Nallan, A. N. | Search bioRxiv

bioRxiv2024

MetaPathways v3.5: Modularity and Scalability Improvements for Pathway Inference from Environmental Genomes

Over the past decade MO_SCPLOWETAC_SCPLOWPO_SCPLOWATHWAYSC_SCPLOW has advanced as a modular pipeline for constructing environmental pathway genome databases (ePGDBs), increasing our understanding of microbial metabolism at the individual, population and community levels of biological organization. With this release, we have addressed several user experience issues related to installation, module integration, and database management. With a refactored code base, MO_SCPLOWETAC_SCPLOWPO_SCPLOWATHWAYSC_SCPLOW v3.5 enhances the user experience through streamlined installation via package indexes or containers, refined modules, and interface upgrades. It boasts updated algorithm support for sequence feature prediction, annotation, metabolic inference, and coverage metrics including genome resolved metagenomes. Tested and refined on synthetic datasets, MO_SCPLOWETAC_SCPLOWPO_SCPLOWATHWAYSC_SCPLOW v3.5 demonstrates improved performance and usability; facilitating more in-depth exploration of microbial interactions and metabolic functions in environmental genomes that scales with con-temporary sequencing throughput. Availability and ImplementationMO_SCPLOWETAC_SCPLOWPO_SCPLOWATHWAYSC_SCPLOW v3.5 is available via AO_SCPLOWNACONDAC_SCPLOW, DO_SCPLOWOCKERC_SCPLOW, and AO_SCPLOWPPTAINERC_SCPLOW. The source code is available on BO_SCPLOWITC_SCPLOWBO_SCPLOWUCKETC_SCPLOW:https://bitbucket.org/BCB2/metapathways/ The documentation is available via RO_SCPLOWEADC_SCPLOWTO_SCPLOWHEC_SCPLOWDO_SCPLOWOCSC_SCPLOW:https://metapathways.readthedocs.io Contactshallam@mail.ubc.ca

bioinformatics↗

bioRxiv2022

ES30L: A large subunit rRNA expansion segment enriched in mammals and birds

Ribosomes, the molecular machines that are central to protein synthesis, have gradually been gaining prominence for their regulatory role in translation. Eukaryotic cytosolic ribosomes are typically larger than bacterial ones, partly due to multi-nucleotide insertions at specific conserved positions in the ribosomal RNAs (rRNAs). Such insertions called expansion segments (ESs) are present primarily on the ribosomal surface, with their role in translation and its regulation remaining under-explored. One such ES in the ribosomal large subunit (LSU) is ES30L, which is present only in mammals and birds among eukaryotes. In this study, we show that ES30L possesses complementarity to many protein-coding transcripts in humans and that the complementarity is enriched around the start codon, hinting at a possible role in translation regulation. Further, our in silico analysis analyses and pull-down assays indicate that ES30L may bind to secondary structures in the 5 UTR of several transcripts and RNA binding proteins (RBPs) that are essential for translation. Thus, we have identified a potential regulatory role for ES30L in translation.

molecular biology↗