Category: Publications

The targeting of plant cellular systems by injected type III effector proteins

Posted on by biota in Publications

Lewis JD, Guttman DS, Desveaux D

Semin. Cell Dev. Biol. 2009 Dec;20(9):1055-63

PubMed PMID: 19540926

Abstract

The battle between phytopathogenic bacteria and their plant hosts has revealed a diverse suite of strategies and mechanisms employed by the pathogen or the host to gain the higher ground. Pathogens continually evolve tactics to acquire host resources and dampen host defences. Hosts must evolve surveillance and defence systems that are sensitive enough to rapidly respond to a diverse range of pathogens, while reducing costly and damaging inappropriate misexpression. The primary virulence mechanism employed by many bacteria is the type III secretion system, which secretes and translocates effector proteins directly into the cells of their plant hosts. Effectors have diverse enzymatic functions and can target specific components of plant systems. While these effectors should favour bacterial fitness, the host may be able to thwart infection by recognizing the activity or presence of these foreign molecules and initiating retaliatory immune measures. We review the diverse host cellular systems exploited by bacterial effectors, with particular focus on plant proteins directly targeted by effectors. Effector-host interactions reveal different stages of the battle between pathogen and host, as well as the diverse molecular strategies employed by bacterial pathogens to hijack eukaryotic cellular systems.

An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell

Posted on by biota in Publications

Gong Y, Kakihara Y, Krogan N, Greenblatt J, Emili A, Zhang Z, Houry WA

Mol. Syst. Biol. 2009;5:275

PubMed PMID: 19536198

Abstract

Molecular chaperones are known to be involved in many cellular functions, however, a detailed and comprehensive overview of the interactions between chaperones and their cofactors and substrates is still absent. Systematic analysis of physical TAP-tag based protein-protein interactions of all known 63 chaperones in Saccharomyces cerevisiae has been carried out. These chaperones include seven small heat-shock proteins, three members of the AAA+ family, eight members of the CCT/TRiC complex, six members of the prefoldin/GimC complex, 22 Hsp40s, 1 Hsp60, 14 Hsp70s, and 2 Hsp90s. Our analysis provides a clear distinction between chaperones that are functionally promiscuous and chaperones that are functionally specific. We found that a given protein can interact with up to 25 different chaperones during its lifetime in the cell. The number of interacting chaperones was found to increase with the average number of hydrophobic stretches of length between one and five in a given protein. Importantly, cellular hot spots of chaperone interactions are elucidated. Our data suggest the presence of endogenous multicomponent chaperone modules in the cell.

Lesion mimic mutants: A classical, yet still fundamental approach to study programmed cell death

Posted on by biota in Publications

Moeder W, Yoshioka K

Plant Signal Behav 2008 Oct;3(10):764-7

PubMed PMID: 19513227

Abstract

Over the last decade a substantial number of lesion mimic mutants (LMM) have been isolated and a growing number of the genes have been cloned. It is now becoming clear that these mutants are valuable tools to dissect various aspects of programmed cell death (PCD) and pathogen resistance pathways in plants. Together with other forward genetics approaches LMMs shed light on the PCD machinery in plant cells and revealed important roles for sphingolipids, Ca(2+) and chloroplast-derived porphyrin-metabolites during cell death development.

Polymorphic genes of major effect: consequences for variation, selection and evolution in Arabidopsis thaliana

Posted on by biota in Publications

Stinchcombe JR, Weinig C, Heath KD, Brock MT, Schmitt J

Genetics 2009 Jul;182(3):911-22

PubMed PMID: 19416942

Abstract

The importance of genes of major effect for evolutionary trajectories within and among natural populations has long been the subject of intense debate. For example, if allelic variation at a major-effect locus fundamentally alters the structure of quantitative trait variation, then fixation of a single locus can have rapid and profound effects on the rate or direction of subsequent evolutionary change. Using an Arabidopsis thaliana RIL mapping population, we compare G-matrix structure between lines possessing different alleles at ERECTA, a locus known to affect ecologically relevant variation in plant architecture. We find that the allele present at ERECTA significantly alters G-matrix structure-in particular the genetic correlations between branch number and flowering time traits-and may also modulate the strength of natural selection on these traits. Despite these differences, however, when we extend our analysis to determine how evolution might differ depending on the ERECTA allele, we find that predicted responses to selection are similar. To compare responses to selection between allele classes, we developed a resampling strategy that incorporates uncertainty in estimates of selection that can also be used for statistical comparisons of G matrices.

Evolution in plant populations as a driver of ecological changes in arthropod communities

Posted on by biota in Publications

Johnson MT, Vellend M, Stinchcombe JR

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2009 Jun;364(1523):1593-605

PubMed PMID: 19414473

Abstract

Heritable variation in traits can have wide-ranging impacts on species interactions, but the effects that ongoing evolution has on the temporal ecological dynamics of communities are not well understood. Here, we identify three conditions that, if experimentally satisfied, support the hypothesis that evolution by natural selection can drive ecological changes in communities. These conditions are: (i) a focal population exhibits genetic variation in a trait(s), (ii) there is measurable directional selection on the trait(s), and (iii) the trait(s) under selection affects variation in a community variable(s). When these conditions are met, we expect evolution by natural selection to cause ecological changes in the community. We tested these conditions in a field experiment examining the interactions between a native plant (Oenothera biennis) and its associated arthropod community (more than 90 spp.). Oenothera biennis exhibited genetic variation in several plant traits and there was directional selection on plant biomass, life-history strategy (annual versus biennial reproduction) and herbivore resistance. Genetically based variation in biomass and life-history strategy consistently affected the abundance of common arthropod species, total arthropod abundance and arthropod species richness. Using two modelling approaches, we show that evolution by natural selection in large O. biennis populations is predicted to cause changes in the abundance of individual arthropod species, increases in the total abundance of arthropods and a decline in the number of arthropod species. In small O. biennis populations, genetic drift is predicted to swamp out the effects of selection, making the evolution of plant populations unpredictable. In short, evolution by natural selection can play an important role in affecting the dynamics of communities, but these effects depend on several ecological factors. The framework presented here is general and can be applied to other systems to examine the community-level effects of ongoing evolution.

Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins

Posted on by biota in Publications

Park SY, Fung P, Nishimura N, Jensen DR, Fujii H, Zhao Y, Lumba S, Santiago J, Rodrigues A, Chow TF, Alfred SE, Bonetta D, Finkelstein R, Provart NJ, Desveaux D, Rodriguez PL, McCourt P, Zhu JK, Schroeder JI, Volkman BF, Cutler SR

Science 2009 May;324(5930):1068-71

PubMed PMID: 19407142

Abstract

Type 2C protein phosphatases (PP2Cs) are vitally involved in abscisic acid (ABA) signaling. Here, we show that a synthetic growth inhibitor called pyrabactin functions as a selective ABA agonist. Pyrabactin acts through PYRABACTIN RESISTANCE 1 (PYR1), the founding member of a family of START proteins called PYR/PYLs, which are necessary for both pyrabactin and ABA signaling in vivo. We show that ABA binds to PYR1, which in turn binds to and inhibits PP2Cs. We conclude that PYR/PYLs are ABA receptors functioning at the apex of a negative regulatory pathway that controls ABA signaling by inhibiting PP2Cs. Our results illustrate the power of the chemical genetic approach for sidestepping genetic redundancy.

Web-queryable large-scale data sets for hypothesis generation in plant biology

Posted on by biota in Publications

Brady SM, Provart NJ

Plant Cell 2009 Apr;21(4):1034-51

PubMed PMID: 19401381

Abstract

The approaching end of the 21st century’s first decade marks an exciting time for plant biology. Several National Science Foundation Arabidopsis 2010 Projects will conclude, and whether or not the stated goal of the National Science Foundation 2010 Program-to determine the function of 25,000 Arabidopsis genes by 2010-is reached, these projects and others in a similar vein, such as those performed by the AtGenExpress Consortium and various plant genome sequencing initiatives, have generated important and unprecedented large-scale data sets. While providing significant biological insights for the individual laboratories that generated them, these data sets, in conjunction with the appropriate tools, are also permitting plant biologists worldwide to gain new insights into their own biological systems of interest, often at a mouse click through a Web browser. This review provides an overview of several such genomic, epigenomic, transcriptomic, proteomic, and metabolomic data sets and describes Web-based tools for querying them in the context of hypothesis generation for plant biology. We provide five biological examples of how such tools and data sets have been used to provide biological insight.

The wound-, pathogen-, and ultraviolet B-responsive MYB134 gene encodes an R2R3 MYB transcription factor that regulates proanthocyanidin synthesis in poplar

Posted on by biota in Publications

Mellway RD, Tran LT, Prouse MB, Campbell MM, Constabel CP

Plant Physiol. 2009 Jun;150(2):924-41

PubMed PMID: 19395405

Abstract

In poplar (Populus spp.), the major defense phenolics produced in leaves are the flavonoid-derived proanthocyanidins (PAs) and the salicin-based phenolic glycosides. Transcriptional activation of PA biosynthetic genes leading to PA accumulation in leaves occurs following herbivore damage and mechanical wounding as well as infection by the fungal biotroph Melampsora medusae. In this study, we have identified a poplar R2R3 MYB transcription factor gene, MYB134, that exhibits close sequence similarity to the Arabidopsis (Arabidopsis thaliana) PA regulator TRANSPARENT TESTA2 and that is coinduced with PA biosynthetic genes following mechanical wounding, M. medusae infection, and exposure to elevated ultraviolet B light. Overexpression of MYB134 in poplar resulted in transcriptional activation of the full PA biosynthetic pathway and a significant plant-wide increase in PA levels, and electrophoretic mobility shift assays showed that recombinant MYB134 protein is able to bind to promoter regions of PA pathway genes. MYB134-overexpressing plants exhibited a concomitant reduction in phenolic glycoside concentrations and other minor alterations to levels of small phenylpropanoid metabolites. Our data provide insight into the regulatory mechanisms controlling stress-induced PA metabolism in poplar, and the identification of a regulator of stress-responsive PA biosynthesis constitutes a valuable tool for manipulating PA metabolism in poplar and investigating the biological functions of PAs in resistance to biotic and abiotic stresses.

Global robustness and identifiability of random, scale-free, and small-world networks

Posted on by biota in Publications

Gong Y, Zhang Z

Ann. N. Y. Acad. Sci. 2009 Mar;1158:82-92

PubMed PMID: 19348634

Abstract

We are interested in the relationships among network topology, robustness, and identifiability, and their implications in improving network reconstruction. We used three different types of artificial gene networks (AGNs) with distinct topologies: topologies random (RND), scale-free (SF), and small-world (SW), to investigate their robustness and identifiability. The robustness of a network is represented by structural reachability (existence of pathways between two nodes) and dynamic reachability (response on one node upon perturbation on another node). The identifiability of the network edges is assessed in silico with an established reverse-engineering algorithm. We found that (1) structural reachability does not always lead to dynamic reachability; (2) network robustness is high and identifiability is low in all surveyed AGNs; (3) robustness is more sensitive to network topologies than is identifiability. We also devised a method for network dissection in which three subnets (set of alternative pathways or feedbacks, referred to as pathnet) are related to each node pair. This method allows us to identify the fine structural features underlying the distinct behaviors of the networks. For example, pathnet of the edge tail negatively contributes to the edge identifiability, and it is likely that extra perturbation at this pathnet would improve edge identifiability. We provide a case study to prove that double perturbations decrease the edge robustness and increase structural identifiability with a T helper cell-differentiation network model.

Neurogenic potential of isolated precursor cells from early post-gastrula somitic tissue

Posted on by biota in Publications

Tropepe V, Alton K, Sachewsky N, Cheng V, Kuo C, Morshead CM

Stem Cells Dev. 2009 Dec;18(10):1533-42

PubMed PMID: 19326969

Abstract

Adult tissues are known to contain rare populations of stem cells with multilineage differentiation potential that are distinct from other resident tissue-specific stem cells. However, whether multilineage stem cells are involved in tissue development is uncertain, primarily because the identification and characterization of these cells in embryonic tissue primordia is not well established. We tested whether stem cells with multilineage potential are present within the early post-gastrula somite tissue. We show that clonally derived precursor cells generate colonies with self-renewal capacity and have both neurogenic and myogenic lineage potential. Somite colonies contain cells that express Sox2, nestin, and Sca1, but do not express genes indicative of somitic mesoderm specification. Furthermore, we demonstrate that this multilineage potential is not due to colony cells with a pluripotent epiblast identity or the selection of p75 receptor-positive neural crest stem cells. Despite utilizing a highly undifferentiated tissue source, colony formation was not enhanced relative to reported estimates of multilineage stem cells from adult muscle, a derivative of the embryonic somite. Thus, our findings suggest that a permissive in vitro environment is sufficient for the isolation of a discrete population of stem cells in the embryonic somite that may represent the earliest developmental precursor to adult muscle multilineage stem cells.