Initial characteristics of RbcX proteins from Arabidopsis thaliana

Form I of Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) is composed of eight large (RbcL) and eight small (RbcS) subunits. Assembly of these subunits into a functional holoenzyme requires the assistance of additional assembly factors. One such factor is RbcX, which has been demonstrated to act as a chaperone in the assembly of most cyanobacterial Rubisco complexes expressed in heterologous system established in Escherichia coli cells. Analysis of Arabidopsis thaliana genomic sequence revealed the presence of two genes encoding putative homologues of cyanobacterial RbcX protein: AtRbcX1 (At4G04330) and AtRbcX2 (At5G19855). In general, both RbcX homologues seem to have the same function which is chaperone activity during Rubisco biogenesis. However, detailed analysis revealed slight differences between them. AtRbcX2 is localized in the stromal fraction of chloroplasts whereas AtRbcX1 was found in the insoluble fraction corresponding with thylakoid membranes. Search for putative “partners” using mass spectrometry analysis suggested that apart from binding to RbcL, AtRbcX1 may also interact with β subunit of chloroplast ATP synthase. Quantitative RT-PCR analysis of AtRbcX1 and AtRbcX2 expression under various stress conditions indicated that AtRbcX2 is transcribed at a relatively stable level, while the transcription level of AtRbcX1 varies significantly. In addition, we present the attempts to elucidate the secondary structure of AtRbcX proteins using CD spectroscopy. Presented results are the first known approach to elucidate the role of RbcX proteins in Rubisco assembly in higher plants

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services

Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology

Background: Switchgrass (Panicum virgatum L.) is a C4 perennial grass and widely popular as an important bioenergy crop. To accelerate the pace of developing high yielding switchgrass cultivars adapted to diverse environmental niches, the generation of genomic resources for this plant is necessary. The large genome size and polyploid nature of switchgrass makes whole genome sequencing a daunting task even with current technologies. Exploring the transcriptional landscape using next generation sequencing technologies provides a viable alternative to whole genome sequencing in switchgrass. Principal Findings: Switchgrass cDNA libraries from germinating seedlings, emerging tillers, flowers, and dormant seeds were sequenced using Roche 454 GS-FLX Titanium technology, generating 980,000 reads with an average read length of 367 bp. De novo assembly generated 243,600 contigs with an average length of 535 bp. Using the foxtail millet genome as a reference greatly improved the assembly and annotation of switchgrass ESTs. Comparative analysis of the 454-derived switchgrass EST reads with other sequenced monocots including Brachypodium, sorghum, rice and maize indicated a 70– 80 % overlap. RPKM analysis demonstrated unique transcriptional signatures of the four tissues analyzed in this study. More than 24,000 ESTs were identified in the dormant seed library. In silico analysis indicated that there are more than 2000 EST-SSRs in this collection. Expression of several orphan ESTs was confirmed by RT-PCR. Significance: We estimate that about 90 % of the switchgrass gene space has been covered in this analysis. This study nearl

A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system

Over the past few decades, several plant species, including Arabidopsis thaliana, Brachypodium distachyon and rice (Oryza sativa), have been adopted as model plants for various aspects of research. These species, especially Arabidopsis, have had vital roles in making fundamental discoveries and technological advances 1. However, all these model plants use C 3 photosynthe-sis, and discoveries made in these species are not always transferable to, or representative of, C 4 plants such as maize (Zea mays), sor-ghum (Sorghum bicolor) and millets, which are efficient fixers of atmospheric CO 2 into biomass. Thus, it is critical to develop a new model system for studies in these and many other C 4 plants 2. Foxtail millet (S. italica) is a cereal crop that was domesticated from its wild ancestor, green foxtail (Setaria viridis). These two species are evolutionarily close to several bioenergy crops, including switchgrass (Panicum virgatum), napiergrass (Pennisetum purpu-reum) and pearl millet (Pennisetum glaucum), and major cereals such as sorghum, maize and rice 3. In addition, extensive genetic diversity exists in Setaria, with approximately 30,000 accessions preserved in China, India, Japan and the United States 3 as valuable resources for gene-function dissection and elite-allele mining 4. In recent years, the whole-genome sequences of foxtail millet and green foxtail have been made available 5-9 , and both species have been proposed as C 4 model plant systems 3,6. Between these two species, foxtail millet is more suitable as a model plant due to the seed shattering and dor-mancy in green foxtail. Nevertheless, the relatively long life cycle (usually 4-5 months per generation) and large plant size (1-2 m in height) limit the use of foxtail millet as a model plant 3,10-12. To overcome such limitations, we have recently developed a large fox-tail millet ethyl methane sulfonate (EMS)-mutagenized population using Jingu21, a high-yield, high-grain-quality elite variety widely grown in north China in the past few decades. From the mutant population, we identified a miniature mutant (dubbed xiaomi) with a life cycle similar to that of Arabidopsis. Subsequently, we developed genomics and transcriptomics resources and a protocol for efficient transformation of xiaomi, as essential parts of the toolbox for the research community

North American Wild Relatives of Grain Crops

The wild-growing relatives of the grain crops are useful for long-term worldwide crop improvement research. There are neglected examples that should be accessioned as living seeds in gene banks. Some of the grain crops, amaranth, barnyard millet, proso millet, quinoa, and foxtail millet, have understudied unique and potentially useful crop wild relatives in North America. Other grain crops, barley, buckwheat, and oats, have fewer relatives in North America that are mostly weeds from other continents with more diverse crop wild relatives. The expanding abilities of genomic science are a reason to accession the wild species since there are improved ways to study evolution within genera and make use of wide gene pools. Rare wild species, especially quinoa relatives in North American, should be acquired by gene banks in cooperation with biologists that already study and conserve at-risk plant populations. Many of the grain crop wild relatives are weeds that have evolved herbicide resistance that could be used in breeding new herbicide-resistant cultivars, so well-documented examples should be accessioned and also vouchered in gene banks

Cellular differentiation in the maize leaf is disrupted by bundle sheath defective mutations.

The mature maize leaf is characterised by a series of parallel veins that are surrounded by concentric rings of bundle sheath (BS) and mesophyll (M) cells. To identify genes that control cellular differentiation patterns in the leaf, we have isolated a group of mutations that specifically disrupt the differentiation of a single cell type. In maize bundle sheath defective (bsd) mutants, C4 photosynthetic development is perturbed in BS cells while M cells appear to develop normally. Two mutants, bsd1 and bsd2, have been characterised in detail. Analysis of these mutants, and the corresponding Bsd1 and Bsd2 genes is providing an insight into cellular processes regulating photosynthetic cell type differentiation in maize