Biochemical Pathways

The genomic era facilitates the understanding of how transcriptional networks are interconnected to program seed development and filling. However, to date, little information is available regarding dicot seeds with a transient perisperm and a persistent, copious endosperm. Coffea arabica is the subject of increasing genomic research and is a model for nonorthodox albuminous dicot seeds of tropical origin.The aim of this study was to reconstruct the metabolic pathways involved in the biosynthesis of the main coffee seed storage compounds, namely cell wall polysaccharides, triacylglycerols, sucrose, and chlorogenic acids. For this purpose, we integrated transcriptomic and metabolite analyses, combining real-time RT-PCR performed on 137 selected genes (of which 79 were uncharacterized in Coffea) and metabolite profiling.Our map-drawing approach derived from model plants enabled us to propose a rationale for the peculiar traits of the coffee endosperm, such as its unusual fatty acid composition, remarkable accumulation of chlorogenic acid and cell wall polysaccharides.Comparison with the developmental features of exalbuminous seeds described in the literature revealed that the two seed types share important regulatory mechanisms for reserve biosynthesis, independent of the origin and ploidy level of the storage tissue.

The "Microbiology" volume of the new revised and updated Handbook of Enology focuses on the vinification process. It describes how yeasts work and how they can be influenced to achieve better results. It continues to look at the metabolism of lactic acid bacterias and of acetic acid bacterias, and again, how can they be treated to avoid disasters in the winemaking process and how to achieve optimal results. The last chapters in the book deal with the use of sulfur-dioxide, the grape and its maturation process, harvest and prefermentation treatment, and the basis of red, white and speciality wine making.

• Evidence is accumulating that the effect of CO2 on time of flowering involves interactions with photoperiod, but the basis for this interaction is unclear. Here, which components of the photoperiod flowering pathway account for this interaction in Arabidopsis thaliana were examined.• Ten mutants deficient in particular loci in the photoperiod pathway, as well as the wild type, were grown under short and long days at either ambient or elevated CO2. Leaf number at flowering and the number of days required for induction of flowering were determined.• Elevated CO2 interacted with both the photoreceptors and the subsequent transduction reactions in the photoperiod pathway. The direction and magnitude of the effects varied with photoperiod. Elevated CO2 also affected flowering by increasing rate of leaf production.• The net effect of elevated CO2 on time of flowering varies because CO2 has a complex array of effects on different elements of the developmental pathway leading to flower induction that may either hasten or delay flowering depending upon the influence of other environmental factors such as photoperiod.Evidence is accumulating that the effect of CO2 on time of flowering involves interactions with photoperiod, but the basis for this interaction is unclear. Here, which components of the photoperiod flowering pathway account for this interaction in Arabidopsis thaliana were examined.Ten mutants deficient in particular loci in the photoperiod pathway, as well as the wild type, were grown under short and long days at either ambient or elevated CO2. Leaf number at flowering and the number of days required for induction of flowering were determined.Elevated CO2 interacted with both the photoreceptors and the subsequent transduction reactions in the photoperiod pathway. The direction and magnitude of the effects varied with photoperiod. Elevated CO2 also affected flowering by increasing rate of leaf production.The net effect of elevated CO2 on time of flowering varies because CO2 has a complex array of effects on different elements of the developmental pathway leading to flower induction that may either hasten or delay flowering depending upon the influence of other environmental factors such as photoperiod.

In the budding yeast,S. cerevisiae, two-dimensional (2D) gel electrophoresis techniques permit mapping of DNA replication origins to short stretches of DNA (±300 bp). In contrast, in mammalian cells andDrosophila, 2D gel techniques do not permit precise origin localization; the results have been interpreted to suggest that replication initiates in broad zones (several kbp or more). However, alternative techniques (replication timing, nascent strand polarity analysis, nascent strand size analysis) suggest that mammalian origins can be mapped to short DNA stretches, just likeS. cerevisiae origins. Because the fission yeast,Schizosaccharomyces pombe, resembles higher organisms in several ways to a greater extent than doesS. cerevisiae, we thought thatS. pombe replication origins might prove to resemble — and thus be helpful models for — animal cell origins. An attempt to test this possibility using 2D gel techiques resulted in identification of a replication origin near theura4 gene on chromosome III ofS. pombe. The 2D gel patterns produced by thisS. pombe origin indeed resemble the patterns produced by animal cell origins and show that theS. pombe origin cannot be precisely located. The data suggest an initiation zone of 3–5 kbp. Some aspects of the 2D gel patterns detected at theS. pombe origin cannot be explained by the rationale of initiation in broad zones, suggesting that future biochemical and genetic studies of this complex origin are likely to provide information useful in helping to understand the apparent conflict between the 2D gel mapping techniques and other mapping techniques at animal cell origins.

Increases in woody vegetation and declines in grasses in arid and semi-arid ecosystems have occurred globally since the 1800s, but the mechanisms driving this major land-cover change remain uncertain and controversial. Working in a shrub-encroached grassland in the northern Chihuahuan Desert where grasses and shrubs typically differ in leaf-level nitrogen allocation, photosynthetic pathway, and root distribution, we asked if differences in leaf-level ecophysiology could help explain shrub proliferation. We predicted that the relative performance of grasses and shrubs would vary with soil moisture due to the different morphological and physiological characteristics of the two life-forms. In a 2-year experiment with ambient, reduced, and enhanced precipitation during the monsoon season, respectively, the encroaching C(3) shrub (honey mesquite Prosopis glandulosa) consistently and substantially outperformed the historically dominant C(4) grass (black grama Bouteloua eriopoda) in terms ...

The Arabidopsis thaliana K+ channel KAT1 has been suggested to have a key role in mediating the aperture of stomata pores on the surface of plant leaves. Although the activity of KAT1 is thought to be regulated by phosphorylation, the endogenous pathway and the primary target site for this modification remained unknown. In the present study, we have demonstrated that the C-terminal region of KAT1 acts as a phosphorylation target for the Arabidopsis calcium-independent ABA (abscisic acid)-activated protein kinase SnRK2.6 (Snf1-related protein kinase 2.6). This was confirmed by LC-MS/MS (liquid chromatography tandem MS) analysis, which showed that Thr306 and Thr308 of KAT1 were modified by phosphorylation. The role of these specific residues was examined by single point mutations and measurement of KAT1 channel activities in Xenopus oocyte and yeast systems. Modification of Thr308 had minimal effect on KAT1 activity. On the other hand, modification of Thr306 reduced the K+ transport u...

Frank Livingstone played a central role in defining the population genetics of the sickle cell mutation at position 6 of the human beta globin gene, the most famous amino acid substitution in evolutionary biology. Its discovery occurred at a time when traditional, 19th-century principles of natural selection were being joined with the newly discovered mechanics of DNA structure and protein synthesis to produce Neo-Darwinian theory. When combined with the epidemiology of malaria in Africa, differential mortality for both homozygotes, and the resulting advantage of the heterozygote, sickle cell became the classic balanced polymorphism. Human HLA-A has 237 molecular alleles. The histocompatibility system has as its primary function the presentation of peptides to T-cell receptors and plays an essential role in the immune system. Nearly all of the alleles are codominant and fully functional. Despite almost 30 years of disease-association studies with HLA-A, no convincing evidence has been found for differential fertility or mortality at this locus. Yet the dogma in the histocompatibility field is that this extensive human polymorphism is maintained by "balancing selection." Explaining HLA-A polymorphism is what one might call the sickle-cell-effect. This one mutation, coming as it did at the historical convergence of Darwinian theory and modern genetics, and carrying with it the strong relationship between mutation, disease, and allele frequency, has conditioned our discussion of human genetic variation and population genetics. Has the strength of this early idea made evolutionary biologists uncritical of systems like HLA-A and retarded the search for new mechanisms of molecular evolution? Is it now time to move away from a focus on mutation and polymorphism in evolutionary genetics and toward a systems theory that would explain the origin and evolution of hemoglobin and HLA-A and the biochemical pathways that surround them?

We identified and functionally characterized genes encoding three Gα proteins and one Gβ protein in the dimorphic fungal wheat pathogenMycosphaerella graminicola, which we designatedMgGpa1,MgGpa2,MgGpa3, andMgGpb1, respectively. Sequence comparisons and phylogenetic analyses showed that MgGPA1 and MgGPA3 are most related to the mammalian Gαiand Gαsfamilies, respectively, whereas MgGPA2 is not related to either of these families. On potato dextrose agar (PDA) and in yeast glucose broth (YGB),MgGpa1mutants produced significantly longer spores than those of the wild type (WT), and these developed into unique fluffy mycelia in the latter medium, indicating that this gene negatively controls filamentation.MgGpa3mutants showed more pronounced yeast-like growth accompanied with hampered filamentation and secreted a dark-brown pigment into YGB. Germ tubes emerging from spores ofMgGpb1mutants were wavy on water agar and showed a nested type of growth on PDA that was due to hampered filamenta...

The research that aims at furthering our understanding of plant primary metabolism has intensified during the last decade. The presented study validated a systems biology methodological framework for the analysis of stress-induced molecular interaction networks in the context of plant primary metabolism, as these are expressed during the first hours of the stress treatment. The framework involves the application of time-series integrated full-genome transcriptomic and polar metabolomic analyses on plant liquid cultures. The latter were selected as the model system for this type of analysis, because they provide a well-controlled growth environment, ensuring that the observed plant response is due only to the applied perturbation. An enhanced gas chromatography–mass spectrometry (GC–MS) metabolomic data correction strategy and a new algorithm for the significance analysis of time-series “omic” data are used to extract information about the plant's transcriptional and metabolic response to the applied stress from the acquired datasets; in this article, it is the first time that these are applied for the analysis of a large biological dataset from a complex eukaryotic system. The case-study involved Arabidopsis thaliana liquid cultures subjected for 30 h to elevated (1%) CO2 stress. The advantages and validity of the methodological framework are discussed in the context of the known A. thaliana or plant, in general, physiology under the particular stress. Of note, the ability of the methodology to capture dynamic aspects of the observed molecular response allowed for 9 and 24 h of treatment to be indicated as corresponding to shifts in both the transcriptional and metabolic activity; analysis of the pathways through which these activity changes are manifested provides insight to regulatory processes. Biotechnol. Bioeng. 2009;102: 264–279. © 2008 Wiley Periodicals, Inc.

This chapter on plant-nematode interactions contains sections on nematode parasitism of plants, invasion and migration in host tissue, wound and defence responses of the plant, protection from host responses, molecular and cellular aspects of the development of nematode feeding cells (cellular changes, cell wall and membrane modifications, changes in the cytoskeleton, nuclear changes and cell activation, and signal transduction pathways and transcription factors), nematode signals for feeding site induction (chorismate mutase, CLAVATA3-like peptides, ubiquitin pathway, cytokinins, and nodulation factors), comparative analysis of the invasion process and feeding sites of cyst (Heterodera and Globodera spp.) and root-knot (Meloidogyne sp.) nematodes, and resistance and avirulence genes in host plants.