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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
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...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Conserved Binding Sites01:49

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 analyses the...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...

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Related Experiment Video

Updated: May 24, 2026

Protein Extract Preparation and Co-immunoprecipitation from Caenorhabditis elegans
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Structural evolution and functional diversification analyses of argonaute protein.

Kai-Fa Wei1, Ling-Juan Wu, Juan Chen

  • 1Department of Biological Sciences and Biotechnology, Zhangzhou Normal University, Zhangzhou 363000, Fujian, China. kaifa-wei@163.com

Journal of Cellular Biochemistry
|March 15, 2012
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Summary

Argonaute (AGO) proteins bind small RNAs to regulate gene expression. Evolutionary analysis reveals gene duplication and horizontal gene transfer drive AGO protein diversity and function across species.

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)
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Published on: July 10, 2019

Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genomics

Background:

  • Argonaute (AGO) proteins are central to RNA silencing pathways, binding small RNAs to guide target recognition.
  • Understanding AGO protein evolution is crucial for deciphering gene regulation and host defense mechanisms.

Purpose of the Study:

  • To analyze the evolutionary trajectory and functional diversification of Argonaute (AGO) proteins across diverse species.
  • To identify key evolutionary events and structural features shaping AGO protein function.

Main Methods:

  • Comparative analysis of 135 full-length AGO protein sequences from prokaryotes, archaea, and eukaryotes.
  • Structural and functional domain analysis, including PAZ and PIWI domains.
  • Investigation of nucleotide-binding sites and interactions with small RNAs.

Main Results:

  • Bacteria and archaea AGO proteins form a distinct clade; eukaryotes exhibit multiple AGO paralogs, indicating gene duplication and horizontal gene transfer (HGT).
  • The PAZ domain emerged uniquely in AGO protein evolution.
  • Specific residues and interactions within AGO proteins define small RNA binding sites and influence function, with some PIWI domains lacking slicer activity.

Conclusions:

  • AGO gene expansion and HGT are key drivers of adaptability and biodiversity.
  • Evolutionary and functional analyses of AGO proteins are vital for understanding molecular mechanisms of diversification, host defense, and disease.