Current Proteomics - Volume 13, Issue 4, 2016

Salt stress is one of the main abiotic stresses that limits poplar (Populus spp.) growth and yields in many regions of the world. To cope with salt stress, poplars have evolved complex saltresponsive mechanisms in the proteomics level. Several proteomics-based studies have recently been conducted to characterize the molecular mechanisms in poplar. In this review, we summarize the effects of salt stress on the proteome of poplar. There are 84 salt-responsive proteins in poplar. These proteins are involved in a diverse range of reactions, including photosynthesis, scavenging of reactive oxygen species, carbon metabolism, energy metabolism, signal transduction, protein metabolism and disease resistance protein. These pathways play an important role in poplar under salt stress, with adjusts to the ability of salt tolerance. This review will likely contribute to a more thorough understanding of the different cellular activities in poplar exposed to salt conditions, with implications for the breeding of new poplar cultivars with improved traits.

Diabetes Mellitus is a chronic metabolic disorder that is often associated with various complications including micro- and macro- angiopathies. The increase in mortality rates associated with these complications is one among the major factors that compels to define proper therapeutic strategies. Protein signatures including their post-translational modifications that are modulated under various disease conditions enabled the biomarker discovery processes and thereby facilitate to predict and diagnose the disease onset at an earlier stage. Identification of the post-translationally modified proteins not only enabled the biomarker prediction associated with various disease conditions but also has a great impact in target based drug discovery process. Mass spectrometry based proteome profiling aided the identification and characterization of these site specific modifications that had a huge impact on various functional aspects in a biological context. In this review, we tried to compile and discuss the information available regarding some of the modified proteins with regard to deregulated glucose metabolism. Several commonly observed modifications including glycosylation, hydroxylation, phosphorylation, nitration, nitrosylation and carbonylation that seem to have a major role in the management of diabetes disorders are summarized. Moreover, the importance and impact of less explored post-translational modifications such as palmitoylation, carbamylation, deamidation and SUMOylation that are associated to diabetes related complications are described.

Background: Mesial temporal lobe epilepsy is the most prevalent type of human epilepsy and its pathogenesis still remains unknown. Structures outside the temporal lobe may also play critical roles in the disease’s progress. Objective: The aim of this study was to investigate proteome alterations and to identify differentially expressed proteins in frontoparietal cortex and thalamus regions of 6-month-old amygdala-kindled WAG/Rij rats as a mesial temporal lobe epilepsy model by using bottom-up proteomics approach. Method: Protein extraction from the tissues was followed by two-dimensional gel electrophoresis. Proteins were identified by peptide mass fingerprinting analysis using MALDI-TOF MS followed by MASCOT database search. Results: 58 and 47 proteins were identified in frontoparietal cortex and thalamus, respectively. Differentially expressed proteins in frontoparietal cortex were all up-regulated in the kindled groups compared to kindled-resistant group (p<0.05). These proteins were; Fabp4, Gamma-enolase, Annexin AI, Rab-15, RAB6-interacting golgin, PGAM1, DAB-2 and Fructose-bisphosphate aldolase C. In thalamus, BDNF (in spot 13), TRAPPC2L, Ras-related protein Rab-2A, GTP-binding protein REM 2 and Calcyclin-binding protein were up-regulated (p<0.05); and BDNF (in spot 9), kif3a, Parvalbumin alpha were down-regulated in the kindled groups compared to the kindled-resistant group (p<0,05). Conclusion: In this study, we identified proteins that might have roles in enabling or complicating mesial temporal lobe epilepsy progress. The potential of these proteins as biomarkers needs further research.

Background: Escherichia coli with its large range of pathologies is a major cause of human morbidity and mortality around the world. The increasing prevalence of bacteria resistant to even the most current arsenal of antibiotics is a serious concern for public health globally. The resistant bacteria which cause human infection are thought to emerge in food and animals. Objective: Our goal was to study the proteome of an extended-spectrum β-lactamase (ESBL)- producing Escherichia coli, SU03, strain recovered from faecal samples of pigs slaughtered for human consumption. Method: A full proteomic survey of this strain was made by two-dimensional electrophoresis identifying proteins by MALDI-TOF/MS. Results: This strain exhibited ciprofloxacin resistance associated with mutations in type II topoisomerase structural gene GyrA (Ser83Leu + Asp87Asn) and ParC (Ser80Ile). We studied how the proteome of this strain responded to stress by applying double the minimum inhibitory concentration of ciprofloxacin. The hydrolase L-asparaginase was overexpressed when SU03 was cultured with double the minimum inhibitory concentration of ciprofloxacin. Conclusion: The abundance of this hydrolase may lead to a diverse secondary response by influencing in the production of other proteins or directly mediating ciprofloxacin resistance. Further research should determine how this enzyme contributes to ciprofloxacin resistance.

Background: Apple flowers can be used as a model material to study the disease resistance of apple varieties. Our previous studies indicated that the resistance mechanisms of resistant and susceptible cultivars may involve different defense response-related proteins. Objective: To investigate the intrinsic differences between two previously introduced apple seedlings under normal conditions. Method: Apple flower samples from two seedlings (one resistant to Alternaria alternate and the other susceptible) were analyzed using two-dimensional electrophoresis and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry. Results: These techniques identified 29 differentially accumulated proteins between the two samples, which could be categorized into five classes. Among them, the most abundant accumulated defense response proteins in the resistant apple included polyphenol oxidase, glycine-rich proteins, superoxide dismutase and glutathione S-transferases, which might play crucial roles in the greater resistance capacity of the resistant cultivar. Conclusion: Herein, new information regarding the differences in resistance between two apple cultivars was revealed. Considering the complex biology involved in the disease resistance mechanisms in apples, further investigations may offer more insights into the molecular mechanisms of resistant apple flowers. The data may also promote further investigations of target proteins.

Aims: Breast cancer is the second most common cancer in the world and, by far, the most frequent cancer among women. Scientific literature has hypothesized the association of ACE I/D polymorphism with breast cancer for several decades. Unfortunately the outcomes of studies are inconsistent. Thus the present study was designed to evaluate the association of ACE gene (I/D) polymorphism with breast cancer in Indian population. Methods: Genotyping was performed by PCR (polymerase chain reaction), using genomic DNA extracted from peripheral blood of subjects, with (213 cases) or without (213 controls) breast cancer. Findings: The distribution of ACE genotype frequencies i.e. II, DD and ID in patients was 43.19%, 16.43% and 40.38% respectively. In healthy control group II, DD and ID frequencies were 52.58%, 11.27% and 36.15% respectively. The frequencies of D and I alleles were 29.34% and 70.66% in the healthy subjects, while 36.62% and 63.38% among the patient group. Frequency of D allele was significantly different (p=0.0287) between control and case subjects. Significance: The present study showed an association of D allele of ACE gene with increased genetic risk factor for breast cancer in Indian women. 0.2% increased disease risk was found in patients carrying D allele.

Background: Adiponectin (APN), which was secreted from adipose tissue, was extensively investigated in various diseases such as obesity as well as obesity-related cancers. Method: Here, we investigated serum adiponectin level in gastric cancer (GC) patients and healthy control subjects using a well-established N-succinimidyl 4-(maleimidomethyl) cyclohexanecarboxylate (SMCC) modified protein biochip. Results: We found that serum adiponectin level significantly decreased in the patients with GC when compared with the controls (p<0.01). Women had higher adiponectin level than men in the controls (p=0.024), but no gender difference occurred in the GC patients (p>0.05). Correlation analysis between serum adiponectin expression and clinicopathological characteristics in the GC patients indicated that serum adiponectin level was obviously correlated with tumor location (p=0.008), differentiated degree (p=0.011) and histologic type (p=0.006). Conclusion: Our results revealed that serum adiponectin might potentially reflect location, histogenesis and differentiation of GC. The biochip immunoassay would act as one substitute of conventional clinical assays for measuring serum adiponectin in GC.

Background: The modulation of the chromatin structure and repression of the transcription process has been done by Polycomb Repressive Complex 2 (PRC2) due to trimethylation of LYS27 of histone H3 (H3K27me3). This process is necessary for protein protein interaction (PPI) between EZH2 and EED catalytic subunits. The dysregulation of this complex is responsible for tumorigenesis and progression, making it an important cancer epigenetic therapeutic target. However, until now, there is only one FDA-approved drug called Astemizole has been reported to disrupt interactions between EZH2-EED. Objective: Identification of novel inhibitors for disrupting EZH2-EED interactions through virtual screening, docking and simulation. Methodology: In this study, we identified five compounds from in-silico screening & docking studies of a database of ~70000 compounds, which show better binding affinities than Astemizole. These compounds cause destabilization of PRC2 complex by disrupting the interaction between EZH2- EED and which in turn, inhibits its methyltransferase activity in cancerous cells. Molecular Dynamics (MD) Simulation analysis of the best receptor-ligand complex for 50 ns has exhibited that the top-scoring compound captures the expansion of PRC2-driven lymphomas primarily by deregulating PRC2 complex. Further, ADMET properties were analyzed to check their drug like properties. Results/Conclusion: Our study demonstrates not just the importance of in-silico drug discovery merely but also provides a range of small molecules that can hold the potential to serve as probable lead candidates for disrupting interactions between EZH2-EED. Hence, it has been suggested that the top screened compound C1 can prove to be more potent to inhibit PRC2-driven human cancers.