scholarly journals Structural and Functional Diversity among Five RING Finger Proteins from Carassius Auratus Herpesvirus (CaHV)

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 254
Author(s):  
Zi-Hao Wang ◽  
Fei Ke ◽  
Qi-Ya Zhang ◽  
Jian-Fang Gui
Keyword(s):  
Subcellular Localization ◽  
Carassius Auratus ◽  
Ring Finger ◽  
Structural Diversity ◽  
Full Length ◽  
Ring Domain ◽  
Whole Cells ◽  
Host Interaction ◽  
New Genes ◽  
Ring Finger Proteins

Carassius auratus herpesvirus (CaHV) has been identified as a high-virulence pathogenic virus that infects aquatic animals, but the key factor for virus–host interaction is still unclear. Five Really interesting new genes (RING) finger proteins (39L, 52L, 131R, 136L, and 143R) of CaHV were screened to determine structural diversity. RING finger proteins were also predicted in other known fish herpesviruses, with an arrangement and number similar to CaHV. We performed multifaceted analyses of the proteins, including protein sizes, skeleton structures, subcellular localizations, and ubiquitination activities, to determine their precise roles in virus–host interactions. The five proteins were overexpressed and detected different levels of ubiquitination activities, and 143R showed the highest activity. Then, the prokaryotic expressed and purified full-length proteins (131R and 136L), RING domain isolates (131R12–43 and 136L45–87), and RING domain-deleted mutants (131RΔ12–43 and 136LΔ45–87) were prepared to detect their activities through ubiquitination assays. The results indicate that both full-length proteins and their isolates have activities that catalyze ubiquitination, and the full-length proteins possess higher activity than the isolates, but RING domain-deleted mutants lose their activities. Furthermore, the activities of the five proteins were verified as E3 ubiquitin ligase activity, showing that the RING domains determine the ubiquitination activity. These proteins present different subcellular localization. RING domain-deleted mutants showed similar subcellular localization with their full-length proteins, and all the isolates diffused in whole cells. The current results indicate that the sequence outside the RING domain determines subcellular localization and the level of ubiquitination activity, suggesting that the RING finger proteins of fish herpesviruses might have diverse functions in virus–host interaction.

scholarly journals Full-length transcriptome analysis reveals the mechanism of acupuncture at PC6 improves cardiac function in myocardial ischemia model

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Jing Yuan ◽  
Jun-Meng Wang ◽  
Zhi-Wei Li ◽  
Cheng-Shun Zhang ◽  
Bin Cheng ◽  
...  
Keyword(s):  
Myocardial Ischemia ◽  
Cardiac Function ◽  
Acupuncture Treatment ◽  
Pathological Process ◽  
Full Length ◽  
The Novel ◽  
New Genes ◽  
Myocardial Infraction ◽  
Differential Expression Genes ◽  
Multi Level

Abstract Background The pathological process of myocardial ischemia (MI) is very complicated. Acupuncture at PC6 has been proved to be effective against MI injury, but the mechanism remains unclear. This study investigated the mechanism that underlies the effect of acupuncture on MI through full-length transcriptome. Methods Adult male C57/BL6 mice were randomly divided into control, MI, and PC6 groups. Mice in MI and PC6 group generated MI model by ligating the left anterior descending (LAD) coronary artery. The samples were collected 5 days after acupuncture treatment. Results The results showed that treatment by acupuncture improved cardiac function, decreased myocardial infraction area, and reduced the levels of cTnT and cTnI. Based on full-length transcriptome sequencing, 5083 differential expression genes (DEGs) and 324 DEGs were identified in the MI group and PC6 group, respectively. These genes regulated by acupuncture were mainly enriched in the inflammatory response pathway. Alternative splicing (AS) is a post-transcriptional action that contributes to the diversity of protein. In all samples, 8237 AS events associated with 1994 genes were found. Some differential AS-involved genes were enriched in the pathway related to heart disease. We also identified 602 new genes, 4 of which may the novel targets of acupuncture in MI. Conclusions Our findings suggest that the effect of acupuncture on MI may be based on the multi-level regulation of the transcriptome.

scholarly journals Genetic and Epigenetic Changes Are Rapid Responses of the Genome to the Newly Synthesized Autotetraploid Carassius auratus

2021 ◽  
Vol 11 ◽  
Author(s):  
Chongqing Wang ◽  
Yuwei Zhou ◽  
Huan Qin ◽  
Chun Zhao ◽  
Li Yang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Carassius Auratus ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Enrichment Analysis ◽  
Full Length ◽  
Aflp Analysis ◽  
Whole Genome ◽  
Epigenetic Alterations ◽  
Fish Genome

Whole genome duplication events have occurred frequently during the course of vertebrate evolution. To better understand the influence of polyploidization on the fish genome, we herein used the autotetraploid Carassius auratus (4n = 200, RRRR) (4nRR) resulting from the whole genome duplication of Carassius auratus (2n = 100, RR) (RCC) to explore the genomic and epigenetic alterations after polyploidization. We subsequently performed analyses of full-length transcriptome dataset, amplified fragment length polymorphism (AFLP) and methylation sensitive amplification polymorphism (MSAP) on 4nRR and RCC. By matching the results of 4nRR and RCC isoforms with reference genome in full-length transcriptome dataset, 649 and 1,971 novel genes were found in the RCC and 4nRR full-length geneset, respectively. Compared to Carassius auratus and Megalobrama amblycephala, 4nRR presented 3,661 unexpressed genes and 2,743 expressed genes. Furthermore, GO enrichment analysis of expressed genes in 4nRR revealed that they were enriched in meiosis I, whereas KEGG enrichment analysis displayed that they were mainly enriched in proteasome. Using AFLP analysis, we noted that 32.61% of RCC fragments had disappeared, while 32.79% of new bands were uncovered in 4nRR. Concerning DNA methylation, 4nRR exhibited a lower level of global DNA methylation than RCC. Additionally, 60.31% of methylation patterns in 4nRR were altered compared to RCC. These observations indicated that transcriptome alterations, genomic changes and regulation of DNA methylation levels and patterns had occurred in the newly established autotetraploid genomes, suggesting that genetic and epigenetic alterations were influenced by autotetraploidization. In summary, this study provides valuable novel insights into vertebrate genome evolution and generates relevant information for fish breeding.

Arabidopsis DAL1 and DAL2, two RING finger proteins homologous to Drosophila DIAP1, are involved in regulation of programmed cell death

2010 ◽  
Vol 30 (1) ◽  
pp. 37-48 ◽  
Author(s):  
B. M. Vindhya S. Basnayake ◽  
Dayong Li ◽  
Huijuan Zhang ◽  
Guojun Li ◽  
Nasar Virk ◽  
...  
Keyword(s):  
Cell Death ◽  
Programmed Cell Death ◽  
Ring Finger ◽  
Ring Finger Proteins

scholarly journals A cellular complex of BACE1 and γ-secretase sequentially generates Aβ from its full-length precursor

2019 ◽  
Vol 218 (2) ◽  
pp. 644-663 ◽  
Author(s):  
Lei Liu ◽  
Li Ding ◽  
Matteo Rovere ◽  
Michael S. Wolfe ◽  
Dennis J. Selkoe
Keyword(s):  
Molecular Weight ◽  
Cultured Cells ◽  
Amyloid Β ◽  
Full Length ◽  
Aβ Peptides ◽  
Whole Cells ◽  
Sequential Processing ◽  
Catalytically Active ◽  
Cellular Complex

Intramembrane proteolysis of transmembrane substrates by the presenilin–γ-secretase complex is preceded and regulated by shedding of the substrate’s ectodomain by α- or β-secretase. We asked whether β- and γ-secretases interact to mediate efficient sequential processing of APP, generating the amyloid β (Aβ) peptides that initiate Alzheimer’s disease. We describe a hitherto unrecognized multiprotease complex containing active β- and γ-secretases. BACE1 coimmunoprecipitated and cofractionated with γ-secretase in cultured cells and in mouse and human brain. An endogenous high molecular weight (HMW) complex (∼5 MD) containing β- and γ-secretases and holo-APP was catalytically active in vitro and generated a full array of Aβ peptides, with physiological Aβ42/40 ratios. The isolated complex responded properly to γ-secretase modulators. Alzheimer’s-causing mutations in presenilin altered the Aβ42/40 peptide ratio generated by the HMW β/γ-secretase complex indistinguishably from that observed in whole cells. Thus, Aβ is generated from holo-APP by a BACE1–γ-secretase complex that provides sequential, efficient RIP processing of full-length substrates to final products.

Physiological characteristic changes and full-length transcriptome of rose (Rosa chinensis) roots and leaves in response to drought stress

2020 ◽  
Author(s):  
Wei Li ◽  
Lufeng Fu ◽  
Ziwen Geng ◽  
Xiaojuan Zhao ◽  
Qinghua Liu ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Drought Stress ◽  
Posttranscriptional Regulation ◽  
Regulatory Networks ◽  
Average Length ◽  
Physiological Characteristic ◽  
Full Length ◽  
Rosa Chinensis ◽  
New Genes ◽  
Leaves And Roots

Abstract Rose (Rosa chinensis) is the most important ornamental crops worldwide. However, the physiological and molecular mechanism of rose under drought stress remains elusive. In this study, we analyzed the changes of photosynthetic and phytohormone levels in the leaves and roots of rose seedlings grown under control (no drought/ND), mild (MD), and severe (SD) drought stress. The total chlorophyll content and water use efficiency were significantly enhanced under MD in rose leaves. In addition, the concentration of abscisic acid (ABA) was higher in the leaves compared to the roots, whereas the roots accumulated more indole-3-acetic acid (IAA), methylindole-3-acetic acid (Me-IAA) and indole-3-propionic acid (IPA). We also constructed the first full-length transcriptome for rose, and identified 96,201,862 full-length reads of average length 1,149 bp that included 65,789 novel transcripts. A total of 3,657 and 4,341 differentially expressed genes (DEGs) were identified in rose leaves and roots respectively. KEGG pathway analysis showed enrichment of plant hormone, signal transduction, and photosynthesis are among the DEGs. 42,544 alternatively spliced isoforms were also identified, and alternative 3ʹ splice site was the major alternative splicing (AS) event among the DEGs. Variations in the AS patterns of three genes between leaves and roots indicated the possibility of tissue-specific posttranscriptional regulation in response to drought stress. Furthermore, 2,410 novel long non-coding RNAs were detected that may participate in regulating the drought-induced DEGs. Our findings identified previously unknown splice sites and new genes in the rose transcriptome, and elucidated the drought stress-responsive genes as well as their intricate regulatory networks.

scholarly journals Subcellular Localization of Full-Length and Truncated Trk Receptor Isoforms in Polarized Neurons and Epithelial Cells

1999 ◽  
Vol 19 (14) ◽  
pp. 5823-5833 ◽  
Author(s):  
David Kryl ◽  
Talene Yacoubian ◽  
Annakaisa Haapasalo ◽  
Eero Castren ◽  
Donald Lo ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Subcellular Localization ◽  
Full Length ◽  
Trk Receptor ◽  
Receptor Isoforms

Comparative analysis of testis transcriptomes associated with male infertility in triploid cyprinid fish

2019 ◽  
Vol 31 (2) ◽  
pp. 248 ◽  
Author(s):  
Wuhui Li ◽  
Hui Tan ◽  
Junmei Liu ◽  
Jie Hu ◽  
Jialin Cui ◽  
...  
Keyword(s):  
Male Infertility ◽  
B Cell ◽  
Ring Finger ◽  
B Cell Lymphoma ◽  
Diploid Parent ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Caspase 7 ◽  
Ring Finger Proteins ◽  
Ubiquitin Conjugating Enzymes

Spermatogenesis involves a series of cellular transformations and thousands of regulated genes. Previously, we showed that the triploid fish (3nBY) cannot produce mature spermatozoa. In the present study, evaluation of the testis microstructure revealed that germ cells of 3nBY could develop into round spermatids, but then degenerated, resulting in male infertility. In this study we comparatively analysed the testis transcriptomes from 3nBY and its diploid parent YB and identified a series of differentially expressed genes (DEGs) that were enriched in the Wnt signalling pathway and the apoptotic and ubiquitin-mediated proteolysis processes in 3nBY. Gene ontology functional analyses revealed that some DEGs in 3nBY were directly associated with the process of gamete generation, development and sperm flagellum assembly. In addition, the expression of a number of genes related to meiosis (Inhibitor Of DNA Binding 2 (ID2), Ovo Like Transcriptional Repressor 1 (OVOL1)), mitochondria (ATP1b (ATPase Na+/K+ Transporting Subunit Beta 1), ATP2a (ATPase, Ca++ Transporting, Cardiac Muscle, Slow Twitch 2), ATP5a (ATP Synthase F1 Subunit Alpha), Mitochondrially Encoded Cytochrome C Oxidase I (COX1), NADH Dehydrogenase Subunit 4 (ND4)) and chromatin structure (Histone 1 (H1), Histone 2a (H2A), Histone 2b (H2B), Histone 3 (H3), Histone 4 (H4)) was lower in the testes of 3nBY, whereas the expression of genes encoding ubiquitin (Ubiquitin Conjugating Enzymes (UBEs), Ring Finger Proteins (RNFs)) and apoptosis (CASPs (Caspase 3, Caspase 7,Caspase 8), BCLs (B-Cell Lymphoma 3, B-Cell CLL/Lymphoma 2, B Cell CLL/Lymphoma 10)) proteins involved in spermatid degeneration was higher. These data suggest that the disrupted expression of genes associated with spermatogenesis and the increased expression of mitochondrial ubiquitin, which initiates cell apoptosis, may result in spermatid degeneration in male 3nBY. This study provides information regarding the potential molecular regulatory mechanisms underlying male infertility in polyploid fish.

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