Metagenomics dataset used to characterize microbiome in water and sediments of the lake Solenoe (Novosibirsk region, Russia).

This is data on the microbial diversity in the floating cyanobacterial community and sediment samples from the lake Solenoe (Novosibirsk region, Russia) obtained by metagenomic methods. Such a detailed data of the microbial diversity of the Novosibirsk oblast lake ecosystem was carried out for the first time. The purpose of our work was to reveal microbial taxonomic diversity and abundance, metabolic pathways and new enzyme findings the studied lake ecosystem using the next-generation sequencing (NGS) technology and metagenomic analysis. The data was obtained using metagenomics DNA whole genome sequencing (WGS) on Illumina NextSeq and NovaSeq. The raw sequence data used for analysis is available in NCBI under the Sequence Read Archive (SRA) with the BioProjects and SRA accession numbers: PRJNA493912 (SRR7943696), PRJNA493952 (SRR7943839) and PRJNA661775 (SRR12601635, SRR12601634, SRR12601633) corresponding to floating cyanobacterial community and sediment layers samples, respectively.

Comparative analysis of protein-coding and long non-coding transcripts based on RNA sequence features.

RNA plays an important role in the intracellular cell life and in the organism in general. Besides the well-established protein coding RNAs (messenger RNAs, mRNAs), long non-coding RNAs (lncRNAs) have gained the attention of recent researchers. Although lncRNAs have been classified as non-coding, some authors reported the presence of corresponding sequences in ribosome profiling data (Ribo-seq). Ribo-seq technology is a powerful experimental tool utilized to characterize RNA translation in cell with focus on initiation (harringtonine, lactimidomycin) and elongation (cycloheximide). By exploiting translation starts obtained from the Ribo-seq experiment, we developed a novel position weight matrix model for the prediction of translation starts. This model allowed us to achieve 96% accuracy of discrimination between human mRNAs and lncRNAs. When the same model was used for the prediction of putative ORFs in RNAs, we discovered that the majority of lncRNAs contained only small ORFs ([Formula: see text][Formula: see text]nt) in contrast to mRNAs.

Assessment of translational importance of mammalian mRNA sequence features based on Ribo-Seq and mRNA-Seq data.

Ribosome profiling technology (Ribo-Seq) allowed to highlight more details of mRNA translation in cell and get additional information on importance of mRNA sequence features for this process. Application of translation inhibitors like harringtonine and cycloheximide along with mRNA-Seq technique helped to assess such important characteristic as translation efficiency. We assessed the translational importance of features of mRNA sequences with the help of statistical analysis of Ribo-Seq and mRNA-Seq data. Translationally important features known from literature as well as proposed by the authors were used in analysis. Such comparisons as protein coding versus non-coding RNAs and high- versus low-translated mRNAs were performed. We revealed a set of features that allowed to discriminate the compared categories of RNA. Significant relationships between mRNA features and efficiency of translation were also established.

Hidden coding potential of eukaryotic genomes: nonAUG started ORFs.

It is widely considered that the vast majority of eukaryotic mRNAs contain only one open reading frame (ORF) and encode single protein. However, eukaryotic ribosomes can initiate translation at alternative start codons due to leaky scanning or reinitiation mechanisms that provides an opportunity to synthesize several protein products. Recent investigations also demonstrated that alternative translation from nonAUG start codons and AUG codons in a weak nucleotide context could make an important contribution to eukaryotic proteomes. However, accurate prediction of alternative start codons demands detailed investigation of mRNA features influencing their recognition by eukaryotic ribosomes. In this work, we present the results of computational analysis of characteristics of yeast and mammalian mRNAs potentially involved in the recognition of nonAUG start codons. It was found that sequence features of nonAUG started Saccharomyces cerevisiae upstream ORFs (uORFs) were adjusted for efficient translation and these uORFs could frequently encode functional polypeptides. In particular, our initial studies revealed that predicted tertiary structures downstream of nonAUG start sites in mammalian mRNAs were energetically more stable than those predicted for AUG start sites with strong Kozak context. We hypothesize that presence of such stable tertiary structure downstream of nonAUG start sites could be an important factor for the ribosome to recognize noncanonical start codons.

Tandem termination signal in plant mRNAs.

It was proposed that if some mRNA characteristics resulted in a low efficiency of termination signal, an additional closely located stop codon (tandem stop codons) could be used to prevent the harmful readthrough. However, the role of tandem terminators in higher eukaryotes was not verified and remains hypothetical. In this work the sequence features of Arabidopsis thaliana and Oryza sativa mRNAs were analyzed. It was found that plant mRNAs with UGA terminator were characterized by a higher frequency of nonsense codons in the first triplet position of 3'-UTR that could result from a weak natural selection for "reserve" stop signal. Interestingly, the presence of tandem stop codons positively correlated with a specific amino acid composition in the C-terminal position of the encoded proteins. In particular, C-terminal glycine positively correlated with significantly higher frequencies of reserve terminators at the beginning positions of 3'-UTR in UGA-containing mRNAs. This finding coincides with some earlier observations concerning the role of glycine and its codons in inefficient termination of translation and recoding (e.g., 2A oligopeptide).

Interrelations between the nucleotide context of human start AUG codon, N-end amino acids of the encoded protein and initiation of translation.

It is known that the recognition of AUG triplet by eukaryotic ribosomes as a translation start site strongly depends on its nucleotide context. However, the relative significance of different context positions is not fully clear. In particular, it concerns the role of 3'-end part of the context located at the beginning of the protein-coding sequence. The significant bias observed in nucleotide frequencies in positions +4, +5, +6 (corresponding to the second codon of CDS) could result from different reasons and their contribution to start codon recognition and initiation of translation is under discussion. In this study, we conducted a comparative computational analysis of the human mRNA samples containing different nucleotides (adenine, guanine or pyrimidine) in the essential context position -3. It was found that the presence of G in position +4 could be important for the context variant GnnAUG but not for AnnAUG. Interestingly, the second position of proteins encoded by mRNAs with AnnAUG context variant was specifically and significantly enriched with serine whereas the presence of GnnAUG context also correlated with a higher occurrence of alanine and glycine. It is likely that the efficiency of translation initiation process can depend on the interplay between 5'-context part, 3'-context part and the type of amino acid in the second position of the encoded protein.

uORFs, reinitiation and alternative translation start sites in human mRNAs.

It is known that eukaryotic ribosomes are able to translate small ORFs and reinitiate translation at downstream start codons. However, this mechanism is widely considered to be inefficient and it is not commonly taken into account. We compiled a sample of human mRNAs containing small upstream ORFs overlapping with annotated protein coding sequences. Statistical analysis supported the hypothesis on reinitiation of translation at downstream AUG codons and functional significance of potential alternative ORFs. It may be assumed that some 5'UTR-located upstream ORFs can deliver ribosomes to alternative translation starts, and they should be taken into consideration in the prediction of human mRNA coding potential.