RESUMEN
In Russia and around the world, there are important questions regarding the potential threats to national and biological safety created by genetic technologies and the need to improve or introduce new, justified, and adequate measures for their control, regulation, and prevention. The article shows that a significant volume of the global market is occupied by five major transgenic crops, and producers are ready to switch to crops with an edited genome that has been approved in the United States, Argentina, and other countries. We propose a qualitatively new approach to the risk assessment of edited plants, "Safe Design," and we have also developed an extremely important, fundamentally new approach to the development of methods that combine next-generation sequencing (NGS) and Bioinformatics for the assessment of the crop import biosafety. The proposed mathematical approach provides a detailed analysis of the possible insertions of DNA fragments into the genome of edited crops and a clarification of their biological significance. The developed method can be used in the rapid screening of plants for the presence of potentially dangerous genes, viral sequences, and nonspecific promoter sequences.
RESUMEN
A new mathematical method for potential reading frameshift detection in protein-coding sequences (cds) was developed. The algorithm is adjusted to the triplet periodicity of each analysed sequence using dynamic programming and a genetic algorithm. This does not require any preliminary training. Using the developed method, cds from the Arabidopsis thaliana genome were analysed. In total, the algorithm found 9,930 sequences containing one or more potential reading frameshift(s). This is â¼21% of all analysed sequences of the genome. The Type I and Type II error rates were estimated as 11% and 30%, respectively. Similar results were obtained for the genomes of Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Rattus norvegicus and Xenopus tropicalis. Also, the developed algorithm was tested on 17 bacterial genomes. We compared our results with the previously obtained data on the search for potential reading frameshifts in these genomes. This study discussed the possibility that the reading frameshift seems like a relatively frequently encountered mutation; and this mutation could participate in the creation of new genes and proteins.
Asunto(s)
Algoritmos , Arabidopsis/genética , Mutación del Sistema de Lectura , Genoma , Sistemas de Lectura Abierta , Análisis de Secuencia de ADN/métodos , Animales , Bacterias/genética , Caenorhabditis elegans/genética , Drosophila melanogaster/genética , Humanos , RatasRESUMEN
A new mathematical method was used for the first time to search for tandem repeats with insertions and deletions in the full-length sequence of the A. thaliana genome. The method is based on a new algorithm for multiple alignment of sequences of certain periods without using paired comparisons of sequences. We identified 13997 periodic sites 2 to 50 characters long, only approximately 30% of which were known earlier. The possible origin and use of the identified sites with tandem repeats are discussed.
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Arabidopsis/genética , Genoma de Planta/genética , Mutagénesis Insercional , Eliminación de Secuencia , Secuencias Repetidas en Tándem/genéticaRESUMEN
A mathematical method was developed in order to search for latent periodicity in protein amino acid and other symbolical sequences using the dynamic programming and random matrixes. The method permits detection of the latent periodicity with insertions and deletions in the previously unknown positions. The developed method was applied to search for the periodicity in the amino acid sequences of some proteins and the periodicity in EUR/USD exchange rate since 2001. The presence of the long period length with insertions and deletions in amino acid sequences was shown. The period length of 7 amino acids was found in proteins containing supercoiled areas (coiled coil), the period length of 6 and 5 and more amino acids was also demonstrated. The existence of the period length of 6 and 7 days as well as 24 and 25 hours in the analyzed financial time series, which can be detected with insertions and deletions only, is revealed. The reasons of the occurence of the latent periodicity with insertions and deletions in the amino acid sequences and financial time series are discussed.
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Secuencia de Aminoácidos/genética , Aminoácidos/genética , Modelos Teóricos , Algoritmos , Mutación INDEL/genética , Proteínas/química , Proteínas/genéticaRESUMEN
We introduce a novel approach for the detection of possible mutations leading to a reading frame (RF) shift in a gene. Deletions and insertions of DNA coding regions are considerable events for genes because an RF shift results in modifications of the extensive region of amino acid sequence coded by a gene. The suggested method is based on the phenomenon of triplet periodicity (TP) in coding regions of genes and its relative resistance to substitutions in DNA sequence. We attempted to extend 326 933 regions of continuous TP found in genes from the KEGG databank by considering possible insertions and deletions. We revealed totally 824 genes where such extension was possible and statistically significant. Then we generated amino acid sequences according to active (KEGG's) and hypothetically ancient RFs in order to find confirmation of a shift at a protein level. Consequently, 64 sequences have protein similarities only for ancient RF, 176 only for active RF, 3 for both and 581 have no protein similarity at all. We aimed to have revealed lower bound for the number of genes in which a shift between RF and TP is possible. Further ways to increase the number of revealed RF shifts are discussed.
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Algoritmos , Mutación del Sistema de Lectura , Mutación INDEL , Sistemas de Lectura Abierta/genética , Secuencia de Bases , Análisis Mutacional de ADN/métodos , Bases de Datos de Ácidos Nucleicos , Datos de Secuencia Molecular , Proteínas/genética , Reproducibilidad de los ResultadosRESUMEN
We conducted classification for 472,288 regions of triplet periodicity found in 578,868 genes from release 29 of KEGG databank. A new concept of triplet periodicity class and a measure of similarity between them are introduced. Totally 2520 classes were created that contain 94% of found triplet periodicity. For 92% of triplet periodicity regions contained in classes an identical linkage of triplet periodicity to reading frame is observed. For the rest triplet periodicity cases a shift between reading frame of a gene and reading frame common for majority of genes contained in a class of triplet periodicity was observed. These periodicity regions were encoded into hypothetical amino acid sequences in accordance with reading frame built by triplet periodicity class. By BLAST program it was shown that 2660 hypothetical amino acid sequences have statistically significant similarity with proteins from UniProt databank. We suppose that 8% of triplet periodicity regions that joined classes mutated by means of reading frame shift. Created classes of triplet periodicity can be used for identification of coding regions of genes as well as for searching for mutations arisen from reading frame shift.
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Bases de Datos Genéticas , Mutación del Sistema de Lectura , Modelos Genéticos , Sistemas de Lectura Abierta/genética , Análisis de Secuencia de Proteína/métodos , Repeticiones de Trinucleótidos/genéticaRESUMEN
We introduce a new concept of triplet periodicity class (TPC) and a measure of similarity between such classes. We performed classification of 472288 triplet periodicity (TP) regions found in 578868 genes from 29th release of KEGG databank. Totally 2520 classes were obtained. They contain 94% of 472288 found cases of TP. For 92% of TP regions contained in classes the same linkage of TP to open reading frame (ORF) is observed. For 8% of TP cases we revealed a shift between ORF of a gene and ORF common for majority of genes contained in a TPC. For these 8% of periodic regions the hypothetical amino acid sequences corresponding to ORF built by TPC were made. BLAST program has shown that 2679 hypothetical amino acid sequences have statistically significant similarity with proteins from UniProt databank. We suppose that 8% of TP regions contained in classes possess a mutation originating from ORF shift. Obtained TPCs can be used for identification of genes' coding regions as well as for searching for mutations arisen arising from ORF shift.
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Sistemas de Lectura Abierta , Proteínas/genética , Algoritmos , Secuencia de Aminoácidos , Secuencia de Bases , Clasificación/métodos , Genes , Datos de Secuencia Molecular , Proteínas/química , Análisis de Secuencia de ADN , Análisis de Secuencia de ProteínaRESUMEN
The information decomposition (ID) method has been used for searching dinucleotide periodicities, including latent ones, in plant genomes. In nucleotide sequences of genomes of various plants from the GenBank database, 14766 sequences with a periodicity of two nucleotides have been found. Classification of the periodicity matrices of the detected DNA sequences has yielded 141 classes of dinucleotide periodicity. Since ID does not detect periodicities with nucleotide deletions or insertions, modified profile analysis (MPA) has been applied to the obtained classes to reveal DNA sequences with dinucleotide periodicities containing nucleotide deletions and insertions. Combined use of ID and MPA has permitted the detection of 80 396 DNA sequences with dinucleotide periodicities in the genomes of various plants. The biological role of dinucleotide periodicity in the detected sequences is discussed.
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ADN de Plantas/genética , Repeticiones de Dinucleótido/genética , Genoma de Planta/genética , Modelos Genéticos , Plantas/genética , Análisis de Secuencia de ADNRESUMEN
A recently developed PCR-fingerprinting method, the so-called DIR (diverged inverted repeats)-PCR, was used for quick search for molecular markers of Bacillus thuringiensis subspecies carrying the cry1 genes. The analysis of the fingerprints obtained by this method made it possible to reveal PCR fragments characteristic of the subspecies that produce proteins toxic for insects of the order Lepidoptera. Cloning and sequencing of these fragments allowed systems of SCAR (sequence characterized amplified region) primers to be designed, which are specific to the above group of B. thuringiensis strains. Comparison of the specific fragments with sequences available in the GenBank database revealed their homology with the rpoC gene family and the adjacent spacer region, suggesting chromosomal localization of these markers. This increases the reliability of the designed system of SCAR primers, because plasmids may be lost or transferred by transformation between closely related strains. It was demonstrated that the DIR-PCR method allows markers to be developed that are linked to diagnostic genotypic and phenotypic characteristics of bacteria.
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Bacillus thuringiensis/genética , Genes Bacterianos , Reacción en Cadena de la Polimerasa , Proteínas Bacterianas/genética , Cromosomas Bacterianos/genética , Clonación Molecular , Cartilla de ADN , ARN Polimerasas Dirigidas por ADN/genética , ARN Polimerasas Dirigidas por ADN/metabolismo , Endotoxinas/genética , Insecticidas , Reacción en Cadena de la Polimerasa/métodosRESUMEN
For detection of the latent periodicity of the protein families responsible for various biological functions, methods of information decomposition, cyclic profile alignment, and the method of noise decomposition have been used. The latent periodicity, being specific to a particular family, is recognized in 94 of 110 analyzed protein families. Family specific periodicity was found for more than 70% of amino acid sequences in each of these families. Based on such sequences the characteristic profile of the latent periodicity has been deduced for each family. Possible relationship between the recognized latent periodicity, evolution of proteins, and their structural organization is discussed.
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Proteínas/química , Análisis de Secuencia de Proteína/métodos , Algoritmos , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Animales , Biología Computacional , Evolución Molecular , Datos de Secuencia Molecular , Proteínas/genética , Alineación de SecuenciaRESUMEN
We identified latent periodicity in catalytic domains of approximately 85% of serine/threonine and tyrosine protein kinases. Similar results were obtained for other 22 protein domains. We also designed the method of noise decomposition, which is aimed to distinguish between different periodicity types of the same period length. The method is to be used in conjunction with the cyclic profile alignment, and this combination is able to reveal structure-related or function-related patterns of latent periodicity. Possible origins of the periodic structure of protein kinase active sites are discussed. Summarizing, we presume that latent periodicity is the common property of many catalytic protein domains.
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Algoritmos , Proteínas Serina-Treonina Quinasas/química , Proteínas Tirosina Quinasas/química , Secuencia de Aminoácidos , Animales , Biología Computacional , Bases de Datos de Proteínas , Humanos , Datos de Secuencia Molecular , Homología de Secuencia de AminoácidoRESUMEN
The paper is the first to suggest methods for rapid obtaining and genotypic identification of phenotypic (colonial-morphological) dissociants of bacterial cultures. For revelation of the potential dissociation ability and obtaining of dissociants, the use of bacterial cyst-like refractile cells (CRC) is recommended. These cells are characterized by enhanced variability; upon their first passage, an abrupt increase in the dissociation index is observed as a result of the emergence of cells that form morphologically different types of colonies. The approaches elaborated were tested with Bacillus cereus, B. subtilis, and B. licheniformis, for which colonial-morphological dissociants of various types were obtained after the first passage of CRC (both of those formed in the developmental cycle of bacteria and of those arising as a result of artificial increase of the concentration of anabiosis autoinducers in the cultivation medium). The genomic distinctions between dissociants of B. cereus and B. subtilis were estimated using polymerase chain reaction with a primer system designed based on the analysis of nucleotide sequences of complete prokaryotic genomes available in the GenBank database (DIR-PCR). The application of the suggested method allowed distinctions between the genomes of dissociants of Bacillus cereus and B. subtilis to be revealed, which is in agreement with the hypothesis that suggests reversible intragenomic rearrangements to be the basis of bacterial dissociation into subpopulations.
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Bacillus/genética , Cartilla de ADN , Fenotipo , Bacillus/crecimiento & desarrollo , Bacillus/aislamiento & purificación , Medios de Cultivo , Filogenia , Reacción en Cadena de la Polimerasa/métodos , Especificidad de la EspecieRESUMEN
A program package has been developed to search for hidden tandem repeats of any specified type in the protein sequence databases. The applied algorithm of the locally optimal cyclic alignment is able to find subsequences possessing a certain profile-based periodicity type when no appreciable homology between periods is observed, as well as in the presence of arbitrary insertions/deletions. The profile can be adjusted to search for the periodicity types structurally and functionally important. The Swiss-Prot database has been analyzed to reveal the periodicities undetectable earlier that are caused by the secondary and super-secondary structure regularities of the NAD-binding sites. In particular, a significant periodicity of 24 aa was found to be characteristic of the absolute majority of domains possessing the Rossman (or Rossman-like) fold and displaying the apparent regularity in their secondary structures, not being obvious at the primary structure level.
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NAD/metabolismo , Proteínas/genética , Proteínas/metabolismo , Alineación de Secuencia/métodos , Programas Informáticos , Secuencia de Aminoácidos , Sitios de Unión , Bases de Datos de Proteínas , Datos de Secuencia Molecular , Periodicidad , Pliegue de Proteína , Proteínas/química , Secuencias Repetitivas de Ácidos Nucleicos , Homología Estructural de ProteínaRESUMEN
Method of informational decomposition has been developed, allowing one to reveal hidden periodicity in any symbol sequences. The informational decomposition is calculated without conversion of a symbol sequence into the numerical one, which facilitates finding periodicities in a symbol sequence. The method permits introducing an analog of the autocorrelation function of a symbol sequence. The method developed by us has been applied to reveal hidden periodicities in nucleotide and amino acid sequences, as well as in different poetical texts. Hidden periodicity has been detected in various genes, testifying to their quantum structure. The functional and structural role of hidden periodicity is discussed.
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Algoritmos , Ciencia de la Información/métodos , Periodicidad , Secuencia de Aminoácidos , Secuencia de Bases , Cómputos Matemáticos , Poesía como AsuntoRESUMEN
The existence of a typical latent periodicity of 21 bases from the Tar chemoreceptor gene of Escherichia coli (E. coli) (MCP II) in the bacterial genes has been investigated in this work. Among 583 annotated bacterial genes and ORFs in the GenBank, in which the typical periodicity has been found, the chemoreceptors' genes constituted the most numerous group (18.5%). This typical latent periodicity of 21 bases has been revealed in many different genes of regulatory proteins, DNA polymerases, reductases, kinases and others. The numbers in such gene groups varied from 1 to 4% of the total analyzed genes. The 2D-structures analysis of the amino acid residues, which have been translated from the genes' regions with 21 bases periodicity, has shown that, though the enrichment of alpha-helical structures in such sequences is kept in all cases, it is seen that the latent periodicity of 21 bases is a very sensitively tuned basis, allowing the translated residues to smoothly change from one conformation to another. Interesting results have been obtained for 16S rRNAs genes of proteobacteria. Short sequences-determinants have been revealed in the genes, which select beta and gamma proteobacteria with an accuracy of above 90%.
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ADN Bacteriano/genética , Proteínas de Escherichia coli/genética , Genes Bacterianos/genética , Receptores de Superficie Celular/genética , Proteínas Bacterianas , Secuencia de Bases , Células Quimiorreceptoras , Bases de Datos de Ácidos Nucleicos , Escherichia coli/genética , Datos de Secuencia Molecular , Conformación de Ácido Nucleico , ARN Ribosómico 16S/química , ARN Ribosómico 16S/genética , Alineación de Secuencia/métodos , Homología de Secuencia de Ácido NucleicoRESUMEN
The location of mammalian interspersed repeats (MIRs) and their density have been determined in the complete nucleotide sequence of human chromosome 22. The approach developed by us has allowed detection of 9675 MIRs at a statistically significant level, which by 15% exceeds the MIR number revealed by all previous approaches. It has been demonstrated that a considerable amount of MIRs missed by the algorithms applied earlier occurs in known DNA sequences of the human genome. The study of the MIR density revealed substantial irregularity of their distribution along the chromosome. The data on the MIRs thus found and the computer program searching for diverged sequences are available by E-mail: katrin2@mail.ru or katrin22@mtu-net.ru.
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Cromosomas Humanos Par 22 , Secuencias Repetitivas de Ácidos Nucleicos , Algoritmos , ADN/genética , HumanosRESUMEN
A search for new members of the mammalian interspersed repeat (MIR) family has been done over the coding regions of human genome from GenBank-116. Only 254 nucleotide sequences contained MIRs in coding regions, of which 45 MIR copies were unknown before, including 17 that occurred in translated gene regions. The program developed by the authors has been demonstrated to surpass the CENSOR program in the search power. The evolution of the MIR copies located in translated regions of human genome is discussed.
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Codón , Evolución Molecular , Genoma Humano , Secuencias Repetitivas de Ácidos Nucleicos , Secuencia de Bases , ADN , Humanos , Datos de Secuencia Molecular , Homología de Secuencia de Ácido NucleicoRESUMEN
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.