Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Translation in Prokaryotes

Translation in Prokaryotes

Prokaryote translation is a complex, highly coordinated process that converts genetic information from mRNA into functional proteins. It involves three stages: initiation, elongation, and termination, each facilitated by specific molecular components.Initiation of TranslationThe process begins with the assembly of the ribosomal subunits and initiation factors on the mRNA. In bacteria, the 30S ribosomal subunit recognizes the Shine-Dalgarno sequence in the mRNA, a conserved region upstream of...

Translational Regulation

Translational Regulation

Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...

Initiation of Translation

Initiation of Translation

Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...

Coordination of Gene Expression Processes in Bacteria

Coordination of Gene Expression Processes in Bacteria

The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...

Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

Bacterial Translocation and Protein Secretion

Bacterial Translocation and Protein Secretion

Bacterial protein secretion involves translocation systems to ensure proteins reach their designated locations, including the plasma membrane, periplasm, outer membrane, or the external environment. These translocation systems are vital for bacterial physiology, supporting processes like membrane assembly, enzymatic activity in the periplasm, and interactions with the external environment. The division of labor between Sec and Tat pathways ensures efficiency in handling proteins with diverse...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Multi-Layered Genomic and Clinical Analysis Identifies Novel Variants, Co-Occurring Single Nucleotide Polymorphism Pairs, and Clinical Determinants of Host-Pathogen Interaction in COVID-19 Severity.

Journal of medical virology·2026

Same author

Comprehensive assessment of transcriptome assembly quality using CATS.

Nature communications·2026

Same author

Age-dependent mutational loads in human tRNA genes are tumor-specific and result in chimeric tRNA sequences that could disrupt the genetic code.

Genome research·2026

Same author

The DNA dialect: a comprehensive guide to pretrained genomic language models.

Molecular systems biology·2026

Same author

Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals.

Genome biology·2025

Same author

Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions.

Nature microbiology·2025

Search research articles

Related Experiment Video

Updated: Jun 11, 2026

Rapid In Vivo Fixation and Isolation of Translational Complexes from Eukaryotic Cells

Rapid In Vivo Fixation and Isolation of Translational Complexes from Eukaryotic Cells

Published on: December 25, 2021

Translational selection is ubiquitous in prokaryotes.

Fran Supek¹, Nives Skunca, Jelena Repar

¹Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia.

|June 30, 2010

Summary

Translational selection, driven by codon usage bias, is nearly universal in prokaryotes. A new machine learning method identifies highly expressed genes, revealing conserved optimization trends across microbial genomes.

More Related Videos

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Published on: October 7, 2021

Measurement of Specific Mycobacterial Mistranslation Rates with Gain-of-function Reporter Systems

Measurement of Specific Mycobacterial Mistranslation Rates with Gain-of-function Reporter Systems

Published on: April 26, 2019

Related Experiment Videos

Last Updated: Jun 11, 2026

Rapid In Vivo Fixation and Isolation of Translational Complexes from Eukaryotic Cells

Rapid In Vivo Fixation and Isolation of Translational Complexes from Eukaryotic Cells

Published on: December 25, 2021

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Published on: October 7, 2021

Measurement of Specific Mycobacterial Mistranslation Rates with Gain-of-function Reporter Systems

Measurement of Specific Mycobacterial Mistranslation Rates with Gain-of-function Reporter Systems

Published on: April 26, 2019

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Codon usage bias in prokaryotes is influenced by DNA substitution patterns.
Highly expressed genes may favor codons for efficient and accurate translation.

Purpose of the Study:

To develop a novel supervised machine learning approach to detect translational selection effects on genes.
To control for local nucleotide substitution patterns using intergenic DNA sequence composition.

Main Methods:

Utilized a Random Forest classifier to identify codon usage patterns.
Compared the Random Forest approach to distance measure-based methods like the codon adaptation index.
Analyzed 460 microbial genomes to assess the universality of translational selection.

Main Results:

The Random Forest classifier outperformed previous methods in distinguishing highly expressed ribosomal protein genes.
Translational selection was found to be nearly universal, present in 460 of 461 genomes examined.
Optimized genes, constituting 5-33% of genomes, showed higher mRNA abundance and favored codons with canonical base pairing.

Conclusions:

Translational selection is a widespread phenomenon in prokaryotic genomes.
Gene functional categories exhibit conserved enrichment or depletion of codon optimization.
The study provides insights into gene expression, physiological roles, and potential misannotations.