Sugarcane proteomics: An update on current status, challenges, and future prospects.

Sugarcane is one of the most important commercial crops cultivated worldwide for the production of crystal sugar, ethanol, and other related by-products. Unlike other comparable monocots like sorghum, maize, and rice, sugarcane genome by virtue of its polyploidy nature remains yet to be fully deciphered. Proteomics-an established complementary tool to genomics is at its infancy in sugarcane as compared to the other monocots. However, with the surge in genomics research accomplished by next-generation sequencing platforms, sugarcane proteomics has gained momentum. This review summarizes the available literature from 1970 to 2014, which ensures a comprehensive coverage on sugarcane proteomics-a topic first of its kind to be reviewed. We herewith compiled substantial contributions in different areas of sugarcane proteomics, which include abiotic and biotic stresses, cell wall, organelle, and structural proteomics. The past decade has witnessed a paradigm shift in the pace with which sugarcane proteomics is progressing, as evident by the number of research publications. In addition to extensively reviewing the progress made thus far, we intend to highlight the scope in sugarcane proteomics, with an aspiration to instigate focused research on sugarcane to harness its full potential for the human welfare.

Molecular profiling of systemic acquired resistance (SAR)-responsive transcripts in sugarcane challenged with Colletotrichum falcatum.

Red rot disease of sugarcane caused by Colletotrichum falcatum is one of the serious constraints affecting the productivity of the crop. The strategy of employing systemic acquired resistance (SAR) against red rot yielded consistently good results at field level. However, elucidation of genes involved in the induction of SAR continues to be a challenging area of research for a critical understanding of red rot disease resistance in sugarcane. Here, temporal expression of 22 putative defense-related genes were analyzed by semiquantitative reverse transcription-PCR (RT-PCR) in red rot-susceptible cultivar (CoC 671) with response to priming using various SAR inducers, viz. benzothiadiazole (BTH), salicylic acid (SA), and C. falcatum elicitor. Among the 22 genes studied, 12 transcripts were found to be differentially expressed, of which seven transcripts represent phenylpropanoid pathway and five transcripts represent resistant gene analogues (RGAs). Differentially regulated phenylpropanoid pathway genes such as cinnamic acid 4-hydroxylase, 4-coumarate:coenzyme A ligase, chalcone synthase, and chalcone reductase were reported to play a major role in the regulation of phytoalexin synthesis, whereas R genes such as NBS-LRR genes and basal layer antifungal peptide (BAF) genes were upregulated upon SAR induction in response to pathogen challenge. These upregulated genes presumably play a potential role in SAR induction and might contribute to defense against C. falcatum.

Plant proteomics in India and Nepal: current status and challenges ahead.

Plant proteomics has made tremendous contributions in understanding the complex processes of plant biology. Here, its current status in India and Nepal is discussed. Gel-based proteomics is predominantly utilized on crops and non-crops to analyze majorly abiotic (49 %) and biotic (18 %) stress, development (11 %) and post-translational modifications (7 %). Rice is the most explored system (36 %) with major focus on abiotic mainly dehydration (36 %) stress. In spite of expensive proteomics setup and scarcity of trained workforce, output in form of publications is encouraging. To boost plant proteomics in India and Nepal, researchers have discussed ground level issues among themselves and with the International Plant Proteomics Organization (INPPO) to act in priority on concerns like food security. Active collaboration may help in translating this knowledge to fruitful applications.

Sugarcane proteomics: establishment of a protein extraction method for 2-DE in stalk tissues and initiation of sugarcane proteome reference map.

Sugarcane is an important commercial crop cultivated for its stalks and sugar is a prized commodity essential in human nutrition. Proteomics of sugarcane is in its infancy, especially when dealing with the stalk tissues, where there is no study to date. A systematic proteome analysis of stalk tissue yet remains to be investigated in sugarcane, wherein the stalk tissue is well known for its rigidity, fibrous nature, and the presence of oxidative enzymes, phenolic compounds and extreme levels of carbohydrates, thus making the protein extraction complicated. Here, we evaluated five different protein extraction methods in sugarcane stalk tissues. These methods are as follows: direct extraction using lysis buffer (LB), TCA/acetone precipitation followed by solubilization in LB, LB containing thiourea (LBT), and LBT containing tris, and phenol extraction. Both quantitative and qualitative protein analyses were performed for each method. 2-DE analysis of extracted total proteins revealed distinct differences in protein patterns among the methods, which might be due to their physicochemical limitations. Based on the 2-D gel protein profiles, TCA/acetone precipitation-LBT and phenol extraction methods showed good results. The phenol method showed a shift in pI values of proteins on 2-D gel, which was mostly overcome by the use of 2-D cleanup kit after protein extraction. Among all the methods tested, 2-D cleanup-phenol method was found to be the most suitable for producing high number of good-quality spots and reproducibility. In total, 30 and 12 protein spots commonly present in LB, LBT and phenol methods, and LBT method were selected and subjected to eLD-IT-TOF-MS/MS and nESI-LC-MS/MS analyses, respectively, and a reference map has been established for sugarcane stalk tissue proteome. A total of 36 nonredundant proteins were identified. This is a very first basic study on sugarcane stalk proteome analysis and will promote the unexplored areas of sugarcane proteome research.