Won Cheol Yim

A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world

Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that features nocturnal CO2 uptake, facilitates increased water-use efficiency (WUE), and enables CAM plants to inhabit water-limited environments such as semi-arid deserts or seasonally dry forests. Human population growth and global climate change now present challenges for agricultural production systems to increase food, feed, forage, fiber, and fuel production. One approach to meet these challenges is to increase reliance on CAM crops, such as Agave and Opuntia, for biomass production on semi-arid, abandoned, marginal, or degraded agricultural lands. Major research efforts are now underway to assess the productivity of CAM crop species and to harness the WUE of CAM by engineering this pathway into existing food, feed, and bioenergy crops. An improved understanding of CAM has potential for high returns on research investment. To exploit the potential of CAM crops and CAM bioengineering, it will be necessary to elucidate the evolution, genomic features, and regulatory mechanisms of CAM. Field trials and predictive models will be required to assess the productivity of CAM crops, while new synthetic biology approaches need to be developed for CAM engineering. Infrastructure will be needed for CAM model systems, field trials, mutant collections, and data management.

A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes

The proteins harboring RING finger motif(s) have been shown to mediate protein–protein interactions that are relevant to a variety of cellular processes. In an effort to elucidate the evolutionary dynamics of the rice RING finger protein family, we have attempted to determine their genomic locations, expression diversity, and co-expressed genes via in silico analysis and semi-quantitative RT–PCR. A total of 425 retrieved genes appear to be distributed over all 12 of the chromosomes of rice with different distributions, and are reflective of the evolutionary dynamics of the rice genome. A genome-wide dataset harboring 155 gene expression omnibus sample plates evidenced some degree of differential evolutionary fates between members of RING-H2 and RING-HC types. Additionally, responses to abiotic stresses, such as salinity and drought, demonstrated that some degree of expression diversity existed between members of the RING finger protein genes. Interestingly, we determined that one RING-H2 finger protein gene (Os04g51400) manifested striking differences in expression patterns in response to abiotic stresses between leaf and culm-node tissues, further revealing responses highly similar to the majority of randomly selected co-expressed genes. The gene network of genes co-expressed with Os04g51400 may suggest some role in the salt response of the gene. These findings may shed further light on the evolutionary dynamics and molecular functional diversity of these proteins in complex cellular regulations.

Expression diversity and evolutionary dynamics of rice duplicate genes

Duplicate genes are believed to be a major source of new gene functions over evolutionary time. In order to evaluate the evolutionary dynamics of rice duplicate genes, formed principally by paleoployploidization prior to the speciation of the Poaceae family, we have employed a public microarray dataset including 155 gene expression omnibus sample plates and bioinformatics tools. At least 57.4% of old ~70 million years ago (MYA) duplicate gene pairs exhibit divergences in expression over the given experimental set, whereas at least 50.9% of young ~7.7-MYA duplicate gene pairs were shown to be divergent. When grouping the rice duplicate genes according to functional categories, we noted a striking and significant enrichment of divergent duplicate metabolism-associated genes, as compared to that observed in non-divergent duplicate genes. While both non-synonymous substitution (Ka) and synonymous substitution (Ks) values between non- and divergent duplicate gene pairs evidenced significant differences, the Ka/Ks values between them exhibited no significant differences. Interestingly, the average numbers of conserved motifs of the duplicate gene pairs revealed a pattern of decline along with an increase in expression diversity, partially supporting the subfunctionalization model with degenerative complementation in regulatory motifs. Duplicate gene pairs with high local similarity (HLS) segments, which might be formed via conversion between rice paleologs, evidenced higher expression correlations than were observed in the gene pairs without the HLS segments; this probably resulted in an increased likelihood of gene conversion in promoters of the gene pairs harboring HLS segments. More than 60% of the rice gene families exhibited similar high expression diversity between members as compared to that of randomly selected gene pairs. These findings are likely reflective of the evolutionary dynamics of rice duplicate genes for gene retention.

PLANEX: the plant co-expression database

BackgroundThe PLAnt co-EXpression database (PLANEX) is a new internet-based database for plant gene analysis. PLANEX (http://planex.plantbioinformatics.org) contains publicly available GeneChip data obtained from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI). PLANEX is a genome-wide co-expression database, which allows for the functional identification of genes from a wide variety of experimental designs. It can be used for the characterization of genes for functional identification and analysis of a gene’s dependency among other genes. Gene co-expression databases have been developed for other species, but gene co-expression information for plants is currently limited.DescriptionWe constructed PLANEX as a list of co-expressed genes and functional annotations for Arabidopsis thaliana, Glycine max, Hordeum vulgare, Oryza sativa, Solanum lycopersicum, Triticum aestivum, Vitis vinifera and Zea mays. PLANEX reports Pearson’s correlation coefficients (PCCs; r-values) that distribute from a gene of interest for a given microarray platform set corresponding to a particular organism. To support PCCs, PLANEX performs an enrichment test of Gene Ontology terms and Cohen’s Kappa value to compare functional similarity for all genes in the co-expression database. PLANEX draws a cluster network with co-expressed genes, which is estimated using the k-mean method. To construct PLANEX, a variety of datasets were interpreted by the IBM supercomputer Advanced Interactive eXecutive (AIX) in a supercomputing center.ConclusionPLANEX provides a correlation database, a cluster network and an interpretation of enrichment test results for eight plant species. A typical co-expressed gene generates lists of co-expression data that contain hundreds of genes of interest for enrichment analysis. Also, co-expressed genes can be identified and cataloged in terms of comparative genomics by using the ‘Co-expression gene compare’ feature. This type of analysis will help interpret experimental data and determine whether there is a common term among genes of interest.

Evolution of non-specific lipid transfer protein (nsLTP) genes in the Poaceae family: their duplication and diversity.

Previously, the genes encoding non-specific lipid transfer proteins (nsLTPs) of the Poaceae family appear to evidence different genomic distribution and somewhat different shares of EST clones, which is suggestive of independent duplication(s) followed by functional diversity. To further evaluate the evolutionary fate of the Poaceae nsLTP genes, we have identified Ka/Ks values, conserved, mutated or lost cis-regulatory elements, responses to several elicitors, genome-wide expression profiles, and nsLTP gene-coexpression networks of both (or either) wheat and rice. The Ka/Ks values within each group and between groups appeared to be similar, but not identical, in both species. The conserved cis-regulatory elements, e.g. the RY repeat (CATGCA) element related to ABA regulation in group A, might be reflected in some degree of long-term conservation in transcriptional regulation postdating speciation. In group A, wheat nsLTP genes, with the exception of TaLTP4, evidenced responses similar to those of plant elicitors; however, the rice nsLTP genes evidenced differences in expression profiles, even though the genes of both species have undergone purifying selection, thereby suggesting their independent functional diversity. The expression profiles of rice nsLTP genes with a microarray dataset of 155 gene expression omnibus sample (GSM) plates suggest that subfunctionalization is not the sole mechanism inherent to the evolutionary history of nsLTP genes but may, rather, function in concert with other mechanism(s). As inferred by the nsLTP gene-coexpression networks, the functional diversity of nsLTP genes appears not to be randomized, but rather to be specialized in the direction of specific biological processes over evolutionary time.

Expressional diversity of wheat nsLTP genes: evidence of subfunctionalization via cis -regulatory divergence

Previously, the wheat non-specific lipid transfer proteins (TaLTP), members of a small multigene family, were reported to evidence a complex pattern of expression regulation. In order to assess further the expression diversity of the TaLTP genes, we have attempted to evaluate their expression profiles in responses to abiotic stresses, using semi-quantitative RT-PCR. The expression profiles generated herein revealed that the TaLTP genes in group A evidenced highly similar responses against abiotic stresses, whereas differential expression patterns among genes in each group were also observed. A total of seven promoters were fused to a GUS reporter gene and the recombinants were introduced into Arabidopsis, while three promoters evidenced non-detectible GUS activity. The promoters of TaLTP1, TaLTP7, and TaLTP10 included in group A drove strong expressions during plant development with overlapping patterns, in large part, but also exhibited distinct expression pattern, thereby suggesting subfunctionalization processing over evolutionary time. However, only trace expression in cotyledons, young emerged leaves, and epidermal cell layers of flower ovaries was driven by the promoter of TaLTP3 of group B. These results indicate that their distinct physiological functions appear to be accomplished by a subfunctionalization process involving degenerative mutations in regulatory regions.

Cross experimental analysis of microarray gene expression data from volatile organic compounds treated targets

DNA microarrays have revolutionized environmental research by enabling the discovery of genomic markers that reflect the toxic effect of various chemicals and by providing information on the underlying mechanisms. Microarray-based toxicogenomics approaches have become a popular tool to investigate potential risks of exposure to various environmental contaminants at the DNA level. Especially, the analysis of microarray data that are generated under various experimental conditions is critically important for validation of biomarkers and, thus, diagnosis and treatment of environmental targets. Presently, we identified commonly regulated genes whose expression level varied upon exposure to volatile organic compounds (VOCs) by performing cross-experimental analysis of public gene expression datasets using the RankProd algorithm. VOCs are chemical contaminants that often exhibit long-term adverse effects upon chronic exposure. Since VOCs are often used in household items and residential buildings, it is important to understand their effect on human health in a more systematic way. This cross-experiment resulted in a valid set of commonly regulated genes. The functional analysis of these differentially expressed genes (DEGs) generated several significantly over-represented Gene Ontology terms and identified metabolic pathways tightly-associated with cancer development. The functional analysis of identified up-regulated genes (RPL27, RPS6, RPS11, RPS27A, AURKA, FNTA, HSP90AB1) revealed concordance with genes related to various respiratory symptoms such as non-small cell lung cancer. The selected commonly regulated diseaserelated genes were also compared with the DEGs identified in previous analysis performed individually for validation of biomarkers.

Cross-experimental analysis of microarray gene expression datasets for in silico risk assessment of TiO2 nano-particles

As the production and usage of nanomaterials increase, there are growing concerns on the unidentified detrimental effect of nanoparticles on human health and environmental safety. Systematic assessments of the risks associated with exposure to nanoparticles are needed. DNA microarrays have emerged as a powerful tool for toxicology research. Microarraybased toxicogenomics research provides valuable information for understanding underling mechanisms of toxicological behavior of non-classic contaminants, including ultrafine nanoparticles. In this work, we investigated the effect of nano-titanium oxide exposure on human cells by analyzing the change in transcription levels of cellular DNA. Cross-experimental analysis of heterogeneous gene expression datasets was performed using the RankProd algorithm. Multiple gene expression omnibus series obtained from various experimental conditions were combined and used for risk assessment. Several commonly regulated genes were identified as being unaffected by the laboratory specific conditions. Pathway analysis revealed the genes as being associated with six major pathways: arachidonic acid metabolism, purine metabolism, pentose phosphate pathway, mitogen-activated protein kinase signaling pathway, synthesis and degradation of ketone bodies, and methionine metabolism. The identified differently expressed genes provide a robust set of markers for exposure analysis and risk assessment of titanium oxide nanoparticles.

Characterization of Expressed Genes Under Ozone Stress in Soybean

To identify the genes specifically or predominantly expressed in ozone-fumigated leaves of two soybean cultivars: Jinpumkong and Cheongjakong, expression levels of mRNA were investigated using differential banding patterns on agarose gel. A total of 408 bands differently expressed after ozone fumigation was identified; 153 of which were up-regulated while 225 were down-regulated. Using BLASTx, the putative functions of the expressed sequence tags were determined. The 178 ozone-regulated differentially expressed genes (DEGs) matched with the previously known genes with high significance. The putative functional classes of these DEGs were categorized by two databases: Gene Ontology and MIPS. Based on the Gene Ontology database, majority of the DEGS have molecular function related to transferase activity. Most of them are involved in the cellular and metabolic processes. Cytoplasmic part and cell part were the primary types of cellular component in the ozone-responding DEGs. Whereas findings using the MIPS database revealed the function distribution of up-regulated DEGs across all classes. Most of the ozone-regulated genes identified in this study are related to biotic and abiotic stresses. The characterized ESTs will serve as useful data to provide a better understanding of the molecular basis and transcript profiles.