Fungal Diversity PDF

Fungal diversity Mitja Remus-Emsermann KöLu 12-16 Raum 129 [email protected]  Fungi Mycology – study of fungi Mycologists – scientists who study fungi Mycoses – diseases caused by fungi Mycotoxico...

Fungal diversity Mitja Remus-Emsermann KöLu 12-16 Raum 129 [email protected]  Fungi Mycology – study of fungi Mycologists – scientists who study fungi Mycoses – diseases caused by fungi Mycotoxicology – study of fungal toxins and their effects  Fungi Fungi and animals are more closely related to each other than they are to plants or other eukaryotes Fungi, animals, and their protist relatives form the opisthokonts clade  Fungi DNA evidence suggests that Animals are most closely related to unicellular choanoflagellates (aquatic filter-feeders) Fungi are most closely related to unicellular Salpingoeca rosetta nucleariids (amoeba) This suggests that multicellularity arose separately in animals and fungi Nuclearia thermophila  Fungi The oldest undisputed fossils of fungi are only about 460 million years old Fungi are diverse and widespread, >100,000 species of fungi have been described They are essential for the well-being of most terrestrial ecosystems because they break down organic material and recycle vital nutrients Despite their diversity, fungi share key traits, most Fossil fungal hyphae and spores from importantly the way in which they derive nutrition Ordovician period (~460 million years ago)  Fungi Genomic studies have identified chytrids in the genus Rozella as an early diverging fungal lineage Rozella and other members of the unicellular group, “cryptomycota” lack chitin-rich cell walls Fungi were among the earliest colonizers of land Fossil evidence indicates fungi formed mutualistic relationships with early land plants Rozella allomycis  Fungi Genomic analysis indicates genes involved in mycorrhizal formation, SYM genes, were present in the common ancestor to land plants Molecular analyses have helped clarify evolutionary relationships among fungal groups, although areas of uncertainty remain Recent environmental studies estimate fungal diversity at around 1.5 million species Bonfante P & Genre A (2010) Mechanisms underlying beneficial plant– fungus interactions in mycorrhizal symbiosis. Nature Communications 1, e48 doi:10.1038/ncomms1046  Fungi Traits common to most fungi Absorptive nutrition: secrete enzymes and then absorb the broken-down nutrients Chemoorganoheterotrophs Saprophytes Hyphae: multinucleate cell filaments, which extend and form branches, generating a mycelium Cell walls contain chitin Membranes contain ergosterol C. Ergosterol  Fungi A fungal hyphae expand at the tip Cytoplasmic expansion is driven by turgor pressure against the chitin cell wall - the force enables fungi to penetrate tough materials such as wood Fungal hyphae can extend up to 0.5 centimeter per hour  Unicellular fungi Unicellular fungi are called yeasts Reproduce by budding Some yeasts are asexual Others can undergo sexual alternation of generations Saccharomyces cerevisiae Baker’s and brewer’s yeast Candida albicans An opportunistic pathogen Can grow also as mycelia  Taxonomy of fungi Five major fungal groups Chytridiomycota Zygomycota Glomeromycota Ascomycota Basidiomycota  Classification of fungi Basidiomycota and Ascomycota are dikarya two parental nuclei are initially paired nuclei fuse, undergo meiosis, produce haploid progeny Zygomycota and Chytridiomycota are paraphyletic taxonomic group includes some descendants of a single common ancestor Classification of fungi Classification of fungi  Terminology & lifestyle The most common body structures are multicellular filaments (hyphae) single cells (yeasts) Some species grow as either filaments or yeasts, others grow as both Fungi exhibit diverse lifestyles Decomposers (saprophytes) Parasites Mutualists  Fungal distribution and importance Primarily terrestrial but few aquatic Puccinia graminis global from polar to tropical Many are pathogenic in plants or animals Some form associations lichens Lichen associations with algae or cyanobacteria mycorrhizae associations with plant roots Ectomycorrhizae on pine root  Fungal structure Cell walls composed of chitin polysaccharide Single-celled microscopic fungi = yeasts Fungi consist of mycelia, networks of branched hyphae adapted for absorption Body/vegetative structure of a fungus = thallus (pl. thalli) multicellular fungi are called moulds thallus consists of long, branched hyphae filaments tangled into a mycelium mass  Fungal structure Most fungi have hyphae divided into cells by septa, with pores allowing cell-to-cell movement of organelles Coenocytic fungi lack septa and have a continuous cytoplasmic mass with hundreds or thousands of nuclei Some unique fungi have specialized hyphae called haustoria that allow them to penetrate the tissues of their host  Fungal reproduction Fungi propagate themselves by producing vast numbers of spores, either sexually or asexually Fungi can produce spores from different types of life cycles  Fungal reproduction - sexual Fungal nuclei are normally haploid = 1 chromosome different hypha attracted the exception of transient by pheromones fuse diploid stages formed during the sexual life cycles Sexual reproduction requires the fusion of hyphae from different mating types Fungi use sexual signaling molecules called pheromones to communicate their mating type  Fungal reproduction - sexual Plasmogamy is the union of cytoplasm from two parent although the cells fuse the nuclei don't mycelia In most fungi, the haploid nuclei from each parent do not fuse right away; they coexist in the mycelium, called a heterokaryon In some fungi, the haploid nuclei pair in couples per cell; such a mycelium is called dikaryotic  Fungal reproduction - sexual Hours, days, or even centuries may pass before the occurrence of karyogamy, nuclear fusion During karyogamy, the haploid nuclei fuse, producing diploid cells The diploid phase is short-lived and undergoes meiosis, producing haploid spores The paired processes of karyogamy and meiosis introduce genetic variation  Fungal reproduction - sexual Homothallic: Sexually-compatible gametes are formed on the same mycelium (self-fertilizing) Heterothallic: Require outcrossing between different, yet compatible mycelia Aspergillus nidulans can undergo three reproduction cycles 1) asexual production of conidia spores 2) homothallic sexual reproduction by selfing, generating fruiting bodies (called cleistothecia) containing ascospores 3) parasexual reproduction where heterohyphae fuse to form a heterodikaryon, followed by nuclear fusion to generate diploid hyphae, in which random chromosome loss occurs to restore the haploid chromosome number. Nature Reviews Genetics 3, 683-697 (September 2002) | doi:10.1038/nrg889  Fungal reproduction - asexual Parent cell undergoes mitosis to form daughter cells Mitosis in vegetative cells may be concurrent with budding to produce a daughter cell Moulds produce haploid spores by mitosis and form visible mycelia  Fungal reproduction - asexual Other fungi that can reproduce asexually are yeasts, which are single cells Instead of producing spores, yeasts reproduce asexually by simple cell division and the pinching of “bud cells” from a parent cell Some fungi can grow as yeasts and as filamentous mycelia (dimorphic fungi) Candida spp Histoplasma capsulatum  Fungal reproduction - asexual Many moulds and yeasts have no known sexual stage Mycologists have traditionally called these deuteromycetes These fungi are reclassified once their sexual stage is discovered Mycologists can use genomic techniques to classify fungi  Chytrids Chytrids (phylum Chytridiomycota) are found in terrestrial, freshwater, and marine habitats including hydrothermal vents They can be decomposers, parasites, or mutualists Molecular evidence supports the hypothesis that chytrids diverged early in fungal evolution Chytrids are unique among fungi in having flagellated spores, called zoospores  Chytrids Produce a zoospore with single, posterior, whiplash flagellum most primitive form of spore dispersal flagella lost in higher forms Asexual and sexual reproduction Many members degrade cellulose and keratin  Chytrids The chytrid Batrachochytrium dendrobatidis is likely the cause of the recent decline in amphibians worldwide  Zygomycetes The zygomycetes (phylum Zygomycota) exhibit great diversity of life histories Include fast-growing moulds, parasites, and commensal symbionts Some of industrial importance foods, antibiotics and other drugs, meat tenderizer, and food coloring  Zygomycetes Usually reproduce asexually by spores that develop at the tips of aerial hyphae Hyphae are coenocytic Generate non-motile spores Spore-bearing organ is called the sporangium  Zygomycetes Sexual reproduction occurs when environmental conditions are not favourable requires compatible opposite mating types hormone production causes hyphae to produce gametes gametes fuse, forming a zygote zygote becomes zygospore Zygomycete fungi include Rhizopus: a bread mould Mucor: a soil mould  Zygomycetes The zygomycetes are named for their sexually produced zygosporangia Pilobolus sp. Zygosporangia are the site of karyogamy and then meiosis Zygosporangia, which are resistant to freezing and drying, can survive unfavorable conditions Some zygomycetes, such as Pilobolus, can actually “aim” and shoot their sporangia toward bright light  Glomeromycetes Arbuscular mycorrhizae penetrate root cell wall Mycorrhizal fungi colonize soils by the dispersal of haploid cells called spores Mutualistic relationship fungus helps protect host from stress, delivers soil nutrients (phosphate ions and minerals) to the plant; plant provides carbohydrates to fungus  Glomeromycetes Arbuscular mycorrhizae fungi extend hyphae through the cell walls of root cells and into tubes formed by invagination of the root cell membrane Glomus mosseae Arbuscular mycorrhizae root mycelium  Glomeromycetes The hyphae invade intracellular space (between cell wall and cell membrane) They reproduce asexually through blastic (budding or swelling) development of the hyphal tip to produce large spores (glomerospores; sometimes reach to 800 Glomus diaphanum µm) inside or outside of roots Morton & Walker. DAOM 22702 Sexual reproduction is unknown Gomus proliferum Dalpé and Declerck DAOM 226389  Ascomycetes Ascomycetes (phylum Ascomycota) live in marine, freshwater, and terrestrial habitats Ascomycetes produce sexual spores in saclike asci contained in fruiting bodies called ascocarps Ascomycetes are commonly called sac fungi Ascomycetes vary in size and complexity from unicellular yeasts to elaborate cup fungi and morels Tuber Morchella Galiella melanosporum esculenta rufa  Ascomycetes Ascomycete fungi include Neurospora - a bread mold Morels and truffles - culinary delicacies Aspergillus - forms asexual fruiting bodies called conidiophores  Ascomycetes Ascomycetes include plant pathogens, decomposers, and symbionts Ascomycetes reproduce asexually by enormous numbers of asexual spores called conidia Conidia are not formed inside sporangia, they are produced asexually at the tips of specialised hyphae called conidiophores Neurospora crassa, a bread mould, is a model organism with a well- studied genome Penicillium sp.  Ascomycetes Penicillium roqueforti found in Blue cheese and Roquefort Penicillium camemberti found in Camembert, Brie Penicillium nalgiovense is used to improve the taste of sausages and hams, and to prevent colonization by other moulds and bacteria Penicillium chrysogenum - penicillin  Ascomycetes Aspergillus fumigatus ubiquitous environmental allergies and significant pathogen Aspergillus oryzae production of fermented foods Important in biotechnology  Ascomycetes Cordyceps spp. Endoparasitoids, parasitic mainly on insects and other arthropods  Ascomycetes Ergot is caused Claviceps purpurea and produces toxins More than 40,000 people died from an epidemic of ergotism during the middle ages Ergotism is characterised by gangrene, nervous spasms, burning sensations, hallucinations, and temporary insanity Ergots contain lysergic acid, the raw material for LSD Rye Wheat  Ascomycetes - yeast Alternates between haploid and diploid in nutrient rich, mitosis and budding occurs at non-scarred regions stops after entire mother cell is scarred In nutrient poor, meiosis and haploid ascus containing ascospores formed haploid cells of opposite mating types fuse tightly regulated by pheromones  Basidiomycetes Phylum Basidiomycota Some basidiomycetes form mycorrhizae, and others are plant parasites The phylum is defined by a club-like structure called a basidium, a transient diploid stage in the life cycle The basidiomycetes are also called club fungi Many basidiomycetes are decomposers of wood Basidiomycetes  Basidiomycetes Basidiomycete fungi Amanita phalloides makes a very poisonous toxin α-amanitin inhibits RNA polymerase II Agaricus bisporus (Portobello mushrooms) Prized culinary delight  Basidiomycetes The life cycle of a basidiomycete usually includes a long- lived dikaryotic mycelium In response to environmental stimuli, the mycelium reproduces sexually by producing elaborate fruiting bodies called basidiocarps Mushrooms are examples of basidiocarps The numerous basidia in a basidiocarp are sources of sexual spores called basidiospores  Basidiomycetes The underground secondary mycelia of some mushrooms form mycorrhizae with tree roots  Basidiomycetes Decomposers Edible, non-edible mushrooms and hallucinogenic Amethyst deceiver Cantharellus cibarius Psilocybe semilanceata  Basidiomycetes Corn smut is a plant disease caused by the pathogenic fungus Ustilago maydis forms galls on all above-ground parts of maize  Fungi – plant mutualism Mycorrhizae are enormously important in natural ecosystems and agriculture Plants harbor harmless symbiotic endophytes, fungi that live inside leaves or other plant parts Endophytes make toxins that deter herbivores and defend against pathogens Most endophytes are ascomycetes  Fungi – animal mutualism Some fungi share their digestive services with animals These fungi help break down plant material in the guts of cows and other grazing mammals Many species of ants use the digestive power of fungi by raising them in “farms” Leucoagaricus gongylophorus  Fungi as decomposers Fungi are efficient decomposers of organic material including cellulose and lignin They perform essential recycling of chemical elements between the living and nonliving world Pleurotus ostreatus Stropharia semiglobata  Lichens A lichen is a symbiotic association between a photosynthetic microorganism and a fungus Millions of photosynthetic cells are held in a mass of fungal hyphae The photosynthetic component is green algae or cyanobacteria The fungal component is most often an ascomycete  Lichens Algae or cyanobacteria occupy an inner layer below the lichen surface algae provide carbon compounds cyanobacteria also provide organic nitrogen fungi provide the environment for growth Fungi of lichens can reproduce sexually and asexually  Fungi as pathogens The general term for a fungal infection in animals is mycosis Ringworm and athlete’s foot are examples of human mycoses Systemic mycoses spread through the body For example, coccidioidomycosis produces tuberculosis-like symptoms Some mycoses are opportunistic For example, Candida albicans, which causes yeast infections  Acellular agents Mitja Remus-Emsermann KöLu 12-16 Raum 129 [email protected]  Acellular agents Viruses – protein and nucleic acid Viroids – only RNA Satellites – only nucleic acids Prions – proteins only  Importance of viruses Major cause of disease also importance as a new source of therapy new viruses are emerging Important members of aquatic world move organic matter from particulate to dissolved Important in evolution transfer genes between bacteria, others Important model systems in molecular biology  What is a virus? A virus is a acellular entity that must infect a host cell, where it replicates It typically subverts the cell’s machinery and directs it to produce viral particles The virus particle, or virion, consists of nucleic acid (DNA or RNA) contained within a protective protein capsid  Properties of viruses Virion complete virus particle consists of >1 molecule of DNA or RNA enclosed in coat of protein may have additional layers cannot reproduce independent of living cells nor carry out cell division but can exist extracellularly  Host of viruses Viruses are ubiquitous in all environments Viruses are part of our daily lives Respiratory pathogens such as rhinovirus (the common cold) and Epstein-Barr virus (infectious mononucleosis) Sexually transmitted viruses such as herpes simplex virus (HSV) and papillomavirus (e.g. genital warts) Different viruses infect every group of organisms Each species of virus infects a particular group of host species, or host range Bacterial viruses called bacteriophages (phages)  Virus structure Virion size range is ~10–400 nm in diameter and most viruses can only be viewed with an electron microscope All virions contain a nucleocapsid which is composed of nucleic acid (DNA or RNA) and a protein coat (capsid) some viruses consist only of a nucleocapsid, others have additional components Some viruses have membrane envelopes Virus morphology  Virus capsids Large macromolecular structures which serve as protein coat of virus Protect viral genetic material and aids in its transfer between host cells Made of protein subunits called capsomer / protomers Capsids can be Helical Icosahedral Asymmetric and complex  Helical capsids Shaped like hollow tubes with protein walls Capsomer / protomers self assemble Size of capsid is a function of nucleic acid  Icosahedral capsids Are polyhedral with 20 identical triangular faces Have a structure that exhibits rotational symmetry  Capsids of complex symmetry In some icosahedral viruses, the capsid is enclosed in an envelope, formed from the host cell’s membrane. The envelope contains glycoprotein spikes, which are encoded by the virus Between the envelope and capsid, tegument proteins may be found  Enveloped viruses Enveloped viruses usually have flexible membranous outer layer Animal virus envelopes (lipids and carbohydrates) usually arise from host cell plasma or nuclear membranes  Viral genomes Viral genomes can be: DNA or RNA Single- or double-stranded (e.g ssDNA or dsDNA) Linear or circular Include genes encoding viral proteins Capsid Envelope proteins (if need be) Any polymerase not found in host cell  Classification of viruses The International Committee on Taxonomy of Viruses (ICTV) has devised a classification system, based on several criteria: Genome composition and structure Capsid symmetry Envelope Size of the virion Host range Baltimore classification  Animal viruses - tissue tropism Animal viruses bind specific receptor proteins on their host cell Receptors determine the viral tropism Ebola virus exhibits broad tropism, infecting many kinds of host tissues Papillomavirus shows tropism for only epithelial tissues Most animal viruses enter host as virions Internalised virions undergo uncoating, where the genome is released from its capsid Can occur in several different ways  Virus replication All animal viruses make proteins with host ribosomes Translation occurs in the cytoplasm Assembly of new virions Capsid and genome May occur in the cytoplasm or nucleus Envelope proteins are inserted into a membrane Cell membrane or organelle membrane Release of progeny viruses from host cell Lysis of cell Budding  Eukaryotic viruses Cytocidal infection results in cell death through lysis Persistent infections may last years Cytopathic effects degenerative changes abnormalities Transformation to malignant (cancer) cell  Viruses and cancer Oncogenic viruses transform the host cell to become cancerous Mechanisms of oncogenesis include: Insertion of an oncogene into the host genome Integration of the entire viral genome Expression of viral proteins that interfere with host cell cycle regulation  Plant viruses Entry of plant viruses into host cells usually requires mechanical transmission Most plant viruses enter by one of three routes: Contact with damaged tissues Transmission by an animal vector Transmission through seed  Plant viruses Within a plant, the thick cell walls prevent a lytic burst or budding out of virions Instead, plant viruses are transmitted to uninfected cells by plasmodesmata Membrane channels that connect adjacent plant cells Inner channel connects the ER  Animal and plant host defences Since viruses are ubiquitous, a wide range of defence mechanisms have evolved in animals and plants Genetic resistance Hosts continually experience mutations Immune system “Innate immunity”—interferons “Adaptive immunity”—antibodies RNA interference (RNAi) Widespread among eukaryotes and archaea  Bacteriophages Virulent phage multiplies immediately upon entry lyses bacterial host cell Temperate phages two reproductive options: reproduce lytically as virulent phages do remain within host cell without destroying it many temperate phages integrate their genome into host genome (becoming a ‘prophage’ in a ‘lysogenic bacterium’) in a relationship called lysogeny Bacteriophages  Bacteriophages - lysogeny Temperate phage changes phenotype of its host bacteria become immune to superinfection phage may express pathogenic toxin or enzyme Lysogeny has advantages for the virus phage remains viable but may not replicate Under appropriate conditions infected bacteria will lyse and release phage particles occurs when conditions in the cell cause the prophage to initiate synthesis of new phage particles, a process called induction An evolutionary arms race  Satellites Infectious nucleic acids (DNA or RNA) Satellite viruses encode their own capsid proteins when helped by a helper virus Satellite RNAs/DNAs do NOT encode their own capsid proteins Encode one or more gene products Require a helper virus for replication human hepatitis D virus is satellite Requires human hepatitis B virus  Viroids Infectious agents composed of closed, circular ssRNAs do not encode gene products Requires host cell DNA-dependent RNA polymerase to replicate Cause plant diseases Prions - Proteinaceous infectious particles Cause a variety of degenerative diseases in humans and animals Scrapie in sheep Bovine spongiform encephalopathy (BSE) or mad cow disease Creutzfeldt-Jakob disease (CJD) and variant CJD (vCJD) in humans Kuru in humans  Viral ecology Viruses exist naturally within host organisms in complex ecosystems Their persistence is significant for human health and for agricultural plants and animals Viral ecologists consider viruses as living entities, playing roles comparable to those of cellular organisms Example: “predator” or “parasite” Some viruses interact positively with hosts, by expressing host genes and by protecting hosts from other organisms  Emergence of viral pathogens Certain human-infecting viruses are well known to persist in the wild, such as rabies virus and West Nile virus. Their persistence requires a broad host range But how does a seemingly “new” virus emerge to sicken humans? As a result of human consumption of wildlife “SARS” coronavirus