Related Experiment Video
Updated: May 10, 2025
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
3.3K
Expanding kinetoplastid genome annotation through protein structure comparison
Juan Manuel Trinidad-Barnech1,2, José Sotelo-Silveira3,4, Darío Fernández Do Porto5,6
1Laboratorio de Bioinformática, Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, Uruguay.
Plos Pathogens
|April 21, 2025
Summary
A new pipeline, Annotation by Structural Comparisons (ASC), uses protein structure to annotate kinetoplastid proteins. This method successfully identified functions for thousands of previously uncharacterized proteins, enhancing our understanding of these early-divergent eukaryotes.
Area of Science:
- Eukaryotic genomics
- Bioinformatics
- Parasitology
Background:
- Kinetoplastids are early-divergent eukaryotes with growing genomic data.
- Traditional sequence-based homology methods struggle to assign functions to kinetoplastid proteins.
- Advancements in in-silico protein structure prediction offer new annotation possibilities.
Purpose of the Study:
- To develop and apply a protein structure-based homology search pipeline for kinetoplastid protein annotation.
- To improve the functional annotation of kinetoplastid proteomes.
- To identify uncharacterized kinetoplastid proteins with potential biological functions.
Main Methods:
- Development of the Annotation by Structural Comparisons (ASC) pipeline.
- Application of ASC to all kinetoplastid proteins in TriTrypDB.
- Large-scale protein structure comparison and annotation transfer.
Main Results:
- ASC assigned structural similarity to a substantial portion of kinetoplastid proteins, enhancing current annotations.
- Identified structural homologs for 6,700 uncharacterized proteins across 33 kinetoplastid species.
- Detected structural homologs to ubiquitous eukaryotic proteins missed by sequence-based methods.
Conclusions:
- Protein structure-based homology searching is effective for annotating kinetoplastid proteins.
- The Kinetoplastid Annotation by Structural Comparison (KASC) resource provides valuable biological insights.
- Open access to KASC facilitates further research into kinetoplastid biology and function.
More Related Videos
Related Concept Videos
03:36Genome Annotation and Assembly
18.7K
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.
18.7K
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
11.9K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
11.9K
02:54Evolutionary Relationships through Genome Comparisons
5.6K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.6K
01:24Protein Organization
6.0K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
The primary structure of a protein is its amino acid sequence....
6.0K
02:26Conservation of Protein Domains Over Different Proteins
10.6K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.6K
02:15Protein and Protein Structure
77.3K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
A protein's shape is critical to its function. For example, an enzyme...
77.3K