Plant Microbiome Interactions Flashcards

Question

Bacterial habitat modifications in the phyllosphere

Answer 1

Syringomycin= affects release of nutrients from plant cells and bacterial cell dispersal. Is a phytotoxin and surfactant (breaks-down hydrophobic nature or disperses across) Auxin secretion= release of saccharides from plant cell wall EPS in bacterial aggregates= protection from environmental stresses such as tolerance to UV and dessication

Answer 2

Antibiotic and biosurfactant (enzyme) release- controlled by quorum sensing signalling molecules released Pigment release for UV and radiation protection Auxin for protection

Answer 3

Ice-nucleation active (INA+) Function as nuclei for the formation of ice crystals that can spread into plant tissues Prevent supercoiling of leaves so frost damage is initiated at -3deg instead of -8deg= agricultural problem Dependent on production of INA outer-membrane protein

Answer 4

Used in snow making machines on mountains Kill bacteria, proteins are on surface so still able to be used Put bacteria into water= produce ice at warmer temperatures of -3deg on mountains for snow sport

Answer 5

Swept into atmosphere by wind, adaptations allow their survival by making rain and snow, can also be found in the middle of hail Come back down to earth Allows spreading to different plants

Answer 6

Caused by erwinia amylovora of pear and apples from flowers (bees get it from flowers and bring to fruit trees) Spray inoculation with suspension of P.fluorescens and rapid multiplication of the antagonist occurs Then when infection arrives by bees, no disease occurs as colonisation by the other bacteria is so high

Answer 7

Bear seeds in pods eg soybeans, clover, beans, peas, alfalfa, gorse

Answer 8

Infection of legume roots by rhizobia leads to root nodule formation and nitrogen fixation (conversion of N gas to combined N in form of ammonia) Host specificity high- one rhizobium nodulates one legume type- 2 compatible partners need to recognise each other Symbiosis adds over 200 million tonnes of N to soils worldwide every year

Answer 9

Gram negative rod shaped soil bacteria Can form nodules on atleast one particular legume Symbiosis characterised by high degree of host specificity Not all able to fix nitrogen Diverse between alpha and beta proteobacteria, then after diversity formed, ability to do symbiosis, create nodules and fix nitrogen occurred from HGT

Answer 10

Recognition of correct plant partner by rhizobia and attachment to root hairs Root hair curling, rhizobia trapped in the curl, leads to cortical cell division of once terminally differential cells (due to signal) Invasion of root hair by formation of infected thread (tube produced by the plant cell wall and membrane as a response)

Answer 11

Rhizobia travel to root cortex via infection thread Bacterial release from infection thread into plant cytoplasm by endocytosis (surrounded by a membrane) Formation of misshapen bacterial cells (bacteriods- become terminally differential) within plant root nodule cells and development of a nitrogen fixing state Plant provides carbon for energy to fix nitrogen, bacteria produce nitrogen as ammonia for the plant- transport through surrounding vascular tissues

Answer 12

Cell division stops after a short period of time and the cell expands to further grow= finite division

Answer 13

Legume produces flavonoid (many types with different chemical groups in certain areas) Flavonoid is recognised by particular bacterium which turns on the expression of nod genes from accessory genetic element Nod leads to creation of a nod factor which is a lipochito-oligosaccharide of N-acetyl glucosamine, fatty acid attached and differences in bound chemical groups depend on the rhizobium type to make it unique for their legume= host specificity Recognised be receptors in legume, allows induction of N fixation

Answer 14

Borne on accessory genetic elements eg plasmid OR IGE or symbiosis island on chromosome (not on core chromosome) Sym plasmids in Rhizobium and Sinorhizobium and islands in mesorhizobium loti

Answer 15

Nodulates legumes of genus lotus (incl L.corniculatus and L.japonicus) Studies contribute to understanding bacterial and plant components of the symbiosis Symbiosis genes are on the chormosome

Answer 16

Site lacked indigenous rhizobia capable of nodulating plant and uninoculated seedlings die from nitrogen deficiency within a year Sampling 7 years later found diverse strains in nodules containing chromosomal symbiotic DNA identical to that of R7A= original nodulation had transferred to others

Answer 17

Integrative and conjugative element ~10% of genome Converts non-symbiotic into Lotus symbionts in environment and lab Integrates into a phe-tRNA gene in a process mediated by a phage-type integrase Converts by a one off transfer event- excise from chromosome and transfer by conjugation and insert into chromosome recipient

Answer 18

Regulatory= nodD gene product turns on other nod genes in response to flavonoid signal from plant Structural= responsible for synthesis of a lipochito-oligosaccaride signalling molecule Nod factor

Answer 19

Host legume secretes signal molecule i root exudate Different factor for each legume/rhizobium pair (mostly flavonoids= three ring compounds) Different NodD’s recognise different flavonoids= host-specificity

Answer 20

Recognises nod factor via receptor Influx of calcium at root hair tip Calcium spiking in root hair nucleus Deformation (curling) of root hair Initiation of cortical cell division Nod factors are like plant hormones as they share similar characteristics= changes in plant growth and can induce a new organ

Answer 21

Nfr1 and Nfr5 are receptor for Nod factor Extracellular LysM domains bind Nod factors= symbiotic signals through intracellular kinase domain of Nfr1 Leads to downstream signalling cascades= rhizobial infection and nodulation Cascade involves several additional genes and includes activation of Ca-calmodulin kinase through calcium spiking Multiple steps leads to infection thread formation and organogenesis= infected nodule

Answer 22

Rhizobia genes needed are nif and fix Requires high energy and low O2 (O2 inactivates nitrogenase enzyme, inhibit transcription of nif and fix)

Answer 23

Bacteroids have high O2 affinity ETC= can have low O2 to be just as efficient Plant compound leghaemoglobin facilitates diffusion of O2 to bacteroids at high flux but low concentration Nitrogen fixation only expressed in absence of intracellular oxygen regulated by FixLJ

Answer 24

FixL= Membrane spanning with majority in the cytoplasm Contains a heme domain in the cytoplasm area, when O2 is present, FixL phsophatase dephosphorylates FixJ and target genes arent expressed When no intracellular O2, autophosphorylation of his in FixL occurs= kinase leading to phosphorylation of FixJ= activates target genes involved in nitrogen fixation (P from His transferred to Asp on FixJ)

Answer 25

Host supplies bacteroids with C4 dicarboxylic acids as energy into CAC to make electrons- enters through 2 transporters one in symbiosome membrane and one in bacteroid membrane Bacteria reduce N2 to NH3= translocated to host and bacteria make amino acids for itself with NH3 Plant has adaptations for O2, C and N metabolism

Answer 26

NH3 enters host cytosol by passive diffusion (not used by bacteria) NH3 assimilated through actions of glutamine synthetase and glutamate synthetase= glutamine and glutamate Used to synthesise amides or ureides which are transported to the rest of the plant via the xylem

Answer 27

Mycorrhixa fungi= root fungus Integrated into physical structure of roots Widespread occurrence: >90% of land plants (350,000 species), and >50,000 taxa of fungi Little species specificity

Answer 28

Ectomycorrhizae Endomycorrhizae- orchid, ericoid, arbuscular

Answer 29

Carbohydrates and fatty acids (FAs needed as they are FA auxotrophs)

Answer 30

Essential for the movement of plants from the ocean to land Crucial role in land colonisation

Answer 31

Form a sheath around root with little intercellular penentration and no intracellular penetration (can go around/ between cells a little bit, doesnt go in) Hyphae spread out from the sheath and can form networks with others in other plants= nutrient exchange through sheath Found mostly in temperate forest trees eg conifers, beech, oak Root system is long and short Short roots are colonised by micorrhizae which prevents pathogen attach Can form fruity bodies Mycelium in roots, rhizomorphs (where exchange of carbs to outer and stuff for plant occurs), fungal mantle/ sheath, hartig net (fungus/ plant interface)

Answer 32

Restricted to orchids Non-pathogenic penetration of root cortex by septate fungal hyphae= intracellular coils Orchids need the fungus (obligatory mycorrhizal) Fungus mildly pathogenic- balance by plant to control growth using orchanol (so doesnt become parasitic)

Answer 33

Restricted by ericaceae eg rhododendron, blueberry) Non-pathogenic penetration of root cortex by septate fungal hyphae that form intracellular coils (like orchid) The plants here are also obligatory mycorrhizal

Answer 34

Most common type- in most crops Can be grown in culture by addition of FA to medium (discovered in 2019) Makes a hyphopodium which allows the fungus to put pressure on the plant cell and enter Inter and intracellular: non-septate (long with multiple nuclei rather than many divisions between) hyphae in cortex, directly linked to external mycelia that spread into soil and form loose netowrk around the root= high SA between (arbuscule)

Answer 35

Each fungal branch in a plant surrounded by plant-derived periarbuscular membrane (PAM)- continues with plant plasma membrane, excludes fungus from plant cytoplasm When arbuscule goes into cell, it is surrounded by this PAM Space between fungal cell wall and PAM is periarbuscular space made of fungal and plant cell wall material Causes fungus to never be free in cytoplasm, prevents it from becoming pathogenic

Answer 36

Plant lets out strigolactones, sensed by AM fungal spore, causes germination and mycelia growth which then expand Expanding mycelia exude signalling molecules eg lipochitooligosaccharides (LCOs) and chitoologosaccharides (COs) Molecules lead to reactions in the plant root: cytosol Ca increases= AM fungal induced gene expression= formation of pre-penetration apparatus Reacting root secretes cutin monomers= fungi form hyphopodium and initiates arbuscular growth

Answer 37

Fungal lipochitooligosaccharide similar to a nod factor (same thing) In fungus however, not all of them have lipid, can be chitoologosaccharide Common symbiotic signalling pathway between Nod and Myc factors leading to nodulation and mycorrhization Suggests AM symbiosis is ancient and rhizobium have taken over and modified the method to become symbiotic (evolved from AM symbiosis) Possibly use the same receptor too

Answer 38

Essential for colonisation and growth of plants in nutrient-poor environments (key in nutrient and carbon cycle in forests) Main effects from provision of P, N and other minerals and possibly water Improved nutrient absorption by mycorrhizal plants due to greater SA provided by fungal micelia= enhanced resistance to drought stress from high water gathering ability due to same reason Protection against some pathogens especially with ectomycorrhiza Link together into communities= more resilient to stress and disturbance than single plants Enable plant to plant communication Less P needed to reach their maximum growth

Answer 39

Eg molecules providing systemic resistance can be transferred Carbon and nutrients can be transferred Eg donor plant infested with aphids increases defence by emitting volatiles which are repellent to pea aphids and attract parasitic wasps that parasitise on aphids. Can share with other plants to increase their defenses (plants without system cant)

Answer 40

Most plant pathogens only attack one or limited no of plant species Often find resistant varieties to a particular pathogen within a plant species In susceptible plants, pathogen damage usually limited Plants often able to recognise pathogen and mount co-ordinated defence against it Once induced, plant defence response is usually effective

Answer 41

Basal and gene-for-gene

Answer 42

Induce upon infection by almost all microbes Based on recognition of general elicitors- PAMPs by pattern recognition receptors (PRRs) Rapid activation of defence but generally without ‘hyper-sensitive’ response Similar in principle to innate immunity in mammals

Answer 43

Induced upon infection by specialised pathogens Based on recognition of highly specific Avr-gene products- effectors, recognised by matching R-gene products Rapid reaction usually including ‘hypersensitive response’

Answer 44

Plant has PAMP recognition Pathogen develops non-eliciting PAMPs that arent recognised by plant receptors= susceptible plant Pathogen evolves effectors= susceptible plant (produces proteins that interfere with cellular signalling) Plant evolves gene-for-gene defence

Answer 45

Bacteria- flagellin, elongation factor EF-Tu, lipopolysaccharide, cold shock protein Fungi- chitin, B-glucan, ergosterols

Answer 46

Main building block of the flagellum N-terminal and C-terminal domains highly conserved 22 aa sequence in N-terminal= flg22 which is recognised by plant FLS2 Leucine rich repeats with protein-protein interaction domains

Answer 47

In Arabidopsis, is a receptor-like kinase Recognises= immediate changes (ion fluxes and generation of ROS) Protein phosphorylation, mitogen activated phosphorylation (MAP) kinase activation= activation of transcription factors from them being phosphorylated-> gene expression of about 1000 genes (R-genes, RLKs, antimicrobials called phytoalexins) Ethylene production Callose deposition= strengthen cell wall (ROS earlier on can also strengthen cell wall) Rapid oxidative cross-linking of hydroxy-proline rich proteins= cross link and strengthen

Answer 48

Because plant cells have multiple PRRs on their cell surfaces which each leads to an effect and prevents different diseases

Answer 49

CERK1 is a PRR for chitin Related to Nod factor receptors- both similar structure with 3 LysM domains CERK1 homologous to legume Nod factor receptors NRF1 and NRF5 (mediates perception of lipo-chitin nod factors) Likely Nod receptors evolved from CERK1

Answer 50

If a host is susceptible and a pathogen virulent, disease occurs

Answer 51

If host is resistant and pathogen avirulent, no disease occurs

Answer 52

Biotypes of pathogens that vary in their pattern of compatible or incompatible reactions on a set of host plant cultivars

Answer 53

No disease if a plant had a dominant resistance gene AND pathogen had dominant avirulent gene Resistance is able to recognise the avirulent gene and give resistance (as avirulent on its own can still have virulence factors, just not as well) Plant may have several R genes directed against a pathogen, pathogen must lack all relevant avirulence genes to escape recognition Leads to hypersensitive response

Answer 54

Rapid death of infected cells at point of infection (kills cells when R gene recognises avirulent)

Answer 55

Systemic acquired resistance One recognises and spreads the resistance to the rest of the plant

Answer 56

Secreted into host cell cytoplasm by type III secretion systems Called effector proteins (the avr genes) Most can be mutated to restore pathogenicity Most encoded hydrophilic proteins with no functional homologues in databases

Answer 57

In absence of R gene, avr effectors suppress basal defence

Answer 58

Most encode hydrophilic proteins with nucleotide-binding site and leucine rich repeat Involved in protein-protein interactions Others are protein kinases eg Pto NB-LRR class further sub-divided based on N-terminal structure features

Answer 59

TIR-NB-LRR= homology to intracellular signalling domains to Drosophila Toll and mammalian interleukin CC-NB-LRR= contain coiled-coil domains

Answer 60

R-protein is linked to the host target protein of the effector Senses the binding and is released or causes interactions= response to the infection

Answer 61

NB-LRR R gene is attached to host effector target and when bound to effector, R gene is released and causes effect NB-LRR R gene is activated in response to effector target complex (R gene not bound to target)

Answer 62

AvrB/ AvrRpm1 bind to RIN4 which is then P by RIP kinase= inactive= recognition by RPM1 resistance gene (R gene) leading to activation of the R protein and effector triggered immunity AvrRpt2 is a protease, binds to RIN4 and cleaves it which makes it inactive= RPS2 resistance gene (R gene) recognises the cleavage and leads to R gene activation and effector triggered immunity

Answer 63

Binds and blocks kinase domain of PRRs which prevents PAMP triggered immunity R gene Pto mimics kinase domain= binds AvrPto, R gene Prf recognises this binding and leads to effector triggered immunity Prf is a member of NB-LRR family

Answer 64

Use next-gen seq to seq genomes of pathogens causing disease in local fields Use bioinformatics to identify most successful core effectors in strains Identify R genes activated by the effectors Deploy multiple stacked R genes that recognise defined core effectors to reduce change pathogens overcome resistance Identify and edit genome disease susceptibility genes to reduce pathogen growth and symptom development Identify and deploy antipathogenic probiotic and/or antipathogenic microbial mixtures as seed coats

Answer 65

Tumor growth on plants Important in stone fruits, rose, grapes and apples Only wounded cells can be transformed through freezing damage, grafting and mechanical injury Majority of genes for crown gall induction are located on Ti plasmid, not part of core chromosome

Answer 66

Loose attachment via acidic capsular polysaccharide Production of cellulose fibrils that enmesh large numbers of bacteria at wound surface Vir genes expressed and T-DNA excised as single strand, transferred to plant nucleus via inter-kingdom sex/ conjugation Integrated into plant cell DNA= expressed leading to tumor (from synthesis of cytokinin and auxin) and production of opines

Answer 67

Plant produces acetosyringone as part of its defence response Activates virulence genes in the bacteria

Answer 68

T-DNA and vir genes and opine catabolism genes Only part of T-DNA required for transfer are borders- 25 bp sequences Transfer occurs through action of expressed vir genes T-DNA contains oncogenesis genes and opine synthesis genes

Answer 69

Enzymes for auxin and cytokinin synthesis= hormone imbalance= tumour formation Opine synthesis genes eg octopine, nopaline Opines are carbon and nitrogen sources for bacteria Contains bacterial genes which have plant transcription sites on them to allow expression in the plants eg poly-A tails Bacteria lack the appropriate set of transcription factors meaning these genes are only expressed in plants

Answer 70

Condensation product of arginine and pyruvic acid

Answer 71

Condensation product of arginine and alpha-ketoglutaric acid

Answer 72

VirA is part of a 2 component sensory system which resides in bacterial membrane VirA detects phenolic compounds released from plant due to wound Leads to autophosphorylation of virA Phosphate is then transferred to virG which acts as a transcription factor activator for the expression of other vir genes

Answer 73

VirD2 nicks T-DNA at 5’/ right border, attaches to this end by covalent bonding to a Trp Single strand of T-DNA unwinds, released from Ti by nicking at the left border VirE single strand binding proteins bind to the excised T-DNA to stop it from coiling Gap in the Ti-plasmid is repaired

Answer 74

Transferred through pilus encoded by virB operon VirD4 also required VirD2 acts as pilot protein and leads ss-T-DNA to the mating pore which has been formed by virB Things secreted into bacterial cell by type IV secretion system (virF, virD2, virE2) ATP-dependent process (type IV secretion) and allows transfer of effector proteins into cells

Answer 75

VirD2 and vieE2 contain plant-active nuclear localisation sequences (NLS) VirE2 interacts with plant protein VIP1- transcription factor phosphorylated by MAP kinase from Agrobacterium infection (defence response) Phosphorylation targets VIP1 to nucleus, T-DNA goes with it through interaction with virE2 VirD2 required for integration of T-DNA by protecting the 5’ end of the T-DNA Integration occurs by illegitimate recombination at expressed loci (genes which are in loose chromatin from presence of RNA pol and are being synthesised)- leads to mutated DNA Allows cell division and opine synthesis

Answer 76

Each Agrobacterium strain catalyses only the opines synthesised by the tumours it induces- catabolic reactions encoded on Ti plasmid= ecological niche Some opines induce conjugal transfer of Ti plasmid to other strains of Agrobacterium that may be present= way if ensuring plasmid is propagated

Answer 77

Binary vector system Clone DNA to be transferred between border sequences in a cloning vector Transfer vector to disarmed/ defective Agrobacterium strain with mutated Ti plasmid containing vir genes but not T-DNA Use strain to transfer cloned DNA to plant cells using either cells in petri dishes or by dipping flowers Regenerate plant cells into whole plants or screen for transformed seeds