Pseudogenes and Their Genome-Wide Prediction in Plants.

Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pseudogenes are functionless, but recent evidence demonstrates that some of them have potential roles in regulation. The majority of pseudogenes are generated from functional progenitor genes either by gene duplication (duplicated pseudogenes) or retro-transposition (processed pseudogenes). Pseudogenes are primarily identified by comparison to their parent genes. Bioinformatics tools for pseudogene prediction have been developed, among which PseudoPipe, PSF and Shiu's pipeline are publicly available. We compared these three tools using the well-annotated Arabidopsis thaliana genome and its known 924 pseudogenes as a test data set. PseudoPipe and Shiu's pipeline identified ~80% of A. thaliana pseudogenes, of which 94% were shared, while PSF failed to generate adequate results. A need for improvement of the bioinformatics tools for pseudogene prediction accuracy in plant genomes was thus identified, with the ultimate goal of improving the quality of genome annotation in plants.

Identification of drought-induced transcription factors in Sorghum bicolor using GO term semantic similarity.

Stress tolerance in plants is a coordinated action of multiple stress response genes that also cross talk with other components of the stress signal transduction pathways. The expression and regulation of stress-induced genes are largely regulated by specific transcription factors, families of which have been reported in several plant species, such as Arabidopsis, rice and Populus. In sorghum, the majority of such factors remain unexplored. We used 2DE refined with MALDI-TOF techniques to analyze drought stress-induced proteins in sorghum. A total of 176 transcription factors from the MYB, AUX_ARF, bZIP, AP2 and WRKY families of drought-induced proteins were identified. We developed a method based on semantic similarity of gene ontology terms (GO terms) to identify the transcription factors. A threshold value (≥ 90%) was applied to retrieve total 1,493 transcription factors with high semantic similarity from selected plant species. It could be concluded that the identified transcription factors regulate their target proteins with endogenous signals and environmental cues, such as light, temperature and drought stress. The regulatory network and cis-acting elements of the identified transcription factors in distinct families are involved in responsiveness to auxin, abscisic acid, defense, stress and light. These responses may be highly important in the modulation of plant growth and development.

Disease Resistance Gene Analogs (RGAs) in Plants.

Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens' resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed.

Identification of salt treated proteins in sorghum using gene ontology linkage.

Sorghum bicolor (L.) is an important crop of arid and semi arid zones with most of its varieties tolerant to drought, heat and salt stress. Functional identification of many salt tolerant proteins has been reported in Arabidopsis, rice and other plants, however only little functional information has been predicted in sorghum till date. A 2-D gel electrophoresis based proteomic approach with MALDI-TOF mass spectrometer was utilized to analyze the salt stress response of sorghum. Major changes in protein complement were observed at 200 mM NaCl in hydroponic culture after 96 h of salt-stress. Highly expressed five proteins were excised for functional identification. We developed shortest path (SP) analysis based method on Gene Ontology (GO) hierarchy using sum of GO-term's semantic similarities. In this study, we observed that majority of expressed proteins belonged to the functional category of energy production and conversion, signal transduction mechanisms and ribosome maturation. These identified functions suggest a distinct mechanism of salt-stress adaptation in sorghum plant. The proposed method in this paper potentially has great importance to further understanding of newly identified proteins that can help in plant development.

Identification of MFS proteins in sorghum using semantic similarity.

The antiporters, uniporters and symporters are the functional classes of MFS that play major role in ions homeostasis, regulation of pumps and channels, membrane structure, transporters activity in tolerance to abiotic stresses. Major facilitator superfamily (MFS) encodes Na(+)/H(+) antiporter that are considered as being sensors of the molecule transports. A large number of MFS proteins have been identified in several plants, rice, maize, Arabidopsis etc. However, the majority of proteins in sorghum are described as putative, uncharacterized till date. This suggested that identified proteins of MFS in sorghum are far from saturation. Hence, we developed gene ontology (GO) terms semantic similarity based method using GOSemSim measure of R package. As a result, total 2,568 high (100 %) semantic similar orthologous proteins from 7 plant species were obtained. These data were used to predict function of 257 putative uncharacterized proteins from 18 families of MFS in Sorghum. Consequently, the identified proteins belonged to the function of regulation of pumps and channels, membrane structure, transporters activity, ions homeostasis, transporter mechanisms and binding process. These identified functions appear to have a distinct mechanism of salt-stress adaptation in plants. The proposed method will help in further identifying new proteins that can help in the development of agronomically and economically important plants.

Identification of drought responsive proteins using gene ontology hierarchy.

The availability of the complete genome sequences has facilitated access to essential information to identify proteins. The determination of Arabidopsis genome sequence has had a great impact to annotate data. The genome sequencing of Sorghum bicolor has been only recently completed and hither to the global response to abiotic stresses in this important crop remains largely unexplored. We used 2-D gel electrophoresis based proteomic approach refined with MALDI-TOF to analyze drought-stress response proteins in sorghum. Major changes in protein complement of sorghum were observed in hydroponic cultures at 96 hours under drought stress. Six most highly expressed proteins were excised for functional identification. Here, we developed a method to obtain functional distances between GO terms and analyzed distance values to allocate shortest path (SP) in GO hierarchy. The shortest paths for expressed proteins were noted for most informative common ancestor (MICA) terms, viz. binding, catalytic activity and primary metabolic process. We observed the expressed proteins belonged to the functional group of signal transduction mechanisms, carbohydrate transport and metabolism. These identified functions of proteins suggest a different mechanism of drought-stress tolerant in sorghum. The novel approach applied in this study may have great importance in further identifying proteins involved in abiotic and biotic stress conditions in crops.