Structure & Function of Argonaute Protein

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Argonaut proteins are an essential component of the RNA-induced silencing complex (RISC), responsible for RNA silencing — also known as RNA interference (RNAi). 

The protein name is derived from a mutation created in the Argonaute-1 (AGO1) protein of Arabidopsis thaliana. The mutation leads to a mutant phenotype, appearing in the form of pelagic octopus Argonauta argo.

The Arabidopsis has nine other AGO protein family members than AGO1, which include AGO2, AGO3, AGO4, AGO5, AGO6, AGO7, AGO8, AGO9, and AGO10. The AGO 4 protein is essential to mediate siRNA-guided DNA methylation of chromatin.

Apart from plants, argonaute proteins are also ubiquitously expressed in a wide range of other organisms, including the nematode worm Caenorhabditis elegans, the fission yeast Schizosaccharomyces pombe, Drosophila, the zebrafish, the mouse, and the mammalian cells.

In human cells, the Argonaute protein is present in a cluster with Human Ago1, Ago3, and Ago4 genes in one cluster at chromosome 1 and Ago2 (known as human argonaute2 or human AGO2) at chromosome 8, only which has the slicer activity. However, due to the lack of highly sensitive antibodies, immunofluorescence studies on mammalian cells have not been able to clearly detect AGO proteins.

AGO proteins bind to different classes of non-coding RNAs, such as small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi-interacting RNAs (piRNAs) involved in different RNA-led metabolic processes.

Argonaute proteins are guided by small RNAs to their specific targets through base pairing or sequence complementarity. This leads to translational repression or inhibition in eukaryotes, target mRNA cleavage, and the initiation of mRNA decay.

In this article, we will cover the roles of argonaute proteins in transcriptional, translational, and epigenetic processes of organisms, their work mechanism, and their applications in lab workflows. 

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How Does Argonaute Protein Work?

The AGO gene encodes for six domains, which include Linker-1 (L1), Linker-2 (L2), N- terminal (N), PAZ, Mid, and C-terminal PIWI domains. However, the crystal structure of the higher organism is not yet complete, which can dictate the exact structure.

Figure: The X-ray crystal structure of Argonaute proteins and its six domains.
  • The PAZ domain is a target RNA-binding module. It recognizes the nucleic acid 3’ end of a single strand of miRNA, siRNA, and piRNA. The domain contains a characteristic two-nucleotide 3′ overhang resulting from the target digestion of RNA duplex.
  • The PIWI domain structurally resembles the RNase H. It’s required for the cleavage of target RNA. The catalytic activity of the enzyme is facilitated by the active site consisting of the amino acid triad aspartate – aspartate – glutamate, containing divalent ions. 

Some biochemical studies on Arabidopsis thaliana and D. melanogaster have found the domain to work as endonucleases — also referred to as slicer.

The PIWI domain in human argonaute protein also facilitates protein-protein interaction by binding to the dicer enzyme at one of the RNase III domains.

  • The mid domain contains an MC motif that mimics the structure of the cab-binding motif. However, no functions of cap-binding have been observed in the protein.
Figure: An illustration of the mechanism of RNA interference in mammalian cells.

Argonaute Protein Forms

AGO proteins are localized in the cytoplasm. They are mainly concentrated in cytoplasmic processing bodies (P-bodies). However, their localization and distribution can change based on the phosphorylation of the protein. 

The Argonaute protein family can be divided into two major groups:

  • AGO protein subfamily: these proteins are ubiquitously expressed in a wide range of organisms.
  • PIWI protein subfamily: It’s mostly restricted to germline or germ cells. Thye bind to Piwi-interacting proteins (piRNAs) to carry out metabolic processes in organisms.

What is Argonaute Protein Used For?

Argonaute protein has a spectrum of functions in organisms, such as in:

  • miRNA biogenesis
  • Cell differentiation
  • Stem cell maintenance
  • Genome editing with CRISPR/Cas system
  • RNAi pathway
  • Transposon silencing in mouse testes

Additionally, the protein also has a role in fighting diseases, such as cancers linked with mutated endogenous gene sequences. It’s mainly due to their high sequence specificity to RNA sequences.

Gene Expression Regulation

Argonaute proteins have extensive application in gene silencing or gene expression inhibition through the RNA interference pathway. They can either be by destructing target RNA or suppressing protein translation.

The pathway is initiated by DICER, which cleaves RNA duplex into short 20 nucleotide siRNAs. The double-stranded RNA is then separated into two single-strand RNAs, named the guide RNA and the passenger strand. 

The passenger strand is degraded, and the guide RNA is incorporated into the RISC complex, mediating gene silencing activity. The argonaute protein in the RISC complex facilitates the cleavage of the target mRNA sequence.

Figure: An illustration of Argonaute protein roles guided by different RNAs.

What Industries Use Argonaute Protein? 

Argonaute proteins are extensively used in a range of life science labs, such as molecular biology, biochemistry, and plant biology in a myriad of in vitro and in vivo studies.

Pharmaceutical 

Argonaute proteins have been found to be associated with cancer. Especially in cancers like pancreatic cancer, where the elevated expression of a particular gene or selective gene expression is involved, gene silencing is considered to be an effective treatment.

RNA interference is an ancient mechanism to protect organisms from viruses with RNA as their genetic material. Moreover, the role of AGO4 as an effective antiviral strategy is still under study.

Biotechnology

Scientists are studying the potential of prokaryotic Argonaute proteins in genome editing as an artificial restriction enzyme, along with guide RNA. Moreover, Argonaute proteins isolated from Pyrococcus furiosus are used to store data on native DNA sequences. It is done by the mechanism of DNA nicking.

The protein is used in research labs to study gene expression, create mutants, and study the resultant phenotype caused due to mutation.

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Argonaute protein is a protein family playing a central role in gene silencing through RNA interference pathways. The protein is ubiquitously present in most organisms and acts in a sequence-specific manner. 

Structurally, it’s composed of six domains that facilitate its functioning. It includes N-terminal, Linker 1 and 2, PAZ domain, Mid domain, and PIWI domain.

The protein target and bind with the different classes of RNAs, such as Piwi-interacting RNAs (piRNAs), microRNAs (miRNAs), and small interfering RNAs (siRNAs), and mediate processes like mRNA decay or cleavage and translation inhibition.

The main role of Argonaute proteins in RNA destruction makes it a crucial tool in life science and molecular biology lab. It’s involved in a range of workflows, such as gene expression studies, genome editing, and translational studies to understand the roles and working mechanism of genes in organisms’ metabolic processes.

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