Molecular dissection of meiotic silencing by unpaired DNA

2015 ◽  
Author(s):  
◽  
Logan M. Decker
Keyword(s):  
Messenger Rnas ◽  
Meiotic Silencing ◽  
University Of Missouri ◽  
A Genome ◽  
Unpaired Region ◽  
The University ◽  
Surveillance Mechanism ◽  
Interfering Rna ◽  
Identification And Characterization

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Meiotic silencing by unpaired DNA (MSUD) is a genome surveillance mechanism that uses RNAi to protect against genetic parasites such as retrotransposons and viruses. This is accomplished by scanning the genome for DNA segments not paired with a homologous partner during meiosis and targeting the corresponding messenger RNAs for destruction. MSUD begins when a single-stranded RNA is made from the unpaired region and subsequently converted into small interfering RNA (siRNA), which are used as sequence specific guides for mRNA destruction. To date, nine meiotic silencing genes have been characterized and here we report the identification and characterization of two new candidates that are orthologous to the conserved proteins CBP80 and EPS15.

scholarly journals Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family

2006 ◽  
Vol 394 (3) ◽  
pp. 575-579 ◽  
Author(s):  
Sergey V. Novoselov ◽  
Deame Hua ◽  
Alexey V. Lobanov ◽  
Vadim N. Gladyshev
Keyword(s):  
Mammalian Cells ◽  
Insertion Sequence ◽  
Phylogenetic Analyses ◽  
Dependent Manner ◽  
Putative Active Site ◽  
A Genome ◽  
Sequence Elements ◽  
Identification And Characterization ◽  
Insertion Sequence Elements

Sec (selenocysteine) is a rare amino acid in proteins. It is co-translationally inserted into proteins at UGA codons with the help of SECIS (Sec insertion sequence) elements. A full set of selenoproteins within a genome, known as the selenoproteome, is highly variable in different organisms. However, most of the known eukaryotic selenoproteins are represented in the mammalian selenoproteome. In addition, many of these selenoproteins have cysteine orthologues. Here, we describe a new selenoprotein, designated Fep15, which is distantly related to members of the 15 kDa selenoprotein (Sep15) family. Fep15 is absent in mammals, can be detected only in fish and is present in these organisms only in the selenoprotein form. In contrast with other members of the Sep15 family, which contain a putative active site composed of Sec and cysteine, Fep15 has only Sec. When transiently expressed in mammalian cells, Fep15 incorporated Sec in an SECIS- and SBP2 (SECIS-binding protein 2)-dependent manner and was targeted to the endoplasmic reticulum by its N-terminal signal peptide. Phylogenetic analyses of Sep15 family members suggest that Fep15 evolved by gene duplication.

scholarly journals Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y

2010 ◽  
Vol 190 (5) ◽  
pp. 777-791 ◽  
Author(s):  
Sonja M. Wiedemann ◽  
Silke N. Mildner ◽  
Clemens Bönisch ◽  
Lars Israel ◽  
Andreas Maiser ◽  
...  
Keyword(s):  
Cell Cycle Control ◽  
Histone H3 ◽  
Cellular Responses ◽  
Histone Variants ◽  
Brain Regions ◽  
Messenger Rnas ◽  
Cellular Density ◽  
Identification And Characterization

Nucleosomal incorporation of specialized histone variants is an important mechanism to generate different functional chromatin states. Here, we describe the identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. Their messenger RNAs are found in certain human cell lines, in addition to several normal and malignant human tissues. In keeping with their primate specificity, H3.X and H3.Y are detected in different brain regions. Transgenic H3.X and H3.Y proteins are stably incorporated into chromatin in a similar fashion to the known H3 variants. Importantly, we demonstrate biochemically and by mass spectrometry that endogenous H3.Y protein exists in vivo, and that stress stimuli, such as starvation and cellular density, increase the abundance of H3.Y-expressing cells. Global transcriptome analysis revealed that knockdown of H3.Y affects cell growth and leads to changes in the expression of many genes involved in cell cycle control. Thus, H3.Y is a novel histone variant involved in the regulation of cellular responses to outside stimuli.

A genome-wide identification and characterization of mircoRNAs and their targets in ‘Suli’ pear (Pyrus pyrifolia white pear group)

Planta ◽  
2013 ◽  
Vol 238 (6) ◽  
pp. 1095-1112 ◽  
Author(s):  
Qingfeng Niu ◽  
Minjie Qian ◽  
Guoqin Liu ◽  
Fengxia Yang ◽  
Yuanwen Teng
Keyword(s):  
Pyrus Pyrifolia ◽  
Genome Wide ◽  
A Genome ◽  
Identification And Characterization

scholarly journals Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible FungusPleurotus ostreatus

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Jibin Qu ◽  
Mengran Zhao ◽  
Tom Hsiang ◽  
Xiaoxing Feng ◽  
Jinxia Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Noncoding Rnas ◽  
Genome Sequences ◽  
Small Noncoding Rnas ◽  
Basidiomycetous Fungus ◽  
A Genome ◽  
Genome Assemblies ◽  
Genome Scale ◽  
Identification And Characterization

Noncoding RNAs (ncRNAs) have been identified in many fungi. However, no genome-scale identification of ncRNAs has been inventoried for basidiomycetes. In this research, we detected 254 small noncoding RNAs (sncRNAs) in a genome assembly of an isolate (CCEF00389) ofPleurotus ostreatus, which is a widely cultivated edible basidiomycetous fungus worldwide. The identified sncRNAs include snRNAs, snoRNAs, tRNAs, and miRNAs. SnRNA U1 was not found in CCEF00389 genome assembly and some other basidiomycetous genomes by BLASTn. This implies that if snRNA U1 of basidiomycetes exists, it has a sequence that varies significantly from other organisms. By analyzing the distribution of sncRNA loci, we found that snRNAs and most tRNAs (88.6%) were located in pseudo-UTR regions, while miRNAs are commonly found in introns. To analyze the evolutionary conservation of the sncRNAs inP. ostreatus, we aligned all 254 sncRNAs to the genome assemblies of some other Agaricomycotina fungi. The results suggest that most sncRNAs (77.56%) were highly conserved inP. ostreatus, and 20% were conserved in Agaricomycotina fungi. These findings indicate that most sncRNAs ofP. ostreatuswere not conserved across Agaricomycotina fungi.

Investigating the role of arginine 21 in the structure and function of human [alpha]a-crystallin

2018 ◽  
Author(s):  
◽  
Ashutosh Shripad Phadte
Keyword(s):  
Functional Characterization ◽  
Lens Fiber Cell ◽  
University Of Missouri ◽  
Mutant Proteins ◽  
Plausible Mechanism ◽  
And Function ◽  
The University

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Cataractogenesis in the eye lens occurs as a result of protein aggregation. Of the multiple mutations in [alpha]A-crystallins associated with the development of congenital hereditary cataract, three identified mutations target R21 within the N- terminal domain of the protein. On structural and functional characterization of a recently identified mutant of [alpha]A-crystallin, [alpha]A-R21Q, we revealed the contribution of R21 in dictating the interaction of [alpha]A-crystallin with other proteins. [alpha]A-R21Q showed and enhanced chaperone-like function, and increased binding to lens fiber cell membranes. Transduction of mutant proteins in ARPE-19 cells prevented their apoptosis in the presence of oxidative stress, suggesting a role for R21 in modulating the anti-apoptotic function of [alpha]A-crystallin. In addition, the R21Q point mutation rescued the chaperone-like activity of [alpha]A-G98R crystallin as well as palliated [alpha]A-G98R mediated cytotoxicity otherwise observed in transduction experiments. Although another mutation, R157Q rescued the chaperone-like activity of [alpha]A-G98R, the double mutant exhibited a loss of its cytoprotective function. The results therefore implicate an important role of R21 in regulating the functional aspect of [alpha]A-crystallin. [alpha]A-crystallin derived peptides have been shown to prevent non-specific aggregation of unfolding proteins in vitro. We show that the [alpha]A-crystallin derived mini-chaperone (mini-[alpha]A) mediated stabilization of self-aggregating [alpha]A-G98R crystallin and bovine [subscript]-crystallin occurs via compensation of lost surface charge. The observation therefore suggests a plausible mechanism of action of [alpha]A-crystallin derived peptides of therapeutic interest.

scholarly journals Identification and Characterization of the Glutathione Peroxidase (GPX) Gene Family in Watermelon and Its Expression under Various Abiotic Stresses

Agronomy ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 206 ◽  
Author(s):  
Yong Zhou ◽  
Jingwen Li ◽  
Junhong Wang ◽  
Wenting Yang ◽  
Youxin Yang
Keyword(s):  
Abiotic Stress ◽  
Glutathione Peroxidase ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome ◽  
Identification And Characterization ◽  
Lower Expression

Plant glutathione peroxidase (GPX) is an important antioxidant enzyme to maintain H2O2 homeostasis and regulate plant response to abiotic stress. In this paper, we present the first report of a genome-wide identification of GPX genes in watermelon. A total of six genes (ClGPX1–ClGPX6) were identified, which were unevenly located on four chromosomes of the watermelon genome. Based on phylogenetic analysis, the GPX genes of Arabidopsis, rice, cucumber, and sorghum were classified into four groups. Through analyzing the promoter regions of ClGPX genes, many development-, stress-, and hormone-responsive cis-acting regulatory elements were also identified. Expression pattern analysis by qRT-PCR indicated that all ClGPX genes were actively expressed in flowers and fruits, and exhibited relatively lower expression in other tissues, particularly roots and stems. In addition, the expression of ClGPX genes was significantly induced by salt, drought, and cold stresses, as well as abscisic acid (ABA) treatment at different time points, suggesting that they may be involved in response to abiotic stress and ABA. Taken together, our findings demonstrated that ClGPX genes might function in watermelon development, especially in flower and fruit tissue, as well as in response to abiotic stress and hormones.

scholarly journals Life's (more than) a BLAST™: Proteomics software

2002 ◽  
Vol 24 (4) ◽  
pp. 21-23 ◽  
Author(s):  
Ronan O’Malley
Keyword(s):  
Proteomics Data ◽  
Software Suite ◽  
Efficient Manner ◽  
Exponential Increase ◽  
A Genome ◽  
Recent Developments ◽  
Automated Processing ◽  
Protein Complement ◽  
Identification And Characterization

Proteomics, the study of the expressed protein complement of a genome, centres on the identification and characterization of protein mixtures isolated from biological systems. Mass spectrometry (MS), in combination with one or more pre-separation steps, is currently the preferred method for analysing protein samples. Recent developments in these disciplines, particularly the emergence of high-throughput, automated techniques, have led to an exponential increase in data quantity -- gigabytes of data can be produced daily. A major challenge lies in processing these data to extract the maximum amount of information in a time- and labour-efficient manner. To meet this challenge, Micromass UK Ltd has developed a comprehensive proteomics software suite, ProteinLynxTM GlobalSERVER 2.0, which enables the automated processing, analysis, storage and reporting of proteomics data.

scholarly journals Genome-Wide Characterization and Expression Analysis Provide Basis to the Biological Function of Cotton FBA Genes

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhong-Qing Li ◽  
Yao Zhang ◽  
He Li ◽  
Ting-Ting Su ◽  
Cheng-Gong Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Function Analysis ◽  
Pcr Analysis ◽  
Functional Domain ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Identification And Characterization

Fructose-1,6-biphosphate aldolase (FBA) is a multifunctional enzyme in plants, which participates in the process of Calvin-Benson cycle, glycolysis and gluconeogenesis. Despite the importance of FBA genes in regulating plant growth, development and abiotic stress responses, little is known about their roles in cotton. In the present study, we performed a genome-wide identification and characterization of FBAs in Gossypium hirsutum. Totally seventeen GhFBA genes were identified. According to the analysis of functional domain, phylogenetic relationship, and gene structure, GhFBA genes were classified into two subgroups. Furthermore, nine GhFBAs were predicted to be in chloroplast and eight were located in cytoplasm. Moreover, the promoter prediction showed a variety of abiotic stresses and phytohormone related cis-acting elements exist in the 2k up-stream region of GhFBA. And the evolutionary characteristics of cotton FBA genes were clearly presented by synteny analysis. Moreover, the results of transcriptome and qRT-PCR analysis showed that the expression of GhFBAs were related to the tissue distribution, and further analysis suggested that GhFBAs could respond to various abiotic stress and phytohormonal treatments. Overall, our systematic analysis of GhFBA genes would not only provide a basis for the understanding of the evolution of GhFBAs, but also found a foundation for the further function analysis of GhFBAs to improve cotton yield and environmental adaptability.

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