Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Initiation of Translation02:33

Initiation of Translation

34.4K
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...
34.4K
Improving Translational Accuracy02:07

Improving Translational Accuracy

11.8K
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...
11.8K
Leaky Scanning02:28

Leaky Scanning

5.2K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.2K
Translation01:31

Translation

142.9K
Lesson: Translation
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
Translation Produces the Building Blocks of...
142.9K
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

8.6K
Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
8.6K
Translation in Prokaryotes01:29

Translation in Prokaryotes

122
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...
122

You might also read

Related Articles

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

Sort by
Same author

Symbiotic bacteria produce non-lytic vesicles with nucleic acid cargo.

Nature communications·2026
Same author

Expression of a phage RecET recombinase system improves detection of shorter DNA fragments by an <i>Acinetobacter baylyi</i> ADP-ISx antibiotic gene biosensor strain.

microPublication biology·2026
Same author

Refactored genetic parts for modular assembly of the E. coli MccV type I secretion system used to screen class II microcin candidates from plant-associated bacteria.

BMC biotechnology·2026
Same author

Phages use contingency loci as a bet-hedging strategy.

bioRxiv : the preprint server for biology·2025
Same author

Evolutionary loss of an antibiotic efflux pump increases Pseudomonas aeruginosa quorum sensing mediated virulence in vivo.

Nature communications·2025
Same author

Evolution in response to prophage activation attenuates the virulence of culturable <i>Serratia symbiotica</i> relatives of aphid endosymbionts.

mBio·2025
Same journal

ggpedigree: Visualizing Pedigrees with 'ggplot2' and 'plotly'.

Journal of open source software·2026
Same journal

ACHR.cu: GPU-accelerated sampling of metabolic networks.

Journal of open source software·2026
Same journal

svZeroDSolver: A modular package for lumped-parameter cardiovascular simulations.

Journal of open source software·2026
Same journal

baysc: An R package for Bayesian survey clustering.

Journal of open source software·2026
Same journal

FastPCA: An R package for fast singular value decomposition.

Journal of open source software·2026
Same journal

Napari-3D-Counter: A manual cell counter for napari.

Journal of open source software·2026
See all related articles

Related Experiment Video

Updated: Aug 27, 2025

Analysis of Translation Initiation During Stress Conditions by Polysome Profiling
10:59

Analysis of Translation Initiation During Stress Conditions by Polysome Profiling

Published on: May 19, 2014

18.4K

OSTIR: open source translation initiation rate prediction.

Cameron T Roots1, Alexandra Lukasiewicz2, Jeffrey E Barrick1

  • 1Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin.

Journal of Open Source Software
|September 30, 2022
PubMed
Summary
This summary is machine-generated.

Predicting bacterial translation initiation rates is now possible using thermodynamic models. The OSTIR Python package enables accurate predictions for systems and synthetic biology applications.

More Related Videos

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

3.7K
Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale
10:56

Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale

Published on: May 17, 2014

68.8K

Related Experiment Videos

Last Updated: Aug 27, 2025

Analysis of Translation Initiation During Stress Conditions by Polysome Profiling
10:59

Analysis of Translation Initiation During Stress Conditions by Polysome Profiling

Published on: May 19, 2014

18.4K
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

3.7K
Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale
10:56

Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale

Published on: May 17, 2014

68.8K

Area of Science:

  • Molecular Biology
  • Systems Biology
  • Synthetic Biology

Background:

  • Ribosome-mediated translation of messenger RNAs into proteins is essential for gene expression in bacteria.
  • Accurate prediction of translation initiation rates can be achieved using thermodynamic models of RNA folding and ribosome binding.

Purpose of the Study:

  • To develop a computational tool for predicting bacterial translation initiation rates.
  • To provide a resource for systems and synthetic biology applications.

Main Methods:

  • Utilized thermodynamic models of RNA folding and ribosome binding.
  • Developed a Python package and command line tool named OSTIR (Open Source Translation Initiation Rates).

Main Results:

  • OSTIR accurately predicts translation initiation rates in bacteria based on sequences surrounding the start codon.
  • The tool has applications in understanding bacterial physiology and reprogramming bacterial cells.

Conclusions:

  • The OSTIR package offers a valuable tool for researchers in systems and synthetic biology.
  • Accurate prediction of translation initiation rates facilitates metabolic engineering and optimization of chemical production in bacteria.