scholarly journals Comparative analysis of viral RNA signatures on different RIG-I-like receptors

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Raul Y Sanchez David ◽  
Chantal Combredet ◽  
Odile Sismeiro ◽  
Marie-Agnès Dillies ◽  
Bernd Jagla ◽  
...  
Keyword(s):  
Rna Virus ◽  
Affinity Purification ◽  
Viral Rna ◽  
Coding Region ◽  
Chikv Infection ◽  
Rna Molecules ◽  
Positive Sense ◽  
Rna Ligands ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The RIG-I-like receptors (RLRs) play a major role in sensing RNA virus infection to initiate and modulate antiviral immunity. They interact with particular viral RNAs, most of them being still unknown. To decipher the viral RNA signature on RLRs during viral infection, we tagged RLRs (RIG-I, MDA5, LGP2) and applied tagged protein affinity purification followed by next-generation sequencing (NGS) of associated RNA molecules. Two viruses with negative- and positive-sense RNA genome were used: measles (MV) and chikungunya (CHIKV). NGS analysis revealed that distinct regions of MV genome were specifically recognized by distinct RLRs: RIG-I recognized defective interfering genomes, whereas MDA5 and LGP2 specifically bound MV nucleoprotein-coding region. During CHIKV infection, RIG-I associated specifically to the 3’ untranslated region of viral genome. This study provides the first comparative view of the viral RNA ligands for RIG-I, MDA5 and LGP2 in the presence of infection.

scholarly journals Autophagy is involved in assisting the replication of Bamboo mosaic virus in Nicotiana benthamiana

2019 ◽  
Vol 70 (18) ◽  
pp. 4657-4670 ◽  
Author(s):  
Ying-Ping Huang ◽  
Ying-Wen Huang ◽  
Yung-Jen Hsiao ◽  
Siou-Cen Li ◽  
Yau-Huei Hsu ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Fluorescent Protein ◽  
Rna Virus ◽  
Critical Role ◽  
Viral Rna ◽  
Autophagosome Formation ◽  
Orange Fluorescent Protein ◽  
Positive Sense ◽  
Trigger Cell Death

Abstract Autophagy plays a critical role in plants under biotic stress, including the response to pathogen infection. We investigated whether autophagy-related genes (ATGs) are involved in infection with Bamboo mosaic virus (BaMV), a single-stranded positive-sense RNA virus. Initially, we observed that BaMV infection in Nicotiana benthamiana leaves upregulated the expression of ATGs but did not trigger cell death. The induction of ATGs, which possibly triggers autophagy, increased rather than diminished BaMV accumulation in the leaves, as revealed by gene knockdown and transient expression experiments. Furthermore, the inhibitor 3-methyladenine blocked autophagosome formation and the autophagy inducer rapamycin, which negatively and positively affected BaMV accumulation, respectively. Pull-down experiments with an antibody against orange fluorescent protein (OFP)-NbATG8f, an autophagosome marker protein, showed that both plus- and minus-sense BaMV RNAs could associate with NbATG8f. Confocal microscopy revealed that ATG8f-enriched vesicles possibly derived from chloroplasts contained both the BaMV viral RNA and its replicase. Thus, BaMV infection may induce the expression of ATGs possibly via autophagy to selectively engulf a portion of viral RNA-containing chloroplast. Virus-induced vesicles enriched with ATG8f could provide an alternative site for viral RNA replication or a shelter from the host silencing mechanism.

scholarly journals Identification of a cis-Acting Replication Element within the Poliovirus Coding Region

2000 ◽  
Vol 74 (10) ◽  
pp. 4590-4600 ◽  
Author(s):  
Ian Goodfellow ◽  
Yasmin Chaudhry ◽  
Andrew Richardson ◽  
Janet Meredith ◽  
Jeffrey W. Almond ◽  
...  
Keyword(s):  
Rna Virus ◽  
Site Directed Mutagenesis ◽  
Evolutionary Significance ◽  
Rna Structures ◽  
Coding Region ◽  
Rna Sequences ◽  
Stem Loop ◽  
Cis Acting ◽  
Function Recovery ◽  
Positive Sense

ABSTRACT The replication of poliovirus, a positive-stranded RNA virus, requires translation of the infecting genome followed by virus-encoded VPg and 3D polymerase-primed synthesis of a negative-stranded template. RNA sequences involved in the latter process are poorly defined. Since many sequences involved in picornavirus replication form RNA structures, we searched the genome, other than the untranslated regions, for predicted local secondary structural elements and identified a 61-nucleotide (nt) stem-loop in the region encoding the 2C protein. Covariance analysis suggested the structure was well conserved in the Enterovirus genus of the Picornaviridae. Site-directed mutagenesis, disrupting the structure without affecting the 2C product, destroyed genome viability and suggested that the structure was required in the positive sense for function. Recovery of revertant viruses suggested that integrity of the structure was critical for function, and analysis of replication demonstrated that nonviable mutants did not synthesize negative strands. Our conclusion, that this RNA secondary structure constitutes a novel polioviruscis-acting replication element (CRE), is supported by the demonstration that subgenomic replicons bearing lethal mutations in the native structure can be restored to replication competence by the addition of a second copy of the 61-nt wild-type sequence at another location within the genome. This poliovirus CRE functionally resembles an element identified in rhinovirus type 14 (K. L. McKnight and S. M. Lemon, RNA 4:1569–1584, 1998) and the cardioviruses (P. E. Lobert, N. Escriou, J. Ruelle, and T. Michiels, Proc. Natl. Acad. Sci. USA 96:11560–11565, 1999) but differs in sequence, structure, and location. The functional role and evolutionary significance of CREs in the replication of positive-sense RNA viruses is discussed.

scholarly journals Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1894
Author(s):  
Orian Gilmer ◽  
Erwan Quignon ◽  
Anne-Caroline Jousset ◽  
Jean-Christophe Paillart ◽  
Roland Marquet ◽  
...  
Keyword(s):  
Historical Perspective ◽  
Detection Methods ◽  
Rna Structures ◽  
Viral Rnas ◽  
Rna Molecules ◽  
Rna Biology ◽  
Key Players ◽  
The 1960S ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.

scholarly journals PEMANFAATAN TEKNOLOGI SEKUENSING GENOM UNTUK MEMPERCEPAT PROGRAM PEMULIAAN TANAMAN

2016 ◽  
Vol 34 (4) ◽  
pp. 159
Author(s):  
I Made Tasma
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Coding Region ◽  
Protein Coding ◽  
Snp Chip ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Sumber daya genetik (SDG) tanaman menyediakan materi dasar untuk program pemuliaan tanaman. Namun, baru sebagian kecil (<1%) koleksi SDG yang dimanfaatkan untuk pemuliaan tanaman. Karakterisasi SDG sudah banyak dilakukan dengan menggunakan karakter morfologi, namun metode ini lambat, menyita waktu, dan memerlukan banyak tenaga. Teknologi sekuensing modern menghasilkan peta genom rujukan suatu spesies tanaman yang   dapat mempercepat karakterisasi SDG menggunakan teknik next generation sequencing (NGS). Tulisan ini mengulas pemanfaatan teknologi sekuensing genom untuk karakterisasi, proteksi, dan pemanfaatan SDG untuk mempercepat program pemuliaan tanaman. Di Indonesia, teknologi NGS telah dimanfaatkan sejak 2010 untuk resekuensing genom komoditas unggulan nasional seperti kedelai, kakao, jagung, dan cabai merah. Jutaan SNP dan Indel telah diidentifikasi pada setiap komoditas sebagai sumber daya pemuliaan yang bernilai tinggi. Sebagian kecil SNP/Indel tersebut berada pada protein coding region yang potensial untuk penemuan gen-gen unggul. Selain SNP yang diidentifikasi pada semua genotipe, ditemukan SNP pada genotipe tertentu (SNP unik). Koleksi SNP dalam jumlah besar ini digunakan untuk mensintesis SNP chip untuk genotyping SDG secara cepat dan komprehensif. Didukung data fenotipe, SNP chip bermanfaat untuk melabel gen-gen unggul. Marka SNP yang berpautan dengan karakter unggul digunakan untuk menyeleksi individu pembawa karakter unggul tersebut. Dengan teknologi NGS, perakitan VUB tanaman dapat dilakukan lebih cepat, akurat, dan efisien. Dengan demikian, teknologi NGS dapat memfasilitasi karakterisasi dan pemanfaatan SDG untuk mem-percepat program pemuliaan tanaman.

RNA Sequencing of Formalin-Fixed and Paraffin-Embedded Tissue as a Complementary Method in Ophthalmopathology

2020 ◽  
Vol 237 (07) ◽  
pp. 860-866
Author(s):  
Günther Schlunck ◽  
Stefaniya Boneva ◽  
Julian Wolf ◽  
Anja Schlecht ◽  
Thomas Reinhard ◽  
...  
Keyword(s):  
Cost Effective ◽  
Messenger Rnas ◽  
Rna Molecules ◽  
Complementary Method ◽  
High Throughput Method ◽  
Next Generation Sequencing Ngs ◽  
Insight Into ◽  
Generation Sequencing ◽  
Formalin Fixed ◽  
Methodological Strategy

AbstractThe high-throughput method of “Next Generation Sequencing” (NGS) allows cost-effective decoding of the nucleotide sequences of millions of RNA molecules in a sample. This makes it possible to determine the number of distinct RNA molecules in tissues or cells and to use these data to draw conclusions. The entirety of RNAs, in particular mRNAs (messenger RNAs) as potential precursors of proteins, provides a comprehensive insight into the functional state of the cells and tissues under investigation. In addition to cell cultures or unfixed tissue, formalin-fixed and paraffin-embedded (FFPE) tissue can also be analysed for this purpose using specific methods. In this overview, the methodological strategy and its application to the field of ophthalmic histopathology are presented.

scholarly journals Near-Complete Genome Sequences of New Strains of Nylanderia Fulva Virus 1 from Solenopsis invicta

2020 ◽  
Vol 9 (15) ◽  
Author(s):  
Margaret L. Allen
Keyword(s):  
Solenopsis Invicta ◽  
Reference Strain ◽  
Rna Virus ◽  
Fire Ant ◽  
Red Imported Fire Ant ◽  
Coding Region ◽  
Genome Sequences ◽  
Nylanderia Fulva ◽  
Positive Sense ◽  
Imported Fire Ant

Nylanderia fulva virus 1 (NfV-1) is a single-stranded positive-sense RNA virus that infects the tawny crazy ant. Three near-complete genomes of NfV-1SI (92% to 94% nucleotide identity to reference strain NfV-1) found infecting the red imported fire ant were determined. The genomes have 10,904 to 10,918 nucleotides and include most of the coding region for the polyprotein.

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