Search

Sugarcane (Saccharum spp.) is an economically vital crop that is a primary source of sugar in our food and is also used for ethanol production. Various studies have been performed to understand the molecular mechanisms underlying sugar accumulation in sugarcane, but the complex, polyploid genome has posed many challenges. Here, we analyzed the recently sequenced genomes of two sugarcane varieties: Saccharum spontaneum, a geographically widespread, stress tolerant, and low sugar-accumulating wild relative of domesticated sugarcane, and Saccharum officinarum, a high sugar-accumulating variety, to investigate the composition and roles of two sugar transporter protein families, Sucrose Transporters (SUTs) and Tonoplast Sugar Transporters (TSTs). We found an increase in the number of alleles for various SUT and TST genes in S. officinarum and S. spontaneum compared to sorghum and other grass species, and we identified new putative TST genes previously uncharacterized. We analyzed expression levels of these genes in various tissues at different stages and identified SUTs and TSTs likely involved in sugar transport and storage. We hypothesize that these sugar transporter genes in S. officinarum, particularly TSTs, contribute to the ability of modern sugarcane hybrid varieties to accumulate large amounts of sugar in the stem. [ABSTRACT FROM AUTHOR]

Protein clustering is useful for refining protein annotations and searching for proteins by their phylogenetic profile. We have performed the clustering of proteins encoded in the plastoms of Rhodophyta, as well as other plastid-containing species related to the Rhodophyta branch. The corresponding database and cluster search according to protein phylogenetic profile are available at . Plastome-encoded proteins specific for small taxonomic groups of algae and protozoa have been found based on this database, and the search for and analysis of RNA polymerase in the nuclear genomes of Apicomplexa has been performed. [ABSTRACT FROM AUTHOR]

New distributed computing platforms (grids) are based on interconnections of a large number of processing elements. A most important issue for their effective utilization is the optimal use of resources through proper task scheduling. It consists of allocating the tasks of a parallel program to processors on the platform and to determine at what time the tasks will start their execution. As data may be subject to uncertainties or disturbances, it is practically impossible to precisely predict the input parameters of the task scheduling problem. We briefly survey existing approaches for dealing with data uncertainties and discuss their relevance in the context of grid computing. We describe the stabilization process and analyze a scheduling algorithm that is intrinsically stable (i.e., it mitigates the effects of disturbances in input data at runtime). This algorithm is based on a decomposition of the application graph into convex sets of vertices. Finally, it is compared experimentally to pure on-line and well-known off-line algorithms. [ABSTRACT FROM AUTHOR]

Abstract   Agrobacterium rhizogenes is the etiological agent for hairy-root disease (also known as root-mat disease). This bacterium induces the neoplastic growth of plant cells that differentiate to form “hairy roots.” Morphologically, A. rhizogenes-induced hairy roots are very similar in structure to wild-type roots with a few notable exceptions: Root hairs are longer, more numerous, and root systems are more branched and exhibit an agravitropic phenotype. Hairy roots are induced by the incorporation of a bacterial-derived segment of DNA transferred (T-DNA) into the chromosome of the plant cell. The expression of genes encoded within the T-DNA promotes the development and production of roots at the site of infection on most dicotyledonous plants. A key characteristic of hairy roots is their ability to grow quickly in the absence of exogenous plant growth regulators. As a result, hairy roots are widely used as a transgenic tool for the production of metabolites and for the study of gene function in plants. Researchers have utilized this tool to study root development and root–biotic interactions, to overexpress proteins and secondary metabolites, to detoxify environmental pollutants, and to increase drought tolerance. In this review, we provide an up-to-date overview of the current knowledge of how A. rhizogenes induces root formation, on the new uses for A. rhizogenes in tissue culture and composite plant production (wild-type shoots with transgenic roots), and the recent development of a disarmed version of A. rhizogenes for stable transgenic plant production. [ABSTRACT FROM AUTHOR]

The Actinobacteria constitute one of the main phyla of Bacteria. Presently, no morphological and very few molecular characteristics are known which can distinguish species of this highly diverse group. In this work, we have analyzed the genomes of four actinobacteria (viz. Mycobacterium leprae TN, Leifsonia xyli subsp. xyli str. CTCB07, Bifidobacterium longum NCC2705 and Thermobifida fusca YX) to search for proteins that are unique to Actinobacteria. Our analyses have identified 233 actinobacteria-specific proteins, homologues of which are generally not present in any other bacteria. These proteins can be grouped as follows: (i) 29 proteins uniquely present in most sequenced actinobacterial genomes; (ii) 6 proteins present in almost all actinobacteria except Bifidobacterium longum and another 37 proteins absent in B. longum and few other species; (iii) 11 proteins which are mainly present in Corynebacterium, Mycobacterium and Nocardia (CMN) subgroup as well as Streptomyces, T. fusca and Frankia sp., but they are not found in Bifidobacterium and Micrococcineae; (iv) 8 proteins that are specific for T. fusca and Streptomyces species, plus 2 proteins also present in the Frankia species; (v) 13 proteins that are specific for the Corynebacterineae or the CMN group; (vi) 14 proteins only found in Mycobacterium and Nocardia; (vii) 24 proteins unique to different Mycobacterium species; (viii) 8 proteins specific to the Micrococcineae; (ix) 85 proteins which are distributed sporadically in actinobacterial species. Additionally, many examples of lateral gene transfer from Actinobacteria to Magnetospirillum magnetotacticum have also been identified. The identified proteins provide novel molecular means for defining and circumscribing the Actinobacteria phylum and a number of subgroups within it. The distribution of these proteins also provides useful information regarding interrelationships among the actinobacterial subgroups. Most of these proteins are of unknown function and studies aimed at understanding their cellular functions should reveal common biochemical and physiological characteristics unique to either all actinobacteria or particular subgroups of them. The identified proteins also provide potential targets for development of drugs that are specific for actinobacteria. [ABSTRACT FROM AUTHOR]

Abstract Xylella fastidiosa is a xylem-limited phytopathogen responsible for diseases in several plants such as citrus and coffee. Analysis of the bacterial genome revealed some putative pathogenicity-related genes that could help to elucidate the molecular mechanisms of plantpathogen interactions. In the present work, the transcription of three genes of the bacterium, grown in defined and rich media and also in media containing host plant extracts (sweet orange, ponkan and coffee) was analyzed by RT-PCR. The pilS gene, which encodes A sensor histidine kinase responsible for the biosynthesis of fimbriae, was transcribed when the bacterium was grown in more complex media such as PW and in medium containing plant extracts. The xps genes (xpsL and xpsE) which are related to the type II secretion system were also detected when the bacterium was grown in rich media and media with ponkan and coffee extracts. It was thus observed that pilS and xpsEL genes of X. fastidiosa can be modulated by environmental factors and their expression is dependent on the nutritional status of the growth medium. [ABSTRACT FROM AUTHOR]

Hydroxyphenylpyruvate reductase (HPPR) is an enzyme involved in the biosynthesis of rosmarinic acid in Lamiaceae reducing hydroxyphenylpyruvates in dependence of NAD(P)H to the corresponding hydroxyphenyllactates. The HPPR protein was purified from suspension cells of Coleus blumei accumulating high levels of rosmarinic acid by ammonium sulfate precipitation, anion exchange chromatography, hydroxylapatite chromatography, chromatography on 2',5'-ADP-Sepharose 4B and SDS-polyacrylamide gel electrophoresis. The protein was tryptically digested and the peptides sequenced. Sequence information was used to isolate a full-length cDNA-clone for HPPR (EMBL accession number AJ507733) by RT-PCR, screening of a C. blumei cDNA-library and 5'-RACE-PCR. The open reading frame of the HPPR-cDNA consists of 939 nucleotides encoding a protein of 313 amino acid residues. The sequence showed that HPPR belongs to the family of D-isomer-specific 2-hydroxyacid dehydrogenases. The HPPR-cDNA was heterologously expressed in Escherichia coli and the protein was shown to catalyse the NAD(P)H-dependent reduction of 4-hydroxyphenylpyruvate to 4-hydroxyphenyllactate and 3,4-dihydroxyphenylpyruvate to 3,4-dihydroxyphenyllactate. [ABSTRACT FROM AUTHOR]