MODULE 4 - Plant-Microbe Interactions Flashcards
1
Q
what part of a plant hosts microbial communities?
A
every single part from leaves to roots and even the soil around it
2
Q
what is the rhizosphere?
A
zone of root influence - extends less than 5mm from root
3
Q
what is the rhizoplane?
A
root surface
4
Q
outline the microbial community in the rhizosphere?
A
populations around plant roots usually 20-100x more than surrounding soil (called the rhizosphere effect)
home to a vast array of species but beta and alpha proteobacteria often predominate, their growth is dependent on root exudates
around the root tip is where many microbes accumulate sloughed off cells make this area nutrient rich
bacteria grow as microcolonies over about 5% of the root surface meaning it is mostly sterile
microbes prefer to colonise the gaps between plants cells and around the root tip
5
Q
what are the bacterial communities in the rhizosphere strongly influenced by?
A
soil type and genetic constitution of host plant
6
Q
what are the four main phylum of bacteria which dominate the rhizosphere of many plants?
A
actinobacteria, bacteroidetes, firmicutes and proteobacteria
of these, alpha and beta-proteobacteria are the two most dominant classes of bacteria
7
Q
outline the multi-step process of how bacteria colonise plant roots?
A
bacteria swim up a gradient of exudates to reach root surface; especially root tip
primary attachment occurs (reversible) which is initially weak and mediated by hydrophobic and electrostatic forces
adhesion strengthened by something like flagella, fimbriae, adhesins or pili)
secondary attachment occurs (irreversible) where cellulose is produced further strengthening attachment
micro colonies form at site of adhesion and biofilms form through secretion of exopolysaccharides
8
Q
what are the three groups which the rhizosphere microbiome can be classified in?
A
beneficial microbes
commensals (neutral) (however they do modulate ability of beneficial and pathogenic bacteria to colonise root through normal microbe-microbe interactions)
pathogens (can infect plant root or secrete compounds which harm plant root)
9
Q
how might rhizosphere research help us reduce reliance on agrochemicals such as pesticides and fertilisers?
A
by tipping the balance of rhizosphere microbes in the favour of the beneficial ones
10
Q
what are some examples of rhizosphere microbes that have harmful effects on plant growth?
A
pathogenic fungi, oomycetes, nematodes and bacteria
root rot fungi such as fusarium, pythium
phytophthora agathidicida causes kauri dieback
11
Q
what are some of the harmful effects of pathogenic rhizosphere microbes other than the diseases they cause?
A
major problem for food production and ecosystem stability worldwide
e.g. pathogen resistance to applied agents, environmental impacts of pesticides, cost of pesticides, demand for pesticide-free food
12
Q
what are beneficial rhizosphere bacteria called?
A
plant growth-promoting rhizobacteria (PGPR)
13
Q
what are some of the direct beneficial effects of rhizosphere microbes like PGPR?
A
facilitate uptake of nutrients from enviro e.g. phosphate solubilisation, associative nitrogen fixation, siderophore production (iron acquisition)
synthesise compounds that affect plant growth e.g. plant growth regulators such as IAA which produces ACC deaminase that inactivates precursor of stress-hormone ethylene
14
Q
what do auxin-producing bacteria do?
A
promote plant growth
e.g. Pseudomonas corrugata with radish plants, Azospirillum with maize
15
Q
how do ACC deaminase-producing bacteria benefit plants?
A
halotolerant bacteria which protect plants from salt stress
16
Q
what are some indirect effects of beneficial rhizosphere microbes such as PGPR?
A
lessen or prevent effects of plant pathogens
e.g. pseudomonas fluorescens can control root rots caused by fungal pathogens such as Ggt which causes take-all disease
17
Q
how does Pseudomonas fluorescens prevent take-all disease from occurring in wheat and how was this discovered?
A
produces antibiotic (2,4-DAPG) which is toxic to Ggt, the take-all causing pathogen
this was sound out as many cases where wheat grown year after year in same soil and natural suppression of fungus occurred which is referred to as take-all decline (TAD)
TAD correlated with development of specific fluorescent Pseudomonas
important example of how bacteria control pathogens (biocontrol)
18
Q
why is soil type important in shaping the rhizosphere bacterial community?
A
it is recruited from the microorganisms present in the soil, thus soil type important in shaping rhizosphere microbiome
19
Q
why is plant genotype important in shaping the plant microbiome?
A
is a driving force for selection of specific elements from the bulk soil microbial community
when under stress/threat, evidence shows that plants can modify their rhizosphere microbiome to select for specific elements
20
Q
what are the three main mechanisms of biocontrol of plant diseases by bacteria in the rhizosphere?
A
antibiosis
induced systematic resistance
competition for nutrients and niches
21
Q
what is antibiosis?
A
bacterium colonises root system and delivers antibiotic molecules around the root thereby harming pathogens that approach the root
also commonly used to kill fungal pathogens which colonise same area as bacteria (gaps between plant cells)
22
Q
what is induced systematic resistance (ISR)?
A
local root colonisation is sufficient to induce ISR. Many bacterial products induce systemic signalling via plant receptors which can result in protection of the whole plant against diseases caused by different organisms
23
Q
how does biocontrol occur through competition for nutrients and niches?
A
biocontrol bacteria acting through this mechanism excel in fast chemotactic movement along the growing root in their efficient hunt for root exudate components, thereby outcompeting the pathogen in scavenging nutrients and in occupying niches on the root
basically just colonise quick as a form of niche exclusion
24
Q
what is the phylloplane?
A
leaf surface
25
what is the phyllosphere?
the total surface area of the plant above ground
26
why is the phyllosphere much harsher than the rhizosphere?
cause its exposed to rapid moisture fluctuations, rapid temperature fluctuations and UV radiation
so to colonise this enviro you have to be able to withstand these conditions
27
describe the microbial population in the phylloplane?
microbial populations fluctuate rapidly
common inhabitants include epiphytic bacteria, gram negative bacteria e.g. Pseudomonas, Erwinia, Xanthomonas
28
where are bacteria mostly concentrated in the phyllosphere?
large populations of bacteria around the trichome, majority of the leaf is sterile
29
what are three Pseudomonas syringae methods of colonising the phylosphere?
production of syringomycin which acts as phytotoxin and surfactant to force release of nutrients by damaging plant cells and breaking down the waxy cuticle to allow its dispersal
auxin production and secretion by bacteria which provokes release of saccharides from plant cell wall
production of exopolysaccharide by bacteria to form biofilm which provides protection from environmental stresses
30
what are some common bacterial traits involved in adaptation to the phyllosphere?
quorum sensing signalling molecules
antibiotics (often controlled by above so all released at same time)
pigments to protect from UV
auxin production
protective proteins
efflux pumps
EPS production
biosurfactants (get through waxy cuticle)
metabolic adaptations
31
how does Pseudomonas syringae worsen frost damage?
it is ice nucleation active meaning that the bacteria can function as a nuclei for formation of ice crystals that can spread into plant tissues
this prevents supercooling of leaves so that frost damage occurs at -3 degs rather than the usual -8 degs without bacterial presence
this process is dependent on production of INA outer-membrane protein
32
what has been done to try and prevent frost damage caused by P. syringae involving competitive exclusion?
production of mutant INA- strains of P. syringae released into environment to see if they competitively exclude INA+ wild type which are a problem for orchards
33
how are INA+ strains of P. syringae used commercially?
in snow making machines to allow snow production at much warmer temperatures
34
what bacteria can live in the atmosphere and induce rain/hail and why is this?
P. syringae
due to its adaptations to surviving in the phyllosphere, it can survive in the atmosphere
being swept up by wind and then inducing and falling with precipitation could be a method of spreading the bacteria to other plants
35
what bacteria causes fireblight?
Erwinia amylovora
spread by pollinating insects
36
how can we use Pseudomonas strains to prevent fireblight?
you can spray blossom with fast-colonising Pseudomonas strain which can't cause disease but can competitively exclude and produce antibiotics to prevent Erwinia amylovora colonisation which is the pathogen causing fireblight
37
what are legumes?
plants which have seeds in pods such as soybeans, clover, beans etc.
only plant that has developed ability to form symbiotic relationship with rhizobia
38
what does infection of legume roots by rhizobia lead to?
root nodule formation and nitrogen fixation, a process where gaseous nitrogen is converted to combined nitrogen
39
how is there host specificity in the rhizobium-legume symbiosis?
only a specific strain of rhizobia is able to nodulate a specific type of legume
40
what are rhizobia?
gram-negative rod shaped soil bacteria that can form nodule on legume
rhizobia very diverse and fall into two groups - alpha-proteobacteria and beta-proteobacteria
nodule forming ability was passed around through HGT, this ability was developed AFTER they split into all these different genera
41
what is the rhizobia-legume symbiosis characterised by?
a high degree of host specificity
42
what are the stages of forming the rhizobia-legume symbiosis?
recognition of correct plant partner by rhizobia and then attachment of rhizobia to root hairs
this causes root hair to curl and induces cortical cell division opposite to where rhizobia binds (one side growing faster causes root hair to curl)
micro colony now trapped in curled root, plant cell wall begins to grow inwards forming an infection threat which rhizobia enters (meaning rhizobia always protected from plant cell cytoplasm)
cortical cell division induced in cells of inner cortex of plant root which forms organ which will be nodule
infection thread branches to contact dividing cells and rhizobia bud off into plant cell via endocytosis surrounded by membrane of plant origin
here the rhizobia terminally differentiate into misshapen bacterial cells called bacteroids which can fix nitrogen
nutrient transmission across plant cell membrane to bacteroid provides carbon source so bacteroid can make energy for N fixation in form of ammonia which it sends back across membrane
43
what is a determinate nodule?
nodule grows not only by plant cells dividing but also by plant cells expanding after division
44
what are the developmental stages which are present (can be seen in cross section) in a nodule?
meristematic zone = the part of the nodule where the cells are continuing to divide making it larger and larger
infection zone = where rhizobia are budding into dividing plant cells
nitrogen-fixing zone = where all the plant cells have bacteroids in them fixing nitrogen
45
what is the purpose of the non-differentiated rhizobia living in the nitrogen-fixing zone?
these released back into soil when the nodule dies off to go infect other plants i.e. nodule provided an ideal sheltered space for rhizobia to grow and proliferate
46
how does host specificity occur in the rhizobia-legume symbiosis i.e. how does it recognise its specific host?
host legume releases exudates into rhizosphere incl phenolic-like compounds called flavonoids
rhizobia can recognise particular flavonoid as opposed to other kinds of flavonoid so that it knows its in presence of specific host legume
rhizobia then induces a set of genes called nod genes which are required for nodule formation. These nod genes make a chemical of their own which has complex oligosaccharide structure which has a fatty acid which differs between rhizobia
so particular nod factors unique for particular rhizobia and legume recognises this via receptors on plant cells
so basically there is two-way signalling between host legume and rhizobia to induce nodule formation/N fixation
47
what are nod genes encoded on?
encoded on a accessory genetic elements called symbiosis islands
e.g. large Sym plasmids in Rhizobium
e.g. chromosomal symbiosis islands in Mesorhizobium loti
this means that nod genes are part of the accessory genome
48
what is Mesorhizobium loti?
rhizobia which modulates the legumes of the genus Lotus
symbiosis genes are on the chromosome
49
what is the Mesorhizobium loti R7A symbiosis island?
mobile, chromosomally integrated element which integrates into a phe-tRNA gene in a process mediated by phage-type integrase
can excise from chromosome and transfer via conjugation (involving oriT, trb and tra genes) thus inserting itself into chromosome of recipient
has been shown in lab and in enviro to convert non-symbiotic mesorhizobia to symbionts (due to HGT of symbiosis island)
50
what are the two groups of nod genes?
regulatory - the nodD gene product turns on other nod genes in response to flavonoid signal from plant
structural - responsible for synthesis of a lipochito-oligosaccharide signalling molecule called nod factor
so once recognition of flavonoid occurs by nodD gene transcription is activated for structural genes which make nod factor
51
how are nod genes turned on?
host legume secretes specific signal molecule in root exudate. These are different for each rhizobia/legume pair and most are secondary plant metabolites called flavonoids (three-ring aromatic compound)
different nodD genes recognise different flavonoids and then turn on other nod genes which are recognised by receptors on legume and allow for nodulation to occur
(two-way signalling)
52
what do nod genes produce?
a nod factor
this is an oligomer of N-acetyl-glucosamine (called a lipochitooligosaccharide) which is decorated by species specific bells and whistles (main one is a fatty acid (acyl group) which is unique for different rhizobia)
it is these bells and whistles that allow for host-specificity
53
what are the plant responses to nod factors?
influx of calcium at root hair tip
calcium spiking in root hair nucleus
curling of root hair
initiation of cortical cell division
(nod factor share many characteristics with plant hormones)
54
what is calcium spiking?
big calcium conc. changes through effluxes and influxes of root hair nucleus which occur about 10 minutes after adding nod factor
55
what are NFR1 and NFR5?
two genes in Lotus japonicus which make proteins which form a receptor for nod factor
extracellular LysM domains bind nod factors and then transduce the symbiotic signals through the intracellular kinase domain of NFR1 to downstream signalling cascades
this leads to rhizobia infection and nodulation
the cascade includes activation of calcium-calmodulin kinase through calcium spiking
56
what are the two pathways which can lead to formation of an infected nodule in Lotus japonicus?
both start with nod-factor perception by NFR1 and NFR5 and both end with infected nodule being formed
pathway 1 involves formation of infection thread
pathway 2 involves organogenesis
57
outline the infection thread pathway to nodule formation?
nod-factor perception and then root hair curling which is followed by rearrangements of actin and then growth down infection thread to infect nodule
58
outline the organogenesis pathway to nodule formation?
nod-factor perception and then signal transduction through a bunch of receptors which leads to calcium spiking and this eventually leads to organogenesis which leads to infected nodule
59
what does cross-signalling between the two pathways to nodule formation in L. japonicus allow?
keeps the pathways in tune with each other (idk just know that there is cross-signalling)
60
what two rhizobia genes are essential for symbiotic N fixation?
nif and fix genes
61
outline the reaction involved in nitrogen fixation in root nodules?
reaction is catalysed by nitrogenase enzyme and has a very high energy requirement
rhizobia are obligate aerobes cause they needa make lots of ATP for N fixation and so have oxygen as terminal electron acceptor
problem is oxygen denatures the nitrogenase enzyme and inhibits expression of nif genes
62
how do rhizobia allow for efficient aerobic respiration while protecting the nitrogenase enzyme?
their ECT has a very high oxygen affinity so can function well at low oxygen concentrations
plants have leg-haemoglobin which serves as an oxygen carrier within the nodule and facilitates diffusion of oxygen to bacteroids electron acceptors at high flux but low conc. i.e. ensures that its getting enough O2 for respiration but it is in a bound form so that it cannot harm nitrogenase inside the bacteria
N fixation genes only expressed in absence of intracellular oxygen - regulated by FixLJ
63
what nutrient exchanges are occurring in the nodule between the plant and bacteroid?
host plant supplies bacteroid w C4-dicarboxylic acids as energy source
bacteria reduce N2 to NH3 which is translocated to host and assimilated in plant cell cytoplasm
64
what happens to rhizobium mutants which are defective in C4-dicarboxylic acid transport?
they form ineffective nodules as no carbon source to turn into energy
65
what is ammonium assimilation?
NH3 enters host cytosol via passive diffusion
NH3 assimilated through actions of glutamine synthetase and glutamate synthetase producing glutamine and glutamate
these products are used to synthesise amides or ureides (other nitrogen containing compounds) which are transported to the rest of the plant as a nitrogen source
66
what nutrients do mycorrhizal fungi get from plants and what do they give in return?
carbs and lipids from plant
give back phosphates, nitrogen, water and also increase surface area tapped by roots
67
why do many arbuscular mycorrhizae absolutely need the fatty acids synthesised by the host plant?
many of them are fatty acid auxotrophs
68
what is the difference between ectomycorrhizae and endomycorrhizae?
ecto stay on outside of plant cells
endo form an intracellular infection
69
describe ectomycorrhizae?
form sheath around root with little intercellular penetration and no intracellular penetration
found mostly in temperate forest trees
colonises short roots and forms sheath around root which protects from pathogens
70
what is the main interface between fungi and plant where nutrients are exchanged?
the Hartig net
71
describe endomycorrhizae?
three types - orchid, erichoid and arbuscular
orchid - restricted to orchids and characterised by non-pathogenic penetration of root cortex by septate fungal hyphae that sometimes form intracellular coils. Orchids require fungi to survive but produce orcinol to keep fungal growth checked i.e. fine balance between parasitism and mutualism
ericoid - restricted to Ericaceae and similar morphology to orchid mycorrhizae
arbuscular - most common type and found in crops, mycelia penetrates plant cells and forms branches called arbuscules. Differ from above two endomycorrhizae as hyphae are non-septate. Very little host specificity. Can be cultured w addition of fatty acid
72
describe the arbuscule?
fungal branches inside plant cell from arbuscular endomycorrhizae
each branch surrounded by plant-derived periarbuscular membrane (PAM) which is continuous w plant plasma membrane and so fungus excluded from plant cytoplasm (why it isn't pathogenic)
interface between fungal plasma membrane and PAM is called the periarbuscular space (PAS) which is comprised of both fungal and plant material
73
which type of mycorrhizae forms a mantle on plant cells?
ectomycorrhizae
74
how does communication occur between arbuscular mycorrhizae (AM) and root and what does this allow to form?
plant root secretes strigolactones, fungal spores sense this and germinate causing rapid growth/branching of mycelia
mycorrhizae secretes signalling molecules such as lipochitooligosaccharides with fatty chains (like nod factors)
these molecules trigger reactions in plant root such as calcium spiking which leads to fungal gene expression leading to formation of pre-penetration apparatus
root secretes cutin which signals to fungi to form hypha-odium and initiate arbuscular growth (penetrate and form arbuscules)
this allows symbiosis to form and is a less specific form of communication than that of plant-rhizobia
75
what is the common symbiotic signalling pathway?
there is a common symbiotic signalling pathway shared between mycorrhizae and rhizobia
differences are AM fungus initiates it with myc factor well rhizobium initiates with nod factor
infection thread solely rhizobia and mycorrhizae less specific
however a lot of the genes for the pathways leading to nodulation and mycorrhization are shared
76
what are the benefits of mycorrhizae?
essential for colonisation and growth of plants in nutrient-poor environments so they are key organisms in nutrient/carbon cycles in forest ecosystems
provide phosphate, nitrogen and other minerals and improve nutrient absorption for mycorrhizal plants through greater root SA provided by mycelia
enhanced resistance to drought stress cause greater water acquisition
protection against pathogens (especially ectomycorrhize as form mycelial sheath on plant root)
link plants together into communities which are more stress resilient than single plants
enable plant-plant communication
77
describe how resource sharing occurs in mycorrhizal networks?
one mycorrhizal individual colonises different plants of different species
molecules such as carbon and nitrogen can be acquired by fungus and form nutrient patches which can then be passed between plants via the fungus
78
how does plant-plant communication occur via common AM fungal networks?
plant infected with aphids increases its defences against them by emitting chemicals which are repellent to aphids but attract wasps which kill aphids
it is connected to other plants via underground hyphal network which also start to emit the same chemicals despite no aphids
when there is no hyphal network the other plants to not up regulate their defences
79
what are some NZ examples of plant pathogens which pose major threats to some plants?
Pseudomonas syringae causing death of kiwifruit vines on orchards
Phytopthora agathidicida causing kauri dieback
Myrtle rust fucking up põhutakawa
80
what kind of pathogens can attack plants?
bacteria, fungi, viruses and nematodes
81
what occurs in most plant-pathogen interactions?
most pathogens only attack one or a limited number of plant species
often find resistant varieties to certain pathogens within plant species
even in susceptible plants, pathogen damage usually limited
plants are often able to recognise pathogen and mount co-ordinated defence against it. Once induced the plant defence response is usually effective
82
what are the two defence systems that plant cells have to detect bacterial and fungal pathogens?
basal defence (PAMP triggered immunity - PTI)
gene-for-gene defence (effector triggered immunity - ETI)
83
outline basal defence?
similar to innate immunity
induced upon infection by almost all microbes and based on recognition of general elicitors known as PAMPS (ubiquitous molecules found in microbes) hence PAMP-triggered immunity (PTI)
defence activated rapidly but generally without a hypersensitive response
84
outline gene-for-gene defence?
induced upon infection by specialised pathogens
based upon recognition of highly specific Avr-gene products (effectors) by specialised, matching R-gene products hence effector-triggered immunity (ETI)
recognition results in rapid reaction called hypersensitive response which kills infected cells
85
outline the plant-pathogen arms race?
plant pathogens have effector proteins which they secrete into plant cytoplasm which interfere with PAMP recognition by plant PRRs
this allows pathogen to cause disease by suppressing the plant basal defence
in response to this however the plant has evolved resistance proteins which recognise the impact of effector proteins and activates a seperate defence response (effector triggered immunity)
86
why do plant pathogens develop effector proteins rather than just mutate PAMPs so that they are unrecognisable?
PAMPs are on highly conserved proteins
87
what are some common PAMPs in bacteria and fungi?
bacteria: flagellin, elongation factor, LPS, cold-shock protein
fungi: chitin, beta-glucan, ergosterols
88
describe flagellin as a PAMP?
flagellin is the main protein of the flagellum and is very conserved in the N terminal of flagellin where there is a peptide called flg22
FLS2 (flagellin sensing 2) is a receptor like kinase (RLK) which recognises flg22 and triggers ion fluxes, generation of ROS, protein phosphorylation, MAP kinase activation which then activates a shit load of genes which make antibiotics and shit and toughens up the cell wall making penetration harder
ROS also has a role in linking proteins in plant cell wall to make it tougher against penetration as well
so basically all these things protect the cell from infection
89
how has the importance of the FLS2 receptor been shown in the lab?
FLS2- plants clearly more susceptible to infection from bacteria
90
how many PAMP receptors do plants usually have?
lots!
91
what is CERK1?
a PRR for chitin which is a common fungal PAMP
CERK1 PRR is homologous to the nod factor receptors NFR1 and NFR5 which mediate perception of lipo-chitin nod factors
so there is a lot of homology. between defence systems and systems that recognise rhizobia in plants
92
what is it that makes a plant resistant to a particular pathogen?
if it is a pathogen it is virulent i.e. can cause disease
however the pathogen may have an avirulence gene (Avr) and if the plant has a resistance gene which matches the Avr gene, then no disease occurs
so for each resistance gene in the plant there is a corresponding Avr (avirulence) gene in the pathogen. The reason the pathogen cannot cause disease is not cause it lacks a virulence gene but because it has an avirulence gene which the plant will have a corresponding resistance gene for (R gene recognises the Avr gene to induce resistance i.e. no disease (incompatible reaction)
so a plant may have a resistance gene but if the pathogen doesn't have corresponding Avr gene then disease occurs (compatible reaction)
a plant may have several R genes and to escape recognition and cause disease, a pathogen will have to lack all the Avr genes which correspond to the plant's R genes
this is referred to as gene-for-gene complementarity
93
what are the main plant defence responses elicited by pathogen recognition?
rapid oxidative burst w production of H2O2
rapid oxidative cross-linking of pre-existing cell wall proteins; toughens cell wall
expression of antimicrobial compounds called phytoalexins
expression of pathogenesis-related (PR) proteins e.g. things that lyse bacteria
rapid death of infected plant cells (hypersensitive response)
systemic acquired resistance (chemical signals diffuse through plant so other parts of the plant express defence mechanisms despite not having contacted pathogen yet)
94
outline the entire defence response in plants in response to PAMP recognition?
PAMPs such as chito-oligosaccharide (COS) recognised by PRRs. PRR activation triggers MAP kinase pathway leading to up regulation of hundreds of defence related genes. Several WRKY transcription factors activated that are directly responsible for expression of defence genes. Activated basal defences include cell wall fortifications, production of ROS and in the case of ETI (effector-triggered immunity), the hypersensitive response. Other cellular responses include release of phytohormones which activate signalling pathways leading to increased expression of antimicrobial genes, cell wall reinforcement and signal transduction to the whole plant
95
after avr genes were cloned, what were most of them found to encode?
hydrophilic proteins with no functional homologues in data bases
now we know that these proteins are secreted into the host cell cytoplasm by Type III secretion systems and are called effector proteins
96
outline the proteins encoded by avr genes?
effector proteins which are secreted into host cell cytoplasm via type III secretion systems (T3SS)
most can be mutated to restore pathogenicity
can function as virulence factors on hosts lacking the corresponding R gene
in absence of R gene, Avr effectors function to suppress basal defence
97
which is going to be more virulent against a plant without a resistance gene, a pathogen with no avr gene or a pathogen with an avr gene?
pathogen with avr gene as it will encode an effector protein which suppresses the plants basal defence
however if plant had compatible R gene there would be no disease caused as R gene and compatible avr gene leads to incompatible reaction (no disease caused)
note this is only with some avr genes
98
after R genes were cloned, what were most of them found to encode?
most encode hydrophilic proteins with nucleotide-binding (NB) site and leucine-rich-repeat (LRR) region involved in protein-protein interactions. Some others encode protein kinases
the NB-LRR class can be subdivided based on N-terminal structural features:
- many have homology to intracellular signalling domains of the Drosophila Toll and mammalian IL-1 receptors (TIR-NB-LRR) (TIR structure)
- others contain coiled-coil domains (CC-NB-LRR) (coil-coil structure)
99
what is the guard hypothesis for how Avr and R gene products interact?
R protein essentially guarding the target of the effector (Avr) protein and when the pathogen effector protein interacts with its target protein the resistance gene can sense this interaction, know its target is under attack and then is activated so it can signal on for other defence responses
other idea is that the R protein is seperate from the target of the effector but when the effector interacts with the target the R protein is is recruited and this sets off the cascade
bottom line is that the actual interaction is being sensed and it is the effect of that interaction that leads to activation of resistance
100
what is the main point of the guard model/hypothesis and why is this beneficial?
the pathogen virulence proteins are recognised as a consequence of their virulence function, rather than by direct interaction with a plant R protein
this is beneficial because by recognising pathogen virulence proteins based on enzymatic activity rather than their shape, plants could likely detect a large number of pathogen effectors with a limited number of R proteins
101
what are some genomic strategies we could use to breed durable resistance to plant pathogens?
use sequencing technologies to sequence genomes of pathogens causing disease
identify R genes that are activated by effectors
use bioinformatics to identify the most successful effectors in particular strains
102
what bacteria causes crown gall formation?
Agrobacterium tumefaciens
103
what is Agrobacterium tumefaciens?
alpha-proteobacterium closely related to Rhizobium
causes crown-gall disease which is important in stone fruits, grapes, rose, apples
only wounded cells can be transformed from stuff like freeze damage, grafting, mechanical injury
majority of genes for crown gall formation on large plasmid called Ti (tumour inducing) plasmid
104
why can Agrobacterium lose the ability to induce crown galls and other bacteria gain it?
the Ti plasmid encodes most of the genes for crown gall
105
outline the steps in crown gall formation?
first step is attachment - involves loose attachment via acidic scapular polysaccharide followed by production of cellulose fibrils that enmesh large numbers of bacteria at the wound surface
vir genes then expressed and T-DNA excised as single strand and is transferred to plant nucleus and integrated into plant genome so now these genes expressed in plant and not agrobacterium
tumorigenesis occurs in plant
106
what are the two main regions on the Agrobacterium plasmid?
vir region
T-DNA region
107
how does the Agrobacterium tumefaciens recognise the wounded plant cell?
wounded plant cell secretes phenolic compounds (acetosyringone)
these single molecules are recognised by VirA/VirG two-component regulatory system and this activates other vir genes
VirA senses them and VirG is a transcriptional activator which turns on the other virulence genes
108
what parts of the T-DNA on the Ti plasmid are required for transfer?
only the borders required
all the DNA between these borders are transferred
109
what does the T-DNA encode?
enzymes for auxin and cytokinin synthesis which cause hormone imbalance leading to tumour formation
also encodes opine synthesis genes and the bacteria uses the opines (v uncommon compounds) as carbon and nitrogen sources for growth
110
how does the T-DNA get excised from the Ti plasmid of Agrobacterium tumefaciens?
process starts with nicking of T-DNA at its right border by a mob protein called VirD2
VirD2 covalently attaches to nicked strand
single strand of T-DNA unwinds and is released from the Ti plasmid by nicking at the left border
gap in Ti plasmid is repaired
T-strand transferred through a pilus encoded by verb operon; this VirD4 also required
VirD2 mob protein acts as pilot protein leading the strand to mating pore for transfer to plant cell
coating of T-strand with VirE2 occurs within plant cell
111
describe the Type IV Secretion System (T4SS) in Agrobacterium?
bacterial cells contact unidentified host cell receptor using VirB2 pilin and VirB5 adhesin
a DNA-dependent ATPase called VirD4 delivers DNA bound by relaxase VirD2 to inner membrane secretion channel
ATPases VirB4 and VirB11 provide energy for secretion of DNA and effectors through a VirB6 inner membrane channel and a secretion complex in host cell
112
once the T-DNA is inside the plant cell, how does it target the nucleus?
once inside plant cell T-DNA has to get to nucleus
VirD2 and VirE2 both contain two plant-active nuclear localisation (NLS) sequences and are both necessary for nuclear targeting
VirE2 interacts with plant protein VIP1 which is a transcription factor that is phosphorylated by MAP kinase which is activated by Agrobacterium infection as a defence response
Phosphorylation targets VIP1 to nucleus and T-DNA hitches ride through interaction with VirE2
VirD2 required for integration of T-DNA and integration occurs by illegitimate recombination
T-DNA encoded genes then expressed
cell division and opine synthesis occurs
113
what are the responses to the opines synthesised by the tumours?
generally each Agrobacterium strain catabolises only the opines synthesised by the tumours it induces (catabolic genes encoded on Ti plasmid (tumour is their ecological niche)
some opines induce conjugal transfer of the Ti plasmid to other strains of Agrobacterium that may be present (opines are the Ti plasmids way of ensuring its propagated)
