Complex Interactions - Lecture notes 1-20 PDF

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Lecture 1 Plant and Fungal Interactions  Negative interaction: pathogenic fungi  Positive interaction: mycorrhiza  Unknown/neutral: endophytesAlgal and fungal interactions in lichenized fungi  Primary partner = mycobiont; fungal partners  Algal/cyanobacterial partners: photobiont  These two ar...

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Complex Interactions Lecture 1 Plant and Fungal Interactions  Negative interaction: pathogenic fungi  Positive interaction: mycorrhiza  Unknown/neutral: endophytes Algal and fungal interactions in lichenized fungi  Primary partner = mycobiont; fungal partners  Algal/cyanobacterial partners: photobiont  These two are very different when you isolate the fungal partners o Formed only when the symbiotic parts are there  Secondary partners: endolichenic fungi and lichenicolous fungi Phenomena of symbiotic associations:  Nature of relationships can change over evolutionary time and is complex  Evolution of new traits due to biological association; 3 examples o Rice seedling blight fungus  Fungus is a zygomycete belonging to the genus Rhizopus  This plant disease is initiated by an abnormal swelling of the seedling roots  This symptom is caused by the metabolite rhizoxin  Rhizoxin has been isolated from cultures of Rhizopus  The phytotoxin is destructive by binding to rice beta-tubulin which results in inhibition of mitosis  Bacteria were constantly found in Rhizopus hyphae cell associated with the rice seedling blight phenomenon  With confocal laser microscopy, the presence of these bacteria within Rhizopus hyphae was demonstrated  We can remove the bacteria with antibacterial easily and track location  Rhizoxin was produced by the bacteria (interesting!)  The Rhizoxin that the bacteria needs is produced by an antagonistic relationship How does Rhizopus tolerate the toxin and how did the tolerance evolve?  Rhizoxin is highly toxic for all eukaryotes since it blocks mitosis  Paralogs of beta-tubulin are resistant to rhizoxin with mutations at position 100 o 4 different types of paralogs o Some are sensitive to rhizoxin, some are not o AA at position 100 was mapped and sensitivity test was done  Seems like sensitivity differed  Then endosymbiosis relationship with bacteria allowed for tolerance  Why we have resistance in beta-tubulin paralogs o Modeled rhizoxin binding to beta-tubulin at the interface of the alpha and beta heterodimer o Resistance is determined by binding  Summary:

Complex Interactions o Rhizoxin resistance evolved first and enabled endosymbiosis o Certain groups of fungi developed rhizoxin resistance independently o Some species then took up rhizoxin producing bacteria to gain the ecological advantage of becoming plant pathogens o Related species of the endosymbiotic Burkholderia sp. are pathogens: hence shift from parasitism to mutalism in the Rhizopus-Burkholderia system most likely allowed for development of parasitic life-style of Rhizopus against rice Example 2: ergot fungus  A pathogen on grasses, mostly rye  Important disease in medieval Europe o Caused skin lesions and epilepsy  Famous for LSD, first isolated by Hoffmann  Wheat could not be parasitized by this fungi so rye was rare back then Diversity of life-styles in Clavicipitaceae (fungus family)  Fungi on fungi  Fungi on pupa  Fungi on other insects  Fungi on mites  Fungi on plants  Fungi on grass (positive effect!)  One family can have so many different effects and relationship, different hosts (fungi, plants, animals), can be mutualistic or parasitic relationships o Relationships can change throughout an evolutionary tree o Not all fungi that affect fungi are close together Shifts in relationships  5-8 independent and unidirectional interkingdom host jumps have occurred among clavicpitaceous fungi: o 3-5 to fungi o 1-2 to animals o 1 to plants Example 3: sap-feeding insects (suborder: auchenorrhyncha)  2 groups: o Phloem-feeding species (Fulgoromorpha)  Phloem transports nutrients throughout plant o Xylem feeding species (Cicadellinae/Sharpshooters)  Xylem transports water from roots to top of plant  Sap-feeding advantage: constant food supply by tapping xylem or phloem o Disadvantage: nutritionally poor (lack essential AA in phloem, vitamins in xylem) o These insects need a strategy to get their AA and vitamins  So will est symbiotic relationship with the plants to get nutrients

Complex Interactions 

Need to establish symbiosis with microbes to synthesize missing nutrients from precursors Evolutionary steps in the acquisition of bacterial symbionts and sap-feeding lifestyles in the insect group Auchenorrhyncha (Hemiptera), with emphasis on sharpshooters (Cicadellinae)  Ancestor of phloem and xylem feeders developed a relationship with a bacterial genus sulcia (insect abdominal bacteriome) o Allowed for sap-feeding lifestyle  Fulgoromorpha come to be  We see sulcia in these inseccts o Co-evolution of host and gut bacteria  For Cicadellinae/sharpshooters, they gained a new symbiont: baumannia o Allowed for xylem-feeding  Baumannis genome has larger genes for vitamin biosynthesis while sulcia genome is rich in amino acid biosynthesis genes o Codiverisfication of sulcia, baumannia, and sharpshooters o We see brightly colored bacteriomes on each side of the abdomen o They also still have the sulcia muelleri Symbiotic relationships increase likelihood of horizontal gene transfer 2 examples:  1. Sea slug Elysia chlorotica o Green because is filled with algae o Has a straw that just sucks up the green plastids from the algae  Sea slug can now do photosynthesis with the plastids  Symbiotic relationship allowed animal to do photosynthesis  Slugs express psbO which is also found in algae  psbO allows for photosynthesis using plastids o slug eggs have a lot of psbO and it lowers during growth until it takes in plastids again o gene transfer from algae to animal is the symbiotic relationship o Horizontal gene transfer occurs often in animals  2. Cyanobacterial endosymbiont o Movement of genes from plastid to other cellular locations like the nucleus, mito  Nucleus controls the plastid o There are genes available for the plastid to survive Gene loss from chloroplast genomes  Can be tracked with an evolutionary tree again  Number of genes in the chloroplast genome decreases as time progresses Types of Symbiosis (term coined by De Bary)  Heinrich Anton de Bary: studied in Heidelberg o Worked on fungi (fungal parasites and lichens), seminal work on symbiotic relationships  Symbiosis defined as a close association between organisms of different species

Complex Interactions 1. Commensalism: one partner benefits, other has no harm or benefit a. Exp: silverfish follows army ants and share prey with them 2. Mutualism: both partners benefit from symbiosis, term often used interchangeable with symbiosis a. Example: clownfish 3. Parasitism: one partner benefit, other suffers a. Exp: black yeast fungus on humans b. Chromoblastomycosis, caused by the black yeast Fonsecaea i. Fungus belongs to a group of ascomycetes closely related to rock fungi and lichens 4. Cheaters: parasites that evolved from mutualistic relationships a. Exp: yucca moths pollinate yucca and lay eggs in the flower (mutualistic) i. Larvae consume some of the seeds (cheaters) 5. Endosymbiosis: one symbiont lives within the tissues of the other, either in the intracellular space or extracellularly 6. Ectosymbiosis: one symbiont lives on the body surface of the host, including the inner surface of the digestive tract a. Exp: lice 7. Facultative symbiosis: both partners can live outside of symbiotic relationship 8. Obligate symbiosis: highly adapted partners, cannot live independently a. Exp: most lichenized fungi are not known to occur outside of the lichen symbiosis in nature Lecture 2 Endosymbiotic events in the evolution of life Endosymbiosis hypothesis: similarity between cyanobacteria and plastids  Developed by AFW Schimper and K Mereschocowky o Suggested that plastids originated from cyanobacteria  Lynn Margulis used hypothesis to explain where eukaryotes came from o Combo of bacteria with spirochaetes and cyanobacteria form eukaryotic plants cells o Caterpillars evolved from onychophorans by hybridogenesis Endosymbiosis:  Eukaryotic cell (with nucleus) incorporated proteobacteria and some later cyanobacteria to evolve mitochondria and plastids  Basal eukaryotes have no mitochondria  Why do we have a nucleus? Why isn’t our genes just out in the open like prokaryotes Mitochondria  Eukaryotes w mito suddenly evolved via mitochondria  3 groups of basal amitochondrial eukaryotes are interesting to study (no mito) o Evolved right after bacteria and archeae o Microsporidians  Unicellular parasites in insects, fishes, and mammals

Complex Interactions  Live in intestines  No mito, believed to be basal eukaryotes, belong to fungi o Parabasalids  Flagellate protozoa, mostly symbiotic in animals; including guts of termites and cockroaches, many of which have symbiotic bacteria that help them digest wood  Some animal pathogens  Exp: trichomonas vaginalis (STD)  Trichomoniasis:  Men: usually without symptoms (danger of re-infection when partner is not treated)  Women: colored vaginal discharge with strong odor, general discomfort  Anaerobic and lack mito; only found in association with animals  Not basal and lost their mito secondarily o Diplomonads  Unicellular with flagella  No mito  Can’t perform respiration and instead must obtrain their energy by fermentative processes (glycolysis)  Giardia lamblia is an anaerobic parasite  Common in tropics  Found on fruits or contaminated water; affects stomach  Not a basal, anaerobic, lost mito secondarily No amitochondrial eukaryotes known that are basal in the eukaryote tree of life  But why should a nucleus have been evolved before mito have evolved?  What is the main purpose of the membrane surrouding the nucleus? o Separation of transcript and RNA processing from translation (bc splicing slow) Introns  Parts of genes that are transcribed in pre-mRNA but later removed by splicing  3 types: o Group I introns: self-splicing, requires catalytic agent for splcing, occur in rDNA, mtDNA, and plastidal DNA o Group II introns: self-splicing, no catalytic agent necessary, occur in my DNA and plastidal DNA, also rarely in bacteria o Spliceosomal introns: splicing requires spliceosome (protein-RNA particles), most common intron type in eukaryotes. Evolved from degermation of group II introns  Originated from Group II introns which can be found in mito DNA Splicing in the different intron types  Self-splicing: fast (1 AA/sec)  Splicing with spliceosome: slow (0.005-0.01 AA/sec)  Translation in eukaryotes: fast (1 AA/sec) Thus we need to separate splicing from translation because of difference in speed  If not separated, a lot of introns won’t be cut out yet by the spliceosome

Complex Interactions

Why do we need a nucleus in an amitochondrial cell?  Because we need to separate splicing from translation  Nucleus is the border o We need nucleus to separate maturation from RNA processing o Invasion of group II introns and the evolution of spliceosomal introns through mito created selection pressure to separate transcription and translation and the creation of a nucleus o Not a problem if there’s no mito, no nucleus necessary if no mito  All amito eukaryotes derive and lose a mito o No basal amito eukaryote can be found Martin and Koonin, Nature (2006)  Archaebacterial host and proteobacterial symbiont form a endosymbiotic relationship o Symbiont enters host o We have 2 independent prokaryotic gene expression systems  Proteobacterial symbiont divides  Gene transfer through occasional organelle lysis o Genetic chimerism and lipid replacement o Eubacterial genes and group II introns recombine into host chromosomes o Introns disperse and degenerate o Gene expression impeded by co-transcriptional translation of unspliced transcripts  Endomembrane accumulation o Emergence of spliceosome o Need for separation of splicing from translation to solve intron problem  Have transcription and splicing in the nucleus  Translation in the cytosol o Gene transfer continues through lysis Identification of a novel archaeal lineage (Lokiarchaea)  Created a new hypothesis  Archaea found in the deep sea o Tend to cluster near eukaryotes o Was the closest relative to eukaryotes Correspondence of different genes with cellular localizations and functions  Showed similarity between archaea and membrane system of eukaryotes  Endomembrane system seems to be formed first before mito enters 3 hypotheses, how an archaea becomes eukaryotic  Mito-late: nucleus comes in before mito endosymbiont  Mito-early: bacterial cell becomes mito, then eukaryotic organelles form  Mito-intermediate: endomembrane systems (like those found in lokiarchaea) are formed first before mitochondrial endosymbiont enters o Leading hypothesis now

Complex Interactions

Plastids Cyanobacteria: phylogenetically important  First aerobic photsynthetically active organisms o Provided the aerobic atmosphere o Some anaerobic organisms became extinct  Provided plastids for eukaryotic organisms  Cyanobacteria are basically gram negative bacteria but contain chlorophyll a and accessory pigments o Gram-negative: small cell wall that can’t hold dye Prochlorophyta: cyanobacteria with chlorophyll a and b  What is the difference between chlorophyll a and b? o Algae don’t have chlorophyll a and b  Algae and plants evolved several times? o Small difference between the 2  Porphyrin ring is different by a change  CHO in chlorophyll b  CH3 in chlorophyll a o All green plants, wet algae, and all cyanobacteria have chlorophyll a and b o Rest of the structure is the same to maintain job Change of our understanding of prochlorophyte  Cyanobacteria evolved to wet algae  Prochlorophyte evolved to green algae Eukaryote phylogeny  Chromista o algae  Green algae o algae  Plantae  Choanoflagellate  Animalia  Fungi  Primitive flagellates, amoebae, parasitic taxa o algae  Slime molds  Rhodophyta o algade  Alveolates  Radiolaria  Testaceafilosea Algae is like a dust bin for anything that have no morphologic structure but is photosynthetically active. Algae is not a group that is monphyletic

Complex Interactions

Euglenoids  Elongated cells with one or two flagella, 1000 species  Photosynthetically active or lacking chloroplasts and are colorless  Cell covered by flexible coat: pellicle, that allows the cell to change shape  Common in freshwater (ponds), few are parasitic in animals  The chloroplast/plastids is surrounded by 3 membranes o Some species have plastids and others don’t o Some are algae, some are not Cryptomonads: phylogenetic position  Small group of unicelleular algae with plastids that have several membranes and nucleopmorph associated with plastids in addition to nucleus o Plastids are in nucleus o Nucleus is not related to red algae Red algae  Lacking flagella  Plastids with 2 membranes  Chlorophyll a and phycobiliproteids o Similar to cyanobacteria, also in phycobilisomes  Phycobiliproteids (phycoerythrin) responsible for color  One genus unicellular, all others are trichal Stramenopiles  Nutritionally and morphologically highly diverse group, including unicellular flagellate species, algae, and fungi  Common characters include: heterokont flagellation o Photoautrotrophic species with 4 membranes and girdle lamellae Plastid structure  Some plastids have 2, 3, or 4 membranes Brown algae  Highly derived seaweeds with complicated anatomy, no unicellular speices known; only marine species o Thalli up to 60 m long Green algae and land plants  Paraphyletic and are basal to land plants  Green algae: isokont flagella, chlorophyll a and b, marine, in fresh water and on soil  Different morphologies o Green algae/charophytes and closely related to land plants and other groups

Complex Interactions Phylogeny of hosts (A) and plastids (B)  Hosts: o Animals/fungi, haptophtyes, rhodophytes, chlorophytes, filose amoebae/chlorarachniophytes, heterokonts, alveolates, cryptophytes/glaucocystophytes, lobose amobae  Plastids: o Cyanelles, cyanobacteria, rhodoplasts+secondary endosymbionts, chloroplasts+secondary endosymbionts o Cyan ones are primary endosymbiosis o Might use the same plastids but come from different hosts  Different groups of eukaryotes incorporated algae at different rates o We have primary and secondary symbionts Origins of simple and complex plastids via primary and secondary endosymbiosis  Simple plastids (1 eukaryotic cell with a cyanobacteria) primary plastid o Begins with nonphotosynthetic eukaryote o Which gets cyanobacteria by primary endosymbiosis (rare) o Forms green algae (chlorophyta), rhodophyta (red algae), and glaucocystophyta  Complex plastids (2 eukaryotic cells coming together) secondary plastid o Begins with nonphotosynthetic eukaryote o Incorporates eukaryotic algae (one of the 3 simple plastids) o Plastid will degenerate and the nucleomorph in chlorarachniophyta and cryptophyte is just the reminants of the plastids o Nucleomorph is further reduced and lost o Form complex plastid by secondary endosymbiosis  Heterokonta, haptophyta, euglenophyta, dinoflagellates, apicomplexans Plastid membranes  4: means non membrane has been reduced o Eukaryotic algae in eukaryotic host o All membranes are there  3 membranes: one membrane in reduced o Exp: euglenophyta

Complex Interactions

Lecture 3 Bacterial Symbioses: Nitrogen Fixation Diversity of bacterial symbioses  Symbioses with other bacteria o Exp: Bdellovibrio  Parasitizes into other bacteria  Cause other bacteria to lyse after establishment into cell  Septation and development of more bdellovibrio cells before lysis  Can also occur in biofilm or as filamentous cells in liquid  Can again convert to a mobile form to parasitize other bacteria  Bdellovibrio: small, motile bacteria that parasitize on other gram negative bacteria. Can destroy other bacteria  Potential therapeutic agents: o Reduction of food-borne pathogenic bacteria o Decrease of viable gram-neg bacteria in polluted waste water sewage plants o But, concept of living antibiotic not working  Bdellovibrio does not wipe out prey because this would be self-destructive  Also wide prey range  Wipe out host completely would prevent it from having more hosts to replicate itself  Predatory bacteria monophyletic  Related to diverse group of bacteria including human pathogens, marine sulphate-reducing bacteria, bacteria in biofilms  Symbosis with protists o Exp: paralytic shellfish poisoning  Shellfish poisoning from eating bivalves  Bivalves are filter feeders that accumulate toxins like dinoflagellates or have other algae  Dinoflagellates (protist) can occur in huge amounts, red in the sea  Very toxic, found in clams  Originated from an old group of algae  Produce toxins that cause vomiting and stomach issues o Poisonous for animals but amount in shellfish usually too low to cause death in humans o Only few death cases reported o Toxin is heat stable, cooking does not help to prevent poisoning  Who produces this toxins and why? o Unknown, but can kill other microalgae  Why they can have such large amounts in nature o There are bacteria in dinoglafellates that produce toxins  Test using antibiotics and no toxins formed

Complex Interactions

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Symbiosses with animal o Exp: bioluminescence in fishes  Light is generated by bacteria in the deep sea light fish from nemo  Chemical structure of four luciferin is diverse and phylogenetically unreleated  Luciferase reaction in bacteria  Creates luminesce  Aldehyde is oxidezed to fatty acid  Flavin monooxygenase oxidized  Oxygen reduced to water  Catalized by enzyme (luciferase)  FMNH2  FMN reaction exothermic (energy emitted in form of light)  Bioluminescence originated independently in several fish clades  Luminous bacteria in fishes form a monophyletic group and belong to the genus photobacterium  Other luminous bacteria form symbiosis with insects and nematodes  Photobacterium species can be easily isolated and cultivated  Advantage for bacteria: receive nutrients from fish, sheltered environment Symbioses with plants: cyanobacterial symbioses o Cyanobacteria are common symbiotic partners in fungi and plants since they can fix atmospheric nitrogen  Atmospheric N is rare in nature, good that they can attract it  Have relationships with gl...