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

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Inorganic Nitrogen Assimilation01:22

Inorganic Nitrogen Assimilation

Nitrogen is an essential element in biological systems, forming a crucial component of proteins, nucleic acids, and other cellular constituents. Many bacteria and archaea acquire nitrogen in the form of nitrate (NO₃⁻) or ammonia (NH₃), which are then assimilated into biomolecules through specific enzymatic pathways.Assimilatory Nitrate ReductionWhen nitrate enters the cell, it undergoes a two-step reduction process known as assimilatory nitrate reduction. Initially, the enzyme nitrate reductase...
Coordination of Gene Expression Processes in Bacteria01:29

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...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
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...

You might also read

Related Articles

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

Sort by
Same author

An ATAC-seq atlas of chromatin accessibility in mouse tissues.

Scientific data·2019
Same author

Spatially Resolved Electric-Field Manipulation of Magnetism for CoFeB Mesoscopic Discs on Ferroelectrics.

Advanced functional materials·2019
Same author

Rapid Method for Detection of <i>Staphylococcus aureus</i> in Feces.

Journal of biomedical nanotechnology·2019
Same author

Angiotensin II triggers autophagy and apoptosis in PC12 cell line: An in vitro Alzheimer's disease model.

Brain research·2019
Same author

Taylor's power law and its decomposition in urban facilities.

Royal Society open science·2019
Same author

Silane Cross-Linked Sulfonted Poly(Ether Ketone/Ether Benzimidazole)s for Fuel Cell Applications.

Polymers·2019

Related Experiment Video

Updated: May 11, 2026

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

Analysis of synonymous codon usage patterns in the genus Rhizobium.

Xinxin Wang1, Liang Wu, Ping Zhou

  • 1School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, People's Republic of China, wangxx200899@yahoo.com.

World Journal of Microbiology & Biotechnology
|May 9, 2013
PubMed
Summary

Rhizobium genomes exhibit conserved codon usage patterns, influenced by selection pressure and gene expression levels. The study identifies specific codon preferences, particularly for cysteine, as a conserved feature across this bacterial genus.

More Related Videos

Single-plant, Sterile Microcosms for Nodulation and Growth of the Legume Plant Medicago truncatula with the Rhizobial Symbiont Sinorhizobium meliloti
20:01

Single-plant, Sterile Microcosms for Nodulation and Growth of the Legume Plant Medicago truncatula with the Rhizobial Symbiont Sinorhizobium meliloti

Published on: October 1, 2013

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
12:05

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

Published on: August 7, 2021

Related Experiment Videos

Last Updated: May 11, 2026

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

Single-plant, Sterile Microcosms for Nodulation and Growth of the Legume Plant Medicago truncatula with the Rhizobial Symbiont Sinorhizobium meliloti
20:01

Single-plant, Sterile Microcosms for Nodulation and Growth of the Legume Plant Medicago truncatula with the Rhizobial Symbiont Sinorhizobium meliloti

Published on: October 1, 2013

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
12:05

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

Published on: August 7, 2021

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Codon usage patterns are crucial for understanding microbial gene expression.
  • Limited data exists on conserved codon usage within specific rhizobial genera.
  • Rhizobia are vital nitrogen-fixing bacteria with significant ecological roles.

Purpose of the Study:

  • To analyze conserved codon usage patterns in the genus Rhizobium.
  • To identify factors shaping codon usage in Rhizobium genomes.
  • To establish a baseline for comparative genomic studies of rhizobial codon bias.

Main Methods:

  • Analysis of complete genome sequences from six Rhizobium strains.
  • Application of relative neutrality plots to assess selection pressure.
  • Utilized Spearman's rank correlation and Correspondence Analysis (COA).
  • Calculated codon adaptation index (CAI) and effective number of codons (ENC).

Main Results:

  • Selection pressure significantly influences codon usage in Rhizobium.
  • Gene expression level and ENC are key drivers of codon usage patterns.
  • Relative synonymous codon usage of cysteine codons is a conserved feature.
  • Twenty unique preferred codons are shared across Rhizobium genomes, indicating conservation.

Conclusions:

  • Codon usage in Rhizobium is shaped by both selection and gene expression.
  • Cysteine codon usage and a set of 20 preferred codons represent conserved features of the genus.
  • This study provides the first comprehensive analysis of codon usage patterns in the genus Rhizobium.