L40: plants and pathogens

How much crop losses occur from biotic factors

40% or more of yields = $200 billion annually

biotic factors causing crop loss

• disease

• pests

• weeds

how are weeds controlled in the developed world

herbicide use

How are weeds controlled in the developing world

removed by hand: whole families are involved in this labourious practice in time children should be getting an education

cause of a decline in Acute oak trees

a bacterial disease which is transmitted by beetle larvae

plant pathogens

• bacteria

• viruses

• fungi (fungal-like organisms)

What are plant pathogenic bacteria responsible for

Average annual crop losses of over 5% = $50bn

What crops are bacterial infections a problem in

a huge variety of crops including

• potatoes

• cereals

• oilseed crops

• very many different vegetables and fruit trees

Direct and Indirect crop losses

• Direct: due to losses in yield or reduction in quality

• Indirect: due to losses in storgae e.g. spoilage

Current solutions for bacterial disease in crop plants

the introduction of genes conferring resistance and the use of chemicals e.g. copper sprays

Problem with suitable resistance genes for breeding

often not available and the chemicals used often have adverse environmental impacts and are becoming increasingly unacceptable

what is Pseudomonas syringae

one of the most widespread and damaging bacterial pathogens globally which causes losses in crops (e.g. tomato, kiwifruit, peppers, olives, cereals, legumes and diverse fruit trees)

what are Pectobacterium spp responsible for

blackleg disease and soft rots in potatoes → annual losses of up to £50m in the UK which is more than any other plant disease

What are viruses a major cause of

economic losses and are particularly serious economic pathogens in Africa and parts of Asia.

Plant viruses are typically transmitted by what

Vectors such as aphids, leafhoppers, whiteflies and nematodes

the result of cassava and sweet potato virus disease

25-50% of yield losses

origin of most plant disease

over 50% of emerging plant diseases are viral in origin

What was responsible for the Irish Potato Famine in 1840s

Fungal like organism: Phytophthora infestans (Late Potato Blight/ Potato Late Blight)

Impact of the irish potato famine

• one million deaths

• emigration of about 1.5million people to other parts of the world

what can happen in moist, cool conditions

the entire foilage of a crop can be destroyed within 2-3 weeks

why is Phytophthora infestans still a huge problem

• because of its ability to evade and overcome resistance

• in parts of the world people cannot afford fungicides

• In Russia for example, Late potato blight can destroy over 15% of the country’s total crop in the worst years

• annual losses and fungicide costs amount to ~ $3billion worldwide

Strategies used by plant pathogens

• Necrotrophs “murderers”: These pathogens grow in dead tissue, invade, secrete cell degrading enzymes to kill host cells and use nutrients released for growth.

• Biotrophs “Confidence Tricksters”: These pathogens can only grow in living tissue, invade, communicate with living host cells, use nutrients released for growth or develop feeding structures to extract nutrients

Plant defence mechanisms against pathogens

• may possess preformed structural barriers or toxic substances that confine infection to particular pathogen species

• may recognise the attacking pathogen and activate defence mechanisms that prevent the pathogen from spreading or localise the infection

• The ability of plants to recognise and defend themselves against pathogens is inherited (innate immunity)

• plants contain hundreds of genes that confer resistance to a variety of pests and pathogens

Type of immunity in plants

lack an adaptive immune system and rely on innate immunity of each cell and mobile signals emanating from infection sites.

2 main branches of plant immune systems

1. Basal

2. Gene-for-Gene

Basal immunity

Plant cells carry proteins on the outside of the plasma membrane that can recognise macromolecules (such as proteins or polysaccharides) that are associated with pathogens. These contain slowly evolving Pathogen Associated Molecular Patterns (PAMPS) such as flagellin, cell wall glycans etc…

Gene-For-Gene immunity

Acts largely within the cell using proteins encoded by Resistance Genes (R-genes). These recognise pathogen-specific effector molecules from diverse kingdoms and activate defence responses

Examples of PAMPs

• Bacterium: Flg22, Elf18, LPS

• Fungi: ergosterol, chitin, B glucans

• Oomycetes: CBEL (cellulose binding elicitor lectin), Peop-13, elicitins

What is essential for motility, translation and a major constituent of the outer membrane

• Motility: Flagellum

• Translation: EF-Tu (elongation factor Tu)

• Outer membrane: LPS (lipopolysaccharide glycolipid)

features of PAMP-triggered immunity

• conserved, exposed molecules from many microbe species

• indispensible to the microbe (critical function)

• not present in the host (non self)

the gene for gene hypothesis

• proposed by Flor in 1940

• states that for resistance to occur, complementary pairs of dominant genes must be present in the host and pathogen

• these genes are referred to as Resistance (host) and Avirulence (pathogen). altering either of these genes leads to susceptibility

What do plants recognise proteins associated with

individual pathogens (often specific isolates of individual pathogens) and they enact defence strategies to limit their speed

What do Avirulent genes encode for

Proteins which are essential for the pathogen to invade and grow in the plant host

Avirulence gene examples

• The protein encoded by the resistance gene Rx (confers resistance to Potato Virus X in potato cultivars like Cara) recognises the major structural protein of the virus capsid and triggers a gene-for-gene defence response

• Bacterial and fungal pathogens inject proteins into the cells of their hosts, for some fungal-like pathogens the number may be several hundreds. These proteins are called effectors: they control host defence responses and are essential for infection. The resistance genes bred into crops usually recognise one or more of these effectors

What is widespread in Gram negative bacteria (pathogens and symbionts in particular)

Type III secretion system (T3ss)

what does the Type III Secretion system do

• Delivers effectors inside host cells (30-40)

• suppresses Basal defence

• Suppresses Programmed cell death

What do Avirulence genes encode for

effector molecules

what have plants evolved

Resistance genes which encode proteins that recognise effector molecules (encoded by avirulence genes) and trigger rapid defence responses

Example of responses to infection in resistant plants

localised responses including programmed cell death

what do defence responses include activating

Systemic Acquired Resistance

What is SAR (Systemic Acquired Resistance) elicited most strongly by

gene-for-gene responses

What acts as a signalling molecule in SAR

Salicylic acid

what do plants acquired with resistance show

reduced susceptibility to a subsequent infection by either virulent or avirulent pathogens

Pathogenesis related proteins

proteins with likely anti-pathogen properties e.g. chitinases (insects), beta1-3 glucanases (bacterial and fungal cell walls)

function of cell wall structural proteins

strengthen cell walls

what can resistance genes be bred into

crops

• this leads to early success in achieving field resistance

• after a few years however, genetic drift in the pathogen or emergence of new races of pathogens lead to loss of resistance

Boom years and Burst years cycle in resistance bred crops

8-12 year cycle for a single plant pathogen control

• Replacement R (resistance gene) introduced

• BOOM YEARS: Effective disease control, use of specific R gene increases

• Selection pressure on the pathogen population steadily rises

• Prevalence of novel races in which the corresponding Avr gene is lost or mutates to a nonfunctioning allele increases

• BURST YEARS: Disease control fails, use of specific R genes decreases

• Plant breeders search for new R gene

How many effector proteins does the Phytophthora infestans genome encode for

• more than 400 effector proteins and some of these are targets for resistance genes

• However, as many of them act redundantly the pathogen can easily evolve to lose or change the Avirulence gene, allowing it to overcome resistance by evading the cognate R-gene protein

what has been identified in the Solanum species (wild relatives of the cultivated potato S. tuberosum)

A number of R genes conferring resistance to strains of P.infestans; these have been bred into cultivated varieties of potato and can confer useful resistance in the field against common P.infestans strains

what does the evolution of the Phytophthora infestans pathogen cause

• the ability of the pathogen to evade resistance

• the emergence of novel strains or races

• the loss of effectiveness of the strategies for resistance against the pathogen

What is conventional resistance

the use of genetic manipulation methods to introduce existing Resistance genes into cultivars or species in which they do not naturally occur.

what is Novel resistance

the use of genetic manipulation methods to introduce genes that function to limit pathogen spread by mechanisms other than via conventional resistance

what did scientists in Norwich do

• screened around 100 wild Solanum spp and identified 2 species that showed particularly good resistance to common UK P. infestans strains

• identified a promising candidate R gene Rpi-vnt1.1 from Solanum venturii

• they engineered this gene into the potato variety “Desiree” and several of the transgenic lines showed good resistance to the pathogen

• field trials began in Norfolk in 2012 with around 1000m2 of potatoes

• similar work in Belgium has led to successful field trials of resistant GM potatoes

features of the Simplot Innate potatoes

• 2 R-genes from wild solanum spp conferring resistance to P.infestans

• One R-gene Ry conferring resistance to Potato Virus Y

• A gene expressing an oligopeptide which is toxic/inhibitory to Potato Cyst Nematode

• Genes conferring improved cooking properties

Describe a non-conventional resistance approach which is not based on R genes

Pathogen derived resistance to a virus: Constitutive expression the major structural protein of Papaya Ringspot Virus (the cause of losses in Hawaii) protects against infection by PRSV. This has also been exploited to obtain resistance against virus diseases of maize, cassava and squash plants