Konstantin Skryabin | Russian academy of sciences (original) (raw)

Papers by Konstantin Skryabin

Herald of the Russian Academy of Sciences, May 3, 2009

New Biotechnology, Nov 30, 2010

Opportunities and Challenges, 2013

FEBS Letters, 1982

... The nucleotide sequence of a cloned cDNA corresponding to one of the gamma-crystallins from t... more ... The nucleotide sequence of a cloned cDNA corresponding to one of the gamma-crystallins from the eye lens of the frog Rana temporaria. Tomarev SI, Krayev AS, Skryabin KG, Bayev AA, Gause GG Jr. PMID: 6982831 [PubMed - indexed for MEDLINE]. MeSH Terms. ...

FEBS Letters, 1983

The nucleotide sequence of a cloned cDNA (clone pRt( 1)297; GENE (1982) 17, 131) coding for a 18 ... more The nucleotide sequence of a cloned cDNA (clone pRt( 1)297; GENE (1982) 17, 131) coding for a 18 kDa polypeptide of the frog eye lens has been determined. The sequence, 791 nucleotide in length has only one long open reading frame (447 nucleotides). The derived amino acid sequence in this frame has >90% homology with the region 25-173 of cuAz-crystallin amino acid sequence from a related frog species Rana pipiens. The 5'-terminal part of mRNA corresponding to the first 24 amino acids of cuAz-crystallin has been lost in cloning and substituted by an artefactual sequence. The 3'-terminal part appears to be intact as follows from the presence of the universal poly(A) addition site and poly(A) tract. The 3 '-nontranslated region present in frog aAz-crystallin mRNA (130 nucleotides) is about 4-times shorter than in mammalian cuAz-crystallin mRNA. Intact cuAz-crystallin mRNA with a size of about 700 nucleotides as determined by Northern blot hybridization is about twice smaller than corresponding mammalian niRNAs.

FEBS Letters, 1984

The nucleotide sequence of a cloned DNA coding for the 35-kDa polypeptide of the eye lens of the ... more The nucleotide sequence of a cloned DNA coding for the 35-kDa polypeptide of the eye lens of the frog (Rana temporaria) has been determined. The sequence without connectors and poly(A) tract is 889 nucleotides in length and shows no homology with sequences coding for other classes of crystallins: cy-, &, y-or S-crystallins. The sequence contains one reading frame 675 nucleotides in length, an apparently intact 3'-non-translated region with the polyadenylation signal sequence and a poly(A) tract; the 5'-nontranslated region is lost along with part of the coding region; this accounts for about l/4 of the total mRNA length. The secondary structure prediction according to the Ptitsin-Finkelstein method shows the presence of predominantly P-strands with only a few a-helical regions. We conclude that the 35-kDa polypeptide from the frog eye lens belongs to a new class of eye lens crystallins for which we propose the name c-crystallin.

Journal of proteome research, Jan 29, 2016

A gene-centric approach was applied for a large-scale study of expression products of a single ch... more A gene-centric approach was applied for a large-scale study of expression products of a single chromosome. Transcriptome profiling of liver tissue and HepG2 cell line was independently performed using two RNA-Seq platforms (SOLiD and Illumina) and also by Droplet Digital PCR (ddPCR) and quantitative RT-PCR. Proteome profiling was performed using shotgun LC-MS/MS as well as selected reaction monitoring with stable isotope-labeled standards (SRM/SIS) for liver tissue and HepG2 cells. On the basis of SRM/SIS measurements, protein copy numbers were estimated for the Chromosome 18 (Chr 18) encoded proteins in the selected types of biological material. These values were compared with expression levels of corresponding mRNA. As a result, we obtained information about 158 and 142 transcripts for HepG2 cell line and liver tissue, respectively. SRM/SIS measurements and shotgun LC-MS/MS allowed us to detect 91 Chr 18-encoded proteins in total, while an intersection between the HepG2 cell line ...

Acta Horticulturae, 2015

ABSTRACT

Febs Letters, May 29, 2006

We report that unprocessed tobacco pectin methylesterase (PME) contains N-terminal pro-sequence i... more We report that unprocessed tobacco pectin methylesterase (PME) contains N-terminal pro-sequence including the transmembrane (TM) domain and spacer segment preceding the mature PME. The mature portion of PME was replaced by green fluorescent protein (GFP) gene and various deletion mutants of pro-sequence fused to GFP were cloned into binary vectors and agroinjected in Nicotiana benthamiana leaves. The PME pro-sequence delivered GFP to the cell wall (CW). We showed that a transient binding of PME TM domain to endoplasmic reticulum membranes occurs upon its transport to CW. The CW targeting was abolished by various deletions in the TM domain, i.e., anchor domain was essential for secretion of GFP to CW. By contrast, even entire deletion of the spacer segment had no influence on GFP targeting.

Mol Gen Genet, 1992

The 5' untranslated leader of potato virus X (PVX) RNA is shown when contiguous to the co... more The 5' untranslated leader of potato virus X (PVX) RNA is shown when contiguous to the coding sequence, to enhance the expression of the neomycin phosphotransferase II gene (NPTII) in Nicotiana tabacum protoplasts in vivo. The level of transient expression of the NPTII gene in protoplasts provided by a plasmid containing the coding sequence of the NPTII gene under the control of 35S cauliflower mosaic virus (CaMV) promoter and terminator elements served as the baseline control. Insertion of the viral 5' untranslated leader sequence upstream of the NPTII ATG codon increased the level of expression 4-fold. An 83 nucleotide (nt) leader sequence (lacking only one nucleotide of the complete PVX leader) and a truncated version with a 28 deletion at the 3' end both had similar enhancing abilities. The 28 nt CA region of the PVX leader alone had no enhancement properties.

Journal of Biomolecular Structure and Dynamics, 1986

The phage lambda operator OR1 and a 18 base pair symmetric lac operator have been studied by high... more The phage lambda operator OR1 and a 18 base pair symmetric lac operator have been studied by high resolution NMR. The imino proton resonances and the resonances of the unexchangeable protons (except the 5' and 5" sugar proton resonances) have been assigned by one- and two-dimensional NOE techniques. The imino proton resonances of OR1 and the symmetric lac operator have been used to monitor changes induced in the operator structure by the formation of a specific complex with the phage lambda cro protein and with the lac repressor N-terminal DNA binding domain ("headpiece"). Two regions within the OR1 sequence could be identified, where changes in the imino proton resonance positions occur: The central part around base pairs CG 9 and 10 and the region around base pairs AT 5 and CG 5. The TA base pair 6 is the only position in the symmetric lac operator, where the complex formation with headpiece induces a change.

Eur Biophys J Biophys Lett, 1985

ABSTRACT

Current Pharmaceutical Design, 2013

Advances in transient expression technologies have allowed the production of milligram quantities... more Advances in transient expression technologies have allowed the production of milligram quantities of proteins within a matter of days using only small amounts (tens of grams) of plant tissue. Among the proteins that have been produced using this approach are the structural proteins of viruses which are capable of forming virus-like particles (VLPs). As such particulate structures are potent stimulators of the immune system, they are excellent vaccine candidates both in their own right and as carriers of additional immunogenic sequences. VLPs of varying complexity derived from a variety of animal viruses have been successfully transiently expressed in plants and their immunological properties assessed. Generally, the plant-produced VLPs were found to have the expected antigenicity and immunogenicity. In several cases, including an M2e-based influenza vaccine candidate, the plant-expressed VLPs have been shown to be capable of stimulating protective immunity. These findings raise the prospect that low-cost plant-produced vaccines could be developed for both veterinary and human use.

Biochemistry and Molecular Biology International, Mar 1, 1998

Sixty-seven bacterial strains were surveyed for the presence of type II restriction endonucleases... more Sixty-seven bacterial strains were surveyed for the presence of type II restriction endonucleases, especially concerning super-rare-cutting enzymes. Fourteen strains were found to contain specific enzymes. One of them CspBI from Corynebacterium species B was purified and characterized as an isoschizomer of NotI, which recognizes the palindromic octanucleotide sequence 5'-GC/GGCCGC-3' and cleaves at the position shown by the arrow. A comparison between the cleavage patterns on different DNAs, obtained with partially purified endonucleases from other detected producents including some strains of Corynebacterium, Cellulomonas and Rhizobium has shown that these enzymes do not belong to super-rare-cutting restriction endonucleases.

ABSTRACT The object of the invention is a protein, termed MF3, or a functional derivative there o... more ABSTRACT The object of the invention is a protein, termed MF3, or a functional derivative there of with a novel structure that surprisingly can induce multiple resistance in plants toward a variety of viral and microbial infections and against pests. The invention also concerns an isolated DNA sequence encoding MF3 protein, as such, or as a part of any DNA sequence, or a fragment thereof, or DNA sequences which have degenerate codons with respect to the DNA sequence defined above. The invention also concerns a method of isolating and purifying the protein MF3 from bacterial cells expressing the said protein and its use as a plant protectant with or without carrier agent. urthennore, the invention concerns a method of obtaining transgenic plants expressing said protein. A further object of the invention is the use of the protein, or of compositions containing the same, as a plant protectant, biopesticide for inducing resistance of plants to viral, microbial phytopathogens and pests.

The restriction endonuclease Eco RI splits the phage τ imm 434 DNA at 6 sites. The smallest of th... more The restriction endonuclease Eco RI splits the phage τ imm 434 DNA at 6 sites. The smallest of the formed fragments Eco RI-G contains the operator OR and promoters PR and Prm, gene cro and N-terminal part of the gene CI of the phage 434. τ DNA portion of the fragment contains the sequences of Po promoter, the gene CII and of the gene O N-terminal part. The complete primary structure of the Eco RI-G fragment was determined. It consists of 1287 base pairs of which 361 belong to the immunity region of the phage 434. The amino-acid sequences of the phage 434 protein cro and N-terminal part of the CI repressor were deduced from the nucleotide sequence. The proposed sequences of the phage τ CII protein and of the N-terminal part of O protein was also obtained. The sequence of the phage 434 promoter-operator region is quite different from that of the phage τ.

Dna Research, 1999

An earlier reported method for revealing latent periodicity of the nucleotide sequences has been ... more An earlier reported method for revealing latent periodicity of the nucleotide sequences has been considerably modified in a case of small samples, by applying a Monte Carlo method. This improved method has been used to search for the latent periodicity of some nucleotide sequences of the EMBL data bank. The existence of the nucleotide sequences' latent periodicity has been shown for some genes. The results obtained have implied that periodicity of gene structure is projected onto the periodicity of primary amino acid sequences and, further, onto spatial protein conformation. Even though the periodic structure of gene sequences has been eroded, it is still retained in primary and/or spatial structures of corresponding proteins. Furthermore, in a few cases the study of genes' periodicity has suggested their possible evolutionary origin by multifold duplications of some gene's fragments.

Biochemistry Engl Tr, 2008

A synthetic gene of the B-subunit of Escherichia coli heat-labile toxin, optimized for expression... more A synthetic gene of the B-subunit of Escherichia coli heat-labile toxin, optimized for expression in plants, was designed and synthesized. The recombinant viral vector was constructed on the basis of potato virus X containing the LTB gene instead of the removed triple block of transport genes and the coat protein gene, which provides for LTB expression in plants. The vector is introduced into the plant cells during cell infiltration by agrobacteria incorporating a binary vector, the T-DNA region of which contains a cDNA copy of the recombinant viral genome. Under conditions of posttranscriptional gene silencing inhibition, the LTB yield in Nicotiana benthamiana plants is 1-2% of total soluble protein; in this case, LTB synthesized in plants forms pentameric complexes analogous to those found in the native toxin. The designed viral system of LTB transient expression can be used to obtain in plants a vaccine against enteropathogenic Escherichia coli.

Herald of the Russian Academy of Sciences, May 3, 2009

New Biotechnology, Nov 30, 2010

Opportunities and Challenges, 2013

FEBS Letters, 1982

... The nucleotide sequence of a cloned cDNA corresponding to one of the gamma-crystallins from t... more ... The nucleotide sequence of a cloned cDNA corresponding to one of the gamma-crystallins from the eye lens of the frog Rana temporaria. Tomarev SI, Krayev AS, Skryabin KG, Bayev AA, Gause GG Jr. PMID: 6982831 [PubMed - indexed for MEDLINE]. MeSH Terms. ...

FEBS Letters, 1983

The nucleotide sequence of a cloned cDNA (clone pRt( 1)297; GENE (1982) 17, 131) coding for a 18 ... more The nucleotide sequence of a cloned cDNA (clone pRt( 1)297; GENE (1982) 17, 131) coding for a 18 kDa polypeptide of the frog eye lens has been determined. The sequence, 791 nucleotide in length has only one long open reading frame (447 nucleotides). The derived amino acid sequence in this frame has >90% homology with the region 25-173 of cuAz-crystallin amino acid sequence from a related frog species Rana pipiens. The 5'-terminal part of mRNA corresponding to the first 24 amino acids of cuAz-crystallin has been lost in cloning and substituted by an artefactual sequence. The 3'-terminal part appears to be intact as follows from the presence of the universal poly(A) addition site and poly(A) tract. The 3 '-nontranslated region present in frog aAz-crystallin mRNA (130 nucleotides) is about 4-times shorter than in mammalian cuAz-crystallin mRNA. Intact cuAz-crystallin mRNA with a size of about 700 nucleotides as determined by Northern blot hybridization is about twice smaller than corresponding mammalian niRNAs.

FEBS Letters, 1984

The nucleotide sequence of a cloned DNA coding for the 35-kDa polypeptide of the eye lens of the ... more The nucleotide sequence of a cloned DNA coding for the 35-kDa polypeptide of the eye lens of the frog (Rana temporaria) has been determined. The sequence without connectors and poly(A) tract is 889 nucleotides in length and shows no homology with sequences coding for other classes of crystallins: cy-, &, y-or S-crystallins. The sequence contains one reading frame 675 nucleotides in length, an apparently intact 3'-non-translated region with the polyadenylation signal sequence and a poly(A) tract; the 5'-nontranslated region is lost along with part of the coding region; this accounts for about l/4 of the total mRNA length. The secondary structure prediction according to the Ptitsin-Finkelstein method shows the presence of predominantly P-strands with only a few a-helical regions. We conclude that the 35-kDa polypeptide from the frog eye lens belongs to a new class of eye lens crystallins for which we propose the name c-crystallin.

Journal of proteome research, Jan 29, 2016

A gene-centric approach was applied for a large-scale study of expression products of a single ch... more A gene-centric approach was applied for a large-scale study of expression products of a single chromosome. Transcriptome profiling of liver tissue and HepG2 cell line was independently performed using two RNA-Seq platforms (SOLiD and Illumina) and also by Droplet Digital PCR (ddPCR) and quantitative RT-PCR. Proteome profiling was performed using shotgun LC-MS/MS as well as selected reaction monitoring with stable isotope-labeled standards (SRM/SIS) for liver tissue and HepG2 cells. On the basis of SRM/SIS measurements, protein copy numbers were estimated for the Chromosome 18 (Chr 18) encoded proteins in the selected types of biological material. These values were compared with expression levels of corresponding mRNA. As a result, we obtained information about 158 and 142 transcripts for HepG2 cell line and liver tissue, respectively. SRM/SIS measurements and shotgun LC-MS/MS allowed us to detect 91 Chr 18-encoded proteins in total, while an intersection between the HepG2 cell line ...

Acta Horticulturae, 2015

ABSTRACT

Febs Letters, May 29, 2006

We report that unprocessed tobacco pectin methylesterase (PME) contains N-terminal pro-sequence i... more We report that unprocessed tobacco pectin methylesterase (PME) contains N-terminal pro-sequence including the transmembrane (TM) domain and spacer segment preceding the mature PME. The mature portion of PME was replaced by green fluorescent protein (GFP) gene and various deletion mutants of pro-sequence fused to GFP were cloned into binary vectors and agroinjected in Nicotiana benthamiana leaves. The PME pro-sequence delivered GFP to the cell wall (CW). We showed that a transient binding of PME TM domain to endoplasmic reticulum membranes occurs upon its transport to CW. The CW targeting was abolished by various deletions in the TM domain, i.e., anchor domain was essential for secretion of GFP to CW. By contrast, even entire deletion of the spacer segment had no influence on GFP targeting.

Mol Gen Genet, 1992

The 5' untranslated leader of potato virus X (PVX) RNA is shown when contiguous to the co... more The 5' untranslated leader of potato virus X (PVX) RNA is shown when contiguous to the coding sequence, to enhance the expression of the neomycin phosphotransferase II gene (NPTII) in Nicotiana tabacum protoplasts in vivo. The level of transient expression of the NPTII gene in protoplasts provided by a plasmid containing the coding sequence of the NPTII gene under the control of 35S cauliflower mosaic virus (CaMV) promoter and terminator elements served as the baseline control. Insertion of the viral 5' untranslated leader sequence upstream of the NPTII ATG codon increased the level of expression 4-fold. An 83 nucleotide (nt) leader sequence (lacking only one nucleotide of the complete PVX leader) and a truncated version with a 28 deletion at the 3' end both had similar enhancing abilities. The 28 nt CA region of the PVX leader alone had no enhancement properties.

Journal of Biomolecular Structure and Dynamics, 1986

The phage lambda operator OR1 and a 18 base pair symmetric lac operator have been studied by high... more The phage lambda operator OR1 and a 18 base pair symmetric lac operator have been studied by high resolution NMR. The imino proton resonances and the resonances of the unexchangeable protons (except the 5' and 5" sugar proton resonances) have been assigned by one- and two-dimensional NOE techniques. The imino proton resonances of OR1 and the symmetric lac operator have been used to monitor changes induced in the operator structure by the formation of a specific complex with the phage lambda cro protein and with the lac repressor N-terminal DNA binding domain ("headpiece"). Two regions within the OR1 sequence could be identified, where changes in the imino proton resonance positions occur: The central part around base pairs CG 9 and 10 and the region around base pairs AT 5 and CG 5. The TA base pair 6 is the only position in the symmetric lac operator, where the complex formation with headpiece induces a change.

Eur Biophys J Biophys Lett, 1985

ABSTRACT

Current Pharmaceutical Design, 2013

Advances in transient expression technologies have allowed the production of milligram quantities... more Advances in transient expression technologies have allowed the production of milligram quantities of proteins within a matter of days using only small amounts (tens of grams) of plant tissue. Among the proteins that have been produced using this approach are the structural proteins of viruses which are capable of forming virus-like particles (VLPs). As such particulate structures are potent stimulators of the immune system, they are excellent vaccine candidates both in their own right and as carriers of additional immunogenic sequences. VLPs of varying complexity derived from a variety of animal viruses have been successfully transiently expressed in plants and their immunological properties assessed. Generally, the plant-produced VLPs were found to have the expected antigenicity and immunogenicity. In several cases, including an M2e-based influenza vaccine candidate, the plant-expressed VLPs have been shown to be capable of stimulating protective immunity. These findings raise the prospect that low-cost plant-produced vaccines could be developed for both veterinary and human use.

Biochemistry and Molecular Biology International, Mar 1, 1998

Sixty-seven bacterial strains were surveyed for the presence of type II restriction endonucleases... more Sixty-seven bacterial strains were surveyed for the presence of type II restriction endonucleases, especially concerning super-rare-cutting enzymes. Fourteen strains were found to contain specific enzymes. One of them CspBI from Corynebacterium species B was purified and characterized as an isoschizomer of NotI, which recognizes the palindromic octanucleotide sequence 5'-GC/GGCCGC-3' and cleaves at the position shown by the arrow. A comparison between the cleavage patterns on different DNAs, obtained with partially purified endonucleases from other detected producents including some strains of Corynebacterium, Cellulomonas and Rhizobium has shown that these enzymes do not belong to super-rare-cutting restriction endonucleases.

ABSTRACT The object of the invention is a protein, termed MF3, or a functional derivative there o... more ABSTRACT The object of the invention is a protein, termed MF3, or a functional derivative there of with a novel structure that surprisingly can induce multiple resistance in plants toward a variety of viral and microbial infections and against pests. The invention also concerns an isolated DNA sequence encoding MF3 protein, as such, or as a part of any DNA sequence, or a fragment thereof, or DNA sequences which have degenerate codons with respect to the DNA sequence defined above. The invention also concerns a method of isolating and purifying the protein MF3 from bacterial cells expressing the said protein and its use as a plant protectant with or without carrier agent. urthennore, the invention concerns a method of obtaining transgenic plants expressing said protein. A further object of the invention is the use of the protein, or of compositions containing the same, as a plant protectant, biopesticide for inducing resistance of plants to viral, microbial phytopathogens and pests.

The restriction endonuclease Eco RI splits the phage τ imm 434 DNA at 6 sites. The smallest of th... more The restriction endonuclease Eco RI splits the phage τ imm 434 DNA at 6 sites. The smallest of the formed fragments Eco RI-G contains the operator OR and promoters PR and Prm, gene cro and N-terminal part of the gene CI of the phage 434. τ DNA portion of the fragment contains the sequences of Po promoter, the gene CII and of the gene O N-terminal part. The complete primary structure of the Eco RI-G fragment was determined. It consists of 1287 base pairs of which 361 belong to the immunity region of the phage 434. The amino-acid sequences of the phage 434 protein cro and N-terminal part of the CI repressor were deduced from the nucleotide sequence. The proposed sequences of the phage τ CII protein and of the N-terminal part of O protein was also obtained. The sequence of the phage 434 promoter-operator region is quite different from that of the phage τ.

Dna Research, 1999

An earlier reported method for revealing latent periodicity of the nucleotide sequences has been ... more An earlier reported method for revealing latent periodicity of the nucleotide sequences has been considerably modified in a case of small samples, by applying a Monte Carlo method. This improved method has been used to search for the latent periodicity of some nucleotide sequences of the EMBL data bank. The existence of the nucleotide sequences' latent periodicity has been shown for some genes. The results obtained have implied that periodicity of gene structure is projected onto the periodicity of primary amino acid sequences and, further, onto spatial protein conformation. Even though the periodic structure of gene sequences has been eroded, it is still retained in primary and/or spatial structures of corresponding proteins. Furthermore, in a few cases the study of genes' periodicity has suggested their possible evolutionary origin by multifold duplications of some gene's fragments.

Biochemistry Engl Tr, 2008

A synthetic gene of the B-subunit of Escherichia coli heat-labile toxin, optimized for expression... more A synthetic gene of the B-subunit of Escherichia coli heat-labile toxin, optimized for expression in plants, was designed and synthesized. The recombinant viral vector was constructed on the basis of potato virus X containing the LTB gene instead of the removed triple block of transport genes and the coat protein gene, which provides for LTB expression in plants. The vector is introduced into the plant cells during cell infiltration by agrobacteria incorporating a binary vector, the T-DNA region of which contains a cDNA copy of the recombinant viral genome. Under conditions of posttranscriptional gene silencing inhibition, the LTB yield in Nicotiana benthamiana plants is 1-2% of total soluble protein; in this case, LTB synthesized in plants forms pentameric complexes analogous to those found in the native toxin. The designed viral system of LTB transient expression can be used to obtain in plants a vaccine against enteropathogenic Escherichia coli.