the plant cell, august 2015 © 2015 2/17/2015 the …...2012/08/28 · have struggled with plant...

The Plant Cell, August 2015 © 2015The American Society of Plant Biologists

2/17/2015

www.plantcell.org/cgi/doi/10.1105/tpc111.tt0811 1

© 2015 American Society of Plant Biologists

Fighting for their lives: Plants and pathogens

Photos courtesy of CIMMYT, Scott Bauer, USDA Agricultural Research Service, IRRI, IRRI, IITA


Plant pathogens are infectious agents that make plants sick

Plant pathogens cause 10 – 30% yield losses annually

Up to 25% of plant genes respond to pathogen infection

Most plants are resistant to most pathogens; disease is the exception, not the rule

The arms race between plants and pathogens drives diversity in defense and pathogenicity genes


Nematodes are large, multicellular animals

Bacteria are prokaryotes

Viruses are non-cellular, and merely packaged nucleic acids

Fungi and oomyctes are eukaryotes

Bacteria

Oomycete

Fungus Fungus

Many kinds of organisms cause plant disease

Large, E.C. 1940. Advance of the Fungi. Jonathan Cape, London.


Lecture Outline

• Brief history of plant pathology

• What makes an interaction into a disease?

• Strategies of pathogenicity• Perception, response,

virulence and resistance• Strategies to prevent and

manage plant diseases

Photo credit: IRRI


Since agriculture began, humans have struggled with plant pathogens

Image credits: Asian Agri-History Foundation and Sacramento Chinese Cultural Foundation

Texts describing best practices to

avoid plant diseases date back

thousands of years


Diseases were often blamed on gods

Image credits: British Museum and VROMA

Once it was thought that

gods and goddesses controlled

natural events

Zeus controlled the weather

Ceres or Demeter was the goddess of grain


Case study: Phytophthora infestans, plant destroyer

Ristaino, J.B. (2002). Tracking historic migrations of the Irish potato famine pathogen, Phytophthora infestans. Microbes and Infection. 4: 1369-1377. Gómez-Alpizar, L., Carbone, I. and Ristaino, J.B. (2007). An Andean origin of Phytophthora infestans inferred from mitochondrial and nuclear gene genealogies. PNAS USA. 104: 3306-3311; Scott Bauer, USDA Agricultural Research Service

Potatoes were brought to Europe from South America starting in the 16th century, but the pathogen Phytophthora infestans was not observed in Europe until the 19th century

1800 1840 1880 1920

2

4

6

8

Po

pu

latio

n o

f Ir

ela

nd

(m

illio

ns)

The late blight epidemics of the 1840s hit Ireland particularly hard, and caused mass starvation and emigration

An outbreak potato late blight, caused by Phytophthora infestans, caused the Great Famine of the 1840s


The 19th century – “some diseases are caused by microorganisms”

Miles Joseph Berkeley, 1846

I believe that the plants are sick because the mold is growing on them

The potato late blight epidemic led to key discoveries in plant pathology

Is mold growing on the plants because the

plants are sick?

Berkeley, M.J. (1846) Observations, botanical and physiological, on the potato murrain. J. Hort. Soc. (Lond) 1: 9 -34, as reprinted in Large, E.C. 1940. Advance of the Fungi. Jonathan Cape, London.


1863 - Anton de Bary showed that Phytophthora causes late blight

De Bary transferred spores from a sick plant to a healthy plant, which then

developed disease symptoms

He also observed the spores entering the leaves of the new host

De Bary, A. 1863. Recherches sur le développement de quelques Champignons parasites, etc. Ann. Sci. Nat. 4e Sér Bot., XX: 1 -148, as reprinted in Large, E.C. 1940. Advance of the Fungi. Jonathan Cape, London.


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Pathologists unite in support of the germ theory

At the same time, Louis Pasteur and Robert Koch showed animal

diseases were caused by microbes, and the germ theory was born Koch’s postulates to establish a microbe

as the causal agent of a disease (1880s):• The microbe is always associated and

isolated from the patient with the disease• The microbe must be grown in pure culture • The microbe can be injected or inoculated

into an animal (plant) and cause disease• The microbe can be re-isolated in pure

culture


Bacterial plant pathogens were described in the 1870s

Paul Bachi, University of Kentucky Research and Education Center, Bugwood.orgClemson University - USDA Cooperative Extension Slide Series

T.J. Burrill (1878) demonstrated that fire blight of pear and apple was caused by a bacterium, Erwinia amylovora

Bacteria oozing away from infected tissue is an important diagnostic tool for bacterial infections


The causal agent of tobacco mosaic was identified as a virus (1890s)

Delft School of Microbiology Archive; Clemson University - USDA Cooperative Extension Slide Series, Bugwood.org

Electron micrograph of TMV

By passing the extract from an infected leaf through an extremely fine filter, pathologists showed that the infectious agent was smaller than a bacterium, and named it “virus”

Dmitri Ivanovsky

Dmitri Ivanovsky

MartinusBeijerinck


Being much larger, plant parasitic nematodes were identified earlier

Wheat seed-gall nematode Anguina triticidescribed by John Turberville Needham, 1743as “Aquatic animals…worms, eels, or serpents, which they very much resemble”

Michael McClure, University of Arizona; Jonathan D. Eisenback x 2, Virginia Polytechnic Institute and State University, Charles Averre, North Carolina State University, Bugwood.org

Experimental nematology began in the 1850s, on the root-knot nematodes affecting these cucumber seedlings, described by M.J. Berkeley


By the end of the 19th century, pathologists knew why plants got sick

Photo by Ken Hammond; Jenkins B, Turn S, Williams R. 1991. Survey documents open burning in the San Joaquin Valley. Cal Ag 45:12-16; Luck, J.E., Lawrence, G.J., Dodds, P.N., Shepherd, K.W. and Ellis, J.G. (2000). Regions outside of the leucine-rich repeats of flax rust resistance proteins play a role in specificity determination. Plant Cell. 12: 1367-1378.

Research in the 20th century focused on the prevention and control of disease outbreaks

Genetics of disease resistance

Chemical warfare Better hygiene(e.g. burning crop residue)

Resistant

Sensitive


What makes an interaction into a disease? (Disease triangle)

Plants are exposed to countless microbes, but very, very few of these interactions lead to disease. Why?

Environment

The disease triangle

(it takes three)

The pathogen must be able to overcome

plant defenses

The environment must tip the balance in favor of the pathogen

The host plant must be

susceptible to the pathogen


Fred Brooks, University of Hawaii at Manoa; Linda Haugen, USDA Forest Service, Bugwood.org

What makes a successful pathogen? • Pathogenesis genes and effectors

allow the pathogen to enter into the plant, evade the plant’s defenses, and survive and reproduce

• Numbers – more pathogens increases the chance of success

What makes a vulnerable host? • Poor health – wounded or weakened

plants can be more vulnerable• A lack of disease resistance genes

Phytophthora colocasiae

Fraser fir (Abies fraseri) killed by phytophthora root disease


Photo by Jack Dykinga

Wind

Nutrient availability

Other organisms

Rain

Moisture content

Temperature

Pollution

Planting density

The environment affects whether the plant or pathogen wins


Example of environmental influence – “blight weather”

0

0.5

1

1.5

2

2.5

3

3.5

4

9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

2.1 ‐ 7.1

7.2 ‐ 11.6

11.7 ‐ 15

15.1 ‐ 26.6

> 26.7

Temp (C)

Se

veri

ty o

f la

te b

ligh

t ris

k

By analyzing patterns of humidity and moisture, it is possible to anticipate the

severity of late blight outbreaks, and decide when to use chemical sprays. The

pathogen thrives in high humidity and moderate temperature conditions

Data from University of California Integrated Pest Management


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Xanthomonas outbreaks follow typhoons and hurricanes

Used with permission from Irey, M., Gottwald, T. R., Graham, J. H., Riley, T. D., and Carlton, G. 2006. Post-hurricane analysis of citrus canker spread and progress towards the development of a predictive model to estimate disease spread due to catastrophic weather events. Online. Plant Health Progress; Donald Groth, Louisiana State University AgCenter; Jeffrey W. Lotz, Florida Department of Agriculture and Consumer Services, Bugwood

Typhoons spread Xanthomonas oryzae pv. oryzae, bacterial blight of rice

Hurricanes spread Xanthomonas axonopodis, citrus canker

Hurricanes regularly hit Florida’s citrus growing regions, spreading citrus canker

Xanthomonas axonopodis


Humans influence diseases

Photos courtesy Scott Bauer and Bob Nichols, USDA, and Geovantage, Inc.

Monoculture

Introduced pathogens and vectors

Growing practices

Migrations of people and plants

Humans add another dimension (making a disease pyramid….)


Case study: The 1970 southern corn leaf blight epidemic

J.C. Wells, North Carolina State University; David B. Langston, University of Georgia, Bugwood.org

Southern Corn Leaf Blight Epidemic of

1970

Warm, wet weather

Although not normally a major pathogen, in 1970 Cochliobolus heterostrophus was responsible for the worst epidemic in US agricultural history


Hybrid seed production requires detasseled or male-sterile plants

Corn drawing by Philip Martin

Female parent – detasseled

Male parent

Pollen is produced in tassel

Female parent– male sterile –pollen is non-

viable

Because detasseling is labor-intensive, genetically male sterile corn was widely adopted in the 20th century

Male sterile “Texas-cytoplasm” (T-cms) corn was used to produce hybrid seed that was planted over much of the US

Egg is produced in ear


Male-sterile, T-cytoplasm corn is highly susceptible to Race-T fungi

T-cytoplasm makes plants male sterile, so it was used in the production of hybrid corn. T-cytoplasm plants make a novel mitochondrial protein

Race-T fungi make a toxin that binds the novel protein and kills the plant

The 1970 Southern corn leaf blight epidemic destroyed more than 15% of the US corn crop, worth more than 1 billion dollars

Extreme genetic uniformity is dangerous

Corn drawing by Philip Martin


Summary - disease involves pathogen, host, environment

Disease onset requires a suitably virulent

pathogen, a susceptible host, and an

environment that favors the pathogen


Strategies of pathogenicity

A successful pathogen must:

• Find the host and attach to it

• Gain entry through the plant’s impermeable defenses

• Avoid the plant’s defense responses

• Grow and reproduce

• Spread to other plants

Clemson University - USDA Cooperative Extension Slide Series, Bugwood.org

Gray mold (Botrytis cinerea)


Wind, water, insects and chemotaxis help pathogens reach their hosts

Jim Plaskowitz, USDA, and Stan Diffie, University of Georgia


Some pathogens use extracellular polysaccharides to attach

Photo by E. W. Kitajima (ESALQ/USP/Brazil); RK Webster, USDA; Talbot, N.J., Kershaw, M.J., Wakley, G.E., de Vries, O., Wessels, J. and Hamer, J.E. (1996). MPG1 encodes a fungal hydrophobin involved in surface interactions during infection-related development of Magnaporthe grisea. Plant Cell. 8: 985-999..

Xylella fastidiosa in a xylem vessel

Many bacteria produce biofilms

A mutant

Magnaporthe grisea, causal agent of rice blast, produces extracellular hydrophobinproteins required for adhesion and penetration; a deficient mutant (shown below) is less pathogenic


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Pathogens must be able to penetrate or circumvent physical barriers

Reprinted by permission from Macmillan Publishers Ltd: Giraldo, M.C., Valent, B. (2013). Filamentous plant pathogen effectors in action. Nat. Rev. Microbiol. 11: 800-814; Kleemann, J., Rincon-Rivera, L.J., Takahara, H., Neumann, U., van Themaat, E.V.L., van der Does, H.C., Hacquard, S., Stüber, K., Will, I., Schmalenbach, W., Schmelzer, E. and O'Connell, R.J. (2012). Sequential delivery of host-induced virulence effectors by appressoria and intracellular hyphae of the phytopathogen Colletotrichumhigginsianum. PLoS Pathog. 8: e1002643;

Appressorium

Some pathogens produce non-melanized but effective appressoria

Melanized appressoria build up high pressure to puncture the cell wall

Some pathogens enter through

stomata and grow extracellularly


Pathogens are biotrophs, necrotrophs or hemibiotrophs

Reprinted by permission from Macmillan Publishers Ltd: Pieterse, C.M.J., Leon-Reyes, A., Van der Ent, S. and Van Wees, S.C.M. (2009). Networking by small-molecule hormones in plant immunity. Nat Chem Biol. 5: 308-316, copyright 2009.

Necrotrophs kill cells and then consume the

contents Biotrophs live within host tissue without causing

death

Hemibiotrophs can switch from biotroph

to necrotroph


Biotrophs live in “pretend harmony”, necrotrophs smash and grab

Necrotrophs: • “Smash and grab”• Produce toxins and cell

wall-degrading enzymes

Biotrophs: • “Pretend harmony”• Fewer cell wall-degrading

enzymes than non-biotrophs• Evade detection and avoid

elicitation of defense responses

See for example Kemen, E. and Jones, J.D.G. (2012). Obligate biotroph parasitism: can we link genomes to lifestyles? Trends Plant Sci. 17:, and Spanu, P.D. (2012). The genomics of obligate (and nonobligate) biotrophs. Annu. Rev. Phytopathol. 50: Van Kan, J.A.L. (2006). Licensed to kill: the lifestyle of a necrotrophic plant pathogen. Trends Plant Sci. 11: 247-253. Laluk K., and Mengiste T. (2010) Necrotroph attacks on plants: Wanton destruction or covert extortion? The Arabidopsis Book 8:e0136. doi:10.1199/tab.0136. Glazebrook, J. (2005). Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu. Rev. Phytopathol. 43: 205–227.


Fungal and oomycete biotrophs usually make haustoria

Photo credit: Emmanuel Boutet

Hyaloperonospora arabidopsidis is a biotrophic oomycete that

infects Arabidopsis Plant cell plasma membrane

Haustorium

Extrahaustorial membrane

Extrahaustorial matrix

Haustoria remain outside the plant plasma membrane, and are specialized for nutrient and signal exchange

Haustoria

Hypha

Hypha


Haustorium

Plant cell wall

Germinated pathogen spore

Biotrophy NecrotrophyCoordinated temporal gene expression

No symptoms

Defense/PCD suppressingsecreted effector proteins

Necrosis inducing secreted effector proteins

Necrosis

Cytoplasm

Extrahaustorialmatrix

Extrahaustorial membrane

Plant plasma membrane

Biotrophy Necrotrophy

PCD/Defense responses

NLPsAvr/R

x x

Asymptomatic Disease

Some pathogens switch from biotrophy to necrotrophy. In this example, Phytophthora infestans initially produces effectors that suppress plant defense responses, but later produces necrosis-inducing effectors

Lee, S.-J. and Rose, J.K.C. (2010). Mediation of the transition from biotrophy to necrotrophy in hemibiotrophic plant pathogens by secreted effector proteins. Plant Signal. Behavior. 5: 769-772, reproduced with permission.


Fungal mimicry - Puccinia monoica and Microbotryum violaceum

Farrar, J.J. (1999) Anatomy of rockcress pseudoflowers caused by Puccinia consimilis. Great Basin Naturalist 59: 384–386;. Roy, B.A. (1993). Floral mimicry by a plant pathogen. Nature. 362: 56-58; Ngugi, H.K. and Scherm, H. (2006). Mimicry in plant-parasitic fungi. FEMS Microbiol. Lett. 257: 171-176. Photos by permission of J.J. Farrar and Michael Hood.

True petal

Uninfected leaf

Pseudopetal

Puccinia monoica induces its host to make pseudoflowers (really leaves). Pollinators visit the pseudoflowers and spread the fungus

Microbotryum violaceum makes its host sterile, but the host still produces flowers and anthers, which are covered with fungal spores. The pollinators visits the flowers, but spreads fungal spores instead of pollen

Smutty anthers

Diseased Dianthus

Healthy Dianthus


Phytoplasmas (a type of bacteria) also induce developmental abnormalities

Phyllody

Oshima, K., Maejima, K. and Namba, S. (2013). Genomic and evolutionary aspects of phytoplasmas. Frontiers Microbiol. 4: 230 . MacLean, A.M., Orlovskis, Z., Kowitwanich, K., Zdziarska, A.M., Angenent, G.C., Immink, R.G.H. and Hogenhout, S.A. (2014). Phytoplasma Effector SAP54 Hijacks Plant Reproduction by Degrading MADS-box Proteins and Promotes Insect Colonization in a RAD23-Dependent Manner. PLoS Biol. 12: e1001835.v; Hoshi, A., Oshima, K., Kakizawa, S., Ishii, Y., Ozeki, J., Hashimoto, M., Komatsu, K., Kagiwada, S., Yamaji, Y. and Namba, S. (2009). A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium. Proc. Natl. Acad. Sci USA 106: 6416-6421, with permission from S. Namba.

In Japanese, this morphology is called tengu-su, the nest of Tengu, a bird-like creature, and a

bacterial effector is named “tengu-su inducer”

Phytoplasma infection can induce phyllody, in which leaf-like tissues are formed in place of flowers. Witch’s broom is another phenotype that can occur

Phyllody

Healthy flowers

Infected plant

Tengu in nest

Tengu


Summary - strategies of pathogenicity

Pathogens must overcome formidable plant defenses

Once inside the plant, they can either co-habitate or kill


Plant immune responses

Plants resist pathogens through active processes that include recognition of the pathogen and defenseresponses to fight it


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The zig-zag model of plant –pathogen interactions

Adapted from Jones and Dangl (2006) The plant immune system. Nature. 444: 323-329.

Am

plit

ud

e o

f de

fen

se

Low

High

Pathogen is recognized:

Pattern Triggered Immunity

Effector is “recognized”:

Effector Triggered Immunity

Pathogen effectors suppress defense

response: Effector Triggered

Susceptibility

Defense responses

Defense responses


Reprinted by permission from Macmillan Publishers Ltd: Wirthmueller, L., Maqbool, A. and Banfield, M.J. (2013). On the front line: structural insights into plant-pathogen interactions. Nat Rev Micro. 11: 761-776

Molecular plant-microbe interactions: Overview


Plants respond to pathogens with large-scale transcriptional changes

Bacterial pathogen

Fungal or oomycete pathogen

Plant cellDefense responses include:• Increased synthesis of

stress hormones• Up-regulation of

pathogenesis-related (PR) genes

• Synthesis of antimicrobial compounds including phytoalexins

• Production of reactive oxygen species (ROS)

• Production of the polysaccharide callose


How are pathogens recognized? Pattern recognition receptors (PRRs)

Many PRRs have an extracellular leucine-

rich repeat domain that recognizes

conserved microbial elements…..

….and an intracellular kinase domain

They are leucine-rich repeat receptor kinases (LRR-RKs)

Bacterial pathogen

Fungal or oomycete pathogen

PRRs recognize pathogens outside the cell and initiate defense responses


Adapted from Wirthmueller, L., Maqbool, A. and Banfield, M.J. (2013). On the front line: structural insights into plant-pathogen interactions. Nat. Rev. Micro. 11: 761-776. See also Heil, M., Land, W.G. (2014). Danger signals – damaged-self recognition across the tree of life. Front. Plant Sci. 5: 578 and Tanaka, K., Choi, J., Cao, Y. and Stacey, G. (2014). Extracellular ATP acts as a damage associated molecular pattern (DAMP) signal in plants. Front. Plant Sci. 5: 446.

Plants also respond to their own cellular damage, through DAMPs

• WAK1 is a receptor-like kinase (RLK) that recognizes cell wall fragments

• DORN1 is an RLK that responds to extracellular ATP, which can be a sign of cellular damage


PRRs recognize PAMPs (pathogen-associated molecular patterns)

Adapted from Segonzac, C. and Zipfel, C. (2011). Activation of plant pattern-recognition receptors by bacteria. Curr. Opin. Microbiol. 14: 54-61.

Only a few PRR / PAMP pairs have been identified

Flagellin EF-Tu Ax21 chitinunknown

FLS2 EFR XA21 OtherLRR-RKs

PRRs

CERK1

unknown

Other LysM PRRs

Leucine-rich repeat receptor kinases

LysM receptor proteins

PAMPSPathogen-associated molecular

patterns (PAMPS) also known as microbe-associated molecular

patterns (MAMPS)

Pattern recognition receptors (PRRs)


Conserved molecules in bacteria and fungi that

can elicit immune responses in plants

include EF-Tu, flagellin, lipopolysaccharide (LPS), peptidoglycan (PGN) and

chitin

Pel, M.J.C., Pieterse, C.M.J. (2013). Microbial recognition and evasion of host immunity. J. Exp. Bot. 64: 1237-1248 by permission of Oxford University Press.


Pathogen recognition triggers defense responses

Defense responses

This response is called pattern triggered immunity (PTI)

Kinase cascade leading to

transcriptional responses

Calcium ion influx

Reactive oxygen

production

HM5


PAMP / PRR interactions activate immune signaling via ROS

Reprinted from Macho, Alberto P. and Zipfel, C. (2014). Plant PRRs and the activation of innate immune signaling. Mol. Cell. 54: 263-272 with permission from Elsevier.

• Conserved PAMPs flagellin (shown as the peptide Flg22) or chitin bind to their cognate receptors FLS2 or AtCERK1.

• PAMP binding triggers phosphorylation of BIK1, which then activates the NADPH oxidase RBOHD, triggering ROS production

ROS = reactive oxygen species

HM5 could add phosphatidic acid production, also extracellular alkalinization (rapid change in H+ gradient), membrane potential depolarization, ion fluxes - summarized in Wu 2014)Herman, Maryann, 23/12/2014


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Phytoalexins and phytoanticipins are chemical defenses

Reprinted from Bednarek, P. and Osbourn, A. (2009). Plant-Microbe Interactions: Chemical Diversity in Plant Defense. Science. 324: 746-748 with permission from AAAS; see also Großkinsky, D.K., van der Graaff, E., Roitsch, T. (2012). Phytoalexin transgenics in crop protection – Fairy tale with a happy end? Plant Sci. 195: 54-70.

Antimicrobial compounds help ward off pathogens; they can be preformed (phytoanticipins) or induced (phytoalexins)

Phytoanticipins and phytoalexins are secondary metabolites, and can be highly variable amongst species

Altering phytoalexin production in plants can contribute to their defense, raise the nutritional quality of some foods, and provide a source of human medicines


Callose, ROS and phytoalexins can arrest pathogen attack

Mellersh, D.G. and Heath, M.C. (2001). Plasma membrane - cell wall adhesion is required for expression of plant defense responses during fungal penetration. Plant Cell. 13: 413-424.

Cell wall

Plasma membrane

Callose

Pathogen

Golgi-mediatedcallose

secretion

Production of phytoalexins,

reactive oxygen

species, and other

defense compounds

Callose, a polysaccharide, acts

as a barrier, and ROS and

phytoalexins are toxic to pathogens

CalloseSpore

Reactive oxygen

Signal

Perception


Pathogens produce effectors that enhance their virulence

Kinase cascade leading to

transcriptional responses

Calcium ion influx

Reactive oxygen

production

Microbial effectors suppress the plant’s immune response and / or contribute to the pathogen’s viability

Plant proteins


Some effectors alter plant behaviour and development

Reprinted from Hogenhout, S.A., Van der Hoorn, R.A.L., Terauchi, R. and Kamoun, S. (2009). Emerging concepts in effector biology of plant-associated organisms. Mol. Plant-Microbe Interact. 22: 115-122.


Effectors act outside the pathogen, in the plant cell or apoplast

Many bacterial effectors are introduced into plant cells through Type-III secretion systems (T3SS) or other secretion systems

Fungal and oomycete effectors are often secreted from haustoria or tips of hyphae Nematode

effectors are introduced through the feeding stylet


Effectors act in many cell compartments

FLS2

AvrBs3

AvrPto

Hop1Hop1 from Pseudomonas syringae disrupts chloroplast structure and function

The transcription activator-like (TAL) effector AvrBs3 from Xanthomonas campestris turns on genes that favor pathogen survival

AvrPto from Pseudomonas syringae targets FLS2 and interferes with signalling

nucleus

plastid

cytoplasm

apoplast

Avr2

Cladosporium fulvum Avr2 inhibits cysteine proteases


TAL effectors provide exciting new tools for biotechnology

Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., Lahaye, T., Nickstadt, A. and Bonas, U. (2009). Breaking the code of DNA binding specificity of TAL-Type III effectors. Science. 326: 1509-1512. Deng, D., Yan, C., Pan, X., Mahfouz, M., Wang, J., Zhu, J.-K., Shi, Y. and Yan, N. (2012). Structural basis for sequence-specific recognition of DNA by TAL effectors. Science. 335: 720-723; see also Boch, J., Bonas, U. and Lahaye, T. (2014). TAL effectors – pathogen strategies and plant resistance engineering. New Phytol. 823-832.

The discovery of this unique protein-to-DNA code means that proteins can be designed to bind any DNA sequence with high specificity. Custom-made nucleases can cut DNA at specific places, and transcriptional activators and repressors can be targeted to specific genes

A transcription activator-like (TAL) effector from Xanthomonas has a set of nearly identical 34-amino acid repeats (red boxes). Within each repeat, amino acids 12 and 13 are variable, and determine the DNA base that the repeat region binds

TAL effector binding to DNA


Effective pathogens show a high rate of effector innovation

Reprinted by permission from Macmillan Publishers Ltd from: Haas, B.J., et al and Nusbaum, C. (2009). Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 461: 393-398; Raffaele S, Win J, Cano LM, Kamoun S. (2010) Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. BMC Genomics. 11: 637.

Why is Phytophthora infestans such an effective pathogen? Its genome is very large and full of duplications and repetitive elements, and ….

Phytophthora effectors are in gene-sparse, transposon-rich regions that generate recombinations and diversity

Effectors are the pathogen’s weapons - effector innovations lead to enhanced pathogenicity

Gene dense regions

Gene sparse regions


Case study: Pseudomonas syringae– a “model” plant pathogen

Katagiri F., Thilmony R., and He S.Y. (2002) The Arabidopsis thaliana- Pseudomonas syringae Interaction. The Arabidopsis Book 1:e0039.; Buell, C.R., etl al. and Collmer, A. (2003). The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 100: 10181-10186.Also see for example Mansfield, J.W. (2009). From bacterial avirulence genes to effector functions via the hrp delivery system: an overview of 25 years of progress in our understanding of plant innate immunity. Mol. Plant Pathol. 10: 721-734.

Arabidopsis thaliana infected with

Pseudomonas syringae

Pseudomonas syringae is a pathogen of several plants including Arabidopsis, and is an excellent model pathogen


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Resistance proteins – intracellular immune receptors

effector

R protein

R protein

R proteins recognize effectors intracellularly

Defense responses


Canonical plant R proteins have a nucleotide binding site and LRR

Wang, C.-I.A., et al and Kobe, B. (2007). Crystal structures of flax rust avirulence proteins AvrL567-A and -D reveal details of the structural basis for flax disease resistance specificity. Plant Cell. 19: 2898-2912.

NBS Nucleotide binding site

LRR Leucine rich-repeat

TIR Toll interleukin receptor

PK Protein Kinase

CC Coiled coil

TM Transmembrane

KINTMeLRR KINTMeLRR

PRR Receptor-like kinase

TIR LRRNBSTIR LRRNBS

CC LRRNBSCC LRRNBS

R proteins NBS-LRR

Canonical R proteins have a leucine-rich repeat (LRR), similar to the PRR extracellular domain (eLRR)

eLRR

LRR

The LRR domain confers specificity to the binding interaction

effector

Slide courtesy Shunyuan Xiao


R type NBS-LRR-encoding genes are very diverse and abundant

Luo, S., Zhang, Y., Hu, Q., Chen, J., Li, K., Lu, C., Liu, H., Wang, W. and Kuang, H. (2012). Dynamic nucleotide-binding site and leucine-rich repeat-encoding genes in the grass family. Plant Physiol. 159: 197-210; see also Marone, D., Russo, M.A., Laidò, G., De Leonardis, A.M., Mastrangelo, A.M. (2013). Plant nucleotide binding site-leucine-rich repeat (NBS-LRR) genes: active guardians in host defense responses. International Journal of Molecular Sciences. 14: 7302-7326.

• Arabidopsis has ~ 149 NBS-LRR genes

• Rice, poplar, grape and potato have > 400 NBS-LRR genes

• R genes are variable even between close relatives

Integrated map of R loci in related grasses Rice


Other R proteins are atypical in sequence

KINKIN CCTM CCTM

TM TMTM TM

Atypical“R” proteins

(Pto)

(Xa13)

(Xa27)

(RPW8)

TMTM TMTM TMTM TMTM TMTM TMTM TMTM TMTM

KINKIN START

ABC

(Yr36)

(Lr34)

KINTMeLRR KINTMeLRR

PRR Receptor-like kinase

eLRR TMeLRR TM

Receptor-like protein (Cf2/4/9)

TIR LRRNBSTIR LRRNBS

CC LRRNBSCC LRRNBS

R proteins NBS-LRR

Identification of R genes is an ongoing process, and other atypical R protein structures are likely to be found

Slide courtesy Shunyuan Xiao


How do R proteins recognize effectors?

Reprinted by permission of Macmillan Publishers Ltd. From Dodds, P.N. and Rathjen, J.P. (2010). Plant immunity: towards an integrated view of plant–pathogen interactions. Nat Rev Genet. 11: 539-548.

In some cases the R protein binds the effector directly

In some cases effector and another factor are recognized by the R protein

In some cases effector modifies the real binding partner of the R protein

R protein

effector


A current model says that R proteins guard key cellular hubs

Reprinted from Mukhtar, M.S., et al. and Dangl, J.L. (2011). Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science. 333: 596-601 with permission from AAAS; see also Weßling, R., et al. (2014). Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Cell Host & Microbe. 16: 364-375..

Plant proteins were identified that interact with R proteins and effectors from the biotrophic oomycete Hyaloperonospora arabidopsidisand Pseudomonas syringae. The results suggest that R proteins guard cellular proteins targeted by effectors

effector

R protein

Common target

Rather than recognizing the effector, some R proteins recognize changes to its cellular targets


Recognition and response to effectors through paired R proteins

Cesari, S., Bernoux, M., Moncuquet, P., Kroj, T. and Dodds, P.N. (2014). A novel conserved mechanism for plant NLR protein pairs: the ‘integrated decoy’ hypothesis. Fronti. Plant Sci 5: 606.

The heterodimer is inactive without an effector (TIR domain of RRS1 represses RPS4)

Two R proteins (RRS1 and RPS4) operate as a pair

+ EffectorEffectors interact with RRS1, relieving repression


R protein activation leads to enhanced defense: ETI

effector

R protein

Transcription responses

Defense responses

ETI is faster, stronger and more prolonged than PTI


Stimulation of R proteins leads to enhanced defense: ETI

Adapted from Jones and Dangl (2006) The plant immune system. Nature. 444: 323-329.

Am

plit

ud

e o

f de

fen

se

Low

High

PTI

ETI

Activated R proteins signal danger, and trigger a heightened defense response that includes:• Production of the stress

hormone salicylic acid (SA)• Production of reactive oxygen

species (ROS)• The hypersensitive cell death

response (HR)• Expression of pathogenesis-

related (PR) proteins• Systemic signals and systemic

acquired resistance (SAR)


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The hypersensitive cell death response can be induced

Reprinted by permission from Macmillan Publishers Ltd. Coll, N.S., Epple, P., and Dangl, J.L. (2011). Programmed cell death in the plant immune system. Cell Death Differ 18: 1247-1256; Torres, M.A., Jones, J.D.G. and Dangl, J.L. (2006). Reactive oxygen species signaling in response to pathogens. Plant Physiol. 141: 373-378..

ROS is generated in the apoplast, in chloroplasts, and mitochondria

ROS and SA act synergisticly

HM8


Systemic acquired resistance (SAR) involves a mobile signal

Uninfected tissues show enhanced resistance to subsequent pathogen challenge. The nature of the mobile signals are still being debated…

In some cases, enhanced resistance is heritable!

Defense responses

SAR

Local response

Systemic response

Sig

na

ls

See Fu, Z.Q., Dong, X. (2013). Systemic acquired resistance: turning local infection into global defense. Annu. Rev. Plant Biol. 64: 839-863 and Gozzo, F., and Faoro, F. (2013). Systemic acquired resistance (50 years after discovery): moving from the lab to the field. J. Agricult. Food Chem. 61: 12473-12491.


Summary - PTI is suppressed by effectors, which sometimes trigger ETI

Effectors suppress PTI

R proteins recognize

effectors and induce ETI

PAMP-triggered immunity

DefenseResponses

DefenseResponses

Effector-triggered immunity

DefenseResponses

Effector triggered suppression

Adapted from Macmillan Publishers Ltd: Pieterse, C.M.J., Leon-Reyes, A., Van der Ent, S. and Van Wees, S.C.M. (2009). Networking by small-molecule hormones in plant immunity. Nat Chem Biol. 5: 308-316,


Case study – the re-emergence of wheat stem rust – Puccinia graminis

Wheat infected with wheat stem rust Puccinia graminis

Rust fungi, including the genus Puccinia, are among the most economically destructive; they produce large numbers of aerially transported spores, and the crops they infect are often grown contiguously over large acreages

In the 1960s, Norman Borlaug bred wheat with stem rust

resistance R genes (e.g. Sr31), which have been incorporated into wheat strains worldwide


Sr31 resistance is not effective against Ug99 – it has been broken

Wheat stem rust strain Ug99 has broken Sr31 resistance,

and is spreading

Newly developed Ug99-resistant wheat varieties are being cultivated in Ug99-affected areas – a modern triumph of plant breeding!

Singh, R.P, et al. (2014). Progress towards genetics and breeding for minor genes based resistance to Ug99 and other rusts in CIMMYT high-yielding spring wheat. J. Integr. Agric. 13: 255-261. Map source: FAO


Plant responses to necrotrophic pathogens

Photo credits: Florida Division of Plant Industry Archive, Florida Department of Agriculture and Consumer Services, David B. Langston, University of Georgia, Bugwood.org; Gary Loake

Arabidopsis plants infected with the fungus Botrytis cinerea

Bacterial soft rot (Pectobacterium

carotovorum)

The oomycete Pythiumon cucumber

There are few known R genes that confer resistance to necrotrophic pathogens, therefore breeding resistance to necrotrophs is more challenging than to biotrophs


Necrotrophs can have a broad or restricted host range

Reproduced from Mengiste, T. (2012). Plant immunity to necrotrophs. Annual Review of Phytopathology. 50: 267-294 with permission of Annual Reviews .

Broad host range necrotrophs produce cell wall degrading enzymes (CWDE), necrosis and ethylene-inducing proteins (NEPs), and also can suppress the plant’s immune response

Host-specific necrotrophs produce specific toxins necessary for their pathogenicity; sometimes these act through specific R genes, in a counterintuitive manner


Case study: Disease susceptibility conferred by a “resistance” gene

Navarre, D.A. and Wolpert, T.J. (1999). Victorin induction of an apoptotic/senescence–like response in oats. Plant Cell. 11: 237-249. Lorang, J., Kidarsa, T., Bradford, C.S., Gilbert, B., Curtis, M., Tzeng, S.-C., Maier, C.S. and Wolpert, T.J. (2012). Tricking the guard: Exploiting plant defense for disease susceptibility. Science. 338: 659-662. Lorang, J.M., Sweat, T.A. and Wolpert, T.J. (2007). Plant disease susceptibility conferred by a “resistance” gene. Proc. Natl. Acad. Sci. USA. 104: 14861-14866. Wolpert, T.J. and Macko, V. (1989). Specific binding of victorin to a 100-kDa protein from oats. Proc. Natl. Acad. Sci. USA. 86: 4092-4096. Image source Plant Pathology, University of Georgia.

The necrotrophic fungus Cochliobolus victoriae causes Victoria blight on oat, but ONLY on oat carrying a particular R gene that confers resistance to Puccinia coronata

Victorin toxin

No R generesistant

R genesusceptible

The fungus similarly affects Arabidopsis

Water control

Victorin toxin

The fungus produces a toxin, which causes disease symptoms in the absence of the fungus


Case study: Disease susceptibility conferred by a “resistance” gene

Reprinted from Lai, Z. and Mengiste, T. (2013). Genetic and cellular mechanisms regulating plant responses to necrotrophic pathogens. Curr. Opin. Plant Biol. 16: 505-512 with permission from Elsevier.

Model: The victorin toxin produced by the necrotrophic fungus C. victoriae interacts with a cellular protein, TRX-h5. This interaction is recognized by the LOV1 R protein, triggering cell death.

The pathogen wins!

The same R protein recognizes an unknown effector from the biotrophicpathogen P. coronata. This interaction triggers the hypersensitive response and resistance.

The plant wins!

HM8 Wu 2014 in virulence paper includes autophagy and catalase in plant cell image (Fig2)Herman, Maryann, 23/12/2014


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Jasmonate can be involved in responses to necrotrophs

Reprinted from Campos, M., Kang, J.-H. and Howe, G. (2014). Jasmonate-triggered plant immunity. J. Chem. Ecol. 40: 657-675 With kind permission from Springer Science and Business Media

Some pathogens, wounding, and herbivores can promote the synthesis of jasmonate (JA)

JA conjugated to the amino acid isoleucine (JA-Ile) induces transcription of defense genes

Some pathogen effectors target the jasmonate pathway


Salicylate and jasmonate are mutually antagonistic

Defense responses

JasmonatesSalicylates

NecrotrophsBiotrophsWhy? Perhaps because the pathogenicity of necrotrophs is enhanced by the hypersensitive response, so HR should be suppressed in the presence of necrotrophs…


Some pathogens take advantage of the defense signal cross-talk

JA SAPseudomonas

syringae producing coronatine

DefenseCoronatine is an excellent mimic of JA-Ile, the active jasmonate hormone. By suppressing biotrophic defenses coronatineproduction significantly enhances the pathogenicity of the bacteria that produce it

For a mechanistic review, see Geng, X., Jin, L., Shimada, M., Kim, M.G., Mackey, D. (2014). The phytotoxin coronatine is a multifunctional component of the virulence armament of Pseudomonas syringae. Planta. 240: 1149-1165.

HM11


Defense pathways intersect with other signaling pathways

Reprinted from Spoel, S.H., and Dong, X. (2008) Making sense of hormone crosstalk during plant immune responses. Cell Host Microbe 3: 348-351 with permission from Elsevier.

Take home message: lots of information is integrated to determine the appropriate response

Defense responses reduce growth rate. Drought stress and abscisic acid (ABA) accumulation suppresses responses to pathogens


Viruses can trigger similar immune responses as other pathogens

Mandadi, K.K., Scholthof, K.G. (2013). Plant immune responses against viruses: how does a virus cause disease? Plant Cell. 25: 1489-1505; see also Nakahara, K.S., Masuta, C. (2014). Interaction between viral RNA silencing suppressors and host factors in plant immunity. Curr. Opin. Plant Biol. 20: 88-95.

Viral components can trigger immune responses through PRRs as well as R proteins, leading to cell death and systemic immunity

Hypersensitive responseNecrosis

SAR

Viruses enter a cell through wounding, introduction by an insect, or cell-to-cell transfer, as virions or viral riboucleoproteins (vRNP)

Within a cell, a virus is disassembled, viral proteins made, the genome replicated, and encapisdated as new viral particles


Plant responses to viruses are largely mediated by siRNAs

Waterhouse, P.M. and Fusaro, A.F. (2006). Viruses face a double defense by plant small RNAs. Science. 313: 54-55; Reprinted by permission from Macmillan Publishers Ltd Lam, E. (2004) Controlled cell death, plant survival and development. Nat. Rev. Mol. Cell Biol. 5: 305 – 315.

Plant defenses against viruses largely occur at the level of RNA-mediated silencing, and through the hypersensitive response to kill infected cells


Summary - Plant immune responses

DefenseResponses

Plants have strong and vigorous immune responses

Plants recognize microbial patterns, and the outcomes of pathogen effectors

Defense responses include production of antimicrobial compounds, the hypersensitive response, and systemic acquired resistance


Strategies to prevent and manage disease

Environment

The disease triangle

(it takes three)

Avoid or eliminate the pathogen

Manipulate the environment to favor the plant

Make the plant resistant through genetic or other

methods


Photos by Photo by James Tourtellotte, US Customs and Border Protection : Keith Parker, Marin County Fire Department.

The best way to prevent disease is to keep pathogens away

Agricultural inspectors check imported plants for pest and pathogens, but many pathogens are spread by wind and water….

Phytophthora ramorum causes sudden oak death

HM11 updated pathway in Geng 2014...probably more detail than needed here though wecould add EthyleneHerman, Maryann, 23/12/2014


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Quarantines slow spread of Tilletia indica, causal agent of Karnal buntTilletia indica is a fungus that attacks wheat kernels. Since first found in 1930 in India, it has been spreading worldwide. Strict quarantine and inspection policies have kept it out of the EU and Australia (so far)….

Photo credits: CIMMYT, Dept. of Agriculture, South Africa


Pathogens’ effects can be minimized by hygiene and rotation

Courtesy J.H. Graham (left) and G. Allen (right). Reproduced by permission from Maloy, O. C. (2005). Plant Disease Management. The Plant Health Instructor. DOI: 10.1094/PHI-I-2005-0202-01.

Rotating crops helps reduce pathogen load in soils

Continuously cultivated

Rotated with corn

Removing and burning an infected citrus grove to eradicate bacterial canker


Certified “pathogen-free” seeds or plantlets are available

Photo sources: CIMMYT, CIMMYT, FAO, University of California

Wheat seeds being propagated in a “pathogen free” field that is rigorously

quarantined and inspected

Sterile tissue culture of vegetatively propagated banana and sweet potato plants

Checking seeds for fungal spores


Cultural practices can help protect plants against pathogens

Photo credits: I.R. Evans and WCPD; Courtesy H.D. Thurston (right). Reproduced by permission , from Maloy, O. C. (2005). Plant Disease Management. The Plant Health Instructor. DOI: 10.1094/PHI-I-2005-0202-01.

Phosphate deficient soil

Plants are more susceptible to disease

when they are malnourished; here wheat succumbs to

Pythium in phosphate-deficient soil

Plastic sleeves on bananas to protect against pests and decay fungi


Case study: Plant-associated human pathogens

Reprinted from Teplitski, M., Barak, J.D. and Schneider, K.R. (2009). Human enteric pathogens in produce: un-answered ecological questions with direct implications for food safety. Curr. Opin. Biotechnol. 20: 166-171 with permission from Elsevier; Photo by Peggy Greb.

In 2011, 50 people died from E. coli -contaminated bean sprouts and 29 people died from Listeria-contaminated cantaloupes. Salmonellaare regularly found in fresh produce

Why are human pathogens living in plants?

E. coli (green) growing on mung bean sprouts


Animal manures are often a source of contamination

From Brandl, M.T. (2008). Plant lesions promote the rapid multiplication of Escherichia coli O157:H7 on postharvest lettuce. Appl. Environ. Microbiol. 74: 5285-5289. Dong, Y., Iniguez, A.L., Ahmer, B.M.M. and Triplett, E.W. (2003). Kinetics and strain specificity of rhizosphere and endophytic colonization by enteric bacteria on seedlings of Medicago sativa and Medicago truncatula. Appl. Environ. Microbiol. 69: 1783-1790.; See also Van Overbeek, L., van Doorn, J., Wichers, J., van Amerongen, A., van Roermund, H. and Willemsen, P. (2014). The arable plant ecosystem as battleground for emergence of human pathogens. Front. Microbiol. 5: 104 and Yaron, S., Römling, U. (2014). Biofilm formation by enteric pathogens and its role in plant colonization and persistence. Microbial Biotechnol. 7: 496-516.

Insects or other vectors Equipment

Surface and groundwater

Human pathogenic bacteria can be carried by farm animals. The bacteria can enter plants through stomates or wounds. Contamination MUST be avoided, because washing does not remove the pathogens that are inside the plant tissues.

E. coli (bright spots) in alfalfa and lettuce

HM15


Chemical controls are critical for eradicating pathogens

Photos by Ken Hammond; J.K. Lindsey

Azostrobulin, a widely used fungicide derived from a

defensive compound produced by Strobilurus fungi

Compounds must be safe and effective, and application protocols must be followed to slow the development of resistance

Because pathogens develop resistance, finding novel compounds to eradicate pathogens is an ongoing process


William M. Brown Jr., Paul Bachi, University of Kentucky Research and Education Center, Stan Diffie, University of Georgia, Whitney Cranshaw, Colorado State University Bugwood.org

Case study: Tomato spotted wilt virus is spread by insects

TSWV on pepper

TSWV on tomato

Frankliniella occidentalis

TSWV is one of the most economically devastating

viruses, and is responsible for more than a billion dollars in

crop losses annually

Small insects called thrips spread the virus, so controlling the virus means controlling the thrips


Case study: Plant pathogenic nematodes

Nematode-infected yam tuber

Photos courtesy of IITA Photo Library and CIMMYT

Wheat infected with root knot nematode (Meloidogyne spp.)

Nematodes are tiny round worms (0.1 mm diameter) that are found ubiquitously. Some are plant pests, some eat plant pests, and some are human pathogens

Globally plant parasitic nematodes cause well over $100 billion in crop losses annually

HM15 could add fig 2. from Yaron 2014 to illustrate how biofilm formation is involved in colonization and persistence of Salmonella on a leaf.Herman, Maryann, 23/12/2014


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Plant pathogens include root-knot and cyst nematodes

Grunewald, W., van Noorden, G., Van Isterdael, G., Beeckman, T., Gheysen, G. and Mathesius, U. (2009). Manipulation of auxin transport in plant roots during rhizobium symbiosis and nematode parasitism. Plant Cell. 21: 2553-2562.

Nematode effectors

modify root cells to become

specialized feeding

cells

Cyst nematodes partially dissolve cell walls between cells to produce a syncytium

Root-knot nematodes induce expansion in five to seven neighboring cells to produce giant cells


The root-knot nematode Meloidogyneincognita infects 1,700 plant species

Scott Bauer, USDA Agricultural Research Service, Edward Sikora, Auburn University, Charles Averre, North Carolina State University Bugwood.org

On pepper

On soybean

On sweet potato


Soybean cyst nematodes are serious threats

Agroscope FAL Reckenholz Archive, Swiss Federal Research Station for Agroecology and Agriculture, Erik Stromberg, Virginia Polytechnic Institute and State University Bugwood.org; Ithal, N., Recknor, J., Nettleton, D., Hearne, L., Maier, T., Baum, T.J. and Mitchum, M.G. (2007). Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean. Mol. Plant-Microbe Interact. 20: 293-305.

The soybean cyst nematode (Heteroderaglycines) is the most serious disease threat to soybeans in the United States

Juveniles (stained pink) attacking soybean root

Syncytium

Feeding stylet

Sensitive and resistant soybeans


Molecular interactions between nematode and plant

Reprinted from Kandoth, P.K., Mitchum, M.G. (2013). War of the worms: how plants fight underground attacks. Curr. Opin. Plant Biol. 16: 457-463 with permission from Elsevier.

Hypersensitive-response (HR) occurs at nematode (N) feeding sites in resistant plants

Nematode resistance involves plasma-membrane and cytosol-localized receptors and resistant proteins

Nematodes produceeffectors

Other genes involved in resistance have been identified


Nematodes are managed by chemical, cultural and genetic

methods

Rosskopf, E. N., Chellemi, D. O., Kokalis-Burelle, N., and Church, G. T. 2005. Alternatives to methyl bromide: A Florida perspective.. Plant Health Progress ;Claverie, M., et al., and Esmenjaud, D. (2011). The Ma gene for complete-spectrum resistance to Meloidogyne species in Prunus Is a TNL with a huge repeated C-terminal post-LRR region. Plant Physiol. 156: 779-792.

Soil application of methyl bromide gas underneath plastic sheeting

Meloidogyne incognita on plum (Prunus cerasifera) roots

Methyl bromide is an

effective nematicide but also a

tightly regulated,

ozone-depleting

compound

Some plants have R genes that confer resistance against nematodes

HM14


Biocontrol agents:• attack the pathogen• compete with the pathogen • enhance the plant’s

defenses through induced systemic resistance (ISR)

• often have multiple effects

Biocontrol refers to the use of other organisms to ward off pathogenic microorganisms and disease

Reprinted by permission from Macmillan Publishers Ltd: Haas, D. and Defago, G. (2005). Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat. Rev. Micro. 3: 307-319.

Biological control of pathogens


Biocontrol: Coniothyrium minitans vs Sclerotinia sclerotiorum

Photo credit: William M. Brown Jr., Gerald Holmes, Valent USA Corporation,Bugwood.org; A. von Tiedemann, K. Hedke & R. Mögling Dept. of Phytomedicine, Faculty of Agriculture, University of Rostock, Germany

Sclerotinia sclerotiorum is a necrotrophic fungal pathogen of > 400 species. It forms durable sclerotia that persist in soil

Infected carrot

Coniothyrium and other mycoparasites are effective biocontrol agents against Sclerotinia sclerotiorum


Take-all decline is a classic example of biocontrol

Take-all decline: Over time, the severity of the disease declines, and yields increase, because the soil accumulates biocontrol agents, which produce antifungal compounds

Take-all disease of wheat is caused by

the fungus Gaeumannomyces

graminis

Disease suppression is transferrable: the wheat on the right was grown in a field inoculated with soil from a field in which the disease had declined. The transferred soil contained the biocontrol agents

2, 4, diacetylphloroglucinol (2,4-DAPG) is a broad-scale antimicrobial made by biocontrol bacteria

Cook, R.J. (2006). Toward cropping systems that enhance productivity and sustainability. Proc. Natl. Acad. Sci. 103: 18389-18394, copyright National Academy of Sciences; Mathre, D. E. 2000. Take-all disease on wheat, barley, and oats. Online. Plant Health Progress doi:10.1094/PHP-2000-0623-01-DG; Take-all control in winter wheat. Home Grown Cereal Authority


Biocontrol agents can induce systemic resistance

Naïve cell with normal defense capacity

Primed cell with dormant signal amplifiers

Amplified signaling leads to heightened response

Adapted from Conrath, U. (2011) Molecular aspects of defense priming. Trends Plant Sci. 16: 524 – 531.

Defense responses

HM14 Kandoth 2013 Fig 1 shows an example of how resistant soybean cultivars respond to nematode feedingHerman, Maryann, 23/12/2014


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Genetic approaches to disease resistance

See Poland, J.A., Balint-Kurti, P.J., Wisser, R.J., Pratt, R.C. and Nelson, R.J. (2009). Shades of gray: the world of quantitative disease resistance. Trends Plant Sci. 14: 21-29; Gust, A.A., Brunner, F. and Nürnberger, T. (2010). Biotechnological concepts for improving plant innate immunity. Curr. Opin Biotechnol. 21: 204-210. Photo by Jack Dykinga

Classic approaches:• Introgression of R genes• Quantitative disease resistance

breedingBiotechnological approaches: • Improving pathogen

recognition• Increasing plant defense

signaling and execution• Interfering with pathogen

virulence• Priming defense responses


Classical approaches – R genes and quantitative disease resistance

Nzungize, J., Gepts, P., Buruchara, R., Male, A., Ragama, P., Busogoro, J.P., and Baudoin, J.P. (2011). Introgression of Pythium root rot resistance gene into Rwandan susceptible common bean cultivars. Afr. J. Plant Sci. 5: 193 – 200; Poland, J.A., Bradbury, P.J., Buckler, E.S. and Nelson, R.J. (2011). Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc. Natl. Acad. Sci. 108: 6893-6898.

Susceptible Resistant

R gene introgression can confer complete resistance by a single gene

Introgression requires backcrossing (BC) to susceptible parental line to restore desired traits

Quantitative disease loci (QDL) are loci that each promote

partial disease resistance. Examples

include protein kinases and

transcription factors

Recombinant inbred lines showing different levels of susceptibility to northern corn leaf blight through different suites of QDLs


Biotechnological approaches –candidate genes for resistance

Reprinted by permission from Macmillan Publishers Ltd : Brutus, A. and Yang He, S. (2010). Broad-spectrum defense against plant pathogens. Nat Biotech. 28: 330-331. See also Lacombe, S., et al. (2010). Interfamily transfer of a plant pattern-recognition receptor confers broad-spectrum bacterial resistance. Nat Biotech. 28: 365-369.

The pattern recognition receptor (PRR) EFR is not present in tomato. Introducing the EFR gene to tomato improved pathogen recognition and conferred broad spectrum resistance


Reprinted from Gust, A.A., Brunner, F. and Nürnberger, T. (2010). Biotechnological concepts for improving plant innate immunity. Curr. Opin. Biotechnol. 21: 204-210 with permission from Elsevier.

Biotech approaches to enhancing immunitya) Introduce or modify

PRR to improve pathogen recognition

b) Overexpress or modify signalling intermediates to stimulate response

c) Detoxify or sequester effectors and virulence factors

d) Biological controls or chemical induction of priming

Pathogen Pathogen

Pathogen Pathogen

Signaling cascades

Virulence targets Potentiation

of responses


Case study: Genetically engineered resistance to papaya ringspot virus

Gonsalves, D., S. Tripathi, J. B. Carr, and J. Y. Suzuki. 2010. Papaya Ringspot virus. The Plant Health Instructor. DOI: 10.1094/PHI-I-2010-1004-01;Photo credits: S. Ferreira.

In the 1980s, PRSV nearly wiped out papaya production in Hawaii. Now most of the papaya produced in Hawaii are genetically resistant

A gene encoding a viral coat protein was introduced into papaya. The modified plants are resistant to viral infection. This was the first commercialized transgenic fruit

Papaya ringspot virus symptoms

Susceptible Resistant


Mycotoxins are fungal toxins that harm humans and animals

Aflatoxin B1

Fumonisin

Fusarium spp on wheat

Photo credits: Mary Burrows, Montana State University, Harry Duncan, North Carolina State University Bugwood

Aspergillus flavus growing on corn

Some fungi produce harmful

toxins called mycotoxins, which can contribute to

birth defects, cancer, kidney

damage and death


Biocontrols and genetic methods reduce exposure to mycotoxins

Spreading fungi that outcompete aflatoxin-producing fungi is an effective biocontrol measure

Identifying plants that resist infection by mycotoxin-producing fungi can lead to genetic resistance. Plants can also be engineered to degrade mycotoxins

Photocredits IITA, Peggy Greb


Summary – strategies to prevent and manage disease

QuarantinesCrop rotationGood hygiene

Control of viral vectors

BiocontrolsChemical controls

• Adequate nutrition• Well drained soils• Genetic diversity to

avoid epidemics• R-gene mediated

resistance• Quantitative

disease resistance• Enhancement of

immune and defense responses

Weaken pathogen

Separate plant & pathogen

Strengthen plant


Plants and Pathogens: Summary

• Plant diseases are major threats to food production

• Pathogens have diverse modes of pathogenicity and rapidly evolving effectors

• Plants are not passive victims - they have sophisticated surveillance and defense mechanisms

• Human practices, particularly migrations and monocultures, have contributed to the magnitude of plant diseases


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Plants and Pathogens: Summary

Reprinted from Dangl, J.L., Horvath, D.M. and Staskawicz, B.J. (2013). Pivoting the plant immune system from dissection to deployment. Science. 341: 746-751 with permission from AAAS

Current model of plant–pathogen interactions1. Membrane-localized receptors

recognize the invader and trigger defense (PTI)

2. Pathogens produce effectors 3. Effectors suppress defense4. R proteins recognize effectors

directly or indirectly5. Activated R proteins (nucleotide-

binding leucine-rich repeat; NLR) trigger ETI and further defense


What does the future hold?

Rapid methods for detection and diagnosis of pathogen

Improved understanding of “pathogenicity”

Effective eradication and biocontrol methods

Improved understanding of what makes plants

susceptible or resistant

Improved genetic resistance

Improved cultural practices for plant health

Challenges: Increasing demands due to increasing population and

meat consumption

Global change

Opportunities: Genomic and biotechnology tools to accelerate research and breeding

Improvements in education and access to information

Louisiana State University AgCenter Archive

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