Plant Kinesin Repertoires Expand with New Domain Architecture and Contract with the Loss of Flagella.

Kinesins are eukaryotic microtubule motor proteins subdivided into conserved families with distinct functional roles. While many kinesin families are widespread in eukaryotes, each organismal lineage maintains a unique kinesin repertoire composed of many families with distinct numbers of genes. Previous genomic surveys indicated that land plant kinesin repertoires differ markedly from other eukaryotes.

Sequential loss of dynein sequences precedes complete loss in land plants.

Dynein motor proteins, often considered to be missing in land plants, are found in plants that reproduce with flagellated sperm.

Use of Dual RNA-seq for Systems Biology Analysis of and Interaction.

The interaction between and is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore, the authors undertook a systems biology approach involving dual RNA-seq to determine the simultaneous response from the host and the pathogen. What was dramatically highlighted in the analysis is the uniformity in the development patterns of gene expression of the host and the pathogen during infection.

Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice.

The interactions between transcription factors (TFs) and cis-acting regulatory elements (CREs) provide crucial information on the regulation of gene expression. The determination of TF-binding sites and CREs experimentally is costly and time intensive. An in silico identification and annotation of TFs, and the prediction of CREs from rice are made possible by the availability of whole genome sequence and transcriptome data.

Evolution of Eukaryal and Archaeal Pseudouridine Synthase Pus10.

In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to mU54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB.

The Pathogenesis-Related Maize Seed () Gene Plays a Role in Resistance to Infection and Aflatoxin Contamination.

is an opportunistic plant pathogen that colonizes and produces the toxic and carcinogenic secondary metabolites, aflatoxins, in oil-rich crops such as maize ( L.). Pathogenesis-related (PR) proteins serve as an important defense mechanism against invading pathogens by conferring systemic acquired resistance in plants.

Image-Based Analysis to Dissect Vertical Distribution and Horizontal Asymmetry of Conspecific Root System Interactions in Response to Planting Densities, Nutrients and Root Exudates in Arabidopsis thaliana.

Intraspecific competition is an important plant interaction that has been studied extensively aboveground, but less so belowground, due to the difficulties in accessing the root system experimentally. Recent in vivo and in situ automatic imaging advances help understand root system architecture. In this study, a portable imaging platform and a scalable transplant technique were applied to test intraspecific competition in .

A Network Approach of Gene Co-expression in the / Pathosystem to Map Host/Pathogen Interaction Pathways.

A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen and its plant host during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in such as jasmonic acid, ethylene, and reactive oxygen species (ROS).

A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize.

Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM) is presented here as an aid to the research community for this valuable crop species.

Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource.

Background: Physcomitrella patens, a haploid dominant plant, is fast becoming a useful molecular genetics and bioinformatics tool due to its key phylogenetic position as a bryophyte in the post-genomic era. Genome sequences from select reference species were compared bioinformatically to Physcomitrella patens using reciprocal blasts with the InParanoid software package. A reference protein interaction database assembled using MySQL by compiling BioGrid, BIND, DIP, and Intact databases was queried for moss orthologs existing for both interacting partners.

Reproductive Toxicity and Life History Study of Silver Nanoparticle Effect, Uptake and Transport in .

Concerns about nanotechnology have prompted studies on how the release of these engineered nanoparticles impact our environment. Herein, the impact of 20 nm silver nanoparticles (AgNPs) on the life history traits of was studied in both above- and below-ground parts, at macroscopic and microscopic scales. Both gross phenotypes (in contrast to microscopic phenotypes) and routes of transport and accumulation were investigated from roots to shoots.

Role of forefinger and thumb loops in production of Ψ54 and Ψ55 in tRNAs by archaeal Pus10.

Pseudouridines (Ψ) are found in structurally and functionally important regions of RNAs. Six families of Ψ synthases, TruA, TruB, TruD, RsuA, RluA, and Pus10 have been identified. Pus10 is present in Archaea and Eukarya.

Phytotoxicity, accumulation and transport of silver nanoparticles by Arabidopsis thaliana.

The widespread availability of nano-enabled products in the global market may lead to the release of a substantial amount of engineered nanoparticles in the environment, which frequently display drastically different physiochemical properties than their bulk counterparts. The purpose of the study was to evaluate the impact of citrate-stabilised silver nanoparticles (AgNPs) on the plant Arabidopsis thaliana at three levels, physiological phytotoxicity, cellular accumulation and subcellular transport of AgNPs. The monodisperse AgNPs of three different sizes (20, 40 and 80 nm) aggregated into much larger sizes after mixing with quarter-strength Hoagland solution and became polydisperse.

A predicted protein interactome for rice.

Background: Protein-protein interactions (PPIs) create the steps in signaling and regulatory networks central to most fundamental biological processes. It is possible to predict these interactions by making use of experimentally determined orthologous interactions in other species.

Results: In this study, prediction of PPIs in rice was carried out by the interolog method of mapping deduced orthologous genes to protein interactions supported by experimental evidence from reference organisms.

A common structural blueprint for plant UDP-sugar-producing pyrophosphorylases.

Plant pyrophosphorylases that are capable of producing UDP-sugars, key precursors for glycosylation reactions, include UDP-glucose pyrophosphorylases (A- and B-type), UDP-sugar pyrophosphorylase and UDP-N-acetylglucosamine pyrophosphorylase. Although not sharing significant homology at the amino acid sequence level, the proteins share a common structural blueprint. Their structures are characterized by the presence of the Rossmann fold in the central (catalytic) domain linked to enzyme-specific N-terminal and C-terminal domains, which may play regulatory functions.

The word landscape of the non-coding segments of the Arabidopsis thaliana genome.

Background: Genome sequences can be conceptualized as arrangements of motifs or words. The frequencies and positional distributions of these words within particular non-coding genomic segments provide important insights into how the words function in processes such as mRNA stability and regulation of gene expression.

Results: Using an enumerative word discovery approach, we investigated the frequencies and positional distributions of all 65,536 different 8-letter words in the genome of Arabidopsis thaliana.

LATERAL ORGAN FUSION1 and LATERAL ORGAN FUSION2 function in lateral organ separation and axillary meristem formation in Arabidopsis.

Plant organs are generated from meristems throughout development. Patterning and elaboration of organ primordia occur as a result of organized cell division and expansion, processes that are likely to be controlled, in part, by meristem-derived signals. Communication between the meristem and lateral organs is crucial for meristem maintenance and organ patterning, and organ boundaries are thought to be important for mediating this communication.

The nematode resistance allele at the rhg1 locus alters the proteome and primary metabolism of soybean roots.

Heterodera glycines, the soybean cyst nematode (SCN), causes the most damaging chronic disease of soybean (Glycine max). Host resistance requires the resistance allele at rhg1. Resistance destroys the giant cells created in the plant's roots by the nematodes about 24 to 48 h after commencement of feeding.

UDP-glucose pyrophosphorylase is not rate limiting, but is essential in Arabidopsis.

UDP-glucose pyrophosphorylase (UGPase) produces UDP-glucose which is essential for sucrose and polysaccharide synthesis. Using Arabidopsis, we demonstrated that two UGPase genes (UGP1 and UGP2) are differentially expressed in a variety of organs, with UGP1 being pre-dominant. Co-expression analyses of UGP genes suggest that UGP1 is closely co-regulated with carbohydrate metabolism genes, late embryogenesis and seed loading, while UGP2 is co-regulated with stress response genes, fertilized flowers and photosynthetic genes.

Novel localization of callose in the spores of Physcomitrella patens and phylogenomics of the callose synthase gene family.

Background And Aims: Callose involvement in spore development is a plesiomorphic feature of land plants. Correlated light, fluorescence and immuno-electron microscopy was conducted on the developing spores of Physcomitrella patens to probe for callose. Using a bioinformatic approach, the callose synthase (PpCalS) genes were annotated and PpCalS and AtCalS gene families compared, testing the hypothesis that an exine development orthologue is present in P.

Impact of chloroplastic- and extracellular-sourced ROS on high light-responsive gene expression in Arabidopsis.

The expression of 28 high light (HL)-responsive genes of Arabidopsis was analysed in response to environmental and physiological factors known to influence the expression of the HL-responsive gene, ASCORBATE PEROXIDASE2 (APX2). Most (81%) of the HL-responsive genes, including APX2, required photosynthetic electron transport for their expression, and were responsive to abscisic acid (ABA; 68%), strengthening the impression that these two signals are crucial in the expression of HL-responsive genes. Further, from the use of mutants altered in reactive oxygen species (ROS) metabolism, it was shown that 61% of these genes, including APX2, may be responsive to chloroplast-sourced ROS.

A predicted interactome for Arabidopsis.

The complex cellular functions of an organism frequently rely on physical interactions between proteins. A map of all protein-protein interactions, an interactome, is thus an invaluable tool. We present an interactome for Arabidopsis (Arabidopsis thaliana) predicted from interacting orthologs in yeast (Saccharomyces cerevisiae), nematode worm (Caenorhabditis elegans), fruitfly (Drosophila melanogaster), and human (Homo sapiens).

Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening.

Systematic identification of direct protein-protein interactions is often hampered by difficulties in expressing and purifying the corresponding full-length proteins. By taking advantage of the modular nature of many regulatory proteins, we attempted to simplify protein-protein interactions to the corresponding domain-ligand recognition and employed peptide arrays to identify such binding events. A group of 12 Src homology (SH) 3 domains from eight human proteins (Swiss-Prot ID: SRC, PLCG1, P85A, NCK1, GRB2, FYN, CRK) were used to screen a peptide target array composed of 1536 potential ligands, which led to the identification of 921 binary interactions between these proteins and 284 targets.

Differential tissue/organ-dependent expression of two sucrose- and cold-responsive genes for UDP-glucose pyrophosphorylase in Populus.

Plant UDP-glucose (UDPG) pyrophosphorylase (UGPase) is involved in the production/metabolism of UDPG, a key metabolite for sucrose and cell wall biosynthesis. Two highly similar cDNAs (UGP1 and UGP2) corresponding to UGPase were isolated from cDNA libraries of hybrid aspen (Populus tremula x tremuloides). Expression of both UGPs, as studied by DNA microarrays and EST abundance, was compared to that of three sucrose synthase genes (SUS1-3), also involved in UDPG synthesis.

Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis.

The whole-genome response of Arabidopsis (Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a cis-element found in its promoter conferred induction (+1), repression (-1), or no transcriptional change (0) during cold stress.