Butenko, A. | bioRxiv Science

bioRxiv2026

A threonine-to-aspartate ACA codon reassignment in uncultivated Acidimicrobiales bacteria

The list of alternative genetic codes continues to grow, yet sense-to-sense codon reassignments remain very rare. Here we analyze a new sense-to-sense codon reassignment in bacteria, where the ACA codon, which canonically specifies threonine, has been predicted to encode aspartate. This so far unprecedented genetic code alteration is confined to a clade within the RAAP-2 family of the order Acidimicrobiales (phylum Actinomycetota). Validated by multiple alignments of highly conserved proteins, the reassignment is further supported by the presence of a tRNAUGU that lacks the G1:C72 threonylation identity element, suggesting that this tRNA is charged with aspartate instead of threonine. Our findings not only expand the set of known natural departures from the canonical genetic code by a novel type of sense-to-sense reassignment but also implicate the ACA codon that was so far considered invariably conserved in its meaning.

genomics↗

bioRxiv2024

Somy evolution in the honey bee infecting trypanosomatid parasite, Lotmaria passim

Lotmaria passim is a ubiquitous trypanosomatid parasite of honey bees nestled within the medically important subfamily Leishmaniinae. Although this parasite is associated with honey bee colony losses, the original draft genome--which was completed before its differentiation from the closely related Crithidia mellificae--has remained the reference for this species despite lacking improvements from newer methodologies. Here we report the updated sequencing, assembly, and annotation of the BRL type strain (ATCC PRA-422) of Lotmaria passim. The nuclear genome assembly has been resolved into 31 complete chromosomes and is paired with an assembled kinetoplast genome consisting of a maxicircle and 30 minicircle sequences. The assembly spans 33.7 Mb and contains very little repetitive content, from which our annotation of both the nuclear assembly and kinetoplast predicted 10,288 protein-coding genes. Analyses of the assembly revealed evidence of a recent chromosomal duplication event within chromosomes 5 and 6 and provides evidence for a high level of aneuploidy in this species, mirroring the genomic flexibility employed by other trypanosomatids as a means of adaptation to different environments. This high-quality reference can therefore provide insights into adaptations of trypanosomatids to the thermally regulated, acidic, and phytochemically rich honey bee hindgut niche, which offers parallels to the challenges faced by other Leishmaniinae during the challenges they undergo within insect vectors, during infection of mammals, and exposure to antiparasitic drugs throughout their multi-host life cycles. This reference will also facilitate investigations of strain-specific genomic polymorphisms, their role in pathogenicity, and the development of treatments for pollinator infection.

genomics↗