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PubMed2026

seq2ribo: structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.

MOTIVATION: Ribosome dynamics are vital in the process of protein expression. Current methods rely on ribosome profiling (Ribo-seq), RNA-seq profiles, and full genomic context. This restricts their use in de novo sequence design, like messenger RNA (mRNA) vaccines. Simulation-only approaches like the Totally Asymmetric Simple Exclusion Process (TASEP) oversimplify translation by focusing solely on codon elongation times. RESULTS: We present seq2ribo, a hybrid simulation and machine learning framework that predicts ribosome A-site locations using only an mRNA sequence as input. Our method first employs a novel structure-aware TASEP (sTASEP), which models translation using a comprehensive set of fitted parameters that include codon wait times and structural features, such as local angles, base-pairing, and discrete positional buckets. The ribosome locations generated by sTASEP are then processed by a polisher model, which learns to refine the simulated ribosome distributions. seq2ribo provides high-fidelity predictions of ribosome locations across diverse cell types (iPSC, HEK293, LCL, and RPE-1), significantly outperforming baselines. seq2ribo is the first method to achieve meaningful positional correlation with observed ribosome profiles from sequence alone, reaching transcript-level Pearson correlations up to 0.920 and within-transcript shape correlations up to 0.186, where all baselines yield near-zero values on these metrics. seq2ribo also reduces elementwise error by up to 37.7% relative to the sequence-only Translatomer baseline. By adding a task-specific head, seq2ribo achieves Pearson correlations up to 0.732 with experimental translation efficiency (TE) across several cell lines, and up to 0.903 with measured protein expression. By operating from sequence alone, seq2ribo provides a new tool for synthetic biology, enabling the rational design and optimization of mRNA sequences without the need for expression-level data or genomic context. AVAILABILITY: seq2ribo is available at https://github.com/Kingsford-Group/seq2ribo.

Machine Learning↗
PubMedDate not supplied

Small subunit ribosomal RNA sequence of Henneguya exilis (class Myxosporea) identifies the actinosporean stage from an oligochaete host.

Several transmission studies, as well as recent molecular data, have indicated that the two classes Myxosporea and Actinosporea represent different life cycle stages of Myxozoa. To evaluate the life cycles of myxozoa in catfish aquaculture systems, the small subunit (18S) ribosomal RNA gene sequences of Henneguya exilis, a myxosporean from channel catfish Ictalurus punctatus, and an actinosporean (previously designated as Aurantiactinomyxon janiszewskai) from the aquatic oligochaete Dero digitata were determined. The sequences were identical, indicating that H. exilis and the actinosporean are alternate life stages of a single species. This is the first report identifying the actinosporean stage of the genus Henneguya.

Animals↗
PubMed2003

RNA sequences that work as transcriptional activating regions.

We describe a set of RNA molecules that work as transcriptional activators when tethered to DNA. These RNA activating regions were found amongst a randomized set of molecules bearing variants of a 10 nt loop attached to an RNA stem. The various RNA activating regions all bear an identical five- residue sequence with an interspersed sixth residue. The result shows that although all natural activating regions characterized thus far are peptidic, this function can be served by other kinds of moieties as well.

Base Sequence↗
PubMed1991

Phylogenetic relationships among species of Saccharomyces, Schizosaccharomyces, Debaryomyces and Schwanniomyces determined from partial ribosomal RNA sequences.

Species of the genera Saccharomyces, Schizosaccharomyces, Debaryomyces and Schwanniomyces were compared from their extent of divergence in three regions from small (18S) and large (25S) subunit ribosomal RNAs comprising a total of 900 nucleotides. With the exception of the closely related Saccharomyces bayanus and S. pastorianus, which appear to have identical sequences, all other species could be distinguished by nucleotide differences in a variable region of the large subunit, and genus-specific nucleotides were discernible in all three regions. The taxon D. tamarii differed markedly from other species and is excluded from Debaryomyces. By contrast, Schwanniomyces occidentalis showed few nucleotide differences with Debaryomyces spp. and its transfer to Debaryomyces is proposed. Schizosaccharomyces proved to be somewhat more divergent than Saccharomyces and Debaryomyces, but species differences appear insufficient for dividing the genus. Some of the factors influencing estimates of phylogenetic distances from rRNA sequences are discussed.

Base Sequence↗
PubMed2001

A molecular phylogeny of Heterodonta (Bivalvia) based on small ribosomal subunit RNA sequences.

Within Heterodonta, phylogenesis has so far been studied almost exclusively on the basis of morphological data. Results have often been discordant, and an exhaustive molecular approach has not yet been attempted. The present study was undertaken to clarify the phylogenetic relationships obtaining among Heterodonta families through the analysis of 18S rRNA gene. To do this, the whole sequence of this gene was analyzed in 29 species of eight superfamilies of the order of Veneroida (Arcticoidea, Cardioidea, Galeommatoidea, Mactroidea, Solenoidea, Tellinoidea, Tridacnoidea, and Veneroidea) and in two superfamilies of Myoida (Pholaloidea and Myoidea). The study was extended by constructing phylogenetic trees using partial sequences. This strategy made it possible to include 11 additional species by introducing three further superfamilies: Chamoidea, Corbiculoidea, and Hiatellinoidea. At variance with the conclusions reached on the basis of morphological features, the molecular data clearly show that the Myoida species included in this study belong to Veneroida, thus undermining the legitimacy of the division of Heterodonta into two orders, and that considerable differences in the phylogenetic relationships obtain among superfamilies.

Animals↗
PubMed2000

Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I and large ribosomal RNA sequences and nuclear internal transcribed spacer I sequences from species of Cyathostominae and Strongylinae (Nematoda, Order Strongylida), parasites of the horse.

Three nucleotide data sets, one nuclear (ITS-2) and two mitochondrial (COI and l-rRNA), have been investigated in order to determine relationships among species of Strongylinae and Cyathostominae, intestinal parasites of the horse. The data exhibited a strong mutational bias towards A and T and in the COI gene, silent sites appeared to saturate rapidly partly due to this substitution bias. Thus, the COI gene was found to be less phylogenetically informative than the l-rRNA and ITS-2 genes. Combined analysis of the l-rRNA and ITS-2 genes supported a monophyletic clade of the cyathostomes with Tridentoinfundibulum gobi, which had previously been classified as a nematode of' uncertain origin'. The Strongylinae grouped consistently outside the clade containing the cyathostomes and T. gobi. Molecular analysis failed to provide strong evidence for the separation of cyathostomes into classical genera, as previously defined by morphological classification.

Animals↗
PubMed2004

Asaia bogorensis peritonitis identified by 16S ribosomal RNA sequence analysis in a patient receiving peritoneal dialysis.

Here the authors report a case of refractory peritonitis leading to multiple hospitalizations and the loss of peritoneal dialysis access in a patient on automated peritoneal dialysis, caused by Asaia bogorensis, a bacterium not previously described as a human pathogen. This organism was identified by sequence analysis of the 16S ribosomal RNA gene. Unusual microbial agents may cause peritonitis, and molecular microbiological techniques are important tools for identifying these agents.

Acetobacteraceae↗
PubMed1990

16S ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs.

16S ribosomal RNAs (rRNA) of 12 methylotrophic bacteria have been almost completely sequenced to establish their phylogenetic relationships. Methylotrophs that are physiologically related are phylogenetically diverse and are scattered among the purple eubacteria (class Proteobacteria). Group I methylotrophs can be classified in the beta- and the gamma-subdivisions and group II methylotrophs in the alpha-subdivision of the purple eubacteria, respectively. Pink-pigmented facultative and non-pigmented obligate group II methylotrophs form two distinctly separate branches within the alpha-subdivision. The secondary structures of the 16S rRNA sequences of 'Methylocystis parvus' strain OBBP, 'Methylosinus trichosporium' strain OB3b, 'Methylosporovibrio methanica' strain 81Z and Hyphomicrobium sp. strain DM2 are similar, and these non-pigmented obligate group II methylotrophs form one tight cluster in the alpha-subdivision. The pink-pigmented facultative methylotrophs, Methylobacterium extorquens strain AM1, Methylobacterium sp. strain DM4 and Methylobacterium organophilum strain XX form another cluster within the alpha-subdivision. Although similar in phenotypic characteristics, Methylobacterium organophilum strain XX and Methylobacterium extorquens strain AM1 are clearly distinguishable by their 16S rRNA sequences. The group I methylotrophs, Methylophilus methylotrophus strain AS1 and methylotrophic species DM11, which do not utilize methane, are similar in 16S rRNA sequence to bacteria in the beta-subdivision. The methane-utilizing, obligate group I methanotrophs, Methylococcus capsulatus strain BATH and Methylomonas methanica, are placed in the gamma-subdivision. The results demonstrate that it is possible to distinguish and classify the methylotrophic bacteria using 16S rRNA sequence analysis.

Base Sequence↗
PubMed1985

The 5S and 5.8S ribosomal RNA sequences of Tetrahymena thermophila and T. pyriformis.

The nucleotide sequences of the 5S rRNAs of Tetrahymena thermophila and two strains of T. pyriformis have been determined to be identical. The 5.8S rRNA sequences have also been determined; these sequences correct several errors in an earlier report. The 5.8S rRNAs of the two species differ at a single position. The sequencing results indicate that the species are of recent common ancestry. Molecular evidence that has been interpreted in the past as suggestive of an ancient divergence has been reviewed and found to be consistent with a T. pyriformis complex radiation beginning approximately 30-40 million years ago.

Animals↗
PubMed1994

The phylogeny of Neospora caninum and Toxoplasma gondii based on ribosomal RNA sequences.

Neospora caninum is a newly described cyst-forming coccidium which is the cause of severe neurological disease in dogs. The parasite is morphologically similar to Toxoplasma gondii, but the two species can be differentiated serologically. In order to define the phylogenetic position of N. caninum, we have determined 16S-like rRNA sequences from three members of the family of Sarcocystidae: N. caninum, T. gondii, and Sarcocystis fusiformis. The 16S-like rRNA genes from the three parasites were amplified by polymerase chain reaction and the sequences were determined by direct solid-phase sequencing. The sequences derived were computer aligned with several other 16S-like rRNA sequences from protozoan parasites to construct phylogenetic trees. The study confirmed that N. caninum should be classified as a member of the family Sarcocystidae. However, because of the close relationship to T. gondii it seems questionable that N. caninum should be placed in a new genus.

Animals↗
PubMed1993

Sensitive detection and strain classification of Trypanosoma cruzi by amplification of a ribosomal RNA sequence.

A sequence of about 100 bp of the 24S alpha ribosomal RNA was investigated for sensitive detection of Trypanosoma cruzi. It was shown that the target sequence is specific for this parasite and no cross-reactivity was observed with different species of pathogenic Leishmania, two strains of Trypanosoma rangeli or human RNA. Amplification of the sequence was obtained by reverse transcription coupled to polymerase chain reaction. Following this procedure the equivalent to 0.1% of the nucleic acid content of a single parasite cell could be detected either by ethidium staining or blot hybridization. The distribution of the target sequence in sixteen strains of T. cruzi was investigated. Positive amplification was obtained for all samples employing the same oligonucleotides as primers. However, amplified fragments of 125 bp were obtained in eight strains, while fragments of 110 bp were detected in the remaining eight isolates. No amplification of both classes of fragments has been detected in any of the strains examined. Dimorphism in the target region was confirmed by hybridization to specific internal probes and sequencing, allowing the division of T. cruzi strains in two groups. It is proposed that sensitive parasite detection could be achieved by rRNA amplification followed by hybridization to two probes derived from the target sequences of both groups of T. cruzi strains. Furthermore, the sequence dimorphism found in this sequence opens the perspective of strain typing simultaneous with parasite detection.

Animals↗
PubMed1983

The 3'-terminal region of mosquito mitochondrial small ribosomal subunit RNA: sequence and localization of methylated residues.

The 3'-terminal 101 residues of the small ribosomal subunit (SSU) RNA of mosquito cell mitochondria have been determined. This stretch includes the four methylated residues of the molecule: an m4C, an m5C, and two m26A residues. The m26A's occur in a typical m26A "arm," and the methylated Cs in the unique subsequence G x m4C . C . m5C . A, which is homologous in position to a conserved methylated GCCCG subsequence of other SSU RNA classes. There is fairly good overall homology between the mosquito mitochondrial sequence and corresponding regions of other SSU RNA classes, except that a domain of 50-100 residues, previously considered universal, is absent. Comparison with mammalian mitochondrial sequences revealed a marked preponderance of transitional base substitutions, supporting earlier evidence that the 3'-terminal region of SSU RNA is under special structural constraints. The extreme 3' end of the mosquito sequence is heterogeneous, three-fourths of the molecules ending in ... GA and one-fourth ending in ... GAA. Evidence is presented indicating that some, at least, of the 3'-terminal A residues may be added post-transcriptionally, as occurs in mammalian mitochondrial systems. Taken together, the results provide modest support for the monophyletic evolutionary origin of insect and mammalian mitochondria from a primitive procaryotic ancestor.

Aedes↗