Category: Publications

Pseudomonas syringae strains naturally lacking the classical P. syringae hrp/hrc Locus are common leaf colonizers equipped with an atypical type III secretion system

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Clarke CR, Cai R, Studholme DJ, Guttman DS, Vinatzer BA

Mol. Plant Microbe Interact. 2010 Feb;23(2):198-210

PubMed PMID: 20064063

Abstract

Pseudomonas syringae is best known as a plant pathogen that causes disease by translocating immune-suppressing effector proteins into plant cells through a type III secretion system (T3SS). However, P. syringae strains belonging to a newly described phylogenetic subgroup (group 2c) are missing the canonical P. syringae hrp/hrc cluster coding for a T3SS, flanking effector loci, and any close orthologue of known P. syringae effectors. Nonetheless, P. syringae group 2c strains are common leaf colonizers and grow on some tested plant species to population densities higher than those obtained by other P. syringae strains on nonhost species. Moreover, group 2c strains have genes necessary for the production of phytotoxins, have an ice nucleation gene, and, most interestingly, contain a novel hrp/hrc cluster, which is only distantly related to the canonical P. syringae hrp/hrc cluster. This hrp/hrc cluster appears to encode a functional T3SS although the genes hrpK and hrpS, present in the classical P. syringae hrp/hrc cluster, are missing. The genome sequence of a representative group 2c strain also revealed distant orthologues of the P. syringae effector genes avrE1 and hopM1 and the P. aeruginosa effector genes exoU and exoY. A putative life cycle for group 2c P. syringae is discussed.

AtMetExpress development: a phytochemical atlas of Arabidopsis development

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Matsuda F, Hirai MY, Sasaki E, Akiyama K, Yonekura-Sakakibara K, Provart NJ, Sakurai T, Shimada Y, Saito K

Plant Physiol. 2010 Feb;152(2):566-78

PubMed PMID: 20023150

Abstract

Plants possess many metabolic genes for the production of a wide variety of phytochemicals in a tissue-specific manner. However, the metabolic systems behind the diversity and tissue-dependent regulation still remain unknown due to incomplete characterization of phytochemicals produced in a single plant species. Thus, having a metabolome dataset in addition to the genome and transcriptome information resources would enrich our knowledge of plant secondary metabolism. Here we analyzed phytochemical accumulation during development of the model plant Arabidopsis (Arabidopsis thaliana) using liquid chromatography-mass spectrometry in samples covering many growth stages and organs. We also obtained tandem mass spectrometry spectral tags of many metabolites as a resource for elucidation of metabolite structure. These are part of the AtMetExpress metabolite accumulation atlas. Based on the dataset, we detected 1,589 metabolite signals from which the structures of 167 metabolites were elucidated. The integrated analyses with transcriptome data demonstrated that Arabidopsis produces various phytochemicals in a highly tissue-specific manner, which often accompanies the expression of key biosynthesis-related genes. We also found that a set of biosynthesis-related genes is coordinately expressed among the tissues. These data suggested that the simple mode of regulation, transcript to metabolite, is an origin of the dynamics and diversity of plant secondary metabolism.

Mating-system variation, demographic history and patterns of nucleotide diversity in the Tristylous plant Eichhornia paniculata

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Ness RW, Wright SI, Barrett SC

Genetics 2010 Feb;184(2):381-92

PubMed PMID: 19917767

Abstract

Inbreeding in highly selfing populations reduces effective size and, combined with demographic conditions associated with selfing, this can erode genetic diversity and increase population differentiation. Here we investigate the role that variation in mating patterns and demographic history play in shaping the distribution of nucleotide variation within and among populations of the annual neotropical colonizing plant Eichhornia paniculata, a species with wide variation in selfing rates. We sequenced 10 EST-derived nuclear loci in 225 individuals from 25 populations sampled from much of the geographic range and used coalescent simulations to investigate demographic history. Highly selfing populations exhibited moderate reductions in diversity but there was no significant difference in variation between outcrossing and mixed mating populations. Population size interacted strongly with mating system and explained more of the variation in diversity within populations. Bayesian structure analysis revealed strong regional clustering and selfing populations were highly differentiated on the basis of an analysis of F(st). There was no evidence for a significant loss of within-locus linkage disequilibrium within populations, but regional samples revealed greater breakdown in Brazil than in selfing populations from the Caribbean. Coalescent simulations indicate a moderate bottleneck associated with colonization of the Caribbean from Brazil approximately 125,000 years before the present. Our results suggest that the recent multiple origins of selfing in E. paniculata from diverse outcrossing populations result in higher diversity than expected under long-term equilibrium.

Characterization of the Arabidopsis thaliana exocyst complex gene families by phylogenetic, expression profiling, and subcellular localization studies

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Chong YT, Gidda SK, Sanford C, Parkinson J, Mullen RT, Goring DR

New Phytol. 2010 Jan;185(2):401-19

PubMed PMID: 19895414

Abstract

*The exocyst is a complex of eight proteins (Sec3p, Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, Exo70p and Exo84p) involved in tethering vesicles to the plasma membrane during regulated or polarized secretion. Here, the plant exocyst complex was explored in phylogenetic, expression, and subcellular localization studies. *Evolutionary relationships of predicted exocyst subunits were examined in the complete genomes of Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Physcomitrella patens. Furthermore, detailed expression profiling of the A. thaliana microarray databases was performed and subcellular localization patterns were studied. *Several plant exocyst subunit genes appear to have undergone gene expansion in a common ancestor and subsequent duplication events in independent plant lineages. Expression profiling revealed that the A. thaliana Exo70 gene family exhibits dynamic expression patterns, while the remaining exocyst subunit genes displayed more static profiles. Subcellular localization patterns for A. thaliana exocyst subunits ranged from cytosolic to endosomal compartments (with enrichment in the early endosomes and the trans-Golgi network). Interestingly, two endosomal-localized AtExo70 proteins also recruited other exocyst subunits to these compartments. *Overall subcellular localization patterns were observed that were also found in yeast and animal cells, and this, coupled with the evolutionary relationships, suggests that the exocyst may perform similar conserved functions in plants.

Plant chemical genetics

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McCourt P, Desveaux D

New Phytol. 2010 Jan;185(1):15-26

PubMed PMID: 19825020

Abstract

The success of the genomics revolution to construct a genetic architecture of a variety of model organisms has placed functional biologists under pressure to show what each individual gene does in vivo. Traditionally, this task has fallen on geneticists who systematically perturb gene function and study the consequences. With the advent of large, easily accessible, small-molecule libraries and new methods of chemical synthesis, biologists now have new ways to probe gene function. Often called chemical genetics, this approach involves the screening of compounds that perturb a process of interest. In this scenario, each perturbing chemical is analogous to a specific mutation. Here, we summarize, with specific examples, how chemical genetics is being used in combination with traditional genetics to address problems in plant biology. Because chemical genetics is rooted in genetic analysis, we focus on how chemicals used in combination with genetics can be very powerful in dissecting a process of interest.

Cellular pathways regulating responses to compatible and self-incompatible pollen in Brassica and Arabidopsis stigmas intersect at Exo70A1, a putative component of the exocyst complex

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Samuel MA, Chong YT, Haasen KE, Aldea-Brydges MG, Stone SL, Goring DR

Plant Cell 2009 Sep;21(9):2655-71

PubMed PMID: 19789280

Abstract

In the Brassicaceae, compatible pollen-pistil interactions result in pollen adhesion to the stigma, while pollen grains from unrelated plant species are largely ignored. There can also be an additional layer of recognition to prevent self-fertilization, the self-incompatibility response, whereby self pollen grains are distinguished from nonself pollen grains and rejected. This pathway is activated in the stigma and involves the ARM repeat-containing 1 (ARC1) protein, an E3 ubiquitin ligase. In a screen for ARC1-interacting proteins, we have identified Brassica napus Exo70A1, a putative component of the exocyst complex that is known to regulate polarized secretion. We show through transgenic studies that loss of Exo70A1 in Brassica and Arabidopsis thaliana stigmas leads to the rejection of compatible pollen at the same stage as the self-incompatibility response. A red fluorescent protein:Exo70A1 fusion rescues this stigmatic defect in Arabidopsis and is found to be mobilized to the plasma membrane concomitant with flowers opening. By contrast, increased expression of Exo70A1 in self-incompatible Brassica partially overcomes the self pollen rejection response. Thus, our data show that the Exo70A1 protein functions at the intersection of two cellular pathways, where it is required in the stigma for the acceptance of compatible pollen in both Brassica and Arabidopsis and is negatively regulated by Brassica self-incompatibility.

Bacterial evolution: dynamic genomes and the power of transformation

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Guttman DS

Curr. Biol. 2009 Sep;19(18):R857-9

PubMed PMID: 19788881

Abstract

Virulence and avirulence genes carried on large, unstable pathogenicity islands (PAI) strongly influence the course and fate of host-pathogen interactions. A recent study shows how one such PAI can be rapidly transferred between two closely related bacteria via transformation in vivo, and how this horizontal gene transfer affects the fitness of the recipient strain.

Temporal expression patterns of hormone metabolism genes during imbibition of Arabidopsis thaliana seeds: a comparative study on dormant and non-dormant accessions

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Preston J, Tatematsu K, Kanno Y, Hobo T, Kimura M, Jikumaru Y, Yano R, Kamiya Y, Nambara E

Plant Cell Physiol. 2009 Oct;50(10):1786-800

PubMed PMID: 19713425

Abstract

Seed imbibition is a prerequisite for subsequent dormancy and germination control. Here, we investigated imbibition responses of Arabidopsis seeds by transcriptomic and hormone profile analyses using dormant [Cape Verde Islands (Cvi)] and non-dormant [Columbia (Col)] accessions. Once imbibed, seeds of both accessions swelled most up to 3 h, reflecting water uptake. Microarray analysis showed that in both accessions, seeds imbibed for 15 min, 30 min and 1 h were less active in gene expression than at 3 h. More than 2,000 genes were either up-regulated or down-regulated in seeds imbibed for 3 h. Some genes up-regulated at 3 h were already induced in seeds imbibed for 1 h, suggestive of genome reprogramming early after the onset of imbibition. Imbibition-induced genes in seeds imbibed for 3 h included those up-regulated in both Col and Cvi (common) or unique to either accession (accession specific). Up-regulated genes that were both common and Cvi-specific were over-represented for sugar metabolism and the pentose phosphate pathway, whereas Col-specific genes were over-represented for ribosomal protein genes. Quantification of plant hormones showed that ABA and salicylic acid (SA) contents were higher, but gibberellin A(4) (GA(4)), N(6)-(Delta(2)-isopentenyl)adenine (iP), jasmonic acid (JA), JA-isoleucine (JA-Ile) and IAA were lower in imbibed seeds of Cvi compared with Col. In addition, changes in IAA and JA were initiated before 1 h, whereas ABA and JA-Ile declined 3 h after the onset of imbibition. An increase in GA(4) and iP appeared to be correlated temporally with the initiation of secondary water uptake, which marks the completion of germination.

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

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Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ

Plant Cell Environ. 2009 Dec;32(12):1633-51

PubMed PMID: 19712066

Abstract

Gene co-expression analysis has emerged in the past 5 years as a powerful tool for gene function prediction. In essence, co-expression analysis asks the question ‘what are the genes that are co-expressed, that is, those that show similar expression profiles across many experiments, with my gene of interest?’. Genes that are highly co-expressed may be involved in the biological process or processes of the query gene. This review describes the tools that are available for performing such analyses, how each of these perform, and also discusses statistical issues including how normalization of gene expression data can influence co-expression results, calculation of co-expression scores and P values, and the influence of data sets used for co-expression analysis. Finally, examples from the literature will be presented, wherein co-expression has been used to corroborate and discover various aspects of plant biology.

Cyclic nucleotide gated channels and ca-mediated signal transduction during plant innate immune response to pathogens

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Ma W, Yoshioka K, Berkowitz GA

Plant Signal Behav 2007 Nov;2(6):548-50

PubMed PMID: 19704555

Abstract

Transitory perturbations in the level of cytosolic Ca(2+) are well known to be involved in numerous cell signaling pathways in both plant and animal systems. However, not much is known at present about the molecular identity of plant plasma membrane Ca(2+) conducting ion channels or their specific roles in signal transduction cascades. A recent study employing genetic approaches as well as patch clamp electrophysiological analysis of channel currents has provided the first such direct evidence linking a specific gene product with inward Ca(2+) currents across the plant cell membrane. This work identified Ca(2+) permeation through (Arabidopsis) cyclic nucleotide gated channel isoform 2 (CNGC2) as contributing to the plant innate immunity signaling cascade initiated upon perception of a pathogen. Here, we expand on the implications of CNGC2 mediated cytosolic Ca(2+) elevations associated with plant cell response to pathogen recognition, and propose some additional steps that may be involved in the innate immunity signal cascade.