Abstract:WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction. WoLF PSORT converts protein amino acid sequences into numerical localization features; based on sorting signals, amino acid composition and functional motifs such as DNA-binding motifs. After conversion, a simple k-nearest neighbor classifier is used for prediction. Using html, the evidence for each prediction is shown in two ways: (i) a list of proteins of known localization with the most similar localization featu… Show more
“…It is generally known that subcellular localization of a protein probably provides significant clues to its function (Horton et al, 2007). As cytosolic proteins with pools of both a soluble and stable form or reversibly connected with components of the cytoskeleton or proteins, annexins mediate interactions between cell and extracellular matrix (Moss & Morgan., 2004).…”
Section: Prognostic Significance Of Annexin A1 Expression In Pamentioning
Annexin A1 is a 37-kDa calcium-and phospholipid-binding protein of the annexin superfamily considered to play an important role in tumorigenesis. However, associations with clinicopathological features in pancreatic ductal adenocarcinoma (PDAC) cases have yet to be fully defined. We therefore investigated the prognostic value of annexin A1 protein as a PDAC biomarker in 83 tumor and matched non-cancerous tissues or normal pancreas tissues. Expression was analyzed using real-time RT-PCR, Western blotting and immunohistochemistry. In non-tumor tissue, myoepithelial cells showed no or weak expression of annexin A1 while expression was strong and sometimes even located in the nuclei of endothelial cells in tumor tissue. High expression was significantly associated with advanced stage (P <0.05) and a worse overall survival (P <0.05). These results provide new insights to better understand the role of annexin A1 in PDAC survival, and might be relevant to prediction of prognosis and development of more effective therapeutic strategies aimed at improving survival.
“…It is generally known that subcellular localization of a protein probably provides significant clues to its function (Horton et al, 2007). As cytosolic proteins with pools of both a soluble and stable form or reversibly connected with components of the cytoskeleton or proteins, annexins mediate interactions between cell and extracellular matrix (Moss & Morgan., 2004).…”
Section: Prognostic Significance Of Annexin A1 Expression In Pamentioning
Annexin A1 is a 37-kDa calcium-and phospholipid-binding protein of the annexin superfamily considered to play an important role in tumorigenesis. However, associations with clinicopathological features in pancreatic ductal adenocarcinoma (PDAC) cases have yet to be fully defined. We therefore investigated the prognostic value of annexin A1 protein as a PDAC biomarker in 83 tumor and matched non-cancerous tissues or normal pancreas tissues. Expression was analyzed using real-time RT-PCR, Western blotting and immunohistochemistry. In non-tumor tissue, myoepithelial cells showed no or weak expression of annexin A1 while expression was strong and sometimes even located in the nuclei of endothelial cells in tumor tissue. High expression was significantly associated with advanced stage (P <0.05) and a worse overall survival (P <0.05). These results provide new insights to better understand the role of annexin A1 in PDAC survival, and might be relevant to prediction of prognosis and development of more effective therapeutic strategies aimed at improving survival.
“…Bioinformatics toolDescriptionWebsiteReferenceTrimmomaticA fast, multithreaded command line tool that can be used to trim and crop Illumina data as well as to remove adapters.http://www.usadellab.org/trimmomatic [80] STARAn algorithm for aligning high-throughput long and short RNA-seq data to a reference genome.http://code.google.com/p/rna-star [81] SignalPSoftware that predicts signal peptide cleavage sites in proteins from eukaryotes and prokaryotes.http://www.cbs.dtu.dk/services/SignalP [82] WoLF PSORTAn algorithm that predicts the subcellular localization sites of proteins based on their amino acid sequences. It makes predictions based on both known sorting signal motifs and some correlative sequence features such as amino acid content.www.wolfpsort.org [83] TargetPTool that predicts subcellular location of eukaryotic proteins.http://www.cbs.dtu.dk/services/TargetP [84] 10.1080/21505594.2018.1504560-F0002Figure 2.Coherent pipeline to identify putative effector proteins of Plasmodiophora brassicae . The pipeline assumes: (1) Researchers are starting with RNA-Seq reads from a host plant infected with P. brassicae ; (2) The draft genomes available for P. brassicae , other plasmodiophorids, oomycetes, and other plant pathogens are used; (3) Motifs mentioned in the review or structural similarities with previously described effector proteins were identified.…”
Section: A Coherent Pipeline To Identify Effectorsmentioning
Clubroot is an economically important disease affecting Brassica plants worldwide. Plasmodiophora brassicae is the protist pathogen associated with the disease, and its soil-borne obligate parasitic nature has impeded studies related to its biology and the mechanisms involved in its infection of the plant host. The identification of effector proteins is key to understanding how the pathogen manipulates the plantâs immune response and the genes involved in resistance. After more than 140Â years studying clubroot and P. brassicae, very little is known about the effectors playing key roles in the infection process and subsequent disease progression. Here we analyze the information available for identified effectors and suggest several features of effector genes that can be used in the search for others. Based on the information presented in this review, we propose a comprehensive bioinformatics pipeline for effector identification and provide a list of the bioinformatics tools available for such.
“…Subcellular localization prediction by WoLF PSORT II (www.wolf psort.org) revealed either a mitochondrial (DNJ-10, also reported 85 ) or cytosolic (DNJ-12, DNJ-19) localization. 86 In consequence, class A J-proteins are missing in the ER. It could be hypothesized whether the presence of the zinc-finger domain in class A proteins is responsible for its lack in the ER.…”
The subcellular compartments of eukaryotic cells are characterized by different redox environments. Whereas the cytosol, nucleus and mitochondria are more reducing, the endoplasmic reticulum represents a more oxidizing environment. As the redox level controls the formation of intra-and inter-molecular disulfide bonds, the folding of proteins is tightly linked to its environment. The proteostasis network of each compartment needs to be adapted to the compartmental redox properties. In addition to chaperones, also members of the thioredoxin superfamily can influence the folding of proteins by regulation of cysteine reduction/oxidation. This review will focus on thioredoxin superfamily members and chaperones of C. elegans, which play an important role at the interface between redox and protein homeostasis. Additionally, this review will highlight recent methodological developments on in vivo and in vitro assessment of the redox state and their application to provide insights into the high complexity of redox and proteostasis networks of C. elegans.
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