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Monday, August 1, 2011

Scientists map attack tactics of plant pathogens

(“Biomechanism.com“) — Every year, plant diseases wipe out millions of tons of crops, lead to the waste of valuable water resources and cause farmers to spend tens of billions of dollars battling them.

Now a new discovery from a University of North Carolina at Chapel Hill-led research team may help tip the war between plants and pathogens in favor of flora.

A leaf infected by a pathogen called an oomycete. The oomycete gains entry into the leaf's intracellular spaces through natural openings and then grows by extending hyphae (filaments) between cells. When the hyphae fill up the leaf, the oomycete releases the next generation of infectious spores (the white tree-like structures emerging from the leaf surface. Oomycetes cause downy mildew diseases of many plants; one was responsible for the Irish Potato Famine and another for Sudden Oak Death Syndrome. Credit: Petra Epple, Dangl Lab, UNC-Chapel Hill.

The finding – published in the July 29, 2011, issue of the journal Science – suggests that while pathogens employ a diverse arsenal of weapons, they use these to attack plants by honing in on a surprisingly limited number of cellular targets.

“This is a major advance in understanding the biomechanisms involved in the ongoing evolutionary battle between plants and pathogens,” said Jeff Dangl, Ph.D., the study’s lead author and John N. Couch Professor of Biology in the College of Arts and Sciences.

The new finding is one of two studies published concurrently in Science related to the first comprehensive plant “interactomes” – maps of the tens of thousands of interactions that link a cell’s proteins. Those connections govern how proteins assemble into complex functional machines that dictate the tasks a cell can perform, such as growth, division and response to light, water and nutrients. And these same machines are often recruited into the battle against infectious agents.

One of the new studies mapped the interactome for about a third of the proteins encoded by the genome of the plant Arabidopsis thaliana, or thale cress. Arabidopsis is widely used for research purposes as a model organism – similar to the way mice are used in medical research – because of traits that make it useful for understanding the workings of many other plant species.

A leaf infected by an oomycete pathogen. Special feeding structures, called haustoria, bulge from the pathogen's hyphae (filaments) into the inside of the plant cells (the purple balloon-like structures inside the clear-colored individual cells). Credit: Petra Epple, Dangl Lab, UNC-Chapel Hill.

Dangl’s group led an additional study incorporating that interactome data with the construction of a second interactome. The second map focused on understanding how two very different pathogens (the bacteria Pseudomonas syringae and the oomycete parasite Hyaloperonospora arabidopsidis) infect plants and how plants fight back.

One method that these pathogens, which live in between cells, use for successful infection is to deploy virulence proteins (known as effectors) into the plant cell. The effectors muzzle the host’s defenses and allow the pathogen to hijack the plant’s cellular machinery.

In the new study, Dangl and his collaborators at institutions including Harvard University, the Salk Institute in La Jolla, Calif., and the University of Warwick, U.K., found that these two pathogens have evolved to focus their effectors onto a limited set of roughly 165 interconnected proteins that act in cellular machines in Arabidopsis cells – despite the fact that they last shared a common ancestor over 2 billion years ago, and use vastly different biomechanisms to colonize plants.

“This likely means that to suppress host plants’ defenses, all plant pathogens have evolved weapons that focus on a relatively small group of cellular machines,” Dangl said. “Knowing this should facilitate faster breeding for disease resistance and development of environmentally sustainable treatments for many devastating plant diseases.”

He said that neither interactome is a complete map, and more work needs to be done fully identify which protein networks are targeted by pathogens.

“We’ve found the needles in the haystack, but we still have to comb through another two-thirds of the hay,” said Dangl. “Our data suggest that there will be only a few hundred targets for effectors from all pathogens, out of the roughly 27,000 proteins encoded in the whole Arabidopsis genome.”

Academic scientists, seed breeders and biotech companies interested in these proteins will benefit from freely available data from both interactomes. The findings also could have implications for human health research.

“Professor Dangl and colleagues have used a powerful combination of network theory and laboratory experimentation to develop an approach to understanding the evolutionary logic by which pathogens and their hosts interact,” said James Anderson, Ph.D., who oversees regulatory biology grants at the National Institutes of Health. “While this study focused on plants, the results illustrate the value of model organisms in revealing fundamental principles that help us understand human responses to infectious diseases and provide the basis for devising new therapeutic strategies.”

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The study, “Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network,” was co-written by researchers from more than a dozen institutions.

The research in Dangl’s lab was funded by the National Institute of General Medical Sciences, part of the National Institutes of Health; the National Science Foundation’s Arabidopsis 2010 Program; and the Department of Energy.

Plant immunity discovery boosts chances of disease-resistant crops

Posted by Biomechanism

(“Biomechanism.com“) — Researchers funded by the Biotechnology and Biological Sciences Research Council (BBSRC) have opened up the black box of plant immune system genetics, boosting our ability to produce disease- and pest-resistant crops in the future. The research is published in the journal Science.

Caption: Broccoli Head rot caused by Downy Mildew. Photo: UMASS

An international consortium of researchers, including Professor Jim Beynon at the University of Warwick, has used a systems biology approach to uncover a huge network of genes that all play a part in defending plants against attacks from pests and diseases – a discovery that will make it possible to explore new avenues for crop improvement and in doing so ensure future food security.

Professor Beynon said “Plants have a basic defence system to keep out potentially dangerous organisms. Unfortunately some of these organisms have, over time, evolved the ability to overcome plant defences and so plant breeders are always looking for new ways to catch them out. Understanding exactly how plant immunity works is key to making developments in this area.”

Professor Beynon’s team looked at downy mildew as an example of a plant disease. This is caused by mould-like organism called Hyaloperonospora parasitica, which, like many organisms that infect plants, produces proteins that it introduces into the plant to undermine its natural defences.

The team studied almost 100 different so-called effector proteins from Hyaloperonospora parasitica that are known to be involved in overcoming a plant’s immune system. They were looking to see how each of these proteins has an effect through interaction with other proteins that are already present in a plant. They found a total of 122 plant proteins from the commonly-studied plant Arabidopsis thaliana that are directly targeted by the proteins from Hyaloperonospora parasitica.

Caption: Broccoli Leaf symptoms caused by Broccoli Downy Mildew. Downy Mildew occurs wherever brassica crops are grown and infects cabbage, Brussels sprout, cauliflower, broccoli, kale, kohlrabi, Chinese cabbage, turnip, radish, and mustard as well as cruciferous weed species. The disease caused by Hyaloperonospora parasitica is particularly important on seedlings but can also cause poor growth and reduced yield and quality of produce at later plant stages. Photo: UMASS Extension

Professor Beynon continued “This shows that there are many more plant proteins involved in immunity than we first thought. By studying the genes that give rise to these proteins we can start to identify key genetic targets for crop improvement.”

The study has also identified many complex connections between the plant proteins suggesting that the network of activity is crucial in plant defences.

Professor Beynon concluded “Our discovery suggests that looking for single genes that confer resistance to pests and diseases is not going to be sufficient. Instead, researchers and breeders will have to work together to produce plants with robust networks of genes that can withstand attack.”

Professor Douglas Kell, Chief Executive, BBSRC said “Understanding the fundamental bioscience of plants is critical if we are to develop new ways of producing sustainable, safe, and nutritious food for a growing population. This discovery opens up a whole realm of possibilities in research about plant-pathogen interactions. It also points the way to new ways of working in this area; with a complex network operating behind the scenes in plant immunity, there is a clear need to take a systems approach to future research.”

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The work was a collaboration between Pascal Braun and Marc Vidal of the Dana Faber Institute, Boston, and Jeff Dangl, University of North Carolina, USA. It also involved a European consortium including Jonathan Jones, The Sainsbury Laboratory, Norwich; Guido van den Ackerveken, Utrecht University; and Jane Parker, Max Planck Institute, Cologne.

Scientists take a giant step for people — with plants!

Posted by Biomechanism

(“Biomechanism.com“) — Salk Institute and Dana Farber Cancer Institute researchers contribute to production of largest-ever map of plant protein interactions.

Science usually progresses in small steps, but on rare occasions, a new combination of research expertise and cutting-edge technology produces a ‘great leap forward.’ An international team of scientists, whose senior investigators include Salk Institute plant biologist Joseph Ecker, report one such leap in the July 29, 2011 issue ofScience. They describe their mapping and early analyses of thousands of protein-to-protein interactions within the cells of Arabidopsis thaliana -a variety of mustard plant that is to plant biology what the lab mouse is to human biology.

Caption: The image shows an Arabidopsis plant overlaid on a network map of protein-protein interactions. The clusters of colors represent "communities" of interacting proteins that are enriched in specific plant processes. Credit: Courtesy of Joseph R. Ecker, Salk Institute for Biological Studies Plant Photo: Joe Belcovson, Salk Institute for Biological Studies Network map: Mary Galli, Salk Institute for Biological Studies and Matija Dreze, Center for Cancer Systems Biology at the Dana-Farber Cancer Institute

“With this one study we managed to double the plant protein-interaction data that are available to scientists,” says Ecker, a professor in the Plant Molecular and Cellular Biology Laboratory. “These data along with data from future ‘interactome’ mapping studies like this one should enable biologists to make agricultural plants more resistant to drought and diseases, more nutritious, and generally more useful to mankind.”

The four-year project was funded by an $8 million National Science Foundation grant, and was headed by Marc Vidal, Pascal Braun, David Hill and colleagues at the Dana Farber Cancer Institute in Boston; and Ecker at the Salk Institute. “It was a natural collaboration,” says Vidal, “because Joe and his colleagues at the Salk Institute had already sequenced the Arabidopsis genome and had cloned many of the protein-coding genes, whereas on our side at the Dana Farber Institute we had experience in making these protein interaction maps for other organisms such as yeast.”

In the initial stages of the project, members of Ecker’s lab led by research technician Mary Galli converted most of their accumulated library of Arabidopsis protein-coding gene clones into a form useful for protein-interaction tests. “For this project, over 10,000 ‘open reading frame’ clones were converted and sequence verified in preparation for protein-interaction screening,” says Galli.

Vidal, Braun, Hill and their colleagues systematically ran these open reading frames through a high quality protein-interaction screening process, based on a test known as the yeast two-hybrid screen. Out of more than forty million possible pair combinations, they found a total of 6,205 Arabidopsis protein- protein interactions, involving 2,774 individual proteins. The researchers confirmed the high quality of these data, for example by showing their overlap with protein interaction datafrom past studies.

The new map of 6,205 protein partnerings represents only about two percent of the full protein- protein “interactome” for Arabidopsis, since the screening test covered only a third of all Arabidopsis proteins, and wasn’t sensitive enough to detect many weaker protein interactions. “There will be larger maps after this one,” says Ecker.

Even as a preliminary step, though, the new map is clearly useful. The researchers were able to sort the protein interaction pairs they found into functional groups, revealing networks and “communities” of proteins that work together. “There had been very little information, for example, on how plant hormone signaling pathways communicate with one another,” says Ecker. “But in this study we were able to find a number of intriguing links between these pathways.”

A further analysis of their map provided new insight into plant evolution. Ecker and colleagues Arabidopsis genome data, reported a decade ago, had revealed that plants randomly duplicate their genes to a much greater extent than animals do. These gene duplication events apparently give plants some of the genetic versatility they need to stay adapted to shifting environments. In this study, the researchers found 1900 pairs of their mapped proteins that appeared to be the products of ancient gene-duplication events.

Using advanced genomic dating techniques, the researchers were able to gauge the span of time since each of these gene-duplication events – the longest span being 700 million years – and compare it with the changes in the two proteins’ interaction partners. “This provides a measure of how evolution has rewired the functions of these proteins,” says Vidal. “Our large, high-quality dataset and the naturally high frequency of these gene duplications in Arabidopsis allowed us to make such an analysis for the first time.”

Caption: Researchers have created an interaction network map for the plant Arabidopsis thaliana, illuminating protein-protein relationships and doubling the knowledge that existed previously. Credit: Courtesy of Zina Deretsky, National Science Foundation

The researchers found evidence that the Arabidopsis protein partnerships tend to change quickly after the duplication event, then more slowly as the duplicated gene settles into its new function and is held there by evolutionary pressure. “Even though the divergence of these proteins’ amino-acid sequences may continue, the divergence in terms of their respective partners slows drastically after a rapid initial change, which we hadn’t expected to see,” Vidal says.

In the July 29 issue of Science researchers from the Arabidopsis interactome mapping study reported yet another demonstration of the usefulness of their approach. Led by Jeffery L. Dangl of the University of North Carolina at Chapel Hill, they examined Arabidopsis protein interactions with the bacterium Pseudomonas syringae (Psy) and a fungus-like microbe called Hyaloperonospora arabidopsidis (Hpa). “Even though these two pathogens are separated by about a billion years of evolution, it turns out that the ‘effector’ proteins they use to subvert Arabidopsis cells during infection are both targeted against the same set of highly connected Arabidopsis proteins,” says Ecker. “We looked at some of these targeted Arabidopsis proteins and found evidence that they serve as ‘hubs’ or control points for the plant immune system and related systems.”

Ecker and his colleagues hope that these studies mark the start of a period of rapid advancement in understanding plant biology, and in putting that knowledge to use for human benefit. “This starts to give us a big, systems-level picture of how Arabidopsis works, and much of that systems-level picture is going to be relevant to – and guide further research on – other plant species, including those used in human agriculture and even pharmaceuticals,”Ecker says.

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The “Arabidopsis Interactome Mapping Consortium” consists of over 20 national and international laboratories that contribute to this study with support from a number of funding agencies including the National Science Foundation and the National Institutes of Health.