Interaction between the Circadian Clock and Regulators of Heat Stress Responses in Plants.

The circadian clock is found ubiquitously in nature, and helps organisms coordinate internal biological processes with environmental cues that inform the time of the day or year. Both temperature stress and the clock affect many important biological processes in plants. Specifically, clock-controlled gene regulation and growth are impacted by a compromised clock or heat stress. The interactions linking these two regulatory pathways include several rhythmic transcription factors that are important for coordinating the appropriate response to temperature stress. Here we review the current understanding of clock control of the regulators involved in heat stress responses in plants

Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis.

In Arabidopsis, a large subset of heat responsive genes exhibits diurnal or circadian oscillations. However, to what extent the dimension of time and/or the circadian clock contribute to heat stress responses remains largely unknown. To determine the direct contribution of time of day and/or the clock to differential heat stress responses, we probed wild-type and mutants of the circadian clock genes CCA1, LHY, PRR7, and PRR9 following exposure to heat (37 °C) and moderate cold (10 °C) in the early morning (ZT1) and afternoon (ZT6). Thousands of genes were differentially expressed in response to temperature, time of day, and/or the clock mutation. Approximately 30% more genes were differentially expressed in the afternoon compared to the morning, and heat stress significantly perturbed the transcriptome. Of the DEGs (~3000) specifically responsive to heat stress, ~70% showed time of day (ZT1 or ZT6) occurrence of the transcriptional response. For the DEGs (~1400) that are shared between ZT1 and ZT6, we observed changes to the magnitude of the transcriptional response. In addition, ~2% of all DEGs showed differential responses to temperature stress in the clock mutants. The findings in this study highlight a significant role for time of day in the heat stress responsive transcriptome, and the clock through CCA1 and LHY, appears to have a more profound role than PRR7 and PRR9 in modulating heat stress responses during the day. Our results emphasize the importance of considering the dimension of time in studies on abiotic stress responses in Arabidopsis

Changes in the nuclear proteome of developing wheat (Triticum aestivum L.) grain

Wheat grain end-use value is determined by complex molecular interactions that occur during grain development, including those in the cell nucleus. However, our knowledge of how the nuclear proteome changes during grain development is limited. Here, we analyzed nuclear proteins of developing wheat grains collected during the cellularization, effective grain-filling, and maturation phases of development, respectively. Nuclear proteins were extracted and separated by two-dimensional gel electrophoresis. Image analysis revealed 371 and 299 reproducible spots in gels with first dimension separation along pH 4-7 and pH 6-11 isoelectric gradients, respectively. The relative abundance of 464 (67%) protein spots changed during grain development. Abundance profiles of these proteins clustered in six groups associated with the major phases and phase transitions of grain development. Using nano liquid chromatography tandem mass spectrometry to analyse 387 variant and non-variant protein spots, 114 different proteins were identified that were classified into 16 functional classes. We noted that some proteins involved in the regulation of transcription, like HMG1/2-like protein and histone deacetylase HDAC2, were most abundant before the phase transition from cellularization to grain-filling, suggesting that major transcriptional changes occur during this key developmental phase. The maturation period was characterized by high relative abundance of proteins involved in ribosome biogenesis. Data are available via ProteomeXchange with identifier PXD002999

Réponse du grain de blé à la nutrition azotée et soufrée : étude intégrative des mécanismes moléculaires mis en jeu au cours du développement du grain par des analyses -omiques

Improving the yield potential of cereals represents a major challenge. In this context, wheat grain quality has to be maintained. Indeed, grain quality is mainly determined by the content and the composition of storage proteins, but there is a strongly negative correlation between yield and grain protein concentration. In addition, grain quality is strongly influenced by the availability of nitrogen and sulfur in soils. Nowadays, the limitation of nitrogen inputs, and also the sulfur deficiency recently observed in soils represent major difficulties to control the quality. Therefore, understanding of molecular mechanisms controlling grain development and accumulation of storage proteins in response to nitrogen and sulfur supply is a major issue. The objective of this thesis was to create knowledge on the comprehension of these regulatory mechanisms. For this purpose, the best strategy to identify molecular actors involved in these processes consisted of -omics approaches. In our studies, the nuclear proteome was an important target. Among these proteins, we revealed some transcriptional regulators likely to be involved in the control of the accumulation of grain storage compounds. Using an approach combining proteomic, transcriptomic and metabolomic data, the characterization of the integrative grain response to the nitrogen and sulfur supply was obtained. Besides, our studies clearly confirmed the major influence of sulfur in the control of the nitrogen/sulfur balance that determines the grain storage protein composition. Among the changes observed in the cell metabolism, some genes were disturbed by the modification of this balance. Thus these genes could coordinate the adjustment of grain composition in response to nutritional deficiencies. These new results contribute in facing the challenge of maintaining wheat grain quality with sustainable agriculture.L’augmentation des rendements est un enjeu majeur chez les céréales. Dans cet objectif, il est nécessaire de maintenir la qualité du grain de blé, qui est principalement déterminée par sa teneur et sa composition en protéines de réserve. En effet, une forte relation négative existe entre le rendement et la teneur en protéines. Par ailleurs, la qualité du grain est fortement influencée par la disponibilité en azote et en soufre dans le sol. La limitation des apports d’intrants azotés à la culture et la carence en soufre récemment observée dans les sols représentent ainsi des difficultés supplémentaires pour maitriser cette qualité. Une meilleure connaissance des mécanismes moléculaires impliqués dans le contrôle du développement du grain et la mise en place de ses réserves protéiques en réponse à la nutrition azotée et soufrée est donc primordiale. L’objectif de cette thèse a ainsi été d’apporter de nouveaux éléments à la compréhension de ces processus de régulation, aujourd’hui peu connus. Pour cela, les approches -omiques sont apparues comme une stratégie de choix pour identifier les acteurs moléculaires mis en jeu. Le protéome nucléaire a été une cible importante dans les travaux menés. L’étude de ces protéines nucléaires a révélé certains régulateurs transcriptionnels qui pourraient être impliqués dans le contrôle de la mise en place des réserves du grain. Dans une approche combinant des données de protéomique, transcriptomique et métabolomique, une vision intégrative de la réponse du grain à la nutrition azotée et soufrée a été obtenue. L’importance d’un apport de soufre dans le contrôle de la balance azote/soufre du grain, déterminante pour la composition du grain en protéines de réserve, a été clairement vérifiée. Parmi les changements observés au niveau du métabolisme cellulaire, certains des gènes affectés par la modification de cette balance pourraient orchestrer l’ajustement de la composition du grain face à des situations de carences nutritionnelles. Ces nouvelles connaissances devraient permettre de mieux maitriser la qualité du grain de blé dans un contexte d’agriculture durable

Wheat grain response to nitrogen and sulfur supply : integrative study of molecular mechanisms involved during the grain development using -omics analyses

L’augmentation des rendements est un enjeu majeur chez les céréales. Dans cet objectif, il est nécessaire de maintenir la qualité du grain de blé, qui est principalement déterminée par sa teneur et sa composition en protéines de réserve. En effet, une forte relation négative existe entre le rendement et la teneur en protéines. Par ailleurs, la qualité du grain est fortement influencée par la disponibilité en azote et en soufre dans le sol. La limitation des apports d’intrants azotés à la culture et la carence en soufre récemment observée dans les sols représentent ainsi des difficultés supplémentaires pour maitriser cette qualité. Une meilleure connaissance des mécanismes moléculaires impliqués dans le contrôle du développement du grain et la mise en place de ses réserves protéiques en réponse à la nutrition azotée et soufrée est donc primordiale. L’objectif de cette thèse a ainsi été d’apporter de nouveaux éléments à la compréhension de ces processus de régulation, aujourd’hui peu connus. Pour cela, les approches -omiques sont apparues comme une stratégie de choix pour identifier les acteurs moléculaires mis en jeu. Le protéome nucléaire a été une cible importante dans les travaux menés. L’étude de ces protéines nucléaires a révélé certains régulateurs transcriptionnels qui pourraient être impliqués dans le contrôle de la mise en place des réserves du grain. Dans une approche combinant des données de protéomique, transcriptomique et métabolomique, une vision intégrative de la réponse du grain à la nutrition azotée et soufrée a été obtenue. L’importance d’un apport de soufre dans le contrôle de la balance azote/soufre du grain, déterminante pour la composition du grain en protéines de réserve, a été clairement vérifiée. Parmi les changements observés au niveau du métabolisme cellulaire, certains des gènes affectés par la modification de cette balance pourraient orchestrer l’ajustement de la composition du grain face à des situations de carences nutritionnelles. Ces nouvelles connaissances devraient permettre de mieux maitriser la qualité du grain de blé dans un contexte d’agriculture durable.Improving the yield potential of cereals represents a major challenge. In this context, wheat grain quality has to be maintained. Indeed, grain quality is mainly determined by the content and the composition of storage proteins, but there is a strongly negative correlation between yield and grain protein concentration. In addition, grain quality is strongly influenced by the availability of nitrogen and sulfur in soils. Nowadays, the limitation of nitrogen inputs, and also the sulfur deficiency recently observed in soils represent major difficulties to control the quality. Therefore, understanding of molecular mechanisms controlling grain development and accumulation of storage proteins in response to nitrogen and sulfur supply is a major issue. The objective of this thesis was to create knowledge on the comprehension of these regulatory mechanisms. For this purpose, the best strategy to identify molecular actors involved in these processes consisted of -omics approaches. In our studies, the nuclear proteome was an important target. Among these proteins, we revealed some transcriptional regulators likely to be involved in the control of the accumulation of grain storage compounds. Using an approach combining proteomic, transcriptomic and metabolomic data, the characterization of the integrative grain response to the nitrogen and sulfur supply was obtained. Besides, our studies clearly confirmed the major influence of sulfur in the control of the nitrogen/sulfur balance that determines the grain storage protein composition. Among the changes observed in the cell metabolism, some genes were disturbed by the modification of this balance. Thus these genes could coordinate the adjustment of grain composition in response to nutritional deficiencies. These new results contribute in facing the challenge of maintaining wheat grain quality with sustainable agriculture

Time of day and genotype sensitivity adjust molecular responses to temperature stress in sorghum

International audienceSUMMARY Sorghum is one of the four major C4 crops that are considered to be tolerant to environmental extremes. Sorghum shows distinct growth responses to temperature stress depending on the sensitivity of the genetic background. About half of the transcripts in sorghum exhibit diurnal rhythmic expressions emphasizing significant coordination with the environment. However, an understanding of how molecular dynamics contribute to genotype‐specific stress responses in the context of the time of day is not known. We examined whether temperature stress and the time of day impact the gene expression dynamics in thermo‐sensitive and thermo‐tolerant sorghum genotypes. We found that time of day is highly influencing the temperature stress responses, which can be explained by the rhythmic expression of most thermo‐responsive genes. This effect is more pronounced in thermo‐tolerant genotypes, suggesting a stronger regulation of gene expression by the time of day and/or by the circadian clock. Genotypic differences were mostly observed on average gene expression levels, which may be responsible for contrasting sensitivities to temperature stress in tolerant versus susceptible sorghum varieties. We also identified groups of genes altered by temperature stress in a time‐of‐day and genotype‐specific manner. These include transcriptional regulators and several members of the Ca 2+ ‐binding EF‐hand protein family. We hypothesize that expression variation of these genes between genotypes along with time‐of‐day independent regulation may contribute to genotype‐specific fine‐tuning of thermo‐responsive pathways. These findings offer a new opportunity to selectively target specific genes in efforts to develop climate‐resilient crops based on their time‐of‐day and genotype variation responses to temperature stress

Proteomic data integration to highlight central actors involved in einkorn grain filling in relation to quality

Proteomic data integration to highlight central actors involved in einkorn grain filling in relation to quality. 3. International Plant Proteomics Organization World Congres

Circadian coordination of cellular processes and abiotic stress responses

Diel changes in the environment are perceived by the circadian clock which transmits temporal information throughout the plant cell to synchronize daily and seasonal environmental signals with internal biological processes. Dynamic modulations of diverse levels of clock gene regulation within the plant cell are impacted by stress. Recent insights into circadian control of cellular processes such as alternative splicing, polyadenylation, and noncoding RNAs are discussed. We highlight studies on the circadian regulation of reactive oxygen species, calcium signaling, and gating of temperature stress responses. Finally, we briefly summarize recent work on the translation-specific rhythmicity of cell cycle genes and the control of subcellular localization and relocalization of oscillator components. Together, this mini-review highlights these cellular events in the context of clock gene regulation and stress responses in Arabidopsis

Could storage protein composition be modified by acting at the transcriptional level?

Could storage protein composition be modified by acting at the transcriptional level?. 7. Colloque du Réseau Français de Biologie des Graine

Proteomic Approach to Identify Nuclear Proteins in Wheat Grain

The nuclear proteome of the grain of the two cultivated wheat species Triticum aestivum (hexaploid wheat; genomes A, B, and D) and T. monococcum (diploid wheat; genome A) was analyzed in two early stages of development using shotgun-based proteomics. A procedure was optimized to purify nuclei, and an improved protein sample preparation was developed to efficiently remove nonprotein substances (starch and nucleic acids). A total of 797 proteins corresponding to 528 unique proteins were identified, 36% of which were classified in functional groups related to DNA and RNA metabolism. A large number (107 proteins) of unknown functions and hypothetical proteins were also found. Some identified proteins may be multifunctional and may present multiple localizations. On the basis of the MS/MS analysis, 368 proteins were present in the two species, and in two stages of development, some qualitative differences between species and stages of development were also found. All of these data illustrate the dynamic function of the grain nucleus in the early stages of development