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A prokaryotic twist on argonaute function.

Willkomm S, Zander A, Gust A, Grohmann D - Life (Basel) (2015)

Bottom Line: Argonaute proteins can be found in all three domains of life.Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic Argonaute proteins, the biological function of bacterial and archaeal Argonautes has remained elusive.We especially focus on archaeal Argonautes when discussing the details of the structural and dynamic features in Argonaute that promote substrate recognition and cleavage, thereby revealing differences and similarities in Argonaute biology.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, University of Lübeck, 23538 Lübeck, Germany. willkomm@imm.uni-luebeck.de.

ABSTRACT
Argonaute proteins can be found in all three domains of life. In eukaryotic organisms, Argonaute is, as the functional core of the RNA-silencing machinery, critically involved in the regulation of gene expression. Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic Argonaute proteins, the biological function of bacterial and archaeal Argonautes has remained elusive. This review discusses new findings in the field that shed light on the structure and function of Argonaute. We especially focus on archaeal Argonautes when discussing the details of the structural and dynamic features in Argonaute that promote substrate recognition and cleavage, thereby revealing differences and similarities in Argonaute biology.

No MeSH data available.


Related in: MedlinePlus

Important structural, functional and dynamic features of Argonaute. Structural elements that are important for Argonaute function are highlighted based on the human Argonaute 2 (hAgo2) structure in complex with a guide (red) and target (blue) strand (PDB: 4W5T). (a) The 5'-end is buried in a binding pocket in the MID domain (orange), where specific interactions with the terminal phosphate of the guide strand and interactions between the protein backbone of the specificity loop (highlighted in purple or orange) contribute to the specific recognition of the first nucleotide (PDB: 3LUD). This interaction network leads to the stable positioning of UTP in hAgo2. In contrast, the Argonaute structure from Pyrococcus furiosus (PfAgo) shows that the specificity loop (orange) is pulled away from the first nucleotide (PDB: 1U04). (b) The PAZ domain (pink) of all Argonaute variants is a mobile element, as revealed by structural, kinetic and single-molecule studies. Shown are the conformational changes (highlighted by a broken arrow) of the PAZ domain between the RNA guide-associated hAgo2 (pink, PDB: 4EI3) and hAgo2 in complex with an RNA guide and an 11-nucleotide RNA target (grey, PDB: 4W5T). The movement of the PAZ domain is more pronounced when comparing the structure of DNA guide-associated Thermus thermophilus Ago (TtAgo, PDB: 3DLH) and the ternary TtAgo complex, which also includes a 19-nucleotide RNA target (PDB: 3HVR). Progression to the ternary complex leads to the release of the 3'-end of the guide from its binding pocket in the PAZ domain. Another flexible element that undergoes a structural change upon ternary complex formation is helix α7 (boxed), which is only found in archaeal-eukaryotic Argonautes. (c) The PIWI domain (green) harbors the active site where the glutamate finger can be found in an “unplugged” or “plugged” conformation (PfAgo in its free state (mint green) with the “unplugged” glutamate finger, PDB: 1U04; cleavage-incompatible ternary TtAgo complex with “unplugged” glutamate finger (PDB: 3F73, corn blue); cleavage-compatible ternary TtAgo complex with “plugged” glutamate finger (PDB: 3DLH, orange); ternary hAgo2 complex with “plugged” glutamate finger (PDB: 4W5T, grey). In the “plugged” conformation, an invariant glutamate sidechain is inserted to complete the tetrad in the catalytic pocket (the broken arrow indicates the relocation of E512).
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life-05-00538-f002: Important structural, functional and dynamic features of Argonaute. Structural elements that are important for Argonaute function are highlighted based on the human Argonaute 2 (hAgo2) structure in complex with a guide (red) and target (blue) strand (PDB: 4W5T). (a) The 5'-end is buried in a binding pocket in the MID domain (orange), where specific interactions with the terminal phosphate of the guide strand and interactions between the protein backbone of the specificity loop (highlighted in purple or orange) contribute to the specific recognition of the first nucleotide (PDB: 3LUD). This interaction network leads to the stable positioning of UTP in hAgo2. In contrast, the Argonaute structure from Pyrococcus furiosus (PfAgo) shows that the specificity loop (orange) is pulled away from the first nucleotide (PDB: 1U04). (b) The PAZ domain (pink) of all Argonaute variants is a mobile element, as revealed by structural, kinetic and single-molecule studies. Shown are the conformational changes (highlighted by a broken arrow) of the PAZ domain between the RNA guide-associated hAgo2 (pink, PDB: 4EI3) and hAgo2 in complex with an RNA guide and an 11-nucleotide RNA target (grey, PDB: 4W5T). The movement of the PAZ domain is more pronounced when comparing the structure of DNA guide-associated Thermus thermophilus Ago (TtAgo, PDB: 3DLH) and the ternary TtAgo complex, which also includes a 19-nucleotide RNA target (PDB: 3HVR). Progression to the ternary complex leads to the release of the 3'-end of the guide from its binding pocket in the PAZ domain. Another flexible element that undergoes a structural change upon ternary complex formation is helix α7 (boxed), which is only found in archaeal-eukaryotic Argonautes. (c) The PIWI domain (green) harbors the active site where the glutamate finger can be found in an “unplugged” or “plugged” conformation (PfAgo in its free state (mint green) with the “unplugged” glutamate finger, PDB: 1U04; cleavage-incompatible ternary TtAgo complex with “unplugged” glutamate finger (PDB: 3F73, corn blue); cleavage-compatible ternary TtAgo complex with “plugged” glutamate finger (PDB: 3DLH, orange); ternary hAgo2 complex with “plugged” glutamate finger (PDB: 4W5T, grey). In the “plugged” conformation, an invariant glutamate sidechain is inserted to complete the tetrad in the catalytic pocket (the broken arrow indicates the relocation of E512).

Mentions: The Argonaute (Ago) protein family was initially discovered in eukaryotes [1,2], but orthologs were found in many archaeal and bacterial organisms [3,4,5]. In eukaryotic organisms, Argonaute represents the principal component of the RNA silencing machinery. Despite the advancements in the understanding of Argonaute function in the eukaryotic field, the biological role of prokaryotic Argonaute proteins (pAgo) remained unknown for a long time. Argonaute proteins are encoded in ~32% and 9% of the sequenced archaeal and bacterial genomes, respectively [6]. PAgos were found to cluster in two groups distinguished by the presence or absence of the PAZ domain [5]. A lack of the PAZ domain often coincides with an apparent inactivation of the nuclease activity [5,6]. Interestingly, pAgos are often found in operons with a diverse range of endonucleolytic DNases (nucleases of the restriction endonuclease fold, a distinctive Sirtuin family domain or TIR domain proteins) and/or helicases (e.g., of the DinG-class) [3,5,7], leading to the hypothesis that the co-action of pAgo and an endo-DNase might act as a plasmid/phage restriction system. However, the subset of pAgos that exhibit a high sequence similarity to their eukaryotic counterpart does not seem to show conserved operonic associations with any other genes. Ago is composed of the N-terminal, PAZ (Piwi-Argonaute-Zwille), middle (MID) and PIWI (P-element-induced wimpy testis) domains interconnected by two structured linker regions (Figure 1 and Figure 2). This review mainly discusses the “long” pAgo variants, which share a comparable domain organization as determined for the eukaryotic Agos. In contrast, short pAgos variants contain the MID and PIWI domain only [5]. Recently, two studies have shed light on the biological role of bacterial Agos [8,9]. Together with our findings on the substrate specificity of an archaeal Ago variant [10], these data point to a paradigm shift in the field, as the spectrum of Argonaute silencing activities now also includes DNA- or RNA-guided DNA interference in prokaryotic organisms.


A prokaryotic twist on argonaute function.

Willkomm S, Zander A, Gust A, Grohmann D - Life (Basel) (2015)

Important structural, functional and dynamic features of Argonaute. Structural elements that are important for Argonaute function are highlighted based on the human Argonaute 2 (hAgo2) structure in complex with a guide (red) and target (blue) strand (PDB: 4W5T). (a) The 5'-end is buried in a binding pocket in the MID domain (orange), where specific interactions with the terminal phosphate of the guide strand and interactions between the protein backbone of the specificity loop (highlighted in purple or orange) contribute to the specific recognition of the first nucleotide (PDB: 3LUD). This interaction network leads to the stable positioning of UTP in hAgo2. In contrast, the Argonaute structure from Pyrococcus furiosus (PfAgo) shows that the specificity loop (orange) is pulled away from the first nucleotide (PDB: 1U04). (b) The PAZ domain (pink) of all Argonaute variants is a mobile element, as revealed by structural, kinetic and single-molecule studies. Shown are the conformational changes (highlighted by a broken arrow) of the PAZ domain between the RNA guide-associated hAgo2 (pink, PDB: 4EI3) and hAgo2 in complex with an RNA guide and an 11-nucleotide RNA target (grey, PDB: 4W5T). The movement of the PAZ domain is more pronounced when comparing the structure of DNA guide-associated Thermus thermophilus Ago (TtAgo, PDB: 3DLH) and the ternary TtAgo complex, which also includes a 19-nucleotide RNA target (PDB: 3HVR). Progression to the ternary complex leads to the release of the 3'-end of the guide from its binding pocket in the PAZ domain. Another flexible element that undergoes a structural change upon ternary complex formation is helix α7 (boxed), which is only found in archaeal-eukaryotic Argonautes. (c) The PIWI domain (green) harbors the active site where the glutamate finger can be found in an “unplugged” or “plugged” conformation (PfAgo in its free state (mint green) with the “unplugged” glutamate finger, PDB: 1U04; cleavage-incompatible ternary TtAgo complex with “unplugged” glutamate finger (PDB: 3F73, corn blue); cleavage-compatible ternary TtAgo complex with “plugged” glutamate finger (PDB: 3DLH, orange); ternary hAgo2 complex with “plugged” glutamate finger (PDB: 4W5T, grey). In the “plugged” conformation, an invariant glutamate sidechain is inserted to complete the tetrad in the catalytic pocket (the broken arrow indicates the relocation of E512).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390867&req=5

life-05-00538-f002: Important structural, functional and dynamic features of Argonaute. Structural elements that are important for Argonaute function are highlighted based on the human Argonaute 2 (hAgo2) structure in complex with a guide (red) and target (blue) strand (PDB: 4W5T). (a) The 5'-end is buried in a binding pocket in the MID domain (orange), where specific interactions with the terminal phosphate of the guide strand and interactions between the protein backbone of the specificity loop (highlighted in purple or orange) contribute to the specific recognition of the first nucleotide (PDB: 3LUD). This interaction network leads to the stable positioning of UTP in hAgo2. In contrast, the Argonaute structure from Pyrococcus furiosus (PfAgo) shows that the specificity loop (orange) is pulled away from the first nucleotide (PDB: 1U04). (b) The PAZ domain (pink) of all Argonaute variants is a mobile element, as revealed by structural, kinetic and single-molecule studies. Shown are the conformational changes (highlighted by a broken arrow) of the PAZ domain between the RNA guide-associated hAgo2 (pink, PDB: 4EI3) and hAgo2 in complex with an RNA guide and an 11-nucleotide RNA target (grey, PDB: 4W5T). The movement of the PAZ domain is more pronounced when comparing the structure of DNA guide-associated Thermus thermophilus Ago (TtAgo, PDB: 3DLH) and the ternary TtAgo complex, which also includes a 19-nucleotide RNA target (PDB: 3HVR). Progression to the ternary complex leads to the release of the 3'-end of the guide from its binding pocket in the PAZ domain. Another flexible element that undergoes a structural change upon ternary complex formation is helix α7 (boxed), which is only found in archaeal-eukaryotic Argonautes. (c) The PIWI domain (green) harbors the active site where the glutamate finger can be found in an “unplugged” or “plugged” conformation (PfAgo in its free state (mint green) with the “unplugged” glutamate finger, PDB: 1U04; cleavage-incompatible ternary TtAgo complex with “unplugged” glutamate finger (PDB: 3F73, corn blue); cleavage-compatible ternary TtAgo complex with “plugged” glutamate finger (PDB: 3DLH, orange); ternary hAgo2 complex with “plugged” glutamate finger (PDB: 4W5T, grey). In the “plugged” conformation, an invariant glutamate sidechain is inserted to complete the tetrad in the catalytic pocket (the broken arrow indicates the relocation of E512).
Mentions: The Argonaute (Ago) protein family was initially discovered in eukaryotes [1,2], but orthologs were found in many archaeal and bacterial organisms [3,4,5]. In eukaryotic organisms, Argonaute represents the principal component of the RNA silencing machinery. Despite the advancements in the understanding of Argonaute function in the eukaryotic field, the biological role of prokaryotic Argonaute proteins (pAgo) remained unknown for a long time. Argonaute proteins are encoded in ~32% and 9% of the sequenced archaeal and bacterial genomes, respectively [6]. PAgos were found to cluster in two groups distinguished by the presence or absence of the PAZ domain [5]. A lack of the PAZ domain often coincides with an apparent inactivation of the nuclease activity [5,6]. Interestingly, pAgos are often found in operons with a diverse range of endonucleolytic DNases (nucleases of the restriction endonuclease fold, a distinctive Sirtuin family domain or TIR domain proteins) and/or helicases (e.g., of the DinG-class) [3,5,7], leading to the hypothesis that the co-action of pAgo and an endo-DNase might act as a plasmid/phage restriction system. However, the subset of pAgos that exhibit a high sequence similarity to their eukaryotic counterpart does not seem to show conserved operonic associations with any other genes. Ago is composed of the N-terminal, PAZ (Piwi-Argonaute-Zwille), middle (MID) and PIWI (P-element-induced wimpy testis) domains interconnected by two structured linker regions (Figure 1 and Figure 2). This review mainly discusses the “long” pAgo variants, which share a comparable domain organization as determined for the eukaryotic Agos. In contrast, short pAgos variants contain the MID and PIWI domain only [5]. Recently, two studies have shed light on the biological role of bacterial Agos [8,9]. Together with our findings on the substrate specificity of an archaeal Ago variant [10], these data point to a paradigm shift in the field, as the spectrum of Argonaute silencing activities now also includes DNA- or RNA-guided DNA interference in prokaryotic organisms.

Bottom Line: Argonaute proteins can be found in all three domains of life.Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic Argonaute proteins, the biological function of bacterial and archaeal Argonautes has remained elusive.We especially focus on archaeal Argonautes when discussing the details of the structural and dynamic features in Argonaute that promote substrate recognition and cleavage, thereby revealing differences and similarities in Argonaute biology.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, University of Lübeck, 23538 Lübeck, Germany. willkomm@imm.uni-luebeck.de.

ABSTRACT
Argonaute proteins can be found in all three domains of life. In eukaryotic organisms, Argonaute is, as the functional core of the RNA-silencing machinery, critically involved in the regulation of gene expression. Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic Argonaute proteins, the biological function of bacterial and archaeal Argonautes has remained elusive. This review discusses new findings in the field that shed light on the structure and function of Argonaute. We especially focus on archaeal Argonautes when discussing the details of the structural and dynamic features in Argonaute that promote substrate recognition and cleavage, thereby revealing differences and similarities in Argonaute biology.

No MeSH data available.


Related in: MedlinePlus