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Article ; Online: Enhancing Capsid Proteins Capacity in Plant Virus-Vector Interactions and Virus Transmission.

Agranovsky, Alexey

2021 Volume 10, Issue 1

Abstract: Vector transmission of plant viruses is basically of two types that depend on the virus helper component proteins or the capsid proteins. A number of plant viruses belonging to disparate groups have developed unusual capsid proteins providing for ... ...

Abstract	Vector transmission of plant viruses is basically of two types that depend on the virus helper component proteins or the capsid proteins. A number of plant viruses belonging to disparate groups have developed unusual capsid proteins providing for interactions with the vector. Thus, cauliflower mosaic virus, a plant pararetrovirus, employs a virion associated p3 protein, the major capsid protein, and a helper component for the semi-persistent transmission by aphids. Benyviruses encode a capsid protein readthrough domain (CP-RTD) located at one end of the rod-like helical particle, which serves for the virus transmission by soil fungal zoospores. Likewise, the CP-RTD, being a minor component of the luteovirus icosahedral virions, provides for persistent, circulative aphid transmission. Closteroviruses encode several CPs and virion-associated proteins that form the filamentous helical particles and mediate transmission by aphid, whitefly, or mealybug vectors. The variable strategies of transmission and evolutionary 'inventions' of the unusual capsid proteins of plant RNA viruses are discussed.
MeSH term(s)	Animals ; Aphids/virology ; Capsid Proteins/chemistry ; Capsid Proteins/metabolism ; Evolution, Molecular ; Plant Viruses/genetics ; Plant Viruses/physiology ; RNA, Viral/genetics
Chemical Substances	Capsid Proteins ; RNA, Viral
Language	English
Publishing date	2021-01-07
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells10010090
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structure and Expression of Large (+)RNA Genomes of Viruses of Higher Eukaryotes.

Agranovsky, Alexey A

Biochemistry. Biokhimiia

2021 Volume 86, Issue 3, Page(s) 248–261

Abstract: Viral positive-sense RNA genomes evolve rapidly due to the high mutation rates during replication and RNA recombination, which allowing the viruses to acquire and modify genes for their adaptation. The size of RNA genome is limited by several factors, ... ...

Abstract	Viral positive-sense RNA genomes evolve rapidly due to the high mutation rates during replication and RNA recombination, which allowing the viruses to acquire and modify genes for their adaptation. The size of RNA genome is limited by several factors, including low fidelity of RNA polymerases and packaging constraints. However, the 12-kb size limit is exceeded in the two groups of eukaryotic (+)RNA viruses - animal nidoviruses and plant closteroviruses. These virus groups have several traits in common. Their genomes contain 5'-proximal genes that are expressed via ribosomal frameshifting and encode one or two papain-like protease domains, membrane-binding domain(s), methyltransferase, RNA helicase, and RNA polymerase. In addition, some nidoviruses (i.e., coronaviruses) contain replication-associated domains, such as proofreading exonuclease, putative primase, nucleotidyltransferase, and endonuclease. In both nidoviruses and closteroviruses, the 3'-terminal part of the genome contains genes for structural and accessory proteins expressed via a nested set of coterminal subgenomic RNAs. Coronaviruses and closteroviruses have evolved to form flexuous helically symmetrical nucleocapsids as a mean to resolve packaging constraints. Since phylogenetic reconstructions of the RNA polymerase domains indicate only a marginal relationship between the nidoviruses and closteroviruses, their similar properties likely have evolved convergently, along with the increase in the genome size.
MeSH term(s)	Amino Acid Sequence ; Animals ; Biological Evolution ; Eukaryota/virology ; Genome, Viral ; Humans ; Open Reading Frames ; RNA Viruses/chemistry ; RNA Viruses/genetics ; RNA Viruses/isolation & purification ; RNA Viruses/metabolism ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-03-26
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1109-5
ISSN	1608-3040 ; 0006-2979 ; 0320-9717
ISSN (online)	1608-3040
ISSN	0006-2979 ; 0320-9717
DOI	10.1134/S0006297921030020
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Article ; Online: The butterfly effect: mutational bias of SARS-CoV-2 affects its pattern of molecular evolution on synonymous and nonsynonymous levels

Voronka, Alexandr / Efimenko, Bogdan / Oreshkov, Sergey / Franco, Melissa / Fleischmann, Zoe / Yurov, Valerian / Trufanova, Arina / Timonina, Valeria / Ree, Natalia / Penfrat, Emma / Junier, Thomas / Agranovsky, Alexey / Khrapko, Konstantin / Gunbin, Konstantin / Fellay, Jacques / Popadin, Konstantin

bioRxiv

Abstract: Evolution is a function of mutagenesis and selection. To analyse the role of mutagenesis on the structure of the SARS-CoV-2 genome, we reconstructed the mutational spectrum, which was highly C>U and G>U biased. This bias suggests that, in weakly ... ...

Abstract	Evolution is a function of mutagenesis and selection. To analyse the role of mutagenesis on the structure of the SARS-CoV-2 genome, we reconstructed the mutational spectrum, which was highly C>U and G>U biased. This bias suggests that, in weakly constrained regions, the SARS-CoV-2 genome becomes increasingly U-rich. We analysed the consequences of this bias on the composition of the most neutral (four-fold degenerate synonymous substitutions) and the least neutral positions (nonsynonymous substitutions). The neutral nucleotide sites of the genome are already saturated by U, suggesting that in the past, an ancestral virus was exposed to similar mutational pressure, and in the future, we don9t expect any significant changes since the system is at equilibrium. However, nonsynonymous changes continue slowly evolve towards equilibrium substituting CG-rich amino-acids ("losers") with U-rich ones ("gainers"). Comparing Coronaviridae with all other positive-stranded RNA viruses, we observed an excess of gainers and a deficit of losers in the former, suggesting that the coronavirus-specific mutational bias affected the amino-acid content of the entire family on the long-term evolutionary scale. We propose the butterfly effect - a tuning of a protein space through permissive amino-acid trajectories by mutational bias, which can be common in species with biased mutagenesis.
Keywords	covid19
Language	English
Publishing date	2022-08-22
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.08.22.504819
Database	COVID19

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Article ; Online: Beet yellows virus replicase and replicative compartments

AlexeyA.Agranovsky / VladimirA.Gushchin / TatyanaN.Erokhina

Frontiers in Microbiology, Vol

parallels with other RNA viruses

2013 Volume 4

Abstract: In eukaryotic virus systems, infection leads to induction of membranous compartments in which replication occurs. Virus-encoded subunits of the replication complex mediate its interaction with membranes. As replication platforms, RNA viruses use the ... ...

Abstract	In eukaryotic virus systems, infection leads to induction of membranous compartments in which replication occurs. Virus-encoded subunits of the replication complex mediate its interaction with membranes. As replication platforms, RNA viruses use the cytoplasmic surfaces of different membrane compartments, e.g., endoplasmic reticulum (ER), Golgi, endo/lysosomes, mitochondria, chloroplasts and peroxisomes. Closterovirus infections are accompanied by formation of multivesicular complexes from cell membranes of ER or mitochondrial origin. So far the mechanisms for vesicles formation have been obscure. In the replication-associated 1a polyprotein of Beet yellows virus (BYV) and other closteroviruses, the region between the methyltransferase (MTR) and helicase (HEL) domains (1a central region, 1a CR) is marginally conserved. Computer-assisted analysis predicts several putative membrane-binding domains in the BYV 1a CR. Transient expression of a hydrophobic segment (referred to here as CR-2) of the BYV 1a in Nicotiana benthamiana led to reorganization of the ER and formation of ~1-m mobile globules. We propose that the CR-2 may be involved in the formation of multivesicular complexes in BYV-infected cells. This provides analogy with membrane-associated proteins mediating the build-up of “virus factories” in cells infected with diverse positive-strand RNA viruses (alpha-like viruses, picorna-like viruses, flaviviruses, and nidoviruses) and negative-strand RNA viruses (bunyaviruses).
Keywords	intracellular traffic ; RNA virus replication ; membrane vesicles ; virus replication factory ; endoplasmatic reticulum modification ; Microbiology ; QR1-502 ; Science ; Q
Subject code	570 ; 612
Language	English
Publishing date	2013-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article: Beet yellows virus replicase and replicative compartments: parallels with other RNA viruses.

Gushchin, Vladimir A / Solovyev, Andrey G / Erokhina, Tatyana N / Morozov, Sergey Y / Agranovsky, Alexey A

Frontiers in microbiology

2013 Volume 4, Page(s) 38

Abstract	In eukaryotic virus systems, infection leads to induction of membranous compartments in which replication occurs. Virus-encoded subunits of the replication complex mediate its interaction with membranes. As replication platforms, RNA viruses use the cytoplasmic surfaces of different membrane compartments, e.g., endoplasmic reticulum (ER), Golgi, endo/lysosomes, mitochondria, chloroplasts, and peroxisomes. Closterovirus infections are accompanied by formation of multivesicular complexes from cell membranes of ER or mitochondrial origin. So far the mechanisms for vesicles formation have been obscure. In the replication-associated 1a polyprotein of Beet yellows virus (BYV) and other closteroviruses, the region between the methyltransferase and helicase domains (1a central region (CR), 1a CR) is marginally conserved. Computer-assisted analysis predicts several putative membrane-binding domains in the BYV 1a CR. Transient expression of a hydrophobic segment (referred to here as CR-2) of the BYV 1a in Nicotiana benthamiana led to reorganization of the ER and formation of ~1-μm mobile globules. We propose that the CR-2 may be involved in the formation of multivesicular complexes in BYV-infected cells. This provides analogy with membrane-associated proteins mediating the build-up of "virus factories" in cells infected with diverse positive-strand RNA viruses (alpha-like viruses, picorna-like viruses, flaviviruses, and nidoviruses) and negative-strand RNA viruses (bunyaviruses).
Keywords	covid19
Language	English
Publishing date	2013-03-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2013.00038
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Article: Original Article. Topical treatment of LdMNPV-infected gypsy moth caterpillars with 18 nucleotides long antisense fragment from LdMNPV IAP3 gene triggers higher levels of apoptosis in infected cells and mortality of the pest

Oberemok, Volodymyr V / Kateryna V. Laikova / Alexey S. Zaitsev / Palmah M. Nyadar / Yuri I. Gninenko / Vladimir A. Gushchin / Valentin V. Makarov / Alexey A. Agranovsky

Journal of plant protection research. 2017 May 9, v. 57, no. 1

2017

Abstract: The high efficiency of baculovirus infection is partially explained by the ability of the virus to suppress host defense machinery connected with the apoptosis pathway. Members of the baculovirus gene family, inhibitors of apoptosis (vIAPs), have been ... ...

Abstract	The high efficiency of baculovirus infection is partially explained by the ability of the virus to suppress host defense machinery connected with the apoptosis pathway. Members of the baculovirus gene family, inhibitors of apoptosis (vIAPs), have been shown to inhibit apoptosis in baculovirus-infected cells. Here we showed that treatment of the LdMNPV-infected 1st instar gypsy moth (Lymantria dispar) caterpillars with sense (oligoBIR) and antisense (oligoRING) DNA oligonucleotides from the LdMNPV IAP3 gene induced elevated mortality of the insects. Apoptotic DNA ladder assay showed that the leading role in this phenomenon is played by the antisense oligoRING fragment of the vIAP3 gene. These results imply that the application of both antisense DNA oligonucleotides from vIAP genes and baculovirus preparations (one following the other) may be a potential method for plant protection against insect pests.
Keywords	Baculoviridae ; Lymantria dispar ; antisense DNA ; apoptosis ; genes ; insect larvae ; insect pests ; instars ; mortality ; oligonucleotides ; plant protection ; viruses
Language	English
Dates of publication	2017-0509
Size	p. 18-24.
Publishing place	De Gruyter Open
Document type	Article
ISSN	1899-007X
DOI	10.1515/jppr-2017-0003
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Structural evolution of the 4/1 genes and proteins in non-vascular and lower vascular plants.

Morozov, Sergey Y / Milyutina, Irina A / Bobrova, Vera K / Ryazantsev, Dmitry Y / Erokhina, Tatiana N / Zavriev, Sergey K / Agranovsky, Alexey A / Solovyev, Andrey G / Troitsky, Alexey V

Biochimie

2015 Volume 119, Page(s) 125–136

Abstract: The 4/1 protein of unknown function is encoded by a single-copy gene in most higher plants. The 4/1 protein of Nicotiana tabacum (Nt-4/1 protein) has been shown to be alpha-helical and predominantly expressed in conductive tissues. Here, we report the ... ...

Abstract	The 4/1 protein of unknown function is encoded by a single-copy gene in most higher plants. The 4/1 protein of Nicotiana tabacum (Nt-4/1 protein) has been shown to be alpha-helical and predominantly expressed in conductive tissues. Here, we report the analysis of 4/1 genes and the encoded proteins of lower land plants. Sequences of a number of 4/1 genes from liverworts, lycophytes, ferns and gymnosperms were determined and analyzed together with sequences available in databases. Most of the vascular plants were found to encode Magnoliophyta-like 4/1 proteins exhibiting previously described gene structure and protein properties. Identification of the 4/1-like proteins in hornworts, liverworts and charophyte algae (sister lineage to all land plants) but not in mosses suggests that 4/1 proteins are likely important for plant development but not required for a primary metabolic function of plant cell.
MeSH term(s)	Amino Acid Sequence ; Base Sequence ; Bryophyta/genetics ; Bryophyta/metabolism ; Charophyceae/genetics ; Charophyceae/metabolism ; Computational Biology ; Conserved Sequence ; Cycadopsida/genetics ; Cycadopsida/metabolism ; Databases, Genetic ; Evolution, Molecular ; Genes, Plant ; Genomic Library ; Magnoliopsida/genetics ; Magnoliopsida/metabolism ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plant Development ; Plant Proteins/chemistry ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Protein Conformation ; Sequence Alignment ; Viridiplantae/genetics ; Viridiplantae/metabolism
Chemical Substances	Plant Proteins
Language	English
Publishing date	2015-12
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120345-9
ISSN	1638-6183 ; 0300-9084
ISSN (online)	1638-6183
ISSN	0300-9084
DOI	10.1016/j.biochi.2015.10.019
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Article ; Online: Original Article. Topical treatment of LdMNPV-infected gypsy moth caterpillars with 18 nucleotides long antisense fragment from LdMNPV IAP3 gene triggers higher levels of apoptosis in infected cells and mortality of the pest

Oberemok Volodymyr V. / Laikova Kateryna V. / Zaitsev Alexey S. / Nyadar Palmah M. / Gninenko Yuri I. / Gushchin Vladimir A. / Makarov Valentin V. / Agranovsky Alexey A.

Journal of Plant Protection Research, Vol 57, Iss 1, Pp 18-

2016 Volume 24

Abstract	The high efficiency of baculovirus infection is partially explained by the ability of the virus to suppress host defense machinery connected with the apoptosis pathway. Members of the baculovirus gene family, inhibitors of apoptosis (vIAPs), have been shown to inhibit apoptosis in baculovirus-infected cells. Here we showed that treatment of the LdMNPV-infected 1st instar gypsy moth (Lymantria dispar) caterpillars with sense (oligoBIR) and antisense (oligoRING) DNA oligonucleotides from the LdMNPV IAP3 gene induced elevated mortality of the insects. Apoptotic DNA ladder assay showed that the leading role in this phenomenon is played by the antisense oligoRING fragment of the vIAP3 gene. These results imply that the application of both antisense DNA oligonucleotides from vIAP genes and baculovirus preparations (one following the other) may be a potential method for plant protection against insect pests.
Keywords	baculoviral infection ; DNA insecticides ; DNA oligonucleotides ; forest and crop protection ; gypsy moth ; IAP genes ; Agriculture ; S ; Plant culture ; SB1-1110
Subject code	570
Language	English
Publishing date	2016-08-01T00:00:00Z
Publisher	De Gruyter Open
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular Alliance of Lymantria dispar Multiple Nucleopolyhedrovirus and a Short Unmodified Antisense Oligonucleotide of Its Anti-Apoptotic IAP-3 Gene: A Novel Approach for Gypsy Moth Control.

Oberemok, Volodymyr V / Laikova, Kateryna V / Zaitsev, Aleksei S / Shumskykh, Maksym N / Kasich, Igor N / Gal'chinsky, Nikita V / Bekirova, Viktoriya V / Makarov, Valentin V / Agranovsky, Alexey A / Gushchin, Vladimir A / Zubarev, Ilya V / Kubyshkin, Anatoly V / Fomochkina, Iryna I / Gorlov, Mikhail V / Skorokhod, Oleksii A

International journal of molecular sciences

2017 Volume 18, Issue 11

Abstract: Baculovirus IAP (inhibitor-of-apoptosis) genes originated by capture of host genes. Unmodified short antisense DNA oligonucleotides (oligoDNAs) from baculovirus IAP genes can down-regulate specific gene expression profiles in both baculovirus-free and ... ...

Abstract	Baculovirus IAP (inhibitor-of-apoptosis) genes originated by capture of host genes. Unmodified short antisense DNA oligonucleotides (oligoDNAs) from baculovirus IAP genes can down-regulate specific gene expression profiles in both baculovirus-free and baculovirus-infected insects. In this study, gypsy moth (
MeSH term(s)	Animals ; Apoptosis ; Genes, Viral/genetics ; Insect Control/methods ; Larva/virology ; Moths/virology ; Nucleopolyhedroviruses/genetics ; Oligodeoxyribonucleotides, Antisense ; Transcriptome ; Viral Proteins/genetics
Chemical Substances	Oligodeoxyribonucleotides, Antisense ; Viral Proteins
Language	English
Publishing date	2017-11-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms18112446
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Article: Completion of the mapping of transcription start sites for the five-gene block subgenomic RNAs of Beet yellows Closterovirus and identification of putative subgenomic promoters.

Vitushkina, Maria V / Rogozin, Igor B / Jelkmann, Wilhelm / Koonin, Eugene V / Agranovsky, Alexey A

Virus research

2007 Volume 128, Issue 1-2, Page(s) 153–158

Abstract: In the positive-sense RNA genome of Beet yellows Closterovirus (BYV), the 3'-terminal open reading frames (ORFs) 2-8 are expressed as a nested set of subgenomic (sg) RNAs. ORFs 2-6, coding for the structural and movement proteins, form a 'five-gene block' ...

Abstract	In the positive-sense RNA genome of Beet yellows Closterovirus (BYV), the 3'-terminal open reading frames (ORFs) 2-8 are expressed as a nested set of subgenomic (sg) RNAs. ORFs 2-6, coding for the structural and movement proteins, form a 'five-gene block' conserved in closteroviruses. We mapped the 5'-end of the ORF 4 sgRNA, which encodes the p64 protein, at adenosine-11169 in the BYV genome. This completes the mapping of the transcription start sites for the five-gene block sgRNAs of BYV. Computer-assisted analysis of the sequences upstream of BYV ORFs 2, 3, 4, 5, and 6 revealed two conserved motifs, which might constitute the subgenomic promoter elements. These motifs are conserved in the equivalent positions upstream of three orthologous genes of Citrus tristeza Closterovirus and two orthologous genes of Beet yellow stunt Closterovirus.
MeSH term(s)	Base Sequence ; Beta vulgaris/virology ; Closterovirus/genetics ; Closterovirus/metabolism ; Gene Expression Regulation, Viral ; Genome, Viral ; Molecular Sequence Data ; Open Reading Frames/genetics ; Promoter Regions, Genetic/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Transcription Initiation Site ; Viral Proteins/genetics
Chemical Substances	RNA, Messenger ; RNA, Viral ; Viral Proteins
Language	English
Publishing date	2007-09
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2007.04.016
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