Current Proteomics - Volume 9, Issue 4, 2012

Flooding is one of the most severe environmental factors which impairs plants growth and yield worldwide. The mechanism of plant response towards flooding includes adjustment of carbohydrate metabolism and disease/defense response. It triggers several signaling pathways that involve regulation of certain genes and changes in protein expression. Plants subjected to flooding stress may adapt many strategies to survive including maintaining the functional conformation of proteins and preventing the aggregation of non-native proteins. Proteomic analyses of response towards flooding stress have been performed in combination with other abiotic stresses. The changes in protein expression in response to flooding stress have been reported but need to link these response mechanisms with specific reference to organ and organelle level is still to be quenched. This chapter will describe the effects of flooding on protein expression at organ and organelles levels which alter various cellular processes. The description of protein changes in flooding stressed plants at various levels of organizations will provide a useful tool for the development of strategies for genetically engineered stress tolerant crop plants.

Among the environmental stresses, drought is the most severe stress in agriculture and improving yield under drought stress is a major goal for plant breeders. Drought or water deficit affects directly the cellular metabolism of plant leading to a significant reduction in growth index and ultimately crop yield. Several reports emphasized the existence of complex network in the cell in response to drought stress. Alterations in the expression of proteins play main role in the network and proteomics has the ability to discover the responsible proteins. The extent of information, that breeders have now, offers them new tools for breeding and the main strategy would be blending all knowledge on the traits sustaining yield under drought and accumulation of the most effective proteins or genes into elite genotypes without detrimental effects on yield potential. It ultimately will result in development of new cultivars with high yield potential and stability in dry environments. Although a number of reviews devoted to plant proteomics are available, review articles dedicated to plant cell proteins response under drought stress are very scanty. In the present review, an attempt has been made to summarize all significant contributions related to drought stresses and their impacts on cell, organelle and plasma membrane proteomes for better understanding of plants abiotic stress tolerance mechanism at protein level. This review provides new insights into the plants drought stress response mechanisms for future development of genetically engineered drought stress tolerant crop plants.

Here we named silicon (Si) as “multitalented micronutrient”. Silicon plays important role in inducing biotic and abiotic stress tolerance in plants. The transport of Si from soil has been studied in detail by numerous research groups and a number of Si transporter genes have been identified in different crop plants. However, there is still a need to mine potential candidate proteins and metabolites, altered due to the application of Si. Research on the impact of Si in animals is still in its infancy, but its impact on bone formation and remedy for osteoporosis has been examined in detail. In this review, we provide an updated-information on the role of Si in plant and animal physiology and metabolism. We also present our views on how OMICS-based approaches can elucidate the role of Si in understanding its involvement in the physiology and metabolism of crops and animals.

The interaction between proteins and sugars, termed as glycation has been a subject of increasing study over the past decade. The aim of the present study was to investigate the non-enzymatic interaction of thiol- proteinase inhibitor (cystatin) with three reducing sugars glucose, fructose and ribose. The behaviour of glycated cystatin was monitored by change in its hyperchromicity at 280nm, tryptophan fluorescence and Maillard fluorescence. The antipapain activity of glycated cystatin was found to be significantly lower than its non-glycated form. It was found that the incubation of cystatin with all the three sugars led to a parallel decrease in tryptophan fluorescence, enhancement in Maillard fluorescence and hyperchromicity in the UV-region. Among the three sugars studied ribose was found to be the most active in inducing structural and conformational alterations in the protein.

Hepatocellular carcinoma (HCC) is currently of great concern due to its poor patient outcome despite the various therapies available. The cause of HCC usually stems from liver cirrhosis, which mainly results from Hepatitis B virus (HBV) or Hepatitis C virus (HCV) infection or environmental and genetic risk factors like alcoholism. Despite the preventive measures available now, the incidence and mortality rates are still high due to chronic infection, making it the third leading cause of cancer –related deaths in the world today and claiming approximately 600,000 lives annually. Patients are usually also diagnosed with HCC later in the stages, leading to a very poor prognosis. It is therefore imperative that a more effective treatment method is developed such that patient survival rates may be improved from current statistics of less than 50%. The role of microRNAs (miRNAs) in the regulation of gene expression and cellular development makes it an important player in cancer initiation and progression. Mir-181a has been shown to be an important miRNA involved in HCC. In this study, we propose to investigate the potential effects of miR-181a in HepG2 cells and also to explore the mechanisms in which it works in controlling cell fate. As chemotherapy is widely used in liver cancer treatment, we also study the use of miR-181a along with chemotherapy (i.e. Cisplatin). Using iTRAQ-coupled 2D LC-MS/MS analysis, we report here the study of protein profile of HepG2 cells transfected with miR-181a mimic and inhibitor separately. Three main types of cellular proteins including metabolic enzymes, protein binding and stress proteins displayed changes. The changes in the level of proteins involved in important cancer processes like cell growth were further supported by a western blot analysis. MiR-181a was subsequently found to increase HepG2 cell viability while the inhibitor displayed the opposite effect. The inhibitor also sensitized HepG2 cells to cisplatin. Cell cycle analysis showed that the inhibitor retards cell cycle progression by decreasing the proportion of cells in S and G2/M phases. Our findings therefore provide molecular evidence on the mechanism of action of miR-181a inhibitor, including its beneficial effects in inhibiting the development of HCC.

Acetylcholine (ACh) biosensor is developed based on mediator-free acetylcholine oxidase (AChOx) by selfassembled monolayer (SAM) onto lab-made micro-chip. The simple cyclic voltammetry (CV) method is utilized in mediator- free system in phosphate buffer solution (PBS, 0.1M) at room conditions. The analytical parameters of AChOx fabricated electrode employed a lower detection limit (DL, 0.136 nM), a wide linear dynamic range (LDR, 1.0 nM to 1.0 mM), good linearity (R= 0.9991), and higher sensitivity (2.7329 μAmM-1cm-2) where a tiny sample volume (70.0 μL) is required. The micro-chip system executes a simple and efficient approach to immobilize the enzymes onto SAM modified surface, which can improve the biosensor performances for a large group of biomolecules in broad scale of biomedical applications in health-care fields.

This paper reports the successful isolation and characterization of a new phenol-degrading bacterium, Achromobacter sp. strain C-1, from an industrial area (Cubatao, Brazil). Achromobacter sp. is a non-motile, strictly aerobic, gram-negative, short-rod or coccobacillary bacterium, which can occur singly, in pairs or in clusters. 16S rRNA gene sequence analysis revealed that Achromobacter sp. strain C-1 belongs to the gamma group of Proteobacteria, with 99% similarity to 16S rRNA gene sequences of Achromobacter xylosoxidans. Strain C-1 can grow aerobically on a number of aromatic compounds, such as phenol, catechol, m-cresol and o-cresol. In particular, it can degrade up to 600 mg/L of phenol at 37°C. In order to understand the phenol degradation pathway used by strain C-1, phenol or glucose cultured C-1 proteomes were comparatively analyzed with two-dimensional SDS-polyacrylamide gel (2D SDS PAGE). Nine protein spots were exclusively induced from phenol-cultures of strain C-1. Of these 9 spots, three phenol-degrading enzymes (phenol degradation meta-pathway protein, hydroxymuconic semialdehyde dehydrogenase and 4-hydroxy-2-oxovalerate aldolase) were identified by peptide mass fingerprinting, and the results were confirmed by tandem mass spectrometry of selected peptides, which suggests that strain C-1 degrades phenol via the β-ketoadipate pathway. Analysis of the metabolite produced from phenol proved that this enzyme is a catechol 2,3 dioxygenase, which is able to utilize phenol as a substrate. These results suggest that comparative proteomic analysis of biodegrading bacteria cultures under different conditions may be a useful initial step toward the elucidation of an aromatic compound degradation pathway and the strain C-1 could be an excellent candidate for the biotreatment of phenol-containing industrial wastewaters.