Publications

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

Posted on by biota in Publications

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

Posted on by biota in Publications

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

Posted on by biota in Publications

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

Posted on by biota in Publications

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

Posted on by biota in Publications

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

Posted on by biota in Publications

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

Posted on by biota in Publications

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.

Vascular system is a node of systemic stress responses: Competence of the cell to synthesize abscisic acid and its responsiveness to external cues

Posted on by biota in Publications

Endo A, Koshiba T, Kamiya Y, Nambara E

Plant Signal Behav 2008 Dec;3(12):1138-40

PubMed PMID: 19704460

Abstract

Activation of abscisic acid (ABA) biosynthesis is a trigger to elicit ABA-mediated biological events. We recently reported that drought-induced ABA biosynthesis occurs predominantly in vascular parenchyma cells. This work also showed that a particular set of drought inducible gene expressions initiated in the vascular system. The spatial constraint of ABA biosynthesis is supposed to be critical for directing systemic stress responses. Cellular competence to synthesize ABA and its responsiveness to developmental and environmental signals is discussed.

Forward and reverse genetics to identify genes involved in the age-related resistance response in Arabidopsis thaliana

Posted on by biota in Publications

Carviel JL, Al-Daoud F, Neumann M, Mohammad A, Provart NJ, Moeder W, Yoshioka K, Cameron RK

Mol. Plant Pathol. 2009 Sep;10(5):621-34

PubMed PMID: 19694953

Abstract

SUMMARY Age-related resistance (ARR) occurs in numerous plant species, often resulting in increased disease resistance as plants mature. ARR in Arabidopsis to Pseudomonas syringae pv. tomato is associated with intercellular salicylic acid (SA) accumulation and the transition to flowering. Forward and reverse genetic screens were performed to identify genes required for ARR and to investigate the mechanism of the ARR response. Infiltration of SA into the intercellular space of the ARR-defective mutant iap1-1 (important for the ARR pathway) partially restored ARR function. Inter- and intracellular SA accumulation was reduced in the mutant iap1-1 compared with the wild-type, and the SA regulatory gene EDS1 was also required for ARR. Combining microarray analysis with reverse genetics using T-DNA insertion lines, four additional ARR genes were identified as contributing to ARR: two plant-specific transcription factors of the NAC family [ANAC055 (At3g15500) and ANAC092 (At5g39610)], a UDP-glucose glucosyltransferase [UGT85A1 (At1g22400)] and a cytidine deaminase [CDA1 (At2g19570)]. These four genes and IAP1 are also required for ARR to Hyaloperonospora parasitica. IAP1 encodes a key component of ARR that acts upstream of SA accumulation and possibly downstream of UGT85A1, CDA1 and the two NAC transcription factors (ANAC055, ANAC092).

Genotype and time of day shape the Populus drought response

Posted on by biota in Publications

Wilkins O, Waldron L, Nahal H, Provart NJ, Campbell MM

Plant J. 2009 Nov;60(4):703-15

PubMed PMID: 19682285

Abstract

As exposure to episodic drought can impinge significantly on forest health and the establishment of productive tree plantations, there is great interest in understanding the mechanisms of drought response in trees. The ecologically dominant and economically important genus Populus, with its sequenced genome, provides an ideal opportunity to examine transcriptome level changes in trees in response to a drought stimulus. The transcriptome level drought response of two commercially important Populus clones (P. deltoides x P. nigra, DN34, and P. nigra x P. maximowiczii, NM6) was characterized over a diurnal period using a 4 x 2 x 2 complete randomized factorial anova experimental design (four time points, two genotypes and two treatment conditions), using Affymetrix Poplar GeneChip microarrays. Notably, the specific genes that exhibited changes in transcript abundance in response to drought differed between the genotypes and/or the time of day that they exhibited their greatest differences. This study emphasizes the fact that it is not possible to draw simple, generalized conclusions about the drought response of the genus Populus on the basis of one species, nor on the basis of results collected at a single time point. The data derived from our studies provide insights into the variety of genetic mechanisms underpinning the Populus drought response, and provide candidates for future experiments aimed at understanding this response across this economically and ecologically important genus.