Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes

<p>Abstract</p> <p>Background</p> <p>Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from other <it>Populus </it>species.</p> <p>Results</p> <p>Using a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought.</p> <p>Conclusions</p> <p>In poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought-sensitive poplar genotype.</p

COORDINATION DES SOINS LIAISON MEDECINE HOSPITALIERE-MEDECINE DE VILLE LE RETOUR D'HOSPITALISATION

LILLE2-BU Santé-Recherche (593502101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Intrafamilial variability in the phenotypic expression of adenylosuccinate lyase deficiency: a report on three patients.

We report on the striking variable expression of adenylosuccinate lyase (ADSL) deficiency in three patients belonging to a family which originates from Portugal. ADSL deficiency is a rare autosomal recessive disorder of the de novo purine synthesis which results in accumulation of succinylpurines in body fluids. As a result, patients may have variable combinations of psychomotor retardation and/or regression, seizures, autistic features and cerebellar vermis hypoplasia. However, intrafamilial variable expression of the phenotype has not been documented to date in this disease and is not commonly observed in metabolic disorders. Here, while the proband had marked psychomotor regression and progressive cerebellar vermis atrophy, the other two affected patients presented mainly autistic features. Mutation analysis of the ADSL gene revealed the presence of a homozygous R426H mutation in this family. Finally, although ADSL deficiency is a rare disorder, this diagnosis should be considered and assessed using a simple urinary screening method for the presence of succinylpurines in any patient with mental retardation of unexplained origin

Homologous DNA exchanges in humans can be explained by the yeast double-strand break repair model : a study of 17p11.2 rearrangements associated with CMT1A and HNPP

Rearrangements in 17p11.2, responsible for the 1.5 Mb duplications and deletions associated, respectively, with autosomal dominant Charcot-Marie-Tooth type 1A disease (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP) are a suitable model for studying human recombination. Rearrangements in 17p11.2 are caused by unequal crossing-over between two homologous 24 kb sequences, the CMT1A-REPs, that flank the disease locus and occur in most cases within a 1.7 kb hotspot. We sequenced this hotspot in 28 de novo patients (25 CMT1A and three HNPP), in order to localize precisely, at the DNA sequence level, the crossing-overs. We show that some chimeric CMT1A-REPs in de novo patients (10/28) present conversion of DNA segments associated with the crossing-over. These rearrangements can be explained by the double-strand break (DSB) repair model described in yeast. Fine mapping of the de novo rearrangements provided evidence that the successive steps of this model, heteroduplex DNA formation, mismatch correction and gene conversion, occurred in patients. Furthermore, the model explains 17p11.2 recombinations between chromosome homologues as well as between sister chromatids. In addition, defective mismatch repair of the heteroduplex DNA, observed in two patients, resulted in two heterozygous chimeric CMT1A-REPs which can be explained, as in yeast, by post-meiotic segregation. This work supports the hypothesis that the DSB repair model of DNA exchange may apply universally from yeasts to humans.8 page(s

Exploring the impact of ZmMYB31 overexpression in maize under contrasted soil water regimes

International audienceWater deficit directly impacts the ability of plants to intercept and convert light into biomass. Because leaf growth is one of the first processes affected by water deficit, many physiological studies concentrated in short-term responses and associated mechanisms. They demonstrated the roles of cellular and metabolic processes such as changes in cell turgor, hydraulic conductance and cell wall plasticity. However, our understanding of how water deficit impacts the cell wall biosynthesis and dynamics is still fragmentary. Here, we report that ZmMYB31, a subgroup 4 R2R3-MYB transcription factor that acts as a repressor of the lignin pathway in Arabidopsis [1-2], is induced by water deficit in the leaf growing zone and colocates with QTLs for lignin content and growth responses to water deficit in maize. To assess the role of ZmMYB31 in maize upon water limitation, we generated maize transgenic lines overexpressing ZmMYB31. We showed, in preliminary experiments, that the leaf growing zone of T1 ZmMYB31 overexpression plants had a higher content of β-O-4-linked lignin units than that of wild-type sister plants grown in the greenhouse under well-watered conditions. A comparative analysis by quantitative RT-PCR revealed significant differences for six lignin biosynthetic genes in the leaf growing zone of T1 ZmMYB31 overexpression plants compared with that of wild-type plants, consistent with the observed changes in -O-4-linked lignin unit content. To obtain additional clues with regard to ZmMYB31 function in maize under water-limited conditions, we are currently combining RNA-seq analysis and shotgun proteomics of the leaf growing zone of homozygous ZmMYB31 overexpression plants and their wild-type siblings grown in the PhenoArch platform under well-watered and moderate water deficit conditions. Integrative statistical approaches shall allow us to infer a ZmMYB31-regulated network and identify variables underpinning maize responses to water deficit

Exploring the impact of ZmMYB31 overexpression in maize under contrasted soil water regimes

International audienceWater deficit directly impacts the ability of plants to intercept and convert light into biomass. Because leaf growth is one of the first processes affected by water deficit, many physiological studies concentrated in short-term responses and associated mechanisms. They demonstrated the roles of cellular and metabolic processes such as changes in cell turgor, hydraulic conductance and cell wall plasticity. However, our understanding of how water deficit impacts the cell wall biosynthesis and dynamics is still fragmentary. Here, we report that ZmMYB31, a subgroup 4 R2R3-MYB transcription factor that acts as a repressor of the lignin pathway in Arabidopsis [1-2], is induced by water deficit in the leaf growing zone and colocates with QTLs for lignin content and growth responses to water deficit in maize. To assess the role of ZmMYB31 in maize upon water limitation, we generated maize transgenic lines overexpressing ZmMYB31. We showed, in preliminary experiments, that the leaf growing zone of T1 ZmMYB31 overexpression plants had a higher content of β-O-4-linked lignin units than that of wild-type sister plants grown in the greenhouse under well-watered conditions. A comparative analysis by quantitative RT-PCR revealed significant differences for six lignin biosynthetic genes in the leaf growing zone of T1 ZmMYB31 overexpression plants compared with that of wild-type plants, consistent with the observed changes in -O-4-linked lignin unit content. To obtain additional clues with regard to ZmMYB31 function in maize under water-limited conditions, we are currently combining RNA-seq analysis and shotgun proteomics of the leaf growing zone of homozygous ZmMYB31 overexpression plants and their wild-type siblings grown in the PhenoArch platform under well-watered and moderate water deficit conditions. Integrative statistical approaches shall allow us to infer a ZmMYB31-regulated network and identify variables underpinning maize responses to water deficit

MYB31 triggers water stress memory responses in maize

International audienceWater deficit directly impacts the ability of plants to intercept and convert light into biomass. Because leaf growth is one of the first processes affected by water deficit, many physiological studies concentrated in short-term responses and associated mechanisms. They demonstrated the roles of cellular and metabolic processes such as changes in cell turgor, hydraulic conductance and cell wall plasticity. However, our understanding of how water deficit impacts cell wall biosynthesis is still fragmentary. Here, we report that ZmMYB31, a R2R3-MYB transcription factor implicated in the regulation of lignin biosynthesis, is induced by water deficit in the growing zone of maize leaves. Consistently, we showed that ZmMYB31 colocates with quantitative trait loci for growth responses to water deficit and anthesis-silking interval (ASI) under water deficit conditions. Furthermore, we showed that increasing ZmMYB31 expression in maize had an impact on ASI that was maintained under water deficit conditions. On the basis of these data, we generated transcriptomic and proteomic data to detect transcripts and proteins that show substantial changes in abundance in the leaf growing zone of three representative independent transgene-positive homozygous maize lines compared with that of transgene-negative sibling plants grown in the PhenoArch platform under well-watered and water deficit conditions. We identified 352 genes that were transcriptionally regulated by ZmMYB31 under well-watered conditions and displayed opposite transcription levels under water deficit conditions, suggesting that ZmMYB31 may function in a water stress memory response pathway, which likely helps the transgenic maize enduring the water deficit stress. Our studies further revealed co-expression relationships between these genes and others from the proteome and a cell wall data sets, suggesting potential regulatory influence

MYB31 triggers water stress memory responses in maize

International audienceWater deficit directly impacts the ability of plants to intercept and convert light into biomass. Because leaf growth is one of the first processes affected by water deficit, many physiological studies concentrated in short-term responses and associated mechanisms. They demonstrated the roles of cellular and metabolic processes such as changes in cell turgor, hydraulic conductance and cell wall plasticity. However, our understanding of how water deficit impacts cell wall biosynthesis is still fragmentary. Here, we report that ZmMYB31, a R2R3-MYB transcription factor implicated in the regulation of lignin biosynthesis [1-2], is induced by water deficit in the growing zone of maize leaves. Consistent with this finding, we also showed that ZmMYB31 colocates with quantitative trait loci for growth responses to water deficit and anthesis-silking interval (ASI) under water deficit conditions. To assess the potential contribution of ZmMYB31 to maize responses to water deficit, we generated transgenic maize overexpressing ZmMYB31. We showed that increasing ZmMYB31 expression in maize maintained ASI under water deficit conditions. On the basis of these data, we generated transcriptomic and proteomic data to detect transcripts and proteins that show substantial changes in abundance in the leaf growing zone of three representative independent transgene-positive homozygous maize lines compared with that of transgene-negative sibling plants grown in PhenoArch under well-watered and water deficit conditions. We identified 352 genes that were transcriptionally regulated by ZmMYB31 under well-watered conditions and displayed opposite transcription levels under water deficit conditions, suggesting that ZmMYB31 may function in a water stress memory response pathway, which likely helps the transgenic maize enduring the water deficit stress. Our studies further revealed co-expression relationships between these genes and others from the proteome and a cell wall data sets, suggesting potential regulatory influence

MYB31 triggers water stress memory responses in maize

International audienceWater deficit directly impacts the ability of plants to intercept and convert light into biomass. Because leaf growth is one of the first processes affected by water deficit, many physiological studies concentrated in short-term responses and associated mechanisms. They demonstrated the roles of cellular and metabolic processes such as changes in cell turgor, hydraulic conductance and cell wall plasticity. However, our understanding of how water deficit impacts cell wall biosynthesis is still fragmentary. Here, we report that ZmMYB31, a R2R3-MYB transcription factor implicated in the regulation of lignin biosynthesis [1-2], is induced by water deficit in the growing zone of maize leaves. Consistent with this finding, we also showed that ZmMYB31 colocates with quantitative trait loci for growth responses to water deficit and anthesis-silking interval (ASI) under water deficit conditions. To assess the potential contribution of ZmMYB31 to maize responses to water deficit, we generated transgenic maize overexpressing ZmMYB31. We showed that increasing ZmMYB31 expression in maize maintained ASI under water deficit conditions. On the basis of these data, we generated transcriptomic and proteomic data to detect transcripts and proteins that show substantial changes in abundance in the leaf growing zone of three representative independent transgene-positive homozygous maize lines compared with that of transgene-negative sibling plants grown in PhenoArch under well-watered and water deficit conditions. We identified 352 genes that were transcriptionally regulated by ZmMYB31 under well-watered conditions and displayed opposite transcription levels under water deficit conditions, suggesting that ZmMYB31 may function in a water stress memory response pathway, which likely helps the transgenic maize enduring the water deficit stress. Our studies further revealed co-expression relationships between these genes and others from the proteome and a cell wall data sets, suggesting potential regulatory influence