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https://www.readbyqxmd.com/read/28315251/fpps-fast-profiling-of-protease-specificity
#1
Matej Vizovišek, Robert Vidmar, Marko Fonović
Profiling of protease specificity is crucial for characterization of these important enzymes that play numerous roles in health and disease. In the past, several proteomic methods have been developed that enable profiling of protease specificities. Although able to identify thousands of protease cleavage events, these degradomics approaches are often time consuming and methodologically challenging, which limits their application to specialized proteomic groups or the laboratories that initially introduced them...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28315250/multiplexed-protease-specificity-profiling-using-isobaric-labeling
#2
Joanna Tucher, Andreas Tholey
The determination of a protease's cleavage site specificity is one of the major goals in degradomics. In the last years, the use of proteome-derived peptide libraries and liquid chromatography-mass spectrometry (LC-MS) in a proteomic identification of protease cleavage sites (PICS) experiment became popular for that purpose.In this chapter, we offer a step-by-step protocol for the execution of a quantitative proteomic identification of protease cleavage sites (Q-PICS) experiment, which enables the relative quantification of proteolytic events by isobaric labeling, e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28315249/determining-protease-substrates-within-a-complex-protein-background-using-the-protein-topography-and-migration-analysis-platform-protomap
#3
R A Fuhrman-Luck, L M Silva, M L Hastie, J J Gorman, J A Clements
The PROtein TOpography and Migration Analysis Platform (PROTOMAP) approach is a degradomics technique used to determine protease substrates within complex protein backgrounds. The method involves protein separation according to protein relative mobility, using sodium dodecyl sulfate polyacrylamide gel electrophoresis. Gel lanes are then sliced into horizontal sections, and in-gel trypsin digestion performed for each gel slice. Extracted peptides and corresponding proteins are identified using liquid chromatography-tandem mass spectrometry and bioinformatics...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28304398/characterization-of-the-polyphenol-oxidase-gene-family-reveals-a-novel-microrna-involved-in-posttranscriptional-regulation-of-ppos-in-salvia-miltiorrhiza
#4
Caili Li, Dongqiao Li, Jiang Li, Fenjuan Shao, Shanfa Lu
Salvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28253861/small-rna-profiling-and-degradome-analysis-reveal-regulation-of-microrna-in-peanut-embryogenesis-and-early-pod-development
#5
Chao Gao, Pengfei Wang, Shuzhen Zhao, Chuanzhi Zhao, Han Xia, Lei Hou, Zheng Ju, Ye Zhang, Changsheng Li, Xingjun Wang
BACKGROUND: As a typical geocarpic plant, peanut embryogenesis and pod development are complex processes involving many gene regulatory pathways and controlled by appropriate hormone level. MicroRNAs (miRNAs) are small non-coding RNAs that play indispensable roles in post-transcriptional gene regulation. Recently, identification and characterization of peanut miRNAs has been described. However, whether miRNAs participate in the regulation of peanut embryogenesis and pod development has yet to be explored...
March 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28241738/response-of-micrornas-to-cold-treatment-in-the-young-spikes-of-common-wheat
#6
Guoqi Song, Rongzhi Zhang, Shujuan Zhang, Yulian Li, Jie Gao, Xiaodong Han, Mingli Chen, Jiao Wang, Wei Li, Genying Li
BACKGROUND: MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important roles in biotic and abiotic stresses by regulating their target genes. For common wheat, spring frost damage frequently occurs, especially when low temperature coincides with plants at early floral organ differentiation, which may result in significant yield loss. Up to date, the role of miRNAs in wheat response to frost stress is not well understood. RESULTS: We report here the sequencing of small RNA transcriptomes from the young spikes that were treated with cold stress and the comparative analysis with those of the control...
February 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28228536/a-viral-satellite-dna-vector-tylccnv-for-functional-analysis-of-mirnas-and-sirnas-in-plants
#7
Zheng Ju, Dongyan Cao, Chao Gao, Jinhua Zuo, Baiqiang Zhai, Shan Li, Hongliang Zhu, Daqi Fu, Yunbo Luo, Benzhong Zhu
With experimental and bioinformatical methods, numerous small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), have been found in plants, and they play vital roles in various biological regulation processes. However, most of these small RNAs remain to be functionally characterized. Until now, only several viral vectors were developed to overexpress miRNAs with limited application in plants. In this study, we reported a new small RNAs overexpression system via viral satellite DNA associated with Tomato yellow leaf curl China virus (TYLCCNV) vector, which could highly overexpress not only artificial and endogenous miRNAs but also endogenous siRNAs in Nicotiana benthamiana...
February 22, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28225779/combined-small-rna-and-degradome-sequencing-reveals-complex-microrna-regulation-of-catechin-biosynthesis-in-tea-camellia-sinensis
#8
Ping Sun, Chunzhen Cheng, Yuling Lin, Qiufang Zhu, Jinke Lin, Zhongxiong Lai
MicroRNAs are endogenous non-coding small RNAs playing crucial regulatory roles in plants. Tea, a globally popular non-alcoholic drink, is rich in health-enhancing catechins. In this study, 69 conserved and 47 novel miRNAs targeting 644 genes were identified by high-throughout sequencing. Predicted target genes of miRNAs were mainly involved in plant growth, signal transduction, morphogenesis and defense. To further identify targets of tea miRNAs, degradome sequencing and RNA ligase-mediated rapid amplification of 5'cDNA ends (RLM-RACE) were applied...
2017: PloS One
https://www.readbyqxmd.com/read/28203245/small-rnas-derived-from-the-t-dna-of-agrobacterium-rhizogenes-in-hairy-roots-of-phaseolus-vulgaris
#9
Pablo Peláez, Alejandrina Hernández-López, Georgina Estrada-Navarrete, Federico Sanchez
Agrobacterium rhizogenes is a pathogenic bacteria that causes hairy root disease by transferring bacterial DNA into the plant genome. It is an essential tool for industry and research due to its capacity to produce genetically modified roots and whole organisms. Here, we identified and characterized small RNAs generated from the transfer DNA (T-DNA) of A. rhizogenes in hairy roots of common bean (Phaseolus vulgaris). Distinct abundant A. rhizogenes T-DNA-derived small RNAs (ArT-sRNAs) belonging to several oncogenes were detected in hairy roots using high-throughput sequencing...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28179412/sharpening-host-defenses-during-infection-proteases-cut-to-the-chase
#10
Natalie C Marshall, B Brett Finlay, Christopher M Overall
The human immune system consists of an intricate network of tightly controlled pathways, where proteases are essential regulators and executioners at multiple levels. Invading microbial pathogens also encode proteases that have evolved to manipulate and dysregulate host proteins including host proteases during the course of disease. The identification of pathogen proteases as well as their substrates and mechanisms of action have empowered significant developments in therapeutics for infectious diseases. Yet for many pathogens, there remains a great deal to be discovered...
February 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28149304/identification-of-submergence-responsive-micrornas-and-their-targets-reveals-complex-mirna-mediated-regulatory-networks-in-lotus-nelumbo-nucifera-gaertn
#11
Qijiang Jin, Yingchun Xu, Neil Mattson, Xin Li, Bei Wang, Xiao Zhang, Hongwei Jiang, Xiaojing Liu, Yanjie Wang, Dongrui Yao
MicroRNAs (miRNAs) are endogenous non-coding RNAs with important regulatory functions in plant development and stress responses. However, their population abundance in lotus (Nelumbo nucifera Gaertn) has so far been poorly described, particularly in response to stresses. In this work, submergence-related miRNAs and their target genes were systematically identified, compared, and validated at the transcriptome-wide level using high-throughput sequencing data of small RNA, Mrna, and the degradome. A total of 128 known and 20 novel miRNAs were differentially expressed upon submergence...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28146558/genome-wide-exonic-small-interference-rna-mediated-gene-silencing-regulates-sexual-reproduction-in-the-homothallic-fungus-fusarium-graminearum
#12
Hokyoung Son, Ae Ran Park, Jae Yun Lim, Chanseok Shin, Yin-Won Lee
Various ascomycete fungi possess sex-specific molecular mechanisms, such as repeat-induced point mutations, meiotic silencing by unpaired DNA, and unusual adenosine-to-inosine RNA editing, for genome defense or gene regulation. Using a combined analysis of functional genetics and deep sequencing of small noncoding RNA (sRNA), mRNA, and the degradome, we found that the sex-specifically induced exonic small interference RNA (ex-siRNA)-mediated RNA interference (RNAi) mechanism has an important role in fine-tuning the transcriptome during ascospore formation in the head blight fungus Fusarium graminearum...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28112201/novel-bioinformatics-based-approach-for-proteomic-biomarkers-prediction-of-calpain-2-caspase-3-protease-fragmentation-application-to-%C3%AE-ii-spectrin-protein
#13
Atlal El-Assaad, Zaher Dawy, Georges Nemer, Firas Kobeissy
The crucial biological role of proteases has been visible with the development of degradomics discipline involved in the determination of the proteases/substrates resulting in breakdown-products (BDPs) that can be utilized as putative biomarkers associated with different biological-clinical significance. In the field of cancer biology, matrix metalloproteinases (MMPs) have shown to result in MMPs-generated protein BDPs that are indicative of malignant growth in cancer, while in the field of neural injury, calpain-2 and caspase-3 proteases generate BDPs fragments that are indicative of different neural cell death mechanisms in different injury scenarios...
January 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28109429/body-fluid-degradomics-and-characterization-of-basic-n-terminome
#14
F Sabino, O Hermes, U Auf dem Keller
Rapid improvements in instrumentation and data analysis make mass spectrometry-based proteomics the method of choice for global characterization of proteomes and discovery of protein-based biomarkers. On the contrary to tissue biopsies, body fluids-e.g., blood, wound fluid, urine, and saliva-are noninvasive and easy to collect and process. However, they are very complex and present high dynamic ranges of protein concentrations, rendering direct shotgun proteomics analysis as inefficient for identification of low-abundance proteins in these specimens...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28090264/drought-stress-induced-changes-of-micrornas-in-diploid-and-autotetraploid-paulownia-tomentosa
#15
Xibing Cao, Guoqiang Fan, Lin Cao, Minjie Deng, Zhenli Zhao, Suyan Niu, Zhe Wang, Yuanlong Wang
Drought stress adversely affects plant productivity. Growth and timber production of Paulownia trees are limited under drought stress. Changes in gene expression patterns and miRNA in different ploidy of Paulownia tomentosa have been investigated. However, the responses of P. tomentosa to drought stress at the microRNA (miRNA) level have not been reported so far. To identify miRNA candidates and their target genes involved in the drought stress response in diploid and tetraploid P. tomentosa, four small RNA and four degradome libraries from diploid and autotetraploid P...
2017: Genes & Genomics
https://www.readbyqxmd.com/read/28064248/mir393-mediated-auxin-signaling-regulation-is-involved-in-root-elongation-inhibition-in-response-to-toxic-aluminum-stress-in-barley
#16
Bin Bai, Hongwu Bian, Zhanghui Zeng, Ning Hou, Bo Shi, Junhui Wang, Muyuan Zhu, Ning Han
High-throughput small RNA sequencing has identified several potential aluminum (Al)-responsive microRNAs (miRNAs); however, their regulatory role remains unknown. Here, we identified two miR393 family members in barley, and confirmed two target genes-HvTIR1 and HvAFB-through a modified form of 5'-RACE (rapid amplification of cDNA ends) as well as degradome data analysis. Furthermore, we investigated the biological function of the miR393/target module in root development and its Al stress response. The investigation showed that miR393 affected root growth and adventitious root number by altering auxin sensitivity...
January 7, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28018404/functional-and-integrative-analysis-of-the-proteomic-profile-of-radish-root-under-pb-exposure
#17
Yan Wang, Liang Xu, Mingjia Tang, Haiyan Jiang, Wei Chen, Wei Zhang, Ronghua Wang, Liwang Liu
Lead (Pb) is one of the most abundant heavy metal (HM) pollutants, which can penetrate the plant through the root and then enter the food chain causing potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots respectively upon Pb(NO3)2 at 500 mg L(-1)(Pb500) and 1000 mg L(-1)(Pb1000), were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification)...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27910907/micrornas-modulate-adaption-to-multiple-abiotic-stresses-in-chlamydomonas-reinhardtii
#18
Xiang Gao, Fengge Zhang, Jinlu Hu, Wenkai Cai, Ge Shan, Dongsheng Dai, Kaiyao Huang, Gaohong Wang
MicroRNAs play an important role in abiotic stress responses in higher plants and animals, but their role in stress adaptation in algae remains unknown. In this study, the expression of identified and putative miRNAs in Chlamydomonas reinhardtii was assessed using quantitative polymerase chain reaction; some of the miRNAs (Cre-miR906-3p) were up-regulated, whereas others (Cre-miR910) were down-regulated when the species was subjected to multiple abiotic stresses. With degradome sequencing data, we also identified ATP4 (the d-subunit of ATP synthase) and NCR2 (NADPH: cytochrome P450 reductase) as one of the several targets of Cre-miR906-3p and Cre-miR910, respectively...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27845893/klk6-proteolysis-is-implicated-in-the-turnover-and-uptake-of-extracellular-alpha-synuclein-species
#19
Georgios Pampalakis, Vasia-Samantha Sykioti, Methodios Ximerakis, Ioanna Stefanakou-Kalakou, Ronald Melki, Kostas Vekrellis, Georgia Sotiropoulou
KLK6 is a serine protease highly expressed in the nervous system. In synucleinopathies, including Parkinson disease, the levels of KLK6 inversely correlate with α-synuclein in CSF. Recently, we suggested that recombinant KLK6 mediates the degradation of extracellular α-synuclein directly and via a proteolytic cascade that involves unidentified metalloproteinase(s). Here, we show that recombinant and naturally secreted KLK6 can readily cleave α-synuclein fibrils that have the potential for cell-to-cell propagation in "a prion-like mechanism"...
November 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27801427/developmental-changes-in-barley-microrna-expression-profiles-coupled-with-mirna-target-analysis
#20
Andrzej Pacak, Katarzyna Kruszka, Aleksandra Swida-Barteczka, Przemyslaw Nuc, Wojciech Karlowski, Artur Jarmolowski, Zofia Szweykowska-Kulinska
MicroRNAs are 19- to 24-nt-long single-stranded RNAs that are crucial regulators of gene expression which control plant development and response to environmental cues. We have analyzed microtranscriptomes of five barley developmental stages. Generally, during the barley development, miR168-3p and miR1432-5p levels increase while the 5'U-miR156-5p level decreases (with exception for the 2-week-old barley). We have identified two miR156-5p izomiRs (called 5'U-miR156-5p [20 nt] and 5'UU-miR156-5p [21 nt]), which were expressed differently during barley development...
2016: Acta Biochimica Polonica
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