Combinatorial natural products: from cloning to analysis.

Medicinal compounds from plants represent one of the largest and most diverse groups of plant secondary metabolites. The advent of advanced bioinformatics tools and modern genetic technology allowed for manipulation of biosynthetic pathways with the potential of generating novel chemical entities. First, public databases of secondary metabolite related enzymes were interrogated to identify relevant plant genes from vinca rosea (Catharanthus roseus) and other species. Genes of interest were tested after cloning by transfection into tobacco cell cultures using DNA viral vectors. The biosynthetic enzymes coded by these genes were over-expressed in the host. Automated solvent extraction procedure was employed to extract secondary metabolites from plant leaf tissues and transfected tobacco cell culture samples. The composition of the extracts was analyzed by state of the art bioanalytical methods such as high performance liquid chromatography and capillary electrophoresis to monitor changes in secondary metabolite patterns.

Identification of putative plant cold responsive regulatory elements by gene expression profiling and a pattern enumeration algorithm.

A pattern enumeration algorithm named GBSSR has been developed to analyse co-expressed gene groups identified through gene chip expression profiling to search for putative cis-regulatory elements, an important step toward understanding transcriptional factors, quantitative trait loci and gene regulatory networks. Without making any statistical assumptions, this algorithm establishes the frequency distribution of all eligible 6-15 bp strings by extensive bootstrap sampling from an entire genome worth of promoters, enabling those over-represented in a co-expressed gene group to be identified. Using a well-studied plant cold responsive gene system as a positive control, several known cold responsive elements were identified as top ranking candidates, along with some potentially novel ones. A typical analysis of 40 co-expressed genes takes a relatively inexpensive Linux cluster with 32 x 1.4 GHz Intel CPUs about 7 days to process.

Transcriptional control of nutrient partitioning during rice grain filling.

Cereal grains accumulate carbohydrates, storage proteins and fatty acids via different pathways during their development. Many genes that participate in nutrient partitioning during grain filling and that affect starch quality have been identified. To understand how the expression of these genes is coordinated during grain development, a genomic approach to surveying the participation and interactions of all the pathways is necessary. Using recently published rice genome information, we designed a rice GeneChip microarray that covers half the rice genome. By monitoring the expression of 21,000 genes in parallel, we identified genes involved in the grain filling process and found that the expression of genes involved in different pathways is coordinately controlled in a synchronized fashion during grain filling. Interestingly, a known promoter element in genes encoding seed storage proteins, AACA, is statistically over-represented among the 269 genes in different pathways with diverse functions that are significantly up-regulated during grain filling. By expression pattern matching, a group of transcription factors that have the potential to interact with this element was identified. We also found that most genes in the starch biosynthetic pathway show multiple distinct spatial and temporal expression patterns, suggesting that different isoforms of a given enzyme are expressed in different tissues and at different developmental stages. Our results reveal key regulatory machinery and provide an opportunity for modifying multiple pathways by manipulating key regulatory elements for improving grain quality and quantity.

Transcription factor binding study by capillary zone electrophoretic mobility shift assay.

Regulation of gene expression through interaction of proteins with specific DNA sequences is a central issue in functional genomics. Capillary electrophoretic mobility shift assay is an efficient novel method for the investigation of sequence specific protein-DNA interactions, allowing rapid and sensitive quantification of the complex formation. In this paper, we present a pilot study on capillary zone electrophoretic mobility shift assay (CZEMSA) to investigate the interaction between the transcription factors of HeLa nuclear extract and Sp1-specific fluorescein-labeled oligonucleotide, using the unlabeled probe as competitor. The mobility shift assay was accomplished by CZE in coated capillaries without polymeric buffer additives. Specificity of the DNA protein complex formation was verified by competition experiments, as well as by supershift assay with an anti-Sp1 antibody. The applied electric field strength did not affect the stability of DNA-protein complex during the electrophoretic analysis, allowing rapid identification and quantification of the protein DNA interaction. A practical application to study the interaction between Oryza sativa MADS-box transcription factor 4 (OsMADS4) and its consensus sequence is also reported.

Development of a system for the study of protein-protein interactions in planta: characterization of a TATA-box binding protein complex in Oryza sativa.

We describe a simple, rapid method for protein complex purification in planta. Using a biotin peptide as an affinity tag with TATA-box binding protein (TBP), 86 unique proteins present in the purified complex were identified by tandem mass spectrometry. We identified proteins known to be associated with TBP, and many other proteins involved in pre-mRNA processing and chromatin remodeling. The identification of these novel protein-protein associations will upon further investigations provide new insights into the mechanisms of mRNA transcription and pre-mRNA processing.

A network of rice genes associated with stress response and seed development.

We used a systematic approach to build a network of genes associated with developmental and stress responses in rice by identifying interaction domains for 200 proteins from stressed and developing tissues, by measuring the associated gene expression changes in different tissues exposed to a variety of environmental, biological, and chemical stress treatments, and by localizing the cognate genes to regions of stress-tolerance trait genetic loci. The integrated data set suggests that similar genes respond to environmental cues and stresses, and some may also regulate development. We demonstrate that the data can be used to correctly predict gene function in monocots and dicots. As a result, we have identified five genes that contribute to disease resistance in Arabidopsis.

Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses.

Numerous studies have shown that transcription factors are important in regulating plant responses to environmental stress. However, specific functions for most of the genes encoding transcription factors are unclear. In this study, we used mRNA profiles generated from microarray experiments to deduce the functions of genes encoding known and putative Arabidopsis transcription factors. The mRNA levels of 402 distinct transcription factor genes were examined at different developmental stages and under various stress conditions. Transcription factors potentially controlling downstream gene expression in stress signal transduction pathways were identified by observed activation and repression of the genes after certain stress treatments. The mRNA levels of a number of previously characterized transcription factor genes were changed significantly in connection with other regulatory pathways, suggesting their multifunctional nature. The expression of 74 transcription factor genes responsive to bacterial pathogen infection was reduced or abolished in mutants that have defects in salicylic acid, jasmonic acid, or ethylene signaling. This observation indicates that the regulation of these genes is mediated at least partly by these plant hormones and suggests that the transcription factor genes are involved in the regulation of additional downstream responses mediated by these hormones. Among the 43 transcription factor genes that are induced during senescence, 28 of them also are induced by stress treatment, suggesting extensive overlap responses to these stresses. Statistical analysis of the promoter regions of the genes responsive to cold stress indicated unambiguous enrichment of known conserved transcription factor binding sites for the responses. A highly conserved novel promoter motif was identified in genes responding to a broad set of pathogen infection treatments. This observation strongly suggests that the corresponding transcription factors play general and crucial roles in the coordinated regulation of these specific regulons. Although further validation is needed, these correlative results provide a vast amount of information that can guide hypothesis-driven research to elucidate the molecular mechanisms involved in transcriptional regulation and signaling networks in plants.

A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).

The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.