Category: Publications

Wilkins O, Nahal H, Foong J, Provart NJ, Campbell MM

Plant Physiol. 2009 Feb;149(2):981-93

PubMed PMID: 19091872

Abstract

The R2R3-MYB proteins comprise one of the largest families of transcription factors in plants. R2R3-MYB family members regulate plant-specific processes, such as the elaboration of specialized cell types, including xylem, guard cells, trichomes, and root hairs, and the biosynthesis of specialized branches of metabolism, including phenylpropanoid biosynthesis. As such, R2R3-MYB family members are hypothesized to contribute to the emergence of evolutionary innovations that have arisen in specific plant lineages. As a first step in determining the role played by R2R3-MYB family members in the emergence of lineage-specific innovations in the genus Populus, the entire Populus trichocarpa R2R3-MYB family was characterized. The Populus R2R3-MYB complement is much larger than that found in other angiosperms with fully sequenced genomes. Phylogenetic analyses, together with chromosome placement, showed that the expansion of the Populus R2R3-MYB family was not only attributable to whole genome duplication but also involved selective expansion of specific R2R3-MYB clades. Expansion of the Populus R2R3-MYB family prominently involved members with expression patterns that suggested a role in specific components of Populus life history, including wood formation and reproductive development. An expandable compendium of microarray-based expression data (PopGenExpress) and associated Web-based tools were developed to better enable within- and between-species comparisons of Populus R2R3-MYB gene expression. This resource, which includes intuitive graphic visualization of gene expression data across multiple tissues, organs, and treatments, is freely available to, and expandable by, scientists wishing to better understand the genome biology of Populus, an ecologically dominant and economically important forest tree genus.

McKay JK, Stinchcombe JR

Evolution 2008 Dec;62(12):2953-7

PubMed PMID: 19055681

Okamoto M, Tanaka Y, Abrams SR, Kamiya Y, Seki M, Nambara E

Plant Physiol. 2009 Feb;149(2):825-34

PubMed PMID: 19036833

Abstract

Levels of endogenous abscisic acid (ABA) are changed dynamically in response to environmental conditions. The ABA 8′-hydroxylase is a key enzyme in ABA catabolism and is encoded by CYP707A genes. In this study, we examined physiological roles of Arabidopsis (Arabidopsis thaliana) CYP707As in the plant’s response to changes in humidity. The cyp707a1 and cyp707a3 mutants displayed lower stomatal conductance under turgid conditions (relative humidity 60%) than the wild type. When wild-type plants were transferred to high-humidity conditions (relative humidity 90%), CYP707A1 and CYP707A3 transcript levels increased, followed by the reduction of ABA levels. The cyp707a3 mutant exhibited high ABA levels even after transferring to high-humidity conditions, whereas, under similar conditions, the cyp707a1 mutant exhibited low ABA levels comparable to the wild type. Analysis of spatial expression patterns by using transgenic plants harboring a promoterbeta-glucuronidase gene indicated that high-humidity-induced expression of CYP707A1 and CYP707A3 occurred primarily in guard cells and vascular tissues, respectively. Furthermore, stomatal closure of the cyp707a1 mutant, but not cyp707a3 mutant, was ABA hypersensitive when epidermal peel was treated with exogenous ABA, suggesting that CYP707A1 is essential for ABA catabolism inside the guard cells. These results implicate that CYP707A3 reduces the amount of mobile ABA in vascular tissues in response to high humidity, whereas CYP707A1 inactivates local ABA pools inside the guard cells. Taken together, ABA catabolism in both vascular tissues and guard cells participates in the systemic ABA action that controls stomatal movement in response to high humidity.

Tropepe V

Cell Stem Cell 2007 Nov;1(5):481-3

PubMed PMID: 18938741

Samis KE, Heath KD, Stinchcombe JR

Evolution 2008 Dec;62(12):2971-83

PubMed PMID: 18752603

Abstract

Using seasonal cues to time reproduction appropriately is crucial for many organisms. Plants in particular often use photoperiod to signal the time to transition to flowering. Because seasonality varies latitudinally, adaptation to local climate is expected to result in corresponding clines in photoperiod-related traits. By experimentally manipulating photoperiod cues and measuring the flowering responses and photoperiod plasticity of 138 Eurasian accessions of Arabidopsis thaliana, we detected strong longitudinal but not latitudinal clines in flowering responses. The presence of longitudinal clines suggests that critical photoperiod cues vary among populations occurring at similar latitudes. Haplotypes at PHYC, a locus hypothesized to play a role in adaptation to light cues, were also longitudinally differentiated. Controlling for neutral population structure revealed that PHYC haplotype influenced flowering time; however, the distribution of PHYC haplotypes occurred in the opposite direction to the phenotypic cline, suggesting that loci other than PHYC are responsible for the longitudinal pattern in photoperiod response. Our results provide previously missing empirical support for the importance of PHYC in mediating photoperiod sensitivity in natural populations of A. thaliana. However, they also suggest that other loci and epistatic interactions likely play a role in the determination of flowering time and that the environmental factors influencing photoperiod in plants vary longitudinally as well as latitudinally.

Singh S, Stavrinides J, Christendat D, Guttman DS

Mol. Biol. Evol. 2008 Oct;25(10):2221-32

PubMed PMID: 18669580

Abstract

The shikimate dehydrogenases (SDH) represent a widely distributed enzyme family with an essential role in secondary metabolism. This superfamily had been previously subdivided into 4 enzyme groups (AroE, YdiB, SdhL, and RifI), which show clear biochemical and functional differences ranging from amino acid biosynthesis to antibiotic production. Despite the importance of this group, little is known about how such essential enzymatic functions can evolve and diversify. We dissected the enzyme superfamily with a phylogenomic analysis of approximately 250 fully sequenced genomes, making use of previously characterized representatives from each enzyme class, and the key substrate-binding residues known to distinguish substrate specificity. We identified 5 major evolutionary and functional SDH subgroups and several other potentially unique functional classes within this complex enzyme family and then validated the functional distinctiveness of each group by characterizing the 5 SDH homologs found in Pseudomonas putida KT2440 biochemically. We identified an entirely novel functionally distinct subgroup, which we designated Ael1 (AroE-like1) and also delineated a new group of shikimate/quinate dehydrogenases (YdiB2), which is phylogenetically distinct from the previously described Escherichia coli YdiB. The combination of biochemical, phylogenetic, and genomic approaches has revealed the broad extent to which the SDH enzyme superfamily has diversified. Five functional groups were validated with the potential for at least 5 additional subgroups. Our analysis also identified a new SDH functional group, which appears to have evolved recently from an ancestral AroE, illustrating a very prominent role of horizontal transmission and neofunctionalizaton in the evolutionary and functional diversification of this enzyme family.

Baxter J, Moeder W, Urquhart W, Shahinas D, Chin K, Christendat D, Kang HG, Angelova M, Kato N, Yoshioka K

Plant J. 2008 Nov;56(3):457-69

PubMed PMID: 18643993

Abstract

We used the chimeric Arabidopsis cyclic nucleotide-gated ion channel AtCNGC11/12 to conduct a structure-function study of plant cyclic nucleotide-gated ion channels (CNGCs). AtCNGC11/12 induces multiple pathogen resistance responses in the Arabidopsis mutant constitutive expresser of PR genes 22 (cpr22). A genetic screen for mutants that suppress cpr22-conferred phenotypes identified an intragenic mutant, #73, which has a glutamate to lysine substitution (E519K) at the beginning of the eighth beta-sheet of the cyclic nucleotide-binding domain in AtCNGC11/12. The #73 mutant is morphologically identical to wild-type plants and has lost cpr22-related phenotypes including spontaneous cell death and enhanced pathogen resistance. Heterologous expression analysis using a K(+)-uptake-deficient yeast mutant revealed that this Glu519 is important for AtCNGC11/12 channel function, proving that the occurrence of cpr22 phenotypes requires active channel function of AtCNGC11/12. Additionally, Glu519 was also found to be important for the function of the wild-type channel AtCNGC12. Computational structural modeling and in vitro cAMP-binding assays suggest that Glu519 is a key residue for the structural stability of AtCNGCs and contributes to the interaction of the cyclic nucleotide-binding domain and the C-linker domain, rather than the binding of cAMP. Furthermore, a mutation in the alpha-subunit of the human cone receptor CNGA3 that causes total color blindness aligned well to the position of Glu519 in AtCNGC11/12. This suggests that AtCNGC11/12 suppressors could be a useful tool for discovering important residues not only for plant CNGCs but also for CNGCs in general.

Stinchcombe JR, Agrawal AF, Hohenlohe PA, Arnold SJ, Blows MW

Evolution 2008 Sep;62(9):2435-40

PubMed PMID: 18616573

Abstract

The use of regression analysis has been instrumental in allowing evolutionary biologists to estimate the strength and mode of natural selection. Although directional and correlational selection gradients are equal to their corresponding regression coefficients, quadratic regression coefficients must be doubled to estimate stabilizing/disruptive selection gradients. Based on a sample of 33 papers published in Evolution between 2002 and 2007, at least 78% of papers have not doubled quadratic regression coefficients, leading to an appreciable underestimate of the strength of stabilizing and disruptive selection. Proper treatment of quadratic regression coefficients is necessary for estimation of fitness surfaces and contour plots, canonical analysis of the gamma matrix, and modeling the evolution of populations on an adaptive landscape.

Lee S, Cheran E, Brudno M

Bioinformatics 2008 Jul;24(13):i59-67

PubMed PMID: 18586745

Abstract

MOTIVATION: Recently, structural genomic variants have come to the forefront as a significant source of variation in the human population, but the identification of these variants in a large genome remains a challenge. The complete sequencing of a human individual is prohibitive at current costs, while current polymorphism detection technologies, such as SNP arrays, are not able to identify many of the large scale events. One of the most promising methods to detect such variants is the computational mapping of clone-end sequences to a reference genome.

RESULTS: Here, we present a probabilistic framework for the identification of structural variants using clone-end sequencing. Unlike previous methods, our approach does not rely on an a priori determined mapping of all reads to the reference. Instead, we build a framework for finding the most probable assignment of sequenced clones to potential structural variants based on the other clones. We compare our predictions with the structural variants identified in three previous studies. While there is a statistically significant correlation between the predictions, we also find a significant number of previously uncharacterized structural variants. Furthermore, we identify a number of putative cross-chromosomal events, primarily located proximally to the centromeres of the chromosomes.

AVAILABILITY: Our dataset, results and source code are available at http://compbio.cs.toronto.edu/structvar/.

Ma W, Guttman DS

Curr. Opin. Plant Biol. 2008 Aug;11(4):412-9

PubMed PMID: 18585954

Abstract

Coevolutionary interactions between plants and their bacterial and eukaryotic pathogens are mediated by virulence effectors. These effectors face the daunting challenge of carrying out virulence functions, while also potentially exposing the pathogen to host defense systems. Very strong selective pressures are imposed by these competing roles, and the subsequent genetic changes leave their footprints in the extant allelic variation. This review examines the evolutionary processes that drive pathogen-host interactions as revealed by the genetic signatures left in virulence effectors, and speculate on the different pressures imposed on bacterial versus eukaryotic pathogens. We find numerous instances of positive selection for new allelic forms, and diversifying selection for genetic variability, which results in altered host-pathogen interactions. We also describe how the genetic structure of both bacterial and eukaryotic virulence effectors may contribute to their rapid generation and turnover.