The Plant Short-Chain Dehydrogenase (SDR) superfamily:genome-wide inventory and diversification patterns

Background Short-chain dehydrogenases/reductases (SDRs) form one of the largest and oldest NAD(P)(H) dependent oxidoreductase families. Despite a conserved 'Rossmann-fold' structure, members of the SDR superfamily exhibit low sequence similarities, which constituted a bottleneck in terms of identification. Recent classification methods, relying on hidden-Markov models (HMMs), improved identification and enabled the construction of a nomenclature. However, functional annotations of plant SDRs remain scarce. Results Wide-scale analyses were performed on ten plant genomes. The combination of hidden Markov model (HMM) based analyses and similarity searches led to the construction of an exhaustive inventory of plant SDR. With 68 to 315 members found in each analysed genome, the inventory confirmed the over-representation of SDRs in plants compared to animals, fungi and prokaryotes. The plant SDRs were first classified into three major types --- 'classical', 'extended' and 'divergent' --- but a minority (10 % of the predicted SDRs) could not be classified into these general types ('unknown' or 'atypical' types). In a second step, we could categorize the vast majority of land plant SDRs into a set of 49 families. Out of these 49 families, 35 appeared early during evolution since they are commonly found through all the Green Lineage. Yet, some SDR families --- tropinone reductase-like proteins (SDR65C), 'ABA2-like'-NAD dehydrogenase (SDR110C), 'salutaridine/menthone-reductase-like' proteins (SDR114C), 'dihydroflavonol 4-reductase'-like proteins (SDR108E) and 'isoflavone-reductase-like' (SDR460A) proteins --- have undergone significant functional diversification within vascular plants since they diverged from Bryophytes. Interestingly, these diversified families are either involved in the secondary metabolism routes (terpenoids, alkaloids, phenolics) or participate in developmental processes (hormone biosynthesis or catabolism, flower development), in opposition to SDR families involved in primary metabolism which are poorly diversified. Conclusion The application of HMMs to plant genomes enabled us to identify 49 families that encompass all Angiosperms ('higher plants') SDRs, each family being sufficiently conserved to enable simpler analyses based only on overall sequence similarity. The multiplicity of SDRs in plant kingdom is mainly explained by the diversification of large families involved in different secondary metabolism pathways, suggesting that the chemical diversification that accompanied the emergence of vascular plants acted as a driving force for SDR evolution

Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato

Members of the TOPLESS gene family emerged recently as key players in gene repression in several mechanisms, especially in auxin perception. The TOPLESS genes constitute, in ‘higher-plant’ genomes, a small multigenic family comprising four to 11 members. In this study, this family was investigated in tomato, a model plant for Solanaceae species and fleshy fruits. Six open reading frames predicted to encode topless-like proteins (SlTPLs) containing the canonical domains (LisH, CTLH, and two WD40 repeats) were identified in the tomato genome. Nuclear localization was confirmed for all members of the SlTPL family with the exception SlTPL6, which localized at the cytoplasm and was excluded from the nucleus. SlTPL genes displayed distinctive expression patterns in different tomato organs, with SlTPL1 showing the highest levels of transcript accumulation in all tissues tested except in ripening fruit where SlTPL3 and SlTPL4 were the most prominently expressed. To gain insight into the specificity of the different TOPLESS paralogues, a protein–protein interaction map between TOPLESS and auxin/indole-3-acetic acid (Aux/IAA) proteins was built using a yeast two-hybrid approach. The PPI map enabled the distinction of two patterns: TOPLESS isoforms interacting with the majority of Aux/IAA, and isoforms with limited capacity for interaction with these protein partners. Interestingly, evolutionary analyses of the TOPLESS gene family revealed that the highly expressed isoforms (SlTPL1, SlTPL3, and SlTPL4) corresponded to the three TPL-related genes undergoing the strongest purifying selection, while the selection was much weaker for SlTPL6, which was expressed at a low level and encoded a protein lacking the capacity to interact with Aux/IAAs

Class I TCP in fruit development: much more than growth

Fruit development can be viewed as the succession of three main steps consisting of the fruit initiation, growth and ripening. These processes are orchestrated by different factors, notably the successful fertilization of flowers, the environmental conditions and the hormones whose action is coordinated by a large variety of transcription factors. Among the different transcription factor families, TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR (TCP) family has received little attention in the frame of fruit biology despite its large effects on several developmental processes and its action as modulator of different hormonal pathways. In this respect, the comprehension of TCP functions in fruit development remains an incomplete puzzle that needs to be assembled. Building on the abundance of genomic and transcriptomic data, this review aims at collecting available TCP expression data to allow their integration in the light of the different functional genetic studies reported so far. This reveals that several Class I TCP genes, already known for their involvement in the cell proliferation and growth, display significant expression levels in developing fruit, although clear evidence supporting their functional significance in this process remains scarce. The extensive expression data compiled in our study provide convincing elements that shed light on the specific involvement of Class I TCP genes in fruit ripening, once these reproductive organs acquire their mature size. They also emphasize their putative role in the control of specific biological processes such as fruit metabolism and hormonal dialogue

Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits

MADS-box transcription factors are key elements of the genetic networks controlling flower and fruit development. Among these, the class D clade gathers AGAMOUS-like genes which are involved in seed, ovule, and funiculus development. The tomato genome comprises two class D genes, Sl-AGL11 and Sl-MBP3 , both displaying high expression levels in seeds and in central tissues of young fruits. The potential effects of Sl-AGL11 on fruit development were addressed through RNAi silencing and ectopic expression strategies. Sl-AGL11-down-regulated tomato lines failed to show obvious phenotypes except a slight reduction in seed size. In contrast, Sl-AGL11 overexpression triggered dramatic modifications of flower and fruit structure that include: the conversion of sepals into fleshy organs undergoing ethylene-dependent ripening, a placenta hypertrophy to the detriment of locular space, starch and sugar accumulation, and an extreme softening that occurs well before the onset of ripening. RNA-Seq transcriptomic profiling high-lighted substantial metabolic reprogramming occurring in sepals and fruits, with major impacts on cell wall-related genes. While several Sl-AGL11-related phenotypes are reminiscent of class C MADS-box genes (TAG1 and TAGL1), the modifications observed on the placenta and cell wall and the Sl-AGL11 expression pattern suggest an action of this class D MADS-box factor on early fleshy fruit development

Functional characterization of SlscADH1, a fruit-ripening associated short-chain alcohol dehydrogenase of tomato

A tomato short-chain dehydrogenase-reductase (SlscADH1) is preferentially expressed in fruit with a maximum expression at the breaker stage while expression in roots, stems, leaves and flowers is very weak. It represents a potential candidate for the formation of aroma volatiles by interconverting alcohols and aldehydes. The SlscADH1 recombinant protein produced in Escherichia coli exhibited dehydrogenase-reductase activity towards several volatile compounds present in tomato flavour with a strong preference for the NAD/NADH co-factors. The strongest activity was observed for the reduction of hexanal (Km = 0.175 mM) and phenylacetaldehyde (Km = 0.375 mM) in the presence of NADH. The oxidation process of hexanol and 1-phenylethanol was much less efficient (Kms of 2.9 and 23.0 mM, respectively), indicating that the enzyme preferentially acts as a reductase. However activity was observed only for hexanal, phenylacetaldehyde, (E)-2-hexenal and acetaldehyde and the corresponding alcohols. No activity could be detected for other aroma volatiles important for tomato flavour, such as methyl-butanol/methyl-butanal, 5-methyl-6-hepten-2-one/5-methyl-6-hepten-2-ol, citronellal/citronellol, neral/nerol, geraniol. In order to assess the function of the SlscADH1 gene, transgenic plants have been generated using the technique of RNA interference (RNAi). Constitutive down-regulation using the 35S promoter resulted in the generation of dwarf plants, indicating that the SlscADH1 gene, although weakly expressed in vegetative tissues, had a function in regulating plant development. Fruitspecific down-regulation using the 2A11 promoter had no morphogenetic effect and did not alter the aldehyde/alcohol balance of the volatiles compounds produced by the fruit. Nevertheless, SlscADH1-inhibited fruit unexpectedly accumulated higher concentrations of C5 and C6 volatile compounds of the lipoxygenase pathway, possibly as an indirect effect of the suppression of SlscADH1 on the catabolism of phospholipids and/or integrity of membranes

Planck 2015 results. XIII. Cosmological parameters

We present results based on full-mission Planck observations of temperature and polarization anisotropies of the CMB. These data are consistent with the six-parameter inflationary LCDM cosmology. From the Planck temperature and lensing data, for this cosmology we find a Hubble constant, H0= (67.8 +/- 0.9) km/s/Mpc, a matter density parameter Omega_m = 0.308 +/- 0.012 and a scalar spectral index with n_s = 0.968 +/- 0.006. (We quote 68% errors on measured parameters and 95% limits on other parameters.) Combined with Planck temperature and lensing data, Planck LFI polarization measurements lead to a reionization optical depth of tau = 0.066 +/- 0.016. Combining Planck with other astrophysical data we find N_ eff = 3.15 +/- 0.23 for the effective number of relativistic degrees of freedom and the sum of neutrino masses is constrained to < 0.23 eV. Spatial curvature is found to be |Omega_K| < 0.005. For LCDM we find a limit on the tensor-to-scalar ratio of r <0.11 consistent with the B-mode constraints from an analysis of BICEP2, Keck Array, and Planck (BKP) data. Adding the BKP data leads to a tighter constraint of r < 0.09. We find no evidence for isocurvature perturbations or cosmic defects. The equation of state of dark energy is constrained to w = -1.006 +/- 0.045. Standard big bang nucleosynthesis predictions for the Planck LCDM cosmology are in excellent agreement with observations. We investigate annihilating dark matter and deviations from standard recombination, finding no evidence for new physics. The Planck results for base LCDM are in agreement with BAO data and with the JLA SNe sample. However the amplitude of the fluctuations is found to be higher than inferred from rich cluster counts and weak gravitational lensing. Apart from these tensions, the base LCDM cosmology provides an excellent description of the Planck CMB observations and many other astrophysical data sets

Le métabolisme de la glycérophosphocholine chez les végétaux (caractérisation d'une glycérophosphodiester phosphodiestérase)

GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF

Caractérisation des interactions protéines-protéines impliquées dans la médiation de l'auxine chez la tomate

La croissance et le développement des plantes sont fortement régulés par plusieurs hormones végétales, dont l auxine qui joue un rôle prépondérant. La modification de l expression de certains gènes en réponse à l auxine est contrôlée par des interactions spécifiques entre les facteurs de transcription ARF (Auxin Response Factors) et les protéines Aux/IAA. Des études sur Arabidopsis thaliana ont aussi montré l implication de corépresseurs de la famille TOPLESS pour réprimer les gènes cibles des ARF. Toutefois, cette régulation transcriptionnelle a surtout été caractérisée chez la plante modèle Arabidopsis et la validité de ce modèle n a pas encore été confortée par l étude d autres modèles. La tomate (Solanum lycopersicon), espèce modèle tant pour les Solanacées que pour les plantes à fruits constitue une bonne alternative pour élucider les caractères généraux liés à la signalisation auxinique. Dans notre travail, nous avons d abord mis en place des protocoles expérimentaux double-hybride, pull-down, complémentation de fluorescence (BiFC, Bifluorescence Complementation) permettant d étudier les interactions protéines-protéines. Ces méthodes ont d abord été validées sur des couples Aux/IAA ARF étant connus chez la tomate pour leur implication dans le développement et la maturation des fruits (SlIAA9, SlARF8, SlIAA3, SlARF4, SlIAA27). L utilisation du double hybride a également permis de construire une carte d interactions entre les Aux/IAA et les ARF de tomate. Dans un deuxième temps, la disponibilité de la séquence du génome de la tomate a permis d entreprendre une étude globale de la famille des corépresseurs TOPLESS. Cette étude a inclus : la caractérisation et le clonage des gènes, l analyse de la séquence protéique, une analyse phylogénétique de la famille sur un ensemble de génome séquencés, la caractérisation du profil d expression des différentes isoformes ainsi qu une analyse comparative de leur capacité d interaction avec les protéines Aux/IAA. Enfin, dans un dernier temps, nous avons souhaité construire des premiers outils permettant d entreprendre une recherche non-ciblée de nouveaux partenaires interagissant avec les protéines ARF ou Aux/IAA en partant de protoplastes de cellules BY-2 de tabac exprimant de façon transitoire des gènes codant des protéines chimères (tagged proteins). Même si ce travail reste préliminaire, il a pu notamment illustrer l importance de l intégrité des noyaux pour la stabilité des Aux/IAA, même en l absence d auxine.The plant hormone auxin plays a central role in plant growth and development. The specific Aux/IAAs and Auxin Response Factors (ARFs) interactions are involved in auxin signaling pathway to regulate the auxin-responsive gene expression. Studies in Arabidopsis showed that TOPLESS family (TPLs) also was recruited by some Aux/IAAs to repress the function of ARFs. The whole machinery of the auxin signaling pathway is not clear yet, and most of this knowledge comes from the research on Arabidopsis. As a reference for Solanaceae and fleshy fruit plant, tomato (Solanum lycopersicon) is a good alternative model to better understand general traits of the auxin regulation process. In our work, we first established in our labs three experimental protocols Yeast two-Hybrid, Pull-down and Bifluorescence complementation to unravel protein-protein interactions. These methods were first challenged on specific Aux/IAA and ARF proteins that were already characterized as major actors in fruit tomato development or ripening (SlIAA9, SlARF8, SlIAA3, SlARF4, SlIAA27). This also enabled us to build an ARF-Aux/IAA interaction map. In a second part, taking advantage of the tomato genome sequence, we carried a whole-genome study on tomato TOPLESS family. This investigation included gene cloning and characterization, protein sequence analysis, phylogenetic analyses, expression pattern and construction of protein-protein interaction maps. In a last part, we developed tools to start a non-targeted approach aiming at identifying new potential partners or protein complex involved in auxin signaling pathway using BY-2 tobacco cell protoplasts transiently expressing tagged-proteins. Although this study is still preliminary, it demonstrated the importance of nucleus integrity for Aux/IAA stability even in absence of auxin.TOULOUSE-INP (315552154) / SudocSudocFranceF

Genes involved in the biosynthesis of aroma volatiles and biotechnological applications

Introduction ; Genes involved in the biosynthesis of aroma volatiles; Genes of amino acid metabolism ; Genes involved in terpenoids biosynthesis ; Genes involved in the generation of aroma volatiles from sugars ; Modification of the glycosylated fraction ; Regulators controlling aromas biosynthesis: transcription factors and hormones ; Conclusions and perspectives ; Acknowledgments ; Reference

Glycerophosphocholine metabolism in higher plant cells. Evidence of a new glyceryl-phosphodiester phosphodiesterase

International audienc