Family-level diversity of extracellular proteases of sedimentary bacteria from the South China Sea

Protease-producing bacteria and their extracellular proteases are key players in degrading organic nitrogen to drive marine nitrogen cycling and yet knowledge on both of them is still very limited. This study screened protease-producing bacteria from the South China Sea sediments and analyzed the diversity of their extracellular proteases at the family level through N-terminal amino acid sequencing. Results of the 16 S rRNA gene sequence analysis showed that all screened protease-producing bacteria belonged to the class Gammaproteobacteria and most of them were affiliated with different genera within the orders Alteromonadales and Vibrionales. The Nterminal amino acid sequence analysis for fourteen extracellular proteases from fourteen screened bacterial strains revealed that all these proteases belonged to the M4 family of metalloproteases or the S8 family of serine proteases. This study presents new details on taxa of marine sedimentary protease-producing bacteria and types of their extracellular proteases, which will help to comprehensively understand the process and mechanism of the microbial enzymatic degradation of marine sedimentary organic nitrogen.

Long noncoding RNAs as diagnostic biomarkers associated with cancer phenotypes

Increasing evidence suggests that long noncoding RNAs(lncRNAs) play vital roles in the transformation and maintenance of cancer phenotypes and have important clinical implications. These lncRNAs control important aspects of tumor biology, including proliferation, angiogenesis, metastasis, and the microenvironment by regulating RNA and protein interactions or through their ability to base pair with RNA and DNA. In this study, we review the mechanism of the function of lncRNAs in cancer and their diagnostic roles in cancer phenotypes, which make them attractive as non-invasive biomarkers from body fluid samples for different types of cancer.

Establishment and Optimization of Two-dimensional Electrophoresis System for Spleen Proteome of Sillago sihama Forsskal

Taking Sillago sihama Forssk?l as the research object,through the optimization of the extraction method,hydration and isoelectric focusing,a two-dimensional electrophoresis system was established for spleen proteome of S. sihama Forssk?l. The results showed that the twpstep hydration and isoelectric focusing method is better than the hydration and isoelectric focusing integrated method. The protein spots of the spleen of S. sihama Forssk?l were detected by two-dimensional electrophoresis mainly at pH 4. 0-7. 0. The establishment of this technical system will lay a foundation for further research on proteomics of S. sihama Forssk?l in the future.

Quantitative Proteomics Using Isobaric Labeling:A Practical Guide

In the past decade,relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological samples.Although its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions,its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification results.Here,we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling method.We also discuss which precautions should be taken at each step of the isobaric labeling workflow,to obtain reliable quantification results in large-scale quantitative proteomics experiments.In the last section,we discuss the broad applications of the isobaric labeling technology in biological and clinical studies,with an emphasis on thermal proteome profiling and proteogenomics.

Oleic Acid and Eicosapentaenoic Acid Reverse Palmitic Acid-induced Insulin Resistance in Human HepG2 Cells via the Reactive Oxygen Species/JUN Pathway

Oleic acid(OA),a monounsaturated fatty acid(MUFA),has previously been shown to reverse saturated fatty acid palmitic acid(PA)-induced hepatic insulin resistance(IR).However,its underlying molecular mechanism is unclear.In addition,previous studies have shown that eicosapentaenoic acid(EPA),aω-3 polyunsaturated fatty acid(PUFA),reverses PA-induced muscle IR,but whether EPA plays the same role in hepatic IR and its possible mechanism involved need to be further clarified.Here,we confirmed that EPA reversed PA-induced IR in HepG2 cells and compared the proteomic changes in HepG2 cells after treatment with different free fatty acids(FFAs).A total of 234 proteins were determined to be differentially expressed after PA+OA treatment.Their functions were mainly related to responses to stress and endogenous stimuli,lipid metabolic process,and protein binding.For PA+EPA treatment,the PA-induced expression changes of 1326 proteins could be reversed by EPA,415 of which were mitochondrial proteins,with most of the functional proteins involved in oxidative phosphorylation(OXPHOS)and tricarboxylic acid(TCA)cycle.Mechanistic studies revealed that the protein encoded by JUN and reactive oxygen species(ROS)play a role in OA-and EPA-reversed PA-induced IR,respectively.EPA and OA alleviated PA-induced abnormal adenosine triphosphate(ATP)production,ROS generation,and calcium(Ca^(2+))content.Importantly,H_(2)O_(2)-activated production of ROS increased the protein expression of JUN,further resulting in IR in HepG2 cells.Taken together,we demonstrate that ROS/JUN is a common response pathway employed by HepG2 cells toward FFA-regulated IR.

Mitochondria in the pathogenesis of diabetes:a proteomic view

Diabetes mellitus is a complex metabolic disorder characterized by chronic hyperglycemia due to absolute or relative lack of insulin.Though great efforts have been made to investigate the pathogenesis of diabetes,the underlying mechanism behind the development of diabetes and its complications remains unexplored.Cumulative evidence has linked mitochondrial modification to the pathogenesis of diabetes and its complications and they are also observed in various tissues affected by diabetes.Proteomics is an attractive tool for the study of diabetes since it allows researchers to compare normal and diabetic samples by identifying and quantifying the differentially expressed proteins in tissues,cells or organelles.Great progress has already been made in mitochondrial proteomics to elucidate the role of mitochondria in the pathogenesis of diabetes and its complications.Further studies on the changes of mitochondrial protein specifically post-translational modifications during the diabetic state using proteomic tools,would provide more information to better understand diabetes.

A study of the protein-protein interactions in the phycocyanin monomer from Synechocystis sp.PCC 6803 using a bacterial two-hybrid system

Investigations into the intramolecular interactions of the native protein in solution are important to understand its structural stability as well as its potential uses in future applications.In this study,we used a bacterial two-hybrid system to investigate the interaction between the phycocyanin𝛼and𝛽subunits that form the phycocyanin monomer.Key amino acid residues responsible for the interaction between the subunits were identified,providing direct experimental evidence for the intramolecular interaction.