Mononucleotide Composition Research Articles

Selective and non-selective evolutionary signatures found in the simplest replicative biological entities.

Mitoviruses, which are considered evolutionary relics of extinct alpha-proteobacteria RNA phages, represent one of the simplest self-replicating biological systems. This study aims to quantitatively describe genomes and identify potential genomic signatures that support the protein phylogenetic-based classification criterion. Genomic variables, such as mononucleotide and dinucleotide composition, codon usage bias, and minimal free energy derived from optimized predicted RNA secondary structure, were analyzed. From the values obtained, the main evolutionary pressures were discussed, indicating that natural selection plays a significant role in shaping mitovirus genomes. However, neutral evolution also makes a significant contribution. This study reveals a significant discovery of structural divergence in Kvaramitovirus. The energy minimization approach employed to study 2D folding in this study reveals a distinct spatial organization of their genomes, providing evidence for the hypothesis of a single evolutionary event of circularization in the most recent common ancestor of the lineage. This hypothesis was discussed in light of recent discoveries by other researchers that partially support the existence of mitoviruses with circular genomes. Finally, this study represents a significant advancement in the understanding of mitoviruses, as it quantitatively describes the nucleotide sequence at the family and genus taxonomic levels. Additionally, we provide hypotheses that can be experimentally validated to inspire new research and address the gaps in knowledge of this fascinating, basally divergent RNA virus lineage.

DFpin: Deep learning–based protein-binding site prediction with feature-based non-redundancy from RNA level

The interaction between proteins and RNA is closely related to various human diseases. Computer-aided drug design can be facilitated by detecting the RNA sites that bind proteins. However, due to the aggregation of binding sites in RNA sequences, high sample similarity occurs when extracting RNA fragments by using a sliding window. Considering these problems, we present a method, DFpin, to predict protein-interacting nucleotides in RNA. To retain more key nucleotide sites, we used the redundancy method based on feature similarity, that is, feature redundancy is removed based on the RNA mono-nucleotide composition to maintain the diversity of RNA samples and avoid the residue of redundant data. In addition, to extract key abstract features and avoid over-fitting, we used the cascade structure of a deep forest model to predict protein-interacting nucleotides. Overall, DFpin demonstrated excellent classification with 85.4% accuracy and 93.3% area under the curve. Compared with other methods, the accuracy of DFpin was better, suggesting that feature-based redundancy removal and deep forest can help predict nucleotides of protein interactions. The source code and all dataset are available at: https://github.com/zhaoxj-tech/DFpin.git.

BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences.

MotivationAccurate motif enrichment analyses depend on the choice of background DNA sequences used, which should ideally match the sequence composition of the foreground sequences. It is important to avoid false positive enrichment due to sequence biases in the genome, such as GC-bias. Therefore, relying on an appropriate set of background sequences is crucial for enrichment analysis.ResultsWe developed BiasAway, a command line tool and its dedicated easy-to-use web server to generate synthetic sequences matching any k-mer nucleotide composition or select genomic DNA sequences matching the mononucleotide composition of the foreground sequences through four different models. For genomic sequences, we provide precomputed partitions of genomes from nine species with five different bin sizes to generate appropriate genomic background sequences.Availability and implementationBiasAway source code is freely available from Bitbucket (https://bitbucket.org/CBGR/biasaway) and can be easily installed using bioconda or pip. The web server is available at https://biasaway.uio.no and a detailed documentation is available at https://biasaway.readthedocs.io.Supplementary informationSupplementary data are available at Bioinformatics online.

Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains

BackgroundWith the remarkable increase of microbial and viral sequence data obtained from high-throughput DNA sequencers, novel tools are needed for comprehensive analysis of the big sequence data. We have developed “Batch-Learning Self-Organizing Map (BLSOM)” which can characterize very many, even millions of, genomic sequences on one plane. Influenza virus is one of zoonotic viruses and shows clear host tropism. Important issues for bioinformatics studies of influenza viruses are prediction of genomic sequence changes in the near future and surveillance of potentially hazardous strains.MethodsTo characterize sequence changes in influenza virus genomes after invasion into humans from other animal hosts, we applied BLSOMs to analyses of mono-, di-, tri-, and tetranucleotide compositions in all genome sequences of influenza A and B viruses and found clear host-dependent clustering (self-organization) of the sequences.ResultsViruses isolated from humans and birds differed in mononucleotide composition from each other. In addition, host-dependent oligonucleotide compositions that could not be explained with the host-dependent mononucleotide composition were revealed by oligonucleotide BLSOMs. Retrospective time-dependent directional changes of mono- and oligonucleotide compositions, which were visualized for human strains on BLSOMs, could provide predictive information about sequence changes in newly invaded viruses from other animal hosts (e.g. the swine-derived pandemic H1N1/09).ConclusionsBasing on the host-dependent oligonucleotide composition, we proposed a strategy for prediction of directional changes of virus sequences and for surveillance of potentially hazardous strains when introduced into human populations from non-human sources. Millions of genomic sequences from infectious microbes and viruses have become available because of their medical and social importance, and BLSOM can characterize the big data and support efficient knowledge discovery.

Causes and implications of codon usage bias in RNA viruses.

Choice of synonymous codons depends on nucleotide/dinucleotide composition of the genome (termed mutational pressure) and relative abundance of tRNAs in a cell (translational pressure). Mutational pressure is commonly simplified to genomic GC content; however mononucleotide and dinucleotide frequencies in different genomes or mRNAs may vary significantly, especially in RNA viruses. A series of in silico shuffling algorithms were developed to account for these features and analyze the relative impact of mutational pressure components on codon usage bias in RNA viruses. Total GC content was a poor descriptor of viral genome composition and causes of codon usage bias. Genomic nucleotide content was the single most important factor of synonymous codon usage. Moreover, the choice between compatible amino acids (e.g., leucine and isoleucine) was strongly affected by genomic nucleotide composition. Dinucleotide composition at codon positions 2-3 had additional effect on codon usage. Together with mononucleotide composition bias, it could explain almost the entire codon usage bias in RNA viruses. On the other hand, strong dinucleotide content bias at codon position 3-1 found in some viruses had very little effect on codon usage. A hypothetical innate immunity sensor for CpG in RNA could partially explain the codon usage bias, but due to dependence of virus translation upon biased host translation machinery, experimental studies are required to further explore the source of dinucleotide bias in RNA viruses.

SVM Model for Prediction and Classification of Drosophila Based on Nucleotide Composition

MicroRNAs (miRNA) are single-stranded RNA molecules of about 21–23 nucleotides in length. MicroRNAs(miRNAs) constitute a large family of non coding RNAs that function to regulate gene expression. Till today wet lab experiments have been used to classify the miRNA of plants and animals. The wet lab techniques are highly expensive, labour intensive and time consuming. Thus there arises a need for computational approach for classification of plants and animal miRNA. These computational approaches are fast and economical as compared to wet lab techniques. In this paper an attempt has been made for the classification of Drosophila and its subclasses.The overall prediction accuracy of SVM modules based on mono nucleotide composition was 83.12% respectively. The accuracy of all the modules was evaluated using a 10-fold cross-validation technique.

Amino acid variation in cellular processes in 108 bacterial proteomes

We have analysed 108 bacterial proteomes in the KEGG database to explore the variation of amino acid composition with respect to protein function. The ratio between the observed amino acid composition and that predicted based on mononucleotide composition was calculated for each functional category. This indicated whether the compositional variation arose from mutation or selection pressure. The results showed that charged amino acids (Lys, Arg and Glu), were found more frequently than expected in proteins involved in genetic information processing (i.e. transcription, translation, etc.) Similarly, in the proteins involved in processing environmental information (e.g. signal transduction), the hydrophobic amino acid Leu was found in excess of values expected from the base composition in the genes.

Plasmid promiscuity: meeting the challenge of DNA immigration control.

Plasmid promiscuity: meeting the challenge of DNA immigration control.

A computer method for finding common base paired helices in aligned sequences: application to the analysis of random sequences

We describe a new computer program that identifies conserved secondary structures in aligned nucleotide sequences of related single-stranded RNAs. The program employs a series of hash tables to identify and sort common base paired helices that are located in identical positions in more than one sequence. The program gives information on the total number of base paired helices that are conserved between related sequences and provides detailed information about common helices that have a minimum of one or more compensating base changes. The program is useful in the analysis of large biological sequences. We have used it to examine the number and type of complementary segments (potential base paired helices) that can be found in common among related random sequences similar in base composition to 16S rRNA from Escherichia coli. Two types of random sequences were analyzed. One set consisted of sequences that were independent but they had the same mononucleotide composition as the 16S rRNA. The second set contained sequences that were 80% similar to one another. Different results were obtained in the analysis of these two types of random sequences. When 5 sequences that were 80% similar to one another were analyzed, significant numbers of potential helices with two or more independent base changes were observed. When 5 independent sequences were analyzed, no potential helices were found in common. The results of the analyses with random sequences were compared with the number and type of helices found in the phylogenetic model of the secondary structure of 16S ribosomal RNA. Many more helices are conserved among the ribosomal sequences than are found in common among similar random sequences. In addition, conserved helices in the 16S rRNAs are, on the average, longer than the complementary segments that are found in comparable random sequences. The significance of these results and their application in the analysis of long non-ribosomal nucleotide sequences is discussed.

Exact computation of pattern probabilities in random sequences generated by Markov chains

Observed patterns in macromolecular sequences are often considered as words and compared with their probabilities of occurring in random sequences. Calculation of these probabilities, however, often lacks rigour. We have developed an algorithm for exact computation of such probabilities for stochastic sequences that follow a Markov chain model. The method is applicable to the case that a random sequence contains one out of two given patterns P and Q, or both simultaneously. Another application yields the probability function P(x) that a sequence contains pattern P exactly x times. An application to patterns that include wild-card characters yields probabilities for homonucleotide clusters of a given length. We prove the probability of multiple runs of single nucleotides in the SV40 genome to be in accordance with the dinucleotide composition of the sequence, although it is in conflict with mononucleotide composition.

Human herpesvirus 6 is closely related to human cytomegalovirus

A sequence of 21,858 base pairs from the genome of human herpesvirus 6 (HHV-6) strain U1102 is presented. The sequence has a mean composition of 41% G + C, and the observed frequency of CpG dinucleotides is close to that predicted from this mononucleotide composition. The sequence contains 17 complete open reading frames (ORFs) and part of another at the 5' end of the sequence. The predicted protein products of two of these ORFs have no recognizable homologs in the genomes of other sequenced human herpesviruses (i.e., Epstein-Barr virus [EBV], human cytomegalovirus [HCMV], herpes simplex virus [HSV], and varicella-zoster virus [VZV]). However, the products of nine other ORFs are clearly homologous to a set of genes that is conserved in all other sequenced herpesviruses, including homologs of the alkaline exonuclease, the phosphotransferase, the spliced ORF, and the major capsid protein genes. Measurements of similarity between these homologous sequences showed that HHV-6 is clearly most closely related to HCMV. The degree of relatedness between HHV-6 and HCMV was commensurate with that observed in comparisons between HSV and VZV or EBV and herpesvirus saimiri and significantly greater than its relatedness to EBV, HSV, or VZV. In addition, the gene for the major capsid protein and its 5' neighbor are reoriented with respect to the spliced ORFs in the genomes of both HHV-6 and HCMV relative to the organization observed in EBV, HSV, and VZV. Three ORFs in HHV-6 have recognizable homologs only in the genome of HCMV. Despite differences in gross composition and size, we conclude that the genomes of HHV-6 and HCMV are closely related.

Relationships between nucleic acid, nitrogen, and growth rate of tobacco cells in suspension culture

Changes in the amount of nucleic acid and nitrogen, and the relationships between these amounts and the growth rate of tobacco cells (Nicotiana tabacum L. cv. Bright Yellow-2) at different initial nitrogen concentrations in the medium, were examined in batch cultures. During culture in basal medium, the amount of intracellular nucleic acid expressed per unit of dry biomass was 36.3 mg RNA g−1 cell and 8.1 mg DNA g−1 cell at the beginning of batch culture. These values increased 2.5 fold for RNA and 1.5 fold for DNA during the exponential growth phase and then gradually decreased with the decline in the growth rate. Similar changes were also observed in the medium containing less nitrogen. The specific growth rate, μ (day−1), of the culture corresponded to the magnitude of the intracellular RNA content (mg RNA g−1 cell), and the linear relationship, RNA=38μ+23 was obtained. In addition, there were remarkable positive correlations between the total and protein nitrogen, and μ during the cultures. The mononucleotide composition of total RNA (AMP+UMP)/(GMP+CMP) which was suggested to be a convenient index of metabolic activity was nearly constant (0.78 to 0.80) during tobacco cell culture in the basal medium.

Acides ribonucléiques messagers de la glande thyroïde de mouton

The messenger character of nuclear and polysomal rapidly‐labeled thyroid RNA has been established using stimulation of amino acid incorporation into trichloracetic‐insoluble material in the Escherichia coli system, mononucleotide composition of the early‐labeled material and tenacity of adsorption on columns of methylated serumalbumin adsorbed on Kieselguhr (MAK columns).A relation between the difficulty to extract nuclear or cytoplasmic thyroid RNA by phenol at 0°, their rapidity of labeling and their capacity to stimulate protein synthesis in vitro has been demonstrated.80% of the nRNA labeled for 15 min was tenaciously bound to MAK columns. After elution with a buffer containing sodium dodecylsulphate at 35–70°, it showed a DNA‐like base composition and sedimented in 4 discrete size classes: 30 S, 22 S, 13 S. The remaining 20% has been identified as preribosomal RNA. After a 9 h‐period of labeling the total nRNA fraction still contained labeled preribosomal RNA, rRNA and DNA‐like RNA.Most of the early‐labeled polysomal RNA has been identified as mRNA by tenacity of adsorption on MAK columns and base composition. Even after a 1 h‐pulse the labeled rRNA accounted only for 30–40% of the total RNA. Absence of preribosomal RNA in polysomes as shown by MAK column chromatography was considered as a good index of the absence of contamination of polysomes by nuclear material. Polysomes pulse‐labeled with [32P]orthophosphate and [14C]protein hydrolysate were dissociated by ethylenediaminetetraacetic acid and fixed with formaldehyde. The buoyant densities of the nucleoprotein particles were determined by banding in CsCI gradients. Under these conditions, the bulk of the material in ribosomes banded at characteristic densities (d= 1.57 and 1.52) but most of RNA with high specific radioactivity banded at a density approximately 1.38. This material contained [32P]RNA and [14C]protein, and was identified as an association of mRNA and protein by base composition of its RNA: (G + C)/(A + U) = 0.83.Purification of pulse‐labeled nuclear mRNA was carried out by the hot‐phenol fractionation procedure of Georgiev et al. [9,10]. Specific radioactivity, specific stimulating activity of protein synthesis in vitro and base composition of the five fractions obtained were determined. The RNAs extracted from nuclei between 55–65° and 65–85° were considerably enriched in mRNA. Sucrose‐density gradient sedimentation showed substantial polydispersity of the stable RNA of all the fractions. However, the main component of the RNA extracted by phenol between 65° and 85° culminated in a metabolically homogeneous 16 S peak. A definite correlation between pulse‐labeled nRNA isolated by the hot‐phenol procedure and pulse‐labeled polysomal RNA was noticed.As compared with 18 S and 28 S rRNA, the fractions of stable polysomal thyroid RNA which corresponded in sedimentation to the rapidly‐labeled RNA (30–40 S, 22 S, 13 S and 7 S) definitely stimulated polypeptide synthesis in vitro.The size of the monocistronic mRNA which codes for the peptide chains of thyroglobulin is discussed. If a molecular weight of 73,000 for the two different chains is assumed, their amino acid sequence might be encoded in the 13 S polysomal RNA. The functional significance of the 30–40 S and 22 S mRNA and the possible importance of polysomal messenger nucleoprotein particles are also discussed.

An endomessenger hypothesis on the mechanism of information transfer in animal cells

Research on the mechanism of information transfer in animal cells is reviewed. It is indicated that the interpretation of experimental results within the framework of the original messenger concept leads to several fundamental controversies. The most important concern the nature of: (a) the rapidly-labelled 45 s nuclear RNA; (b) the cytoplasmic 40 s ribonucleoprotein particle; and (c) the nuclear and cytoplasmic 18 s RNA's. In order to explain the available facts and to avoid the controversies in their interpretation, a new hypothesis is proposed, designated as the endomessenger hypothesis. The main feature of the advanced hypothesis is the consideration of “messenger” RNA's as an integral part of some cellular “ribosomal” RNA's, namely, the “ribosomal” precursor 45 s RNA and the “ribosomal” 18 s RNA. The experimental evidence and the theoretical grounds are discussed, primarily focused on: (a) the synchronous formation and turnover of the two ribosomal subunits and their RNA's correlated with the stability of messenger RNA's in animal cells; (b) the existence of RNA molecules with a hybrid mononucleotide composition, constituted of a “ribosomal” segment and a “messenger” segment; (c) the vectorial transcription of the genome, involving one of the two DNA strands, initiated from the “ribosomal” RNA segments and finished with the “messenger” RNA segments; and (d) the relatively extended time period necessary for the completion of any RNA molecule. The implications derived from the proposed endomessenger hypothesis, on the mechanism of information transfer in animal cells are discussed.

Pattern of [ 32P]orthophosphate incorporation in vitro into ribonucleic acid nucleotides of Ehrlich ascites tumor cells

1. 1. Rapidly labelled RNA from whole Ehrlich ascites tumor cells had the same mononucleotide composition irrespective of conditions used for [ 32P]orthophosphate incorporation ( in vivo or in vitro). It corresponded in each case to 30–40 % d-RNA (RNA similar in mononucleotide composition to DNA) and 60–70 % r-RNA (RNA similar in mononucleotide composition to ribosomal RNA). 2. RNA extracted with phenol-sodium dodecyl sulfate at 65° from nuclei of isolated ascites tumor cells showed three main peaks on agar gel electrophoresis, corresponding to ribosomal RNA (2 peaks) and soluble RNA. Polyvinyl sulfate was necessary to avoid partial degradation of RNA during its isolation and storage. 3. Nuclear RNA isolated from tumor cells labelled in vitro (30 min) with [ 32P]orthophosphate was hydrolyzed with 0.5 N KOH or with snake-venom phosphodiesterase (EC 3.1.4.1). The specific activities of the four nucleoside 2′(3′)-monophosphates were of the same order. The specific activity of GMP was on the average twelve-fold lower than that of the other three nucleoside 5′-monophosphates. Nucleotide incorporation into rapidly labelled nuclear RNA was statistically random. The mononucleotide composition of this RNA corresponds to 50 % d-RNA and 50 % r-RNA. 4. During the step-wise degradation of rapidly labelled nuclear RNA with snake-venom phosphodiesterase the specific activity of CMP increased, while that of AMP and UMP decreased.

Isolation of the mouse mammary tumor virus: chemical and morphological studies.

The course of purification of the mammary tumor virus from milk of infective Columbia RIII strain mice by methods involving velocity gradient (zone) centrifugation in Ficoll, a chemically inert, high molecular weight, synthetic polysaccharide, is described. On a dry weight basis, an approximate 1,000-fold enrichment of virus was achieved. A fraction consisting of what appeared to be incomplete virus was separated in a zone above the main viral particle zone in the gradient tube. The viral particles had an average lipid content of 27 percent and a ribonucleic acid (RN A) content of 0.8 percent on a dry weight basis. Experiments pointed to the essential single-stranded character of the RNA, the mononucleotide composition of which, in moles percent, was: uridine monophosphate, 28.9; guanosine monophosphate, 30.2; cytidine monophosphate, 21.6; adenosine monophosphate, 19.3. The value of 3.7 × 106 daltons was determined for the average RNA content of the virions. In certain morphological features and in aspects of their maturation, largely relating to the arrangement of the nucleic acid-containing structure within the particles, they differed significantly from the myxoviruses, a group which they otherwise resemble in general morphology and gross chemical composition. Substantial tumorigenicity for the mammary gland was found to reside in viral particle preparations, purified by isopyenic gradient centrifugation in rubidium chloride and gradient electrophoresis, methods previously described—the purity of which was attested by electron microscopic examination.

Separation and characterization of Carp egg ribonucleic acids

1. 1. The solubilities in cold sodium chloride of ribonucleoproteins obtained from mature ovarian eggs of Cyprinus carpio differ from those exhibited by the ribonucleoproteins of differentiated tissue. 2. 2. The RNA prepared from the ribonucleoprotein present in a 0·17 M NaCl extract is composed of about 30 per cent acid-soluble RNA and the RNA isolated from a 1 M NaCl extract contains only about 10 per cent acid-soluble RNA. 3. 3. The mononucleotide composition of acid-soluble RNA differs from that of acid-insoluble RNA but the acid-soluble and acid-insoluble RNA of the 0·17 M NaCl extract resemble their acid-soluble and acid-insoluble counterparts in the 1 M NaCl extract. 4. 4. Carp egg RNA from the 0·17 M NaCl extract and the 1 M NaCl extract each can be separated into four fractions by Ecteola cellulose column chromatography. Each fraction has a characteristics content of acid-soluble RNA that apparently determines its order of elution from the column.

フアージ増殖の生化学的研究

It was found that chloramphenicol, when added before T2 infection, blocked the formation of protein and DNA, but not the RNA synthesis after infection. The RNA synthesis after infection seems to be slightly stimulated by the addition of chloramphenicol. This RNA, which is formed without a priori formation of protein after T2 infection, is also characteristic of T2 infection in its mononucleotide composition. These results show that T2 infection induces a synthesis of new RNA, or at least a specific change in RNA metabolism at first without the prior synthesis of new protein.