Category: Publications

Negative regulation of CCaMK is essential for symbiotic infection

Posted on by biota in Publications

Liao J, Singh S, Hossain MS, Andersen SU, Ross L, Bonetta D, Zhou Y, Sato S, Tabata S, Stougaard J, Szczyglowski K, Parniske M

Plant J. 2012 Nov;72(4):572-84

PubMed PMID: 22775286

Abstract

One of the earliest responses of legumes to symbiotic signalling is oscillation of the calcium concentration in the nucleoplasm of root epidermal cells. Integration and decoding of the calcium-spiking signal involve a calcium- and calmodulin-dependent protein kinase (CCaMK) and its phosphorylation substrates, such as CYCLOPS. Here we describe the Lotus japonicus ccamk-14 mutant that originated from a har1-1 suppressor screen. The ccamk-14 mutation causes a serine to asparagine substitution at position 337 located within the calmodulin binding site, which we determined to be an in vitro phosphorylation site in CCaMK. We show that ccamk-14 exerts cell-specific effects on symbiosis. The mutant is characterized by an increased frequency of epidermal infections and significantly compromised cortical infections by Mesorhizobium loti and also the arbuscular mycorrhiza fungus Rhizophagus irregularis. The S337 residue is conserved across angiosperm CCaMKs, and testing discrete substitutions at this site showed that it participates in a negative regulation of CCaMK activity, which is required for the cell-type-specific integration of symbiotic signalling.

Drought induces alterations in the stomatal development program in Populus

Posted on by biota in Publications

Hamanishi ET, Thomas BR, Campbell MM

J. Exp. Bot. 2012 Aug;63(13):4959-71

PubMed PMID: 22760471

Abstract

Much is known about the physiological control of stomatal aperture as a means by which plants adjust to water availability. By contrast, the role played by the modulation of stomatal development to limit water loss has received much less attention. The control of stomatal development in response to water deprivation in the genus Populus is explored here. Drought induced declines in stomatal conductance as well as an alteration in stomatal development in two genotypes of Populus balsamifera. Leaves that developed under water-deficit conditions had lower stomatal indices than leaves that developed under well-watered conditions. Transcript abundance of genes that could hypothetically underpin drought-responsive changes in stomatal development was examined, in two genotypes, across six time points, under two conditions, well-watered and with water deficit. Populus homologues of STOMAGEN, ERECTA (ER), STOMATA DENSITY AND DISTRIBUTION 1 (SDD1), and FAMA had variable transcript abundance patterns congruent with their role in the modulation of stomatal development in response to drought. Conversely, there was no significant variation in transcript abundance between genotypes or treatments for the Populus homologues of YODA (YDA) and TOO MANY MOUTHS (TMM). The findings highlight the role that could be played by stomatal development during leaf expansion as a longer term means by which to limit water loss from leaves. Moreover, the results point to the key roles played by the regulation of the homologues of STOMAGEN, ER, SDD1, and FAMA in the control of this response in poplar.

AtMYB61, an R2R3-MYB transcription factor, functions as a pleiotropic regulator via a small gene network

Posted on by biota in Publications

Romano JM, Dubos C, Prouse MB, Wilkins O, Hong H, Poole M, Kang KY, Li E, Douglas CJ, Western TL, Mansfield SD, Campbell MM

New Phytol. 2012 Sep;195(4):774-86

PubMed PMID: 22708996

Abstract

Throughout their lifetimes, plants must coordinate the regulation of various facets of growth and development. Previous evidence has suggested that the Arabidopsis thaliana R2R3-MYB, AtMYB61, might function as a coordinate regulator of multiple aspects of plant resource allocation. Using a combination of cell biology, transcriptome analysis and biochemistry, in conjunction with gain-of-function and loss-of-function genetics, the role of AtMYB61 in conditioning resource allocation throughout the plant life cycle was explored. In keeping with its role as a regulator of resource allocation, AtMYB61 is expressed in sink tissues, notably xylem, roots and developing seeds. Loss of AtMYB61 function decreases xylem formation, induces qualitative changes in xylem cell structure and decreases lateral root formation; in contrast, gain of AtMYB61 function has the opposite effect on these traits. AtMYB61 coordinates a small network of downstream target genes, which contain a motif in their upstream regulatory regions that is bound by AtMYB61, and AtMYB61 activates transcription from this same motif. Loss-of-function analysis supports the hypothesis that AtMYB61 targets play roles in shaping subsets of AtMYB61-related phenotypes. Taken together, these findings suggest that AtMYB61 links the transcriptional control of multiple aspects of plant resource allocation.

Coevolutionary genetic variation in the legume-rhizobium transcriptome

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Heath KD, Burke PV, Stinchcombe JR

Mol. Ecol. 2012 Oct;21(19):4735-47

PubMed PMID: 22672103

Abstract

Coevolutionary change requires reciprocal selection between interacting species, where the partner genotypes that are favoured in one species depend on the genetic composition of the interacting species. Coevolutionary genetic variation is manifested as genotype × genotype (G × G) interactions for fitness in interspecific interactions. Although quantitative genetic approaches have revealed abundant evidence for G × G interactions in symbioses, the molecular basis of this variation remains unclear. Here we study the molecular basis of G × G interactions in a model legume-rhizobium mutualism using gene expression microarrays. We find that, like quantitative traits such as fitness, variation in the symbiotic transcriptome may be partitioned into additive and interactive genetic components. Our results suggest that plant genetic variation had the largest influence on nodule gene expression and that plant genotype and the plant genotype × rhizobium genotype interaction determine global shifts in rhizobium gene expression that in turn feedback to influence plant fitness benefits. Moreover, the transcriptomic variation we uncover implicates regulatory changes in both species as drivers of symbiotic gene expression variation. Our study is the first to partition genetic variation in a symbiotic transcriptome and illuminates potential molecular routes of coevolutionary change.

BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species

Posted on by biota in Publications

Patel RV, Nahal HK, Breit R, Provart NJ

Plant J. 2012 Sep;71(6):1038-50

PubMed PMID: 22607031

Abstract

Large numbers of sequences are now readily available for many plant species, allowing easy identification of homologous genes. However, orthologous gene identification across multiple species is made difficult by evolutionary events such as whole-genome or segmental duplications. Several developmental atlases of gene expression have been produced in the past couple of years, and it may be possible to use these transcript abundance data to refine ortholog predictions. In this study, clusters of homologous genes between seven plant species – Arabidopsis, soybean, Medicago truncatula, poplar, barley, maize and rice – were identified. Following this, a pipeline to rank homologs within gene clusters by both sequence and expression profile similarity was devised by determining equivalent tissues between species, with the best expression profile match being termed the ‘expressolog’. Five electronic fluorescent pictograph (eFP) browsers were produced as part of this effort, to aid in visualization of gene expression data and to complement existing eFP browsers at the Bio-Array Resource (BAR). Within the eFP browser framework, these expression profile similarity rankings were incorporated into an Expressolog Tree Viewer to allow cross-species homolog browsing by both sequence and expression pattern similarity. Global analyses showed that orthologs with the highest sequence similarity do not necessarily exhibit the highest expression pattern similarity. Other orthologs may show different expression patterns, indicating that such genes may require re-annotation or more specific annotation. Ultimately, it is envisaged that this pipeline will aid in improvement of the functional annotation of genes and translational plant research.

Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage

Posted on by biota in Publications

Mazzaglia A, Studholme DJ, Taratufolo MC, Cai R, Almeida NF, Goodman T, Guttman DS, Vinatzer BA, Balestra GM

PLoS ONE 2012;7(5):e36518

PubMed PMID: 22590555

Abstract

Intercontinental spread of emerging plant diseases is one of the most serious threats to world agriculture. One emerging disease is bacterial canker of kiwi fruit (Actinidia deliciosa and A. chinensis) caused by Pseudomonas syringae pv. actinidiae (PSA). The disease first occurred in China and Japan in the 1980s and in Korea and Italy in the 1990s. A more severe form of the disease broke out in Italy in 2008 and in additional countries in 2010 and 2011 threatening the viability of the global kiwi fruit industry. To start investigating the source and routes of international transmission of PSA, genomes of strains from China (the country of origin of the genus Actinidia), Japan, Korea, Italy and Portugal have been sequenced. Strains from China, Italy, and Portugal have been found to belong to the same clonal lineage with only 6 single nucleotide polymorphisms (SNPs) in 3,453,192 bp and one genomic island distinguishing the Chinese strains from the European strains. Not more than two SNPs distinguish each of the Italian and Portuguese strains from each other. The Japanese and Korean strains belong to a separate genetic lineage as previously reported. Analysis of additional European isolates and of New Zealand isolates exploiting genome-derived markers showed that these strains belong to the same lineage as the Italian and Chinese strains. Interestingly, the analyzed New Zealand strains are identical to European strains at the tested SNP loci but test positive for the genomic island present in the sequenced Chinese strains and negative for the genomic island present in the European strains. Results are interpreted in regard to the possible direction of movement of the pathogen between countries and suggest a possible Chinese origin of the European and New Zealand outbreaks.

A chemical genetics method to uncover small molecules for dissecting the mechanism of ABA responses in Arabidopsis seed germination

Posted on by biota in Publications

Zhao Y

Methods Mol. Biol. 2012;876:107-16

PubMed PMID: 22576089

Abstract

Functional redundancy widely exists in genes encoding receptors and signaling components of plant hormones, particularly the stress hormone abscisic acid (ABA). The redundancy hinders the use of conventional genetic approach to dissecting molecular mechanisms for ABA signal perception and transduction. Chemical genetics approach, in which bioactive small molecules are used to perturb the function of gene products encoded by functionally redundant genes, provides an excellent alternative strategy to investigate ABA signaling. This approach led to the discovery of ABA receptor family, PYR/PYL/RCAR (Zhao et al., Nat Chem Biol 3:716-721, 2007; Park et al., Science 324:1068-1071, 2009). A forward chemical genetics screen uncovered an ABA agonist, pyrabactin, which provides a critical small-molecule probe to the identification of the ABA receptor family and the dissection of its downstream signaling.

Genetic architecture and adaptive significance of the selfing syndrome in Capsella

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Slotte T, Hazzouri KM, Stern D, Andolfatto P, Wright SI

Evolution 2012 May;66(5):1360-74

PubMed PMID: 22519777

Abstract

The transition from outcrossing to predominant self-fertilization is one of the most common evolutionary transitions in flowering plants. This shift is often accompanied by a suite of changes in floral and reproductive characters termed the selfing syndrome. Here, we characterize the genetic architecture and evolutionary forces underlying evolution of the selfing syndrome in Capsella rubella following its recent divergence from the outcrossing ancestor C. grandiflora. We conduct genotyping by multiplexed shotgun sequencing and map floral and reproductive traits in a large (N= 550) F2 population. Our results suggest that in contrast to previous studies of the selfing syndrome, changes at a few loci, some with major effects, have shaped the evolution of the selfing syndrome in Capsella. The directionality of QTL effects, as well as population genetic patterns of polymorphism and divergence at 318 loci, is consistent with a history of directional selection on the selfing syndrome. Our study is an important step toward characterizing the genetic basis and evolutionary forces underlying the evolution of the selfing syndrome in a genetically accessible model system.

Increase in dopaminergic, but not serotoninergic, receptors in T-cells as a marker for schizophrenia severity

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Brito-Melo GE, Nicolato R, de Oliveira AC, Menezes GB, Lélis FJ, Avelar RS, Sá J, Bauer ME, Souza BR, Teixeira AL, Reis HJ

J Psychiatr Res 2012 Jun;46(6):738-42

PubMed PMID: 22497994

Abstract

Schizophrenia is characterized by a slow deteriorating mental illness. Although the pathophysiology mechanisms are not fully understood, different studies have suggested a role for the immune system in the pathogenesis of schizophrenia. To date, an altered expression or signaling of neurotransmitters receptors is observed in immune cells during psychiatric disorders. In the present study, we investigated the expression of different serotonin and dopamine receptors in T-cells of schizophrenic and control patients. We used flow cytometry to determine the pattern of expression of dopamine (D2 and D4) and serotonine receptors (SR1A, SR1C, SR2A, SR2B), as well as serotonin transporter (ST), in T-cell subsets (CD4 and CD8). Expression of serotonin receptors and ST in T-cells of schizophrenic patients were not different from controls. However, the percentages of CD4+D4+ and CD8+D4+ were increased in schizophrenic patients as compared to controls. In addition, increased percentages of CD8+D2+ cells were also observed in schizophrenic patients, albeit this population revealed lower CD4+D2+ cells in comparison to controls. Interestingly, a relationship between clinical symptoms and immunological parameters was also observed. We showed that the Brief Psychiatric Rating Scale (BPRS), the Positive and Negative Syndrome Scale (PANSS) and the Abnormal Involuntary Movement Scale (AIMS) were positively related to CD8+D2+ cells, though AIMS was inversely related to CD4+D4+ cells. In conclusion, the alteration in the pattern of cell population and molecules expressed by them might serve as a promising biomarker for diagnosis of schizophrenia.

Pulmonary bacterial communities in surgically resected noncystic fibrosis bronchiectasis lungs are similar to those in cystic fibrosis

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Maughan H, Cunningham KS, Wang PW, Zhang Y, Cypel M, Chaparro C, Tullis DE, Waddell TK, Keshavjee S, Liu M, Guttman DS, Hwang DM

Pulm Med 2012;2012:746358

PubMed PMID: 22448327

Abstract

Background. Recurrent bacterial infections play a key role in the pathogenesis of bronchiectasis, but conventional microbiologic methods may fail to identify pathogens in many cases. We characterized and compared the pulmonary bacterial communities of cystic fibrosis (CF) and non-CF bronchiectasis patients using a culture-independent molecular approach. Methods. Bacterial 16S rRNA gene libraries were constructed from lung tissue of 10 non-CF bronchiectasis and 21 CF patients, followed by DNA sequencing of isolates from each library. Community characteristics were analyzed and compared between the two groups. Results. A wide range of bacterial diversity was detected in both groups, with between 1 and 21 bacterial taxa found in each patient. Pseudomonas was the most common genus in both groups, comprising 49% of sequences detected and dominating numerically in 13 patients. Although Pseudomonas appeared to be dominant more often in CF patients than in non-CF patients, analysis of entire bacterial communities did not identify significant differences between these two groups. Conclusions. Our data indicate significant diversity in the pulmonary bacterial community of both CF and non-CF bronchiectasis patients and suggest that this community is similar in surgically resected lungs of CF and non-CF bronchiectasis patients.