scholarly journals Engineering, decoding and systems-level characterization of chimpanzee cytomegalovirus

2022 ◽  
Vol 18 (1) ◽  
pp. e1010193
Author(s):  
Quang Vinh Phan ◽  
Boris Bogdanow ◽  
Emanuel Wyler ◽  
Markus Landthaler ◽  
Fan Liu ◽  
...  
Keyword(s):  
Splice Variants ◽  
Artificial Chromosome ◽  
Infection Model ◽  
Cell Tropism ◽  
Close Phylogenetic Relationship ◽  
High Conservation ◽  
Cellular Pathways ◽  
Human Cmv ◽  
Comparative Functional Genomics

The chimpanzee cytomegalovirus (CCMV) is the closest relative of human CMV (HCMV). Because of the high conservation between these two species and the ability of human cells to fully support CCMV replication, CCMV holds great potential as a model system for HCMV. To make the CCMV genome available for precise and rapid gene manipulation techniques, we captured the genomic DNA of CCMV strain Heberling as a bacterial artificial chromosome (BAC). Selected BAC clones were reconstituted to infectious viruses, growing to similar high titers as parental CCMV. DNA sequencing confirmed the integrity of our clones and led to the identification of two polymorphic loci and a deletion-prone region within the CCMV genome. To re-evaluate the CCMV coding potential, we analyzed the viral transcriptome and proteome and identified several novel ORFs, splice variants, and regulatory RNAs. We further characterized the dynamics of CCMV gene expression and found that viral proteins cluster into five distinct temporal classes. In addition, our datasets revealed that the host response to CCMV infection and the de-regulation of cellular pathways are in line with known hallmarks of HCMV infection. In a first functional experiment, we investigated a proposed frameshift mutation in UL128 that was suspected to restrict CCMV’s cell tropism. In fact, repair of this frameshift re-established productive CCMV infection in endothelial and epithelial cells, expanding the options of CCMV as an infection model. Thus, BAC-cloned CCMV can serve as a powerful tool for systematic approaches in comparative functional genomics, exploiting the close phylogenetic relationship between CCMV and HCMV.

scholarly journals ENGINEERING, DECODING AND SYSTEMS-LEVEL CHARACTERIZATION OF CHIMPANZEE CYTOMEGALOVIRUS

2021 ◽  
Author(s):  
Quang Vinh Phan ◽  
Boris Bogdanow ◽  
Emanuel Wyler ◽  
Markus Landthaler ◽  
Fan Liu ◽  
...  
Keyword(s):  
Splice Variants ◽  
Artificial Chromosome ◽  
Infection Model ◽  
Cell Tropism ◽  
Close Phylogenetic Relationship ◽  
High Conservation ◽  
Infected Cells ◽  
Human Cmv ◽  
Comparative Functional Genomics

The chimpanzee cytomegalovirus (CCMV) is the closest relative of human CMV (HCMV). Because of the high conservation between these two species and the ability of human cells to fully support CCMV replication, CCMV holds great potential as a model system for HCMV. To make the CCMV genome available for precise and rapid gene manipulation techniques, we captured the genomic DNA of CCMV strain Heberling as a bacterial artificial chromosome (BAC). Selected BAC clones were reconstituted to infectious viruses, growing to similar high titers as parental CCMV. DNA sequencing confirmed the integrity of our clones and led to the identification of two polymorphic loci within the CCMV genome. To re-evaluate the CCMV coding potential, we analyzed the transcriptome and proteome of infected cells and identified several novel ORFs, splice variants, and regulatory RNAs. We further characterized the dynamics of CCMV gene expression and found that viral proteins cluster into five distinct temporal classes. In addition, our datasets revealed that the host response to CCMV infection and the de-regulation of cellular pathways are in line with known hallmarks of HCMV infection. In a first functional experiment, we investigated a proposed frameshift mutation in UL128 that was suspected to restrict CCMV's cell tropism. In fact, repair of this frameshift re-established productive CCMV infection in endothelial and epithelial cells, expanding the options of CCMV as an infection model. Thus, BAC-cloned CCMV can serve as a powerful tool for systematic approaches in comparative functional genomics, exploiting the close phylogenetic relationship between CCMV and HCMV.

Identification and characterization of novel splice variants of human farnesoid X receptor

2021 ◽  
pp. 108893
Author(s):  
Enni-Kaisa Mustonen ◽  
Serene M.L. Lee ◽  
Hanno Nieß ◽  
Matthias Schwab ◽  
Tatu Pantsar ◽  
...  
Keyword(s):  
Splice Variants ◽  
Farnesoid X Receptor ◽  
Identification And Characterization

scholarly journals Mutation analysis and characterization of alternative splice variants of the Wilson disease gene ATP7B

Hepatology ◽  
2010 ◽  
Vol 52 (5) ◽  
pp. 1662-1670 ◽  
Author(s):  
Lei Wan ◽  
Chang-Hai Tsai ◽  
Chin-Moo Hsu ◽  
Chin-Chang Huang ◽  
Chih-Chao Yang ◽  
...  
Keyword(s):  
Alternative Splice ◽  
Mutation Analysis ◽  
Wilson Disease ◽  
Disease Gene ◽  
Splice Variants ◽  
Alternative Splice Variants

scholarly journals Characterization of splice variants of human caspase-activated DNase with CIDE-N structure and function

FEBS Letters ◽  
2004 ◽  
Vol 566 (1-3) ◽  
pp. 234-240 ◽  
Author(s):  
José R. Bayascas ◽  
Vı́ctor J. Yuste ◽  
Carme Solé ◽  
Isabel Sánchez-López ◽  
Miquel F. Segura ◽  
...  
Keyword(s):  
Splice Variants ◽  
Structure And Function ◽  
Caspase Activated Dnase ◽  
And Function ◽  
Human Caspase

scholarly journals Characterization of bacterial artificial chromosome transgenic mice expressing mCherry fluorescent protein substituted for the murine smooth muscle α-actin gene

genesis ◽  
2010 ◽  
Vol 48 (7) ◽  
pp. 457-463 ◽  
Author(s):  
John J. Armstrong ◽  
Irina V. Larina ◽  
Mary E. Dickinson ◽  
Warren E. Zimmer ◽  
Karen K. Hirschi
Keyword(s):  
Smooth Muscle ◽  
Bacterial Artificial Chromosome ◽  
Transgenic Mice ◽  
Fluorescent Protein ◽  
Artificial Chromosome ◽  
Actin Gene

Characterization of three alternative splice variants associated with the Arabidopsis rhomboid protein gene At1g74130

Botany ◽  
2013 ◽  
Vol 91 (12) ◽  
pp. 840-849 ◽  
Author(s):  
Joshua Powles ◽  
Katharine Sedivy-Haley ◽  
Eric Chapman ◽  
Kenton Ko
Keyword(s):  
Alternative Splicing ◽  
Alternative Splice ◽  
Splice Variant ◽  
Serine Proteases ◽  
Transmembrane Domain ◽  
Splice Variants ◽  
Genes Encoding ◽  
Different Characteristics ◽  
Alternative Splice Variants

Rhomboid serine proteases are grouped into three main types — secretases, presenilin-like associated rhomboid-like (PARL) proteases, and “inactive” rhomboid proteins. Although the three rhomboid groups are distinct, the different types are likely to operate within the same cell or compartment, such as observed in the plastids of Arabidopsis. There are four distinct plastid rhomboid genes at play in Arabidopsis plastids, two for active types (At1g25290 and At5g25752) and two for inactive forms (At1g74130 and At1g74140). The number of working plastid rhomboids is further increased by alternative splicing, as reported for At1g25290. To understand how the plastid rhomboid system works, it is necessary to identify all rhomboid forms in play. To this end, this study was designed to examine the alternative splicing activities of At1g74130, one of the two genes encoding proteolytically “inactive” plastid rhomboids. The exon mapping and DNA sequencing results obtained here indicate the presence of three prominent alternative splice variants in the At1g74130 transcript population. The dominant splice variant, L, encodes the full-length protein. The other two splice variants, M and S, produce proteins lacking sections from the carboxyl transmembrane domain region. The splice variants M and S appear to be at levels with functional potential and appear to adjust relative to each other during development and in response to changes in the level of Tic40, a component of the plastid translocon. The splice variant proteins themselves exhibit different characteristics with respect to rhomboid protein–substrate interactions. These differences were observed in bacterial co-expression pull-down assays and in yeast mitochondrial studies. When considered together, the data suggest that the alternative splicing of At1g74130 bears functional significance in Arabidopsis and is likely to be part of a mechanism for diversifying plastid rhomboid function.

scholarly journals Molecular Characterization of the FCoV-like Canine Coronavirus HLJ-071 in China

2021 ◽  
Author(s):  
Zhige Tian ◽  
Miaomiao Zheng ◽  
Ying Deng ◽  
Dandan Gou ◽  
Peng Guo ◽  
...  
Keyword(s):  
Variable Region ◽  
Open Reading Frames ◽  
Cell Tropism ◽  
Essential Information ◽  
Severe Diarrhea ◽  
S Gene ◽  
Canine Coronavirus ◽  
Complete Sequences ◽  
Feline Coronavirus

Abstract Background According to differences in antigens and genetic composition, canine coronavirus (CCoV) consists of two genotypes, CCoV-Ⅰ and CCoV-Ⅱ. Recently, CCoVs with mutant variations have been found to be pantropic and pathogenic in dogs. Results In this study, we isolated a CCoV, designated HLJ-071, from a dead 5-week-old female Welsh Corgi with severe diarrhea and vomiting. Sequence analysis suggested that HLJ-071 bears a complete ORF3abc when compared with classic CCoV isolates (1–71, K378 and S378). In addition, a variable region was located between the S gene and the open reading frames (ORF) 3a gene, in which HLJ-071 has a deletion of 104 nucleotides (nts) when compared with classic CCoV strains 1–71, S378 and K378. Phylogenetic analysis based on the S gene and complete sequences showed that HLJ-071 is closely related to Feline Coronavirus (FCoV) II. Recombination analysis suggested that HLJ-071 originated from the recombination of FCoV 79-1683, FCoV DF2 and CCoV A76. Finally, cell tropism experiments suggested that HLJ-071 is able to replicate in canine macrophages/monocytes. Conclusion The present study involved the isolation and genetic characterization of a variant CCoV strain. The spike protein and ORF3abc of CCoV might play a key role in viral tropism, which could affect replication in monocyte/macrophage cells. This will provide essential information for further understanding the evolution of CCoV in China.

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