Programmed ribosomal frameshifting has translational costs that may influence codon usage bias.
The genetic code has some redundancy—the same amino acid is often encoded by several codons. However, these codons are not necessarily equal in their effect, as evidenced by the codon usage bias observed in many organisms. The translation efficiency hypothesis posits that some codons are more easily translated than others, and these are the ones more commonly used. Based on this hypothesis, the codon usage bias index of a given mRNA should correlate closely with its translation efficiency—but in a report in G3: Genes|Genomes|Genetics, Garcia et al. explain why this might not always be the case.
Programmed ribosomal frameshifting (PRF) occurs when a ribosome stalls at specific sequences—appropriately termed “slippery sites”—which shifts translation to a new reading frame. The authors were specifically interested in “-1 PRF” cases, where the ribosome moves a single nucleotide backward during translation. This phenomenon is ubiquitous across the tree of life, and it is generally used by eukaryotes as a way to regulate gene expression, but the authors wondered if it could also induce translational costs.
To test this, they used the database PRFdb to examine associations between -1 PRF signals and gene expression in yeast, determining that -1 PRF signals are less common in highly expressed genes. They also found that these signals tend to be present towards the start of open reading frames, which makes sense if the -1 PRF signals are causing translational costs—if the signals occur towards the start of the mRNA, translation is disrupted more quickly, so less energy is wasted. These lines of evidence support the idea that PRF signals do incur translational costs.
The authors then retested the association between codon usage bias and translational efficiency while accounting for the cost of -1 PRF signals. Using a set of mathematical models, they found that incorporating this data generally strengthened support of the translational efficiency hypothesis—that is, more costly transcripts were less often translated, whether the cost was incurred due to codon usage bias or -1 PRF signals. Better understanding these phenomena may help elucidate how translational efficiency is controlled.
CITATION:
Accounting for Programmed Ribosomal Frameshifting in the Computation of Codon Usage Bias Indices
Victor Garcia, Stefan Zoller, Maria Anisimova
https://doi.org/10.1534/g3.118.200185
http://www.g3journal.org/content/8/10/3173
[wysija_form id=”1″]
Science Writing and Communications Intern, Genetics Society of America.
View all posts by Marisa Wexler »Read more in
-
In Memoriam: Ellsworth Herman Grell (1932–2023), a pioneer of Drosophila genome engineering and annotation
Ellsworth (Ed) Grell blessed the Drosophila community through three enduring legacies: as a pioneer of chromosome mechanics, as a primary organizer and synthesizer of genetic knowledge in Drosophila, and as a graceful mentor to those fortunate to have known him personally. Ed grew up in rural Nebraska, completed his undergraduate studies at Iowa State, and…
-
Congratulations to the #Fungal24 Poster Award winners!
We are pleased to announce the recipients of the GSA Poster Awards for posters presented at the 32nd Fungal Genetics Conference! Undergraduate and graduate student members of GSA were eligible for the awards, and a hard-working team of judges made the determinations. Congratulations to all! Felicia Ebot Ojong, The University of Georgia My research is focused…
-
Poster presentation tips for TAGC 2024
You’ve been selected to present a poster at The Allied Genetics Conference 2024 in March—you’ve celebrated, made plans to attend, now what? This is an exciting opportunity to showcase your research and engage with fellow members of the genetics community, so you want to make sure you’re prepared. We wanted to offer you some tips…
-
Maximize your TAGC 2024 experience
A guide to all that National Harbor & DC have to offer Are you joining us for The Allied Genetics Conference 2024 in March? Make the most of your #TAGC24 experience in National Harbor! We know the science will keep you busy, but you deserve to unwind and have some fun, so we’ve curated a…
-
Early Career Leadership Spotlight: Sarah Petrosky
We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates. Sarah PetroskyMultimedia SubcommitteeUniversity of Pittsburgh Research Interest I am interested in understanding adaptation that has been happening recently in populations by dissecting the ways that genes underlying an adaptation…
-
TAGC 2024 Early Career Award Winners
GSA is pleased to announce the winners of the early career awards presented at The Allied Genetics Conference 2024. These awards are specific to particular TAGC communities and recognize early career scientists’ outstanding work on their respective research organisms. The awardees will present their talks in keynote sessions at TAGC 2024. Don’t miss the opportunity…
-
Preeminent geneticists recognized with revamped GSA Awards
In 2022, GSA’s Board of Directors launched an audit to review the five major awards conferred by the Society. Today, we are thrilled to announce the recipients of the reimagined GSA Awards, including the new Genetics Society of America Early Career Medal. The scientists honored this year are recognized by their peers for their outstanding…
-
Fly Board funds outreach programs to spread the word about Drosophila research
In 2020, the Fly Board voted to use part of its reserve fund to support efforts to increase trainee participation as well as equity and diversity in the Drosophila community. An awards committee decides how the money will be spent each year, and from 2020–2022, the committee posted a very broad call for applications from…
-
New members of the GSA Board of Directors: 2024–2026
We are pleased to announce the election of four new leaders to the GSA Board of Directors: 2024 Vice President/2025 President Brenda Andrews Professor, University of Toronto It’s an honor to continue my association with the Society by serving as Vice President of the Board of Directors. I have broad knowledge of the ongoing activities…
-
Parrot plumage study aids breeders and endangered natural populations
Yellow coloration is maladaptive in the wild but prized by breeders. People have long been fascinated with birds, which exhibit one of the widest ranges of coloration among vertebrates. Parrots, in particular, have captivated humans by their ability to mimic human speech and spectacular plumage. Brightly colored feathers are used primarily to attract mates, intimidate…
-
Early Career Leadership Spotlight: Sarah Gilmour
We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates. Sarah GilmourMultimedia SubcommitteeStowers Institute for Medical Research Research Interest Questions of evolution have always fascinated me. I am extremely fortunate to be starting out my research career in a…