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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.


Putative mechanisms of bacterial Ago-mediated silencing pathways. (I) Guide sequences of Thermus thermophilus Ago (TtAgo) and Rhodobacter sphaeroides Ago (RsAgo) are derived from plasmid DNA or RNA transcripts, respectively. (II) TtAgo is loaded with a 13–25-nt guide DNA and RsAgo with a 15–19-nt guide RNA. (III) The target substrates are (a) ssRNA, (b) negatively-supercoiled plasmid DNA and (c) ssDNAs in the case of TtAgo. RsAgo binds plasmid DNA, which will be cleaved, yielding 22–24-nt DNA fragments. Binding of the guide-Ago complex to plasmid DNA furthermore possibly leads to an inhibition of plasmid transcription. The short fragments either stay bound to Argonaute (d) or interact with other RsAgo molecules to constitute DNA-RsAgo complexes and regulate plasmid transcription (e). Figure in part modified from Olovnikov et al. [8].
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life-05-00538-f003: Putative mechanisms of bacterial Ago-mediated silencing pathways. (I) Guide sequences of Thermus thermophilus Ago (TtAgo) and Rhodobacter sphaeroides Ago (RsAgo) are derived from plasmid DNA or RNA transcripts, respectively. (II) TtAgo is loaded with a 13–25-nt guide DNA and RsAgo with a 15–19-nt guide RNA. (III) The target substrates are (a) ssRNA, (b) negatively-supercoiled plasmid DNA and (c) ssDNAs in the case of TtAgo. RsAgo binds plasmid DNA, which will be cleaved, yielding 22–24-nt DNA fragments. Binding of the guide-Ago complex to plasmid DNA furthermore possibly leads to an inhibition of plasmid transcription. The short fragments either stay bound to Argonaute (d) or interact with other RsAgo molecules to constitute DNA-RsAgo complexes and regulate plasmid transcription (e). Figure in part modified from Olovnikov et al. [8].

Mentions: Despite the mechanistic and structural similarities between the archaeal, prokaryotic and eukaryotic Argonaute proteins, a major difference in the fundamental mechanism of silencing was revealed recently. Bacterial Argonautes use either DNA or RNA guide strands to silence complementary DNA strands (Figure 3). In native cells Argonaute from the alphaproteobacterium Rhodobacter sphaeroides (RsAgo) is associated with small RNAs and DNAs [8]. Interestingly, RsAgo belongs to the Ago class with an inactivated catalytic tetrad. However, RsAgo is encoded in an operon with a predicted DNA nuclease. The small RNAs are derived from mRNA precursors that can be mapped to the majority of cellular transcripts and most likely are generated from mRNA degradation products. DNAs associated with RsAgo are largely complementary to the bound RNAs. A current model for the generation of RNA-interacting DNAs (riDNA) proposes that the small RNA directs RsAgo to the complementary DNA target followed by the nucleolytic cleavage of the DNA by a yet unidentified nuclease. Alternatively, RsAgo-RNA complexes loaded onto a complementary stretch of DNA inhibit RNA polymerase loading or block RNA polymerase elongation, leading to transcriptional repression of the target DNA. The enrichment of riDNA for foreign sequences, like plasmid DNA and transposons, suggests that the RsAgo-mediated DNA silencing mechanism is in place to destroy foreign genetic elements. However, the molecular mechanisms that allow the discrimination between self and foreign DNA are not known. Another example of bacterial Ago-mediated DNA silencing was described for TtAgo. Expression of TtAgo in E. coli and subsequent characterization of TtAgo-bound nucleic acids revealed that TtAgo associates primarily with DNA sequences (small interfering DNAs) preferentially derived from its own expression plasmid [9]. The underlying mechanism for DNA guide processing from foreign DNA (e.g., plasmids) has not been deciphered yet. However, loading of TtAgo with guide DNA and subsequent cleavage of target DNA is only observed if the catalytic center of the enzyme is intact, indicating that the nuclease activity of TtAgo is required for guide processing. Even though the experimental characterization of TtAgo in vivo was mainly carried out using plasmid DNA, it is feasible that the DNA-guided DNA silencing mechanism targets replication intermediates from invading genetic elements and DNA taken up by the natural competence system present in Thermus thermophilus. The functional role of archaeal Argonaute still remains elusive. However, in vitro studies showed that MjAgo exclusively cleaves DNA targets when using a DNA guide [10], suggesting that this archaeal Argonaute variant, like the bacterial counterparts, is involved in DNA silencing processes.


A prokaryotic twist on argonaute function.

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

Putative mechanisms of bacterial Ago-mediated silencing pathways. (I) Guide sequences of Thermus thermophilus Ago (TtAgo) and Rhodobacter sphaeroides Ago (RsAgo) are derived from plasmid DNA or RNA transcripts, respectively. (II) TtAgo is loaded with a 13–25-nt guide DNA and RsAgo with a 15–19-nt guide RNA. (III) The target substrates are (a) ssRNA, (b) negatively-supercoiled plasmid DNA and (c) ssDNAs in the case of TtAgo. RsAgo binds plasmid DNA, which will be cleaved, yielding 22–24-nt DNA fragments. Binding of the guide-Ago complex to plasmid DNA furthermore possibly leads to an inhibition of plasmid transcription. The short fragments either stay bound to Argonaute (d) or interact with other RsAgo molecules to constitute DNA-RsAgo complexes and regulate plasmid transcription (e). Figure in part modified from Olovnikov et al. [8].
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Related In: Results  -  Collection

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

life-05-00538-f003: Putative mechanisms of bacterial Ago-mediated silencing pathways. (I) Guide sequences of Thermus thermophilus Ago (TtAgo) and Rhodobacter sphaeroides Ago (RsAgo) are derived from plasmid DNA or RNA transcripts, respectively. (II) TtAgo is loaded with a 13–25-nt guide DNA and RsAgo with a 15–19-nt guide RNA. (III) The target substrates are (a) ssRNA, (b) negatively-supercoiled plasmid DNA and (c) ssDNAs in the case of TtAgo. RsAgo binds plasmid DNA, which will be cleaved, yielding 22–24-nt DNA fragments. Binding of the guide-Ago complex to plasmid DNA furthermore possibly leads to an inhibition of plasmid transcription. The short fragments either stay bound to Argonaute (d) or interact with other RsAgo molecules to constitute DNA-RsAgo complexes and regulate plasmid transcription (e). Figure in part modified from Olovnikov et al. [8].
Mentions: Despite the mechanistic and structural similarities between the archaeal, prokaryotic and eukaryotic Argonaute proteins, a major difference in the fundamental mechanism of silencing was revealed recently. Bacterial Argonautes use either DNA or RNA guide strands to silence complementary DNA strands (Figure 3). In native cells Argonaute from the alphaproteobacterium Rhodobacter sphaeroides (RsAgo) is associated with small RNAs and DNAs [8]. Interestingly, RsAgo belongs to the Ago class with an inactivated catalytic tetrad. However, RsAgo is encoded in an operon with a predicted DNA nuclease. The small RNAs are derived from mRNA precursors that can be mapped to the majority of cellular transcripts and most likely are generated from mRNA degradation products. DNAs associated with RsAgo are largely complementary to the bound RNAs. A current model for the generation of RNA-interacting DNAs (riDNA) proposes that the small RNA directs RsAgo to the complementary DNA target followed by the nucleolytic cleavage of the DNA by a yet unidentified nuclease. Alternatively, RsAgo-RNA complexes loaded onto a complementary stretch of DNA inhibit RNA polymerase loading or block RNA polymerase elongation, leading to transcriptional repression of the target DNA. The enrichment of riDNA for foreign sequences, like plasmid DNA and transposons, suggests that the RsAgo-mediated DNA silencing mechanism is in place to destroy foreign genetic elements. However, the molecular mechanisms that allow the discrimination between self and foreign DNA are not known. Another example of bacterial Ago-mediated DNA silencing was described for TtAgo. Expression of TtAgo in E. coli and subsequent characterization of TtAgo-bound nucleic acids revealed that TtAgo associates primarily with DNA sequences (small interfering DNAs) preferentially derived from its own expression plasmid [9]. The underlying mechanism for DNA guide processing from foreign DNA (e.g., plasmids) has not been deciphered yet. However, loading of TtAgo with guide DNA and subsequent cleavage of target DNA is only observed if the catalytic center of the enzyme is intact, indicating that the nuclease activity of TtAgo is required for guide processing. Even though the experimental characterization of TtAgo in vivo was mainly carried out using plasmid DNA, it is feasible that the DNA-guided DNA silencing mechanism targets replication intermediates from invading genetic elements and DNA taken up by the natural competence system present in Thermus thermophilus. The functional role of archaeal Argonaute still remains elusive. However, in vitro studies showed that MjAgo exclusively cleaves DNA targets when using a DNA guide [10], suggesting that this archaeal Argonaute variant, like the bacterial counterparts, is involved in DNA silencing processes.

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.