrate various cells at bite wound site. Inside cells they transform into amastigotes.
- Amastigotes multiply by binary fission in cells of infected tissues.
- Intracellular amastigotes transform into trypomastigotes, then burst out of the cell and enter the bloodstream
- Triatomine bug takes blood meal.
- Epimastigotes in midgut.
- Multiply in midgut
- Metacyclic trypomastigotes in hindgut.
Invasion of host cells by Trpanosoma cruzi
- Attachment to host-surface receptors.
- Ca2+ signal recruits lysosomes.
- Fusion of lysosomes with plasma membrane
- Invasion
- Secretion of pore-forming protein
- Lysis of surrounding membrane, release of pathogen.
Excavata: Giardia lamblia
Worldwide distribution.
Higher prevalence in developing countries (~20%)
1-6% in temperate countries - zoonotic origins
Most common protozoa found in human stools
~200 million clinical cases per year.
Giardiasis (often asymptomatic, acute or chronic diarrhoea)
Fecal-oral life cycle, extracellular parasite
With reduced mitochondria and mitosomes (without a genome)
Excavata: Trichomonas vaginalis
Most common sexually transmitteed cellular pathogen:
277 million Trichomonas vaginalis
106 million Neisseria gonorrhoeae
105 million Chlamydia trachomatis
11 million Treponema pallidum
Can be very common in resource-limited conditions.
Strongly associated with HIV and mycoplasma.
Linked with pre-natal and post-natal complications.
Positively correlated with cervical and agressive/lethal prostate cancers
Trichomonas vaginalis as an extracellular urogenital pathogen
- Trophozoite in vaginal and prostatic secretions and urine.
- Multiples by longitudinal binary fission
- Trophozoite in vagina or orifice of urethra.
Trichomonas vaginalis as a pathogen of the urinary tract
Prostate gland
Urethra: 100%
Vagina
Urethra: 5% only urehtra, 90% of episode
Chagas’ disease
Acute stage, typically asymptomatic
Followed by decades of latency followed by chronic symptoms - heart and gastrointestinal tract, congestive heart failure in large fraction of patients.
