Session 8: Plant Immunity and the Evolutionary Arms Race between Host and Pathogen

Transcript of Part 1: Introduction to Plant-Pathogen Interactions

00:00:07;13	Hi, I'm Sheng Yang He.
00:00:09;13	I'm a professor at Michigan State University.
00:00:11;09	And I'm an Investigator of the Howard Hughes Medical Institute.
00:00:14;27	Today, I'm going to tell you about the
00:00:17;09	fascinating world of plant-pathogen interactions.
00:00:20;12	Now, why do we care about plant-pathogen interactions?
00:00:23;11	Some of you may know a disease called potato late blight.
00:00:27;23	This disease devastate...
00:00:30;19	devastated the potato crop in the 1840s in Ireland.
00:00:36;04	That event basically killed about a million people,
00:00:42;18	and another million emigrated... forced emigration...
00:00:47;15	out of Ireland.
00:00:48;24	Many of them actually ended up in the United States.
00:00:51;02	So, this just illustrates how a plant disease
00:00:53;26	can have a profound effect on human survival and emigration.
00:00:59;02	There are many such diseases, not to this scale,
00:01:02;18	but they are major threats to our global food securities.
00:01:05;19	So, one of the other diseases, you know,
00:01:07;29	like rice blast, I grew up with in China.
00:01:10;04	I lived in a small village,
00:01:12;17	and it was very severe when I was growing up.
00:01:15;13	But, you know, now I go back 40 years later.
00:01:18;21	It's still a very severe disease.
00:01:20;22	In fact, this is the number one disease in rice production across the globe.
00:01:24;21	There also are new diseases like kiwi bacterial canker,
00:01:28;22	which is caused by a bacterial pathogen that I'm very familiar with
00:01:31;26	called Pseudomonas syringae,
00:01:33;05	sweeping across New Zealand and some European countries right now.
00:01:37;09	So, you see there are old and new diseases.
00:01:39;26	They really pose a great threat to agriculture.
00:01:42;26	And so the... many researchers are, you know,
00:01:45;28	involved in trying very hard to understand the molecular basis of these diseases.
00:01:51;08	And the goal is to... hopefully, to come up with
00:01:55;13	very innovative solutions to solve all these diseases.
00:01:58;22	It's been very challenging.
00:02:01;10	But I think, you know, this is an area that we have to do,
00:02:03;28	because the crop production has to increase
00:02:06;22	to meet the demand of the rising population in the next century, actually.
00:02:12;16	So these diseases are one of the obstacles
00:02:16;26	to increase the yield production.
00:02:18;20	And also quality... you know, disease affects quality as well.
00:02:22;14	And so, in today's... this part of my talk,
00:02:25;29	I'm going to introduce some of the very general concepts
00:02:28;26	dealing with host-pathogen interactions.
00:02:31;19	On the one side, I'm going to talk to you about plant immunity.
00:02:35;06	Yes, plants do have immune responses like a human.
00:02:37;15	But I also want to talk about pathogen virulence factors
00:02:40;29	and so-called effectors.
00:02:43;08	That's Part 1.
00:02:45;19	In Part 2, I'm gonna illustrate these concepts
00:02:48;22	using the model Arabidopsis-Pseudomonas syringae system
00:02:53;04	that we and many others are actually working on.
00:02:55;02	So, I hope you're able to watch both parts,
00:02:57;22	because if you only see one you may not get enough information
00:03:02;03	from this talk.
00:03:04;09	So, what is effector-triggered immunity in plants?
00:03:06;16	There's an older name for this.
00:03:08;19	This is called, actually, gene-for-gene resistance.
00:03:10;23	This is describing a phenomenon, probably noticed by farmers or by,
00:03:15;09	you know, other people, over many years, thousands of years, probably.
00:03:19;03	You know, if you go into the wheat field
00:03:21;15	where there's different cultivars that are planted,
00:03:23;24	some cultivars will be severely diseased in some years.
00:03:27;12	And at the same time, some cultivars will be green and,
00:03:29;24	you know, yielding really well.
00:03:31;15	What's the molecular basis of that?
00:03:33;04	What's the genetic basis of it?
00:03:34;19	And that's been, you know,
00:03:36;00	puzzling for many people for a long time, until this scientist named H. H. Flor.
00:03:42;13	He's a plant breeder and a plant pathologist.
00:03:45;06	He studied a disease called the flax rust disease.
00:03:49;08	It is caused by a fungus.
00:03:50;24	He was very careful.
00:03:52;15	He studied many strains of fungal pathogens,
00:03:55;07	but also many cultivars of the flax plant.
00:04:00;18	And he studied the genetics of the interaction,
00:04:04;07	and came up with this very interesting hypothesis called
00:04:07;02	the gene-for-gene hypothesis.
00:04:09;05	What he thought is that maybe the pathogen
00:04:11;22	has so-called avirulence genes, or Avr genes, some strains.
00:04:15;20	And some cultivars that are resistant
00:04:18;02	contain so-called resistant genes, or R genes. Okay?
00:04:21;10	So, this is the diagram he would use to describe these interactions.
00:04:26;12	If he'd taken a pathogen without any avirulence genes,
00:04:29;06	it's going to infect the plants
00:04:31;27	that either have the R genes or no R genes, right?
00:04:34;13	Because it's virulent, okay?
00:04:36;02	But, if when the pathogen has Avr genes within it,
00:04:39;14	it's going to only infect the plants
00:04:43;01	with no corresponding R genes, okay?, which is depicted right here.
00:04:47;18	If the plant has R genes that can recognize genetically this Avr gene,
00:04:50;26	then the plant will be resistant.
00:04:52;27	So, you needed both the R genes in the plant
00:04:55;09	but also Avr genes in the pathogen
00:04:57;17	for a plant to be resistant.
00:05:00;20	So, this has... you know,
00:05:02;27	was a hypothesis only, okay?
00:05:04;19	But about 10 or, you know, 15 years later,
00:05:07;17	there's actually molecular proof for the existence of these interactions.
00:05:11;20	So, scientists started to clone these so-called Avr genes
00:05:17;11	from different kind of pathogens.
00:05:18;21	The initial few Avr genes were actually cloned from bacteria.
00:05:22;20	And this was done by Brian Staskawicz at UC Berkeley
00:05:25;05	and the late Noel Keen at UC Riverside.
00:05:29;03	And then about ten years later,
00:05:30;25	a number of R genes have been cloned from plants,
00:05:34;21	from different plant species.
00:05:36;15	Okay?
00:05:38;09	So, there were some original predictions of how the Avr proteins and R protein
00:05:41;13	would work, actually, right?
00:05:43;00	So, the idea was really inspired
00:05:45;11	by an animal receptor signaling kind of model.
00:05:49;12	It says that, you know,
00:05:51;03	this Avr protein may be made in the pathogen
00:05:53;15	but is secreted outside of the bacteria. Okay?
00:05:56;16	And the R proteins may be receptors.
00:05:59;13	They may be in the membrane of the plant cell.
00:06:01;20	So, it indicated this classical ligand-receptor kind of interaction.
00:06:08;16	When the Avr genes and R genes are cloned,
00:06:12;23	you know, we'll see whether this model actually holds, right?
00:06:15;16	So, as I said, many R genes have been cloned from different species
00:06:20;20	against different kinds of pathogens.
00:06:21;29	So, we have N gene cloned from tobacco
00:06:24;03	against a viral pathogen.
00:06:25;25	A Cf9 gene... you know, the names... it's not important...
00:06:30;01	but this particular gene is against a fungal disease called leaf mold.
00:06:35;00	There's also, you know, genes...
00:06:37;19	R genes that are against bacterial diseases,
00:06:40;25	in this case, from Arabidopsis.
00:06:42;22	And also some R genes actually
00:06:45;16	against worms, like, nematodes.
00:06:48;20	So, it's very different kinds of pathogens.
00:06:52;06	Initially, we were thinking that maybe there's different kind of R genes,
00:06:53;26	you know, molecularly.
00:06:55;10	But it turns out many of these genes actually share the same kind of motif,
00:06:58;15	including the so-called leucine-rich repeat, or LRR.
00:07:02;25	And this is very exciting because
00:07:04;25	if you line up a sequence against a database,
00:07:07;01	some of the genes that come up are actually
00:07:10;03	involved in animal immune... immunity, so immune receptors,
00:07:13;09	for instance Nod1 is the bottom one diagrammed here.
00:07:17;04	It contains the leucine-rich repeat
00:07:19;24	like the plant receptors here.
00:07:21;06	It also contains so-called NB domains,
00:07:23;13	or nucleotide binding domains.
00:07:25;19	So, here's a very interesting parallel
00:07:27;23	between the animal immune system and the plant immune system.
00:07:31;00	They are based on the same kind of protein
00:07:35;02	to defend against different kinds of pathogens.
00:07:37;06	So, remember this model that I showed you just a few minutes earlier,
00:07:40;22	that indicated that these Avr proteins
00:07:43;16	may be secreted from the pathogen
00:07:45;29	and the R proteins are probably localized
00:07:48;19	to the plasma membrane in the host cell.
00:07:51;11	When you look at the Avr protein sequence, however,
00:07:54;14	you actually don't see this classical signal peptide
00:07:56;20	that indicates the protein will be secreted
00:07:59;02	through the conventional secretion system in the bacteria.
00:08:04;27	So, this model is probably not correct
00:08:07;02	in terms of this particular step.
00:08:09;06	Actually, it turns out most R proteins
00:08:12;09	are also not localized to the plant plasma membrane as originally predicted.
00:08:16;05	Most of them actually localize inside of the cytosol.
00:08:19;27	So, what's going on?
00:08:21;24	Now, this is really Puzzle #1 for a lot of people.
00:08:24;13	It doesn't really make sense.
00:08:26;17	Until we discovered that, actually,
00:08:29;14	most of these Avr proteins from bacteria
00:08:32;12	actually are directly injected into the plant cell
00:08:35;07	through the type III secretion system.
00:08:38;16	And this is actually a very conserved system
00:08:41;04	in bacterial pathogens of plants and animals, again.
00:08:45;02	So, you can see that type III secretion system.
00:08:49;10	You can see it under the electron microscope
00:08:51;24	like a syringe-like thing.
00:08:54;15	The injection system allows bacteria, in this case,
00:08:57;29	to penetrate through the plant cell wall.
00:09:00;22	So, the plant cell has a cell wall, unlike the animal cell.
00:09:04;03	And injecting through the plasma membrane into the cytosol.
00:09:07;07	So, that explains why Avr proteins
00:09:09;20	could be potentially recognized by R proteins
00:09:12;06	located inside the plant cell.
00:09:15;25	And this translocation system actually
00:09:18;14	is very common for other types of plant pathogen:
00:09:21;00	fungus and even, you know, nematodes.
00:09:24;14	They inject these proteins into the plant cell
00:09:28;04	as a very common mechanism during infection.
00:09:31;03	So, gene-for-gene resistance, you know,
00:09:33;24	became effector-triggered immunity, the common term today.
00:09:36;15	This is another way of depicting it.
00:09:38;04	So, you can see that bacteria
00:09:40;12	are injecting these red colored effectors
00:09:43;06	into the plant cell.
00:09:44;25	And they're being recognized by these immune receptors,
00:09:48;16	either containing the coiled-coil domain, CC domain,
00:09:51;16	or the TIR domain, and they are LRR proteins.
00:09:55;28	Okay? So, it's called effector-triggered immunity.
00:09:58;16	So, when the plant genome was sequenced in early 2000,
00:10:03;22	first from Arabidopsis,
00:10:05;08	people were interested to see how many R proteins are there in plants, right?
00:10:09;18	In humans, we know we have these antibodies.
00:10:11;26	You know, it's this endless combination of antibodies
00:10:15;13	that can recognize all kinds of microbes, right?,
00:10:18;00	10^14 specificity.
00:10:20;23	So, we wanted to know how many R proteins
00:10:23;02	are encoded from the plant genome.
00:10:25;15	There was a puzzle, actually.
00:10:27;05	When you see this, there's only hundreds of these genes.
00:10:30;05	How can hundreds of genes, immune receptors,
00:10:32;13	recognize thousands of microbes?
00:10:34;10	So, that's really a big puzzle.
00:10:35;21	And that was the puzzle based on this directed recognition,
00:10:38;20	so, saying that one Avr protein from a pathogen
00:10:42;15	can be recognized by a particular R protein in the plant.
00:10:46;20	So, it can't do this more than a hundred times, right?
00:10:49;19	This puzzle was partially solved by this realization
00:10:53;19	that there's a lot of so-called indirect recognition
00:10:57;00	by R proteins of these Avr proteins.
00:11:00;16	So, this is actually happening in many diseases.
00:11:03;19	So, this is a one example.
00:11:05;19	Imagine that this light blue colored circle
00:11:09;20	is a plant protein called RIN4 in Arabidopsis.
00:11:12;09	This protein is actually attacked
00:11:14;21	by two avirulence proteins, AvrB and AvrRpm1
00:11:18;05	from Pseudomonas syringae.
00:11:19;24	What they do is that these two Avr proteins,
00:11:22;20	well, they attack a RIN4 protein,
00:11:25;09	in this case inducing the phosphorylation of RIN4,
00:11:28;00	of the plant protein.
00:11:29;24	This phosphorylation event induced by two different Avr proteins
00:11:34;08	is recognized by the Rpm1 R protein.
00:11:37;08	Okay, so in this case one R protein recognized
00:11:41;02	two Avr proteins through this common modification
00:11:44;05	of another plant protein.
00:11:46;00	It's called indirect recognition.
00:11:47;29	There's actually another Avr protein called AvrRpt2,
00:11:50;22	which modifies RIN4 differently.
00:11:53;05	It actually cleaves the RIN4 because it's a protease.
00:11:56;02	That is being recognized by another R protein called Rps2.
00:12:00;10	So, you can see there's a lot of variations of so-called indirect recognition
00:12:03;15	that could potentially explain why a limited set of R proteins
00:12:07;20	could potentially recognize many different Avr proteins
00:12:10;29	from different pathogens, because they could induce modification
00:12:15;10	of another plant protein and that modification, then,
00:12:18;11	is sensed by the pathogen to say, this is not normal;
00:12:20;24	it's not my normal thing, okay?
00:12:23;12	So... so then there's another puzzle, okay?
00:12:25;13	I've being telling you these avirulence proteins from pathogens...
00:12:30;01	indicating... when you have these Avr proteins,
00:12:33;02	then the pathogen is avirulent. Okay?
00:12:35;17	Why would a pathogen send avirulence proteins
00:12:37;29	into the plant cell to become avirulent?
00:12:40;01	That... no... no... that makes no sense, okay?
00:12:42;25	And so that's Puzzle #3.
00:12:44;18	Why would the pathogen send avirulence proteins
00:12:46;27	into the plant to be recognized by R proteins?
00:12:49;13	What is the original function of these proteins? Okay?
00:12:52;18	So, I'll remind you of this again.
00:12:54;25	So, we have been talking about this effector-triggered immunity
00:12:57;10	because these particular cells contain R proteins.
00:13:01;16	The plants are resistant against pathogens, okay?
00:13:04;06	In this case, the effector proteins, or avirulence proteins,
00:13:08;07	are basically not good for pathogens.
00:13:11;02	They're being recognized.
00:13:13;04	Actually, in most plants without resistant proteins,
00:13:16;25	these effector proteins or avirulence proteins are doing something else.
00:13:20;12	They're actually suppressing another branch of immune response
00:13:23;28	called pattern-triggered immunity.
00:13:26;00	So, this is depicted on the left.
00:13:28;04	So, pattern-triggered immunity is distinct
00:13:30;13	from effector-triggered immunity.
00:13:32;07	They use different signaling pathways.
00:13:34;28	But they are normally suppressed
00:13:37;09	by these effector proteins to induce disease, okay?
00:13:41;00	So, that's why you want to send these Avr proteins into the plant cells,
00:13:44;13	because the R protein is rare.
00:13:48;01	So, what is pattern-triggered immunity?
00:13:51;03	This branch of immunity is not triggered by effectors
00:13:54;14	of the pathogen,
00:13:55;28	but it's triggered by common patterns from microbes.
00:13:59;13	There can be pathogens.
00:14:01;09	It could be non-pathogens, okay?
00:14:03;17	And so, they've evolved to recognize all kinds of microbes.
00:14:06;25	They are probably more ancient then effector-triggered immunity.
00:14:10;03	They are probably more related to the animal system of the immune system.
00:14:15;02	So, one example of these patterns from bacteria is called bacterial flagellin.
00:14:19;25	This is obviously very common
00:14:21;24	because most bacteria have to swim,
00:14:23;14	so they have to have these traits.
00:14:25;12	And that common trait is now recognized by pattern-triggered immunity.
00:14:29;02	So, one example you can see here...
00:14:32;04	you know, flagellin subunits make up the flagella.
00:14:35;12	It's like about 10,000 copies of this to make
00:14:38;26	a viable flagella.
00:14:40;13	Flagellin has a conserved domain at the N-terminus and the C-terminus,
00:14:43;21	a variable region in the middle of the protein,
00:14:46;28	and there's a peptide called flg22.
00:14:50;27	This is a 22- amino acid peptide,
00:14:54;02	which is now used very commonly in the study of
00:14:57;00	pattern-triggered immunity, called flg22.
00:14:59;03	People have identified the receptor in Arabidopsis for flg22
00:15:04;03	and flagellin.
00:15:06;06	This is done by Thomas Boller's group, very nice work.
00:15:09;15	This receptor looks like a traditional membrane-bound receptor.
00:15:14;14	You have a leucine-rich repeat domain,
00:15:16;27	which recognizes the flagellin or flg22 peptide,
00:15:19;27	but then you have a kinase domain inside the plant cell
00:15:22;25	that transduces the signal to do phosphorylation.
00:15:25;16	So, it's very similar to the animal signal/receptor system.
00:15:29;24	A critical question is,
00:15:32;09	is this receptor important for disease resistance, right? Okay.
00:15:36;14	So, this is done by Cyril Zipfel in Thomas Boller's group,
00:15:42;00	many years ago now.
00:15:44;05	They created this receptor mutant in Arabidopsis.
00:15:47;22	So, this mutant will fail to recognize flagellin of bacteria,
00:15:51;08	including Pseudomonas syringae.
00:15:52;29	On the left, you have a wild type plant
00:15:55;22	containing the full, functional fls2 receptor.
00:15:57;20	On the right is the receptor mutant.
00:16:01;20	And you can see... you see more disease after infection with Pseudomonas
00:16:06;02	in the receptor mutant compared to the wild type,
00:16:07;29	indicating the receptor is very important.
00:16:10;18	The importance of the receptor is actually most obvious
00:16:13;07	if the infection is done by putting bacteria
00:16:15;24	onto the leaf surface, okay?
00:16:18;03	For bacteria to infect the plants,
00:16:20;06	bacteria have to actually go into the leaves.
00:16:22;10	And one of the routes is through stomata.
00:16:25;08	So, these are microscopic pores on plant leaves
00:16:29;10	that allow plants to uptake CO2 to do photosynthesis.
00:16:32;25	But the stomata pores are big enough for bacteria to go in there,
00:16:36;29	so for a long time people thought this is a passive process.
00:16:40;24	The bacteria takes advantage of the open pores
00:16:43;00	to get into the plant tissue.
00:16:46;12	But I just told you...
00:16:48;16	so, the fls2 receptor mutant phenotype
00:16:52;21	is most obvious when you inoculate bacteria
00:16:55;16	onto the surface because they have to go through the stomata to infect.
00:16:59;17	If you inject bacteria directly into the leaf,
00:17:04;02	bypassing the stomata,
00:17:06;08	there's not much difference between the wild type plants
00:17:08;25	and the immune receptor mutant plants.
00:17:10;25	Okay, so, why?
00:17:12;20	It turns out... actually, my group figured out...
00:17:15;16	that this is because...
00:17:18;17	these are stomata cells that...
00:17:20;22	each stomata is actually made up of two guard cells.
00:17:23;02	They actually can recognize flagellin as a molecular pattern
00:17:26;28	and then they close the pore.
00:17:29;08	It's the first line of defense against bacterial infection.
00:17:32;09	So, this is a kind of interesting immune output,
00:17:35;14	very unique to plants.
00:17:37;21	They're recognizing the molecular pattern
00:17:39;24	and do this stomata closure as the first line of defense.
00:17:45;01	So, to summarize this part of the talk,
00:17:48;03	there are two branches of plant innate immune systems.
00:17:53;14	One is involving pattern-triggered immunity,
00:17:55;24	probably very ancient.
00:17:57;16	It evolved to recognize all kinds of pathogens or non-pathogens
00:18:02;05	so the plants won't be eaten by these microbes, then,
00:18:06;05	because plants are really rich in sugars and other nutrients.
00:18:10;18	But then, the pathogen has evolved effectors
00:18:14;02	to shut down the pattern-triggered immunity
00:18:16;09	as a mechanism of pathogenesis.
00:18:18;08	And this is a called effector-trigger susceptibility.
00:18:22;24	But then plants are smart.
00:18:25;11	They evolved this effector-triggered immunity to recognize individual effectors,
00:18:29;02	which used to be called avirulence proteins,
00:18:31;24	to activate the second branch of immunity
00:18:34;20	to fight against these pathogens.
00:18:37;01	So, this... if you go into the wheat field right now,
00:18:40;09	you have this continuation of evolution.
00:18:43;01	Sometimes the pathogen wins; sometimes the plants win.
00:18:45;24	What we want to do is to identify a way
00:18:48;23	to speed up the evolution so that we can fight against plant...
00:18:53;12	emergence of new diseases before they become a problem.
00:18:57;01	So, now I want to acknowledge colleagues
00:19:00;14	who actually gave me some slides for this talk,
00:19:02;06	so, including the slides I had,
00:19:04;13	Cyril Zipfel provided a few interesting slides for this part of my talk.
00:19:08;01	Thank you very much.