Bioinformatics analysis and characterization of a secretory cystatin from Thelohanellus kitauei

Somatic mutation in the KCNJ5 gene is a common driver of autonomous aldosterone overproduction in aldosterone-producing adenomas (APA). KCNJ5 mutations contribute to a loss of potassium selectivity, and an inward Na+ current could be detected in cells transfected with mutated KCNJ5. Among 223 unilateral primary aldosteronism (uPA) individuals with a KCNJ5 mutation, we identified 6 adenomas with a KCNJ5 p.Gly387Arg (G387R) mutation, previously unreported in uPA patients. The six uPA patients harboring mutant KCNJ5-G387R were older, had a longer hypertensive history, and had milder elevated preoperative plasma aldosterone levels than those APA patients with more frequently detected KCNJ5 mutations. CYP11B2 immunohistochemical staining was only positive in three adenomas, while the other three had co-existing multiple aldosterone-producing micronodules. The bioinformatics analysis predicted that function of the KCNJ5-G387R mutant channel could be pathological. However, the electrophysiological experiment demonstrated that transfected G387R mutant cells did not have an aberrantly stimulated ion current, with lower CYP11B2 synthesis and aldosterone production, when compared to that of the more frequently detected mutant KCNJ5-L168R transfected cells. In conclusion, mutant KCNJ5-G387R is not a functional KCNJ5 mutation in unilateral PA. Compared with other KCNJ5 mutations, the observed mildly elevated aldosterone expression actually hindered the clinical identification of clinical unilateral PA. The KCNJ5-G387R mutation needs to be distinguished from functional KCNJ5 mutations during genomic analysis in APA evaluation because of its functional silence.

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Molecular characterization and bioinformatics analysis of Ncoa7B, a novel ovulation-associated and reproduction system-specific Ncoa7 isoform

Reproduction ◽

10.1530/rep-07-0402 ◽

2008 ◽

Vol 135 (3) ◽

pp. 321-333 ◽

Cited By ~ 14

Author(s):

Ketty Shkolnik ◽

Shifra Ben-Dor ◽

Dalia Galiani ◽

Ariel Hourvitz ◽

Nava Dekel

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Oxidative Dna Damage ◽

Bioinformatics Analysis ◽

Cdna Clones ◽

Nuclear Receptor Coactivator ◽

Reproduction System ◽

Preovulatory Follicles ◽

Multiple Signaling

In the present work, we employed bioinformatics search tools to select ovulation-associated cDNA clones with a preference for those representing putative novel genes. Detailed characterization of one of these transcripts, 6C3, by real-time PCR and RACE analyses led to identification of a novel ovulation-associated gene, designatedNcoa7B. This gene was found to exhibit a significant homology to theNcoa7gene that encodes a conserved tissue-specific nuclear receptor coactivator. UnlikeNcoa7,Ncoa7Bpossesses a unique and highly conserved exon at the 5′ end and encodes a protein with a unique N-terminal sequence. Extensive bioinformatics analysis has revealed thatNcoa7Bhas one identifiable domain, TLDc, which has recently been suggested to be involved in protection from oxidative DNA damage. An alignment of TLDc domain containing proteins was performed, and the closest relative identified wasOXR1, which also has a corresponding, highly related short isoform, with just a TLDc domain. Moreover,Ncoa7Bexpression, as seen to date, seems to be restricted to mammals, while other TLDc family members have no such restriction. Multiple tissue analysis revealed that unlikeNcoa7, which was abundant in a variety of tissues with the highest expression in the brain,Ncoa7BmRNA expression is restricted to the reproductive system organs, particularly the uterus and the ovary. The ovarian expression ofNcoa7Bwas stimulated by human chorionic gonadotropin. Additionally, using real-time PCR, we demonstrated the involvement of multiple signaling pathways forNcoa7Bexpression on preovulatory follicles.

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Molecular Characterization of the Transcription Factors in Susceptible Poplar Infected with Virulent Melampsora larici-populina

International Journal of Molecular Sciences ◽

10.3390/ijms20194806 ◽

2019 ◽

Vol 20 (19) ◽

pp. 4806 ◽

Cited By ~ 1

Author(s):

Qiaoli Chen ◽

Jianan Wang ◽

Danlei Li ◽

Zhiying Wang ◽

Feng Wang ◽

...

Keyword(s):

Transcription Factors ◽

Calcium Binding ◽

Bioinformatics Analysis ◽

Pathological Process ◽

Compatible Interaction ◽

Time Points ◽

Time Periods ◽

Two Phases ◽

Transcript Profiles

Transcription factors (TFs) have been shown to play important roles in determining poplar susceptibility. In this study, the transcript profiles of five resistance-related TF groups at different time points were investigated to study the roles of TFs in the compatible interaction between ‘Robusta’ (Populus nigra × P. deltoides) and the virulent E4 race of Melampsora larici-populina. The susceptibility test indicated that the parasitic process of E4 could be divided into two representative time periods: the infection phase and the production phase. Bioinformatics analysis showed that in these two phases, E4 infection induced a network of TFs in ‘Robusta’. Although some TFs responded rapidly and positively, most TFs did not respond to E4, especially during the infection phase. The ethylene, jasmonic acid, and auxin pathways were downregulated, while a calcium-binding protein was upregulated. No other significantly changed phytohormone-related genes were found, which was consistent with the pathological process in the absence of an immune response, suggesting that the lack of response of most TFs during the infection phase of E4 is related to the susceptibility of ‘Robusta’.

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Comprehensive Characterization of Androgen-Responsive lncRNAs Mediated Regulatory Network in Hormone-Related Cancers

Disease Markers ◽

10.1155/2020/8884450 ◽

2020 ◽

Vol 2020 ◽

pp. 1-18

Author(s):

Dan Wang ◽

Mingyue Li ◽

Jing Li ◽

Xuechao Wan ◽

Yan Huang ◽

...

Keyword(s):

Signaling Pathway ◽

Cancer Progression ◽

Regulatory Network ◽

Bioinformatics Analysis ◽

Mapk Signaling ◽

Ppi Network ◽

Network Analyses ◽

Comprehensive Characterization ◽

Upstream Regulators

The AR signaling pathway plays an important role in initiation and progression of many hormone-related cancers including prostate, bladder, kidney, lung, and breast cancer. However, the potential roles of androgen-responsive long noncoding RNAs (lncRNAs) in hormone-related cancers remained unclear. In the present study, we identified 469 novel androgen-responsive lncRNAs using microarray data. After validating the accuracy of the array data, we constructed a transcriptional network which contained more than 30 transcriptional factors using ChIP-seq data to explore upstream regulators of androgen-responsive lncRNAs. Next, we conducted bioinformatics analysis to identify lncRNA-miRNA-mRNA regulatory network. To explore the potential roles of androgen-responsive lncRNAs in hormone-related cancers, we performed coexpression network and PPI network analyses using TCGA data. GO and KEGG analyses showed these lncRNAs were mainly involved in regulating signal transduction, transcription, development, cell adhesion, immune response, cell differentiation, and MAPK signaling pathway. We also highlight the prognostic value of HPN-AS1, TPTEP1, and LINC00623 in cancer outcomes. Our results suggest that androgen-responsive lncRNAs played important roles in regulating hormone-related cancer progression and could be novel molecular biomarkers.

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Functional-Genomics-Based Identification and Characterization of Open Reading Frames Encoding α-Glucoside-Processing Enzymes in the Hyperthermophilic Archaeon Pyrococcus furiosus

Applied and Environmental Microbiology ◽

10.1128/aem.01920-07 ◽

2007 ◽

Vol 74 (4) ◽

pp. 1281-1283 ◽

Cited By ~ 19

Author(s):

Donald A. Comfort ◽

Chung-Jung Chou ◽

Shannon B. Conners ◽

Amy L. VanFossen ◽

Robert M. Kelly

Keyword(s):

Glycoside Hydrolase ◽

Bioinformatics Analysis ◽

Pyrococcus Furiosus ◽

Transcriptional Response ◽

Open Reading Frames ◽

Processing Enzymes ◽

Response Information ◽

Identification And Characterization ◽

Reading Frames

ABSTRACT Bioinformatics analysis and transcriptional response information for Pyrococcus furiosus grown on α-glucans led to the identification of a novel isomaltase (PF0132) representing a new glycoside hydrolase (GH) family, a novel GH57 β-amylase (PF0870), and an extracellular starch-binding protein (1,141 amino acids; PF1109-PF1110), in addition to several other putative α-glucan-processing enzymes.

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A Periplasmic Thioredoxin-Like Protein Plays a Role in Defense against Oxidative Stress in Neisseria gonorrhoeae

Infection and Immunity ◽

10.1128/iai.00714-09 ◽

2009 ◽

Vol 77 (11) ◽

pp. 4934-4939 ◽

Cited By ~ 17

Author(s):

Maud E. S. Achard ◽

Amanda J. Hamilton ◽

Tarek Dankowski ◽

Begoña Heras ◽

Mark S. Schembri ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Bioinformatics Analysis ◽

Biochemical Characterization ◽

Gram Negative Bacteria ◽

Secondary Structure Analysis ◽

Disulfide Reduction ◽

Highly Sensitive ◽

Standard Redox Potential ◽

Disulfide Oxidoreductase

ABSTRACT Thioredoxin-like proteins of the TlpA/ResE/CcmG subfamily are known to face the periplasm in gram-negative bacteria. Using the tlpA gene of Bradyrhizobium japonicum as a query, we identified a locus (NGO1923) in Neisseria gonorrhoeae that encodes a thioredoxin-like protein (NG_TlpA). Bioinformatics analysis indicated that the predicted NG_TlpA protein contained a cleavable signal peptide at the N terminus, and secondary structure analysis identified a thioredoxin fold with a helical insertion (∼25 residues), similar to that found in B. japonicum TlpA but absent in cytoplasmic thioredoxins. Biochemical characterization of a recombinant form of NG_TlpA revealed a standard redox potential (E0′) of −206 mV. This property and the observation that the oxidized form of the protein exhibited greater thermal stability than the reduced species indicated that NG_TlpA is a reducing thioredoxin and not an oxidizing thiol-disulfide oxidoreductase like DsbA. The thioredoxin activity of NG_TlpA was confirmed in an insulin disulfide reduction assay. A tlpA mutant of N. gonorrhoeae strain 1291 was found to be highly sensitive to oxidative killing by paraquat and hydrogen peroxide, indicating an antioxidant role for the NG_TlpA in this bacterium. The tlpA mutant also exhibited reduced intracellular survival in human primary cervical epithelial cells.

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Serological characterization of surface-exposed proteins of Coxiella burnetii

Microbiology ◽

10.1099/mic.0.082131-0 ◽

2014 ◽

Vol 160 (12) ◽

pp. 2718-2731 ◽

Cited By ~ 7

Author(s):

Jun Jiao ◽

Xiaolu Xiong ◽

Yong Qi ◽

Wenping Gong ◽

Changsong Duan ◽

...

Keyword(s):

Coxiella Burnetii ◽

Bioinformatics Analysis ◽

Q Fever ◽

Obligate Intracellular ◽

Rickettsia Rickettsii ◽

Serological Characterization ◽

Vaccine Antigens ◽

Mycoplasma Pneumonia ◽

Dimensional Electrophoresis

The obligate intracellular Gram-negative bacterium Coxiella burnetii causes Q fever, a worldwide zoonosis. Here we labelled Cox . burnetii with biotin and used biotin-streptavidin affinity chromatography to isolate surface-exposed proteins (SEPs). Using two-dimensional electrophoresis combined with mass spectrometry, we identified 37 proteins through bioinformatics analysis. Thirty SEPs expressed in Escherichia coli (recombinant SEPs, rSEPs) were used to generate microarrays, which were probed with sera from mice experimentally infected with Cox. burnetii or sera from Q fever patients. Thirteen rSEPs were recognized as seroreactive, and the majority reacted with at least 50 % of the sera from mice infected with Cox. burnetii but not with sera from mice infected with Rickettsia rickettsii, R. heilongjiangensis, or R. typhi. Further, 13 proteins that reacted with sera from patients with Q fever did not react with sera from patients with brucellosis or mycoplasma pneumonia. Our results suggest that these seroreactive SEPs have potential as serodiagnostic antigens or as subunit vaccine antigens against Q fever.

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