Expanded diversity of pedinophytes provides a window into the evolution of the genetic code in organelles

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61988987%3A17310%2F25%3AA2603CVU" target="_blank" >RIV/61988987:17310/25:A2603CVU - isvavai.cz</a>

Výsledek na webu

<a href="https://dx.plos.org/10.1371/journal.pgen.1011901" target="_blank" >https://dx.plos.org/10.1371/journal.pgen.1011901</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1371/journal.pgen.1011901" target="_blank" >10.1371/journal.pgen.1011901</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Expanded diversity of pedinophytes provides a window into the evolution of the genetic code in organelles

Popis výsledku v původním jazyce

Mitochondria and plastids of various lineages exhibit genetic code alterations.However, the knowledge of the diversity and occurrence, mechanistic underpinnings,and evolutionary origins of codon reassignments in organelles remainsincomplete. To address this gap, we focused on organelles of the neglected greenalgal class Pedinophyceae, as well as pedinophyte-derived secondary plastids ofgreen-coloured dinoflagellates (peDinoflagellates). We isolated and characterized anovel pedinophyte, herein formally described as Oistococcus okinawensis gen. et sp.nov., and phenotypically documented the previously sequenced but morphologicallyuncharacterized strain YPF-701, herein described as Akinorimonas japonica gen.et sp. nov. Based on phylogenetic analyses, both new taxa were classified into theexpanded family Resultomonadaceae. We sequenced the organellar genomes of O.okinawensis, and utilizing existing raw (meta)genomic data we assembled organellargenome sequences from other previously unexplored pedinophyte lineages. Bioinformaticanalyses of the expanded set of pedinophyte organellar genomes painteda complex picture of their genetic code landscape. Concerning mitochondria, thestop-to-Trp reassignment of the UGA codon turned out to have evolved multiple timesin pedinophytes, and the Arg-to-Ala reassignment of AGA/AGG codons was shownto be apomorphic for the whole order Marsupiomonadales. The latter has additionallyconverted UUA and UUG into termination codons, relying on specific mutations in themtRF1a protein. All pedinophyte mitochondria seem to decode AUA as methioninerather than the standard isoleucine, and an analogous reassignment seems to beevolving also in plastids of two separate pedinophyte lineages. Finally, apart fromthe previously reported Ile-to-Met AUA reassignment, peDinoflagellate plastids haveswitched the meaning of the AGA/AGG codons from arginine to another amino acid(most likely alanine), and have modified their pRF2 protein to mediate translationtermination at UUA/UCA codons. Pedinophyte(-derived) organelles present a broad spectrum of codon reassignments and provide important insights into the emergence and mechanisms of non-standard codon translation.

Název v anglickém jazyce

Expanded diversity of pedinophytes provides a window into the evolution of the genetic code in organelles

Popis výsledku anglicky

Mitochondria and plastids of various lineages exhibit genetic code alterations.However, the knowledge of the diversity and occurrence, mechanistic underpinnings,and evolutionary origins of codon reassignments in organelles remainsincomplete. To address this gap, we focused on organelles of the neglected greenalgal class Pedinophyceae, as well as pedinophyte-derived secondary plastids ofgreen-coloured dinoflagellates (peDinoflagellates). We isolated and characterized anovel pedinophyte, herein formally described as Oistococcus okinawensis gen. et sp.nov., and phenotypically documented the previously sequenced but morphologicallyuncharacterized strain YPF-701, herein described as Akinorimonas japonica gen.et sp. nov. Based on phylogenetic analyses, both new taxa were classified into theexpanded family Resultomonadaceae. We sequenced the organellar genomes of O.okinawensis, and utilizing existing raw (meta)genomic data we assembled organellargenome sequences from other previously unexplored pedinophyte lineages. Bioinformaticanalyses of the expanded set of pedinophyte organellar genomes painteda complex picture of their genetic code landscape. Concerning mitochondria, thestop-to-Trp reassignment of the UGA codon turned out to have evolved multiple timesin pedinophytes, and the Arg-to-Ala reassignment of AGA/AGG codons was shownto be apomorphic for the whole order Marsupiomonadales. The latter has additionallyconverted UUA and UUG into termination codons, relying on specific mutations in themtRF1a protein. All pedinophyte mitochondria seem to decode AUA as methioninerather than the standard isoleucine, and an analogous reassignment seems to beevolving also in plastids of two separate pedinophyte lineages. Finally, apart fromthe previously reported Ile-to-Met AUA reassignment, peDinoflagellate plastids haveswitched the meaning of the AGA/AGG codons from arginine to another amino acid(most likely alanine), and have modified their pRF2 protein to mediate translationtermination at UUA/UCA codons. Pedinophyte(-derived) organelles present a broad spectrum of codon reassignments and provide important insights into the emergence and mechanisms of non-standard codon translation.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10602 - Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology

Projekt

<a href="/cs/project/GA23-05764S" target="_blank" >GA23-05764S: Organelární translace jako evoluční hřiště</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

PLOS Genetics

ISSN

1553-7404

e-ISSN

—

Svazek periodika

—

Číslo periodika v rámci svazku

10

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

38

Strana od-do

—

Kód UT WoS článku

001598136200003

EID výsledku v databázi Scopus

2-s2.0-105020600608