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

tRNA Activation02:26

tRNA Activation

Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
Improving Translational Accuracy02:07

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...

You might also read

Related Articles

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

Sort by
Same author

Network Clustering Approach Reveals Key Proteins and Biological Functions in the Response of Whiteleg Shrimp (Penaeus vannamei) to Acute Hepatopancreatic Necrosis Disease.

Marine biotechnology (New York, N.Y.)·2026
Same author

Graph latent diffusion-based molecular representation learning for enhanced generalization in molecular property prediction.

Journal of cheminformatics·2026
Same author

Self-supervised domain adaptation of protein language model based solely on positive enzyme-reaction pairs.

Computational and structural biotechnology journal·2025
Same author

Relationship between Antiviral Activity against Influenza A Virus Induced by Compound Combinations and Changes in the Physical Properties of Lipid Bilayers.

ACS pharmacology & translational science·2025
Same author

Complete genome sequences of <i>Micrococcus luteus</i> isolated from the radioactive element-containing water in Fukushima Daiichi nuclear power station unit 2.

Microbiology resource announcements·2025
Same author

SLFN11-mediated tRNA regulation induces cell death by disrupting proteostasis in response to DNA-damaging agents.

Nucleic acids research·2025

Related Experiment Video

Updated: Jun 6, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

tRNADB-CE 2011: tRNA gene database curated manually by experts.

Takashi Abe1, Toshimichi Ikemura, Junichi Sugahara

  • 1Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan. takaabe@nagahama-i-bio.ac.jp

Nucleic Acids Research
|November 13, 2010
PubMed
Summary

The updated tRNA database (tRNADB-CE) now includes over 287,000 tRNA genes from diverse genomes and environmental samples. Identical tRNA sequences serve as powerful phylogenetic markers for analyzing microbial community structures.

More Related Videos

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Related Experiment Videos

Last Updated: Jun 6, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

  • Genomics
  • Bioinformatics
  • Microbial Ecology

Background:

  • Transfer RNA (tRNA) genes are essential for protein synthesis and play roles in various cellular processes.
  • Previous tRNA databases lacked comprehensive data from diverse genomic and metagenomic sources.
  • Understanding tRNA diversity is crucial for microbial community analysis.

Purpose of the Study:

  • To update and expand the tRNADB-CE with a significantly larger dataset.
  • To provide tools for analyzing tRNA genes and their phylogenetic utility.
  • To enable detailed clarification of microbial community structures using tRNA markers.

Main Methods:

  • Analysis of 939 prokaryotic and eukaryotic genomes, 171 virus genomes, 121 chloroplast genomes.
  • Inclusion of approximately 230 million sequences from 210 environmental metagenomic samples.
  • Compilation of 287,102 tRNA genes with sequence, structure, and similarity data.

Main Results:

  • The updated tRNADB-CE contains over twice the number of tRNA genes compared to previous versions.
  • High phylogenetic preservation of tRNA sequences was observed, particularly at the phylum level.
  • Identical tRNA sequences from metagenomic data matched those from known prokaryotes, validating their use as markers.

Conclusions:

  • The updated tRNADB-CE is a valuable resource for tRNA research and microbial ecology.
  • Identical tRNA sequence groups are effective phylogenetic markers for ecosystem microbial community analysis.
  • Users can leverage tRNADB-CE to identify phylotype-specific markers and analyze microbial communities.