Related Experiment Video

Updated: Aug 9, 2025

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

Evolution of codon and amino acid usage in bacterial protein toxins

Anuj Sharma¹, Shelly Gupta², Karan Paul¹

¹Department of Biochemistry, DAV University, Jalandhar, 144012, India.

Biochemical and Biophysical Research Communications

|February 15, 2023

Abstract:

Toxin proteins are secreted by most pathogens as an integral part of pathogenic mechanism(s). The toxins act by either damaging the host cell membrane (for example, pore-forming toxins and RTX toxins) or by modulation of important cellular pathways (for example, inhibition of protein translation by ribosome-inactivating proteins). The mechanism of action of these toxins provides the pathogen with strategies for adaptation in the unfavorable host environment. Though, secreted by different pathogenic species, the protein toxins seem to share common features that allow the protein to bind to specific molecules and enter the host cell. Earlier studies have suggested role of several events like horizontal gene transfer and insertion-deletion mutations in evolution of protein toxins. The present study involving 125 bacterial protein toxins secreted by 49 pathogenic bacteria focuses on the role and constraints of the bacterial genome on evolution of codon and amino acid usage in respective bacterial protein toxins. We compare the nucleotide composition, codon and dinucleotide usage trends between different classes of bacterial protein toxins and between individual toxins and the parent bacterial genome expressing the toxin(s).

Insights

Bacterial protein toxins evolve under genomic constraints, influencing codon and amino acid usage. This study analyzes toxin evolution across diverse bacterial pathogens, revealing genome-specific adaptation strategies.

Area of Science:

Microbiology
Genomics
Evolutionary Biology

Background:

Pathogenic bacteria secrete toxin proteins crucial for virulence.
Toxins damage host cells or modulate cellular pathways for pathogen survival.
Protein toxins share features enabling host cell binding and entry.

Purpose of the Study:

To investigate the role of bacterial genome constraints on the evolution of codon and amino acid usage in secreted protein toxins.
To compare nucleotide composition, codon usage, and dinucleotide trends among different bacterial toxin classes and their parent genomes.

Main Methods:

Analysis of 125 bacterial protein toxins from 49 pathogenic bacterial species.
Comparative analysis of nucleotide composition and codon usage patterns.
Examination of dinucleotide usage trends.

Main Results:

Significant variations in codon and amino acid usage exist among bacterial protein toxins.
Toxin evolution is influenced by the specific genomic context of the host bacterium.
Nucleotide composition and dinucleotide frequencies show distinct patterns related to toxin function and origin.

Conclusions:

Bacterial genome properties impose selective pressures shaping toxin protein evolution.
Understanding codon usage bias provides insights into toxin adaptation and pathogenicity.
Comparative genomics of toxins and host genomes reveals evolutionary trajectories.

Read full analysis

More Related Videos

Antimicrobial Peptides Produced by Selective Pressure Incorporation of Non-canonical Amino Acids

Antimicrobial Peptides Produced by Selective Pressure Incorporation of Non-canonical Amino Acids

Published on: May 4, 2018

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Published on: August 1, 2016

Related Concept Videos

From DNA to Protein

From DNA to Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...

The Central Dogma

The Central Dogma

tRNA Activation

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...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Leaky Scanning

Leaky Scanning

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...

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

The role of nanoparticles and nanotechnologies in regulating metal(loid) accumulation in rice (Oryza sativa L.) and wheat (Triticum aestivum L.).

Physiology and molecular biology of plants : an international journal of functional plant biology·2026

Forensic Microbiomics and Trace Microbial Evidence: Molecular Innovations for Linking Suspects, Objects, and Environments.

Microorganisms·2026

Mechanochemical three-component radical sulfonamidation enabled by copper catalysis.

Chemical communications (Cambridge, England)·2026

Madhuca longifolia as a Translational Food Biomaterial for Addressing the Triple Burden of Malnutrition.

Foods (Basel, Switzerland)·2026

Sustainable Food Security Through Nanotechnology-Based Seed Priming in Rice and Wheat.

Foods (Basel, Switzerland)·2026

Mechanochemical Electron Donor-Acceptor (EDA)-Complex-Mediated Thioetherification Reaction via Site-Selective C-H Functionalization Using Aryl (DMIX)iodonium Salt.

The Journal of organic chemistry·2026

See all related articles