Microbial volatile emissions promote accumulation of exceptionally high levels of starch in leaves in mono- and di-cotyledonous plants

Trabajo presentado en la X Reunión de Biología Molecular de plantas, celebrada en Valencia del 8 al 10 de julio de 2010.Peer Reviewe

Characterization of the cork oak transcriptome dynamics during acorn development

Background: Cork oak (Quercus suber L.) has a natural distribution across western Mediterranean regions and is a keystone forest tree species in these ecosystems. The fruiting phase is especially critical for its regeneration but the molecular mechanisms underlying the biochemical and physiological changes during cork oak acorn development are poorly understood. In this study, the transcriptome of the cork oak acorn, including the seed, was characterized in five stages of development, from early development to acorn maturation, to identify the dominant processes in each stage and reveal transcripts with important functions in gene expression regulation and response to water. Results: A total of 80,357 expressed sequence tags (ESTs) were de novo assembled from RNA-Seq libraries representative of the several acorn developmental stages. Approximately 7.6 % of the total number of transcripts present in Q. suber transcriptome was identified as acorn specific. The analysis of expression profiles during development returned 2,285 differentially expressed (DE) transcripts, which were clustered into six groups. The stage of development corresponding to the mature acorn exhibited an expression profile markedly different from other stages. Approximately 22 % of the DE transcripts putatively code for transcription factors (TF) or transcriptional regulators, and were found almost equally distributed among the several expression profile clusters, highlighting their major roles in controlling the whole developmental process. On the other hand, carbohydrate metabolism, the biological pathway most represented during acorn development, was especially prevalent in mid to late stages as evidenced by enrichment analysis. We further show that genes related to response to water, water deprivation and transport were mostly represented during the early (S2) and the last stage (S8) of acorn development, when tolerance to water desiccation is possibly critical for acorn viability. Conclusions: To our knowledge this work represents the first report of acorn development transcriptomics in oaks. The obtained results provide novel insights into the developmental biology of cork oak acorns, highlighting transcripts putatively involved in the regulation of the gene expression program and in specific processes likely essential for adaptation. It is expected that this knowledge can be transferred to other oak species of great ecological value.Fundação para a Ciência e a Tecnologi

The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics

Fluid-Phase Endocytosis in Plant Cells

Editors: Jozef ŠamajThe uptake of nutrients by plant cells has been traditionally believed to be mediated by membrane-bound carriers. However, the last decade has seen an increase in evidence pointing to the parallel uptake by fluid-phase endocytosis (FPE). Recent advances in plant endocytosis reveal that this is true for heterotrophic cells, whether storage parenchyma, cell suspensions, or nutrient absorbing cells of carnivorous plants. Uptake of extracellular matrix components, endocytic markers, and sugar analogs in a wide variety of heterotrophic cells has confirmed the uptake of extracellular fluids and their transport to the vacuole. Furthermore, there is evidence to indicate the passage through an intracellular compartment where solutes are distributed. The precise nature of FPE has not been revealed; however, evidence using specific inhibitors, CdSe/ZnS quantum dots in combination with other FPE markers and inhibitors such as ikargalukin, points to the clathrin-independent nature of FPE and its possible association with flotillin. That FPE operates in conjunction with membrane-bound transporters in the uptake of solutes is supported by experiments analyzing uptake kinetics of the fluorescent endocytic marker Alexa-488 in the presence of sucrose and membrane-bound transporters and endocytic inhibitors. The mechanisms of membrane remodeling to accommodate the addition of membrane and aqueous volume to the vacuole during FPE remain unresolved.Peer Reviewe

Starch metabolism, its regulation and biotechnological approaches to improve yields

Trabajo presentado en el Olomouc Biotech. Plant Biotechnology: green for good II, celebrado en Olomouc (República Checa) del 17 al 21 de junio de 2013.Starch is the main storage carbohydrate in vascular plants and structurally composed of the glucose homopolymers amylose and amylopectin.Peer Reviewe

No evidence for the occurrence of substrate inhibition of Arabidopsis thaliana sucrose synthase-1 (AtSUS1) by fructose and UDP-glucose

Sucrose synthase (SuSy) catalyzes the reversible conversion of sucrose and NDP into the corresponding nucleotidesugars and fructose. The Arabidopsis genome possesses six SUS genes (AtSUS1-6) that code for proteins with SuSy activity. As a first step to investigate optimum fructose and UDP-glucose (UDPG) concentrations necessary to measure maximum sucrose-producing SuSy activity in crude extracts of Arabidopsis, in this work we performed kinetic analyses of recombinant AtSUS1 in two steps: (1) SuSy reaction at pH 7.5, and (2) chromatographic measurement of sucrose produced in step 1. These analyses revealed a typical Michaelis-Menten behavior with respect to both UDPG and fructose, with Km values of 50 μM and 25 μM, respectively. Unlike earlier studies showing the occurrence of substrate inhibition of UDP-producing AtSUS1 by fructose and UDP-glucose, these analyses also revealed no substrate inhibition of AtSUS1 at any UDPG and fructose concentration. By including 200 μM fructose and 1 μM UDPG in the SuSy reaction assay mixture, we found that sucrose-producing SuSy activity in leaves and stems of Arabidopsis were exceedingly higher than previously reported activities. Furthermore, we found that SuSy activities in organs of the sus1/sus2/sus3/sus4 mutant were ca. 80-90% of those found in WT plants. © 2012 Landes Bioscience.This research was partially supported by the grant BIO2010-18239 from the Comisión Interministerial de Ciencia y Tecnología and Fondo Europeo de Desarrollo Regional (Spain) and by Iden Biotechnology S.L. G.A. acknowledges a fellowship from the Public University of Navarra.Peer Reviewe

Starch biosynthesis, its regulation and biotechnological approaches to improve crop yields

Structurally composed of the glucose homopolymers amylose and amylopectin, starch is the main storage carbohydrate in vascular plants, and is synthesized in the plastids of both photosynthetic and non-photosynthetic cells. Its abundance as a naturally occurring organic compound is surpassed only by cellulose, and represents both a cornerstone for human and animal nutrition and a feedstock for many non-food industrial applications including production of adhesives, biodegradable materials, and first-generation bioethanol. This review provides an update on the different proposed pathways of starch biosynthesis occurring in both autotrophic and heterotrophic organs, and provides emerging information about the networks regulating them and their interactions with the environment. Special emphasis is given to recent findings showing that volatile compounds emitted by microorganisms promote both growth and the accumulation of exceptionally high levels of starch in mono- and dicotyledonous plants. We also review how plant biotechnologists have attempted to use basic knowledge on starch metabolism for the rational design of genetic engineering traits aimed at increasing starch in annual crop species. Finally we present some potential biotechnological strategies for enhancing starch content.This research was partially supported by the grants BIO2010-18239 from the Comisión Interministerial de Ciencia y Tecnología and Fondo Europeo de Desarrollo Regional (Spain) and IIM010491.RI1 from the Government of Navarra, and by Iden Biotechnology. M.O. was partly supported by grant N. ED0007/01/01Centre of the Region Haná for Biotechnological and Agricultural Research.Peer reviewe

Volatiles from the fungal phytopathogen Penicillium aurantiogriseum

Volatile compounds (VCs) emitted by the fungal phytopathogen Penicillium aurantiogriseum promote root growth and developmental changes in Arabidopsis. Here we characterized the metabolic and molecular responses of roots to fungal volatiles. Proteomic analyses revealed that these compounds reduce the levels of aquaporins, the iron carrier IRT1 and apoplastic peroxidases. Fungal VCs also increased the levels of enzymes involved in the production of mevalonate (MVA)‐derived isoprenoids, nitrogen assimilation and conversion of methionine to ethylene and cyanide. Consistently, fungal VC‐treated roots accumulated high levels of hydrogen peroxide (H2O2), MVA‐derived cytokinins, ethylene, cyanide and long‐distance nitrogen transport amino acids. qRT‐PCR analyses showed that many proteins differentially expressed by fungal VCs are encoded by VC non‐responsive genes. Expression patterns of hormone reporters and developmental characterization of mutants provided evidence for the involvement of cyanide scavenging and enhanced auxin, ethylene, cytokinin and H2O2 signaling in the root architecture changes promoted by fungal VCs. Our findings show that VCs from P. aurantiogriseum modify root metabolism and architecture, and improve nutrient and water use efficiencies through transcriptionally and non‐transcriptionally regulated proteome resetting mechanisms. Some of these mechanisms are subject to long‐distance regulation by photosynthesis and differ from those triggered by VCs emitted by beneficial microorganisms.Peer reviewe