Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli
ABSTRACT Prokaryotic Argonaute (pAgo) proteins are guide-dependent nucleases that function in host defense against invaders. Recently, it was shown that TtAgo from Thermus thermophilus also participates in the completion of DNA replication by decatenating chromosomal DNA. Here, we show that two pAgo...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2023-06-01
|
| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.04146-22 |
| _version_ | 1797803430908002304 |
|---|---|
| author | Anna Olina Aleksei Agapov Denis Yudin Dmitry Sutormin Alina Galivondzhyan Anton Kuzmenko Konstantin Severinov Alexei A. Aravin Andrey Kulbachinskiy |
| author_facet | Anna Olina Aleksei Agapov Denis Yudin Dmitry Sutormin Alina Galivondzhyan Anton Kuzmenko Konstantin Severinov Alexei A. Aravin Andrey Kulbachinskiy |
| author_sort | Anna Olina |
| collection | DOAJ |
| description | ABSTRACT Prokaryotic Argonaute (pAgo) proteins are guide-dependent nucleases that function in host defense against invaders. Recently, it was shown that TtAgo from Thermus thermophilus also participates in the completion of DNA replication by decatenating chromosomal DNA. Here, we show that two pAgos from cyanobacteria Synechococcus elongatus (SeAgo) and Limnothrix rosea (LrAgo) are active in heterologous Escherichia coli and aid cell division in the presence of the gyrase inhibitor ciprofloxacin, depending on the host double-strand break repair machinery. Both pAgos are preferentially loaded with small guide DNAs (smDNAs) derived from the sites of replication termination. Ciprofloxacin increases the amounts of smDNAs from the termination region and from the sites of genomic DNA cleavage by gyrase, suggesting that smDNA biogenesis depends on DNA replication and is stimulated by gyrase inhibition. Ciprofloxacin enhances asymmetry in the distribution of smDNAs around Chi sites, indicating that it induces double-strand breaks that serve as a source of smDNA during their processing by RecBCD. While active in E. coli, SeAgo does not protect its native host S. elongatus from ciprofloxacin. These results suggest that pAgo nucleases may help to complete replication of chromosomal DNA by promoting chromosome decatenation or participating in the processing of gyrase cleavage sites, and may switch their functional activities depending on the host species. IMPORTANCE Prokaryotic Argonautes (pAgos) are programmable nucleases with incompletely understood functions in vivo. In contrast to eukaryotic Argonautes, most studied pAgos recognize DNA targets. Recent studies suggested that pAgos can protect bacteria from invader DNA and counteract phage infection and may also have other functions including possible roles in DNA replication, repair, and gene regulation. Here, we have demonstrated that two cyanobacterial pAgos, SeAgo and LrAgo, can assist DNA replication and facilitate cell division in the presence of topoisomerase inhibitors in Escherichia coli. They are specifically loaded with small guide DNAs from the region of replication termination and protect the cells from the action of the gyrase inhibitor ciprofloxacin, suggesting that they help to complete DNA replication and/or repair gyrase-induced breaks. The results show that pAgo proteins may serve as a backup to topoisomerases under conditions unfavorable for DNA replication and may modulate the resistance of host bacterial strains to antibiotics. |
| first_indexed | 2024-03-13T05:20:44Z |
| format | Article |
| id | doaj.art-f2830c1fdacb426db63824c11cae8b08 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-03-13T05:20:44Z |
| publishDate | 2023-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-f2830c1fdacb426db63824c11cae8b082023-06-15T13:18:32ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972023-06-0111310.1128/spectrum.04146-22Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coliAnna Olina0Aleksei Agapov1Denis Yudin2Dmitry Sutormin3Alina Galivondzhyan4Anton Kuzmenko5Konstantin Severinov6Alexei A. Aravin7Andrey Kulbachinskiy8Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, RussiaInstitute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, RussiaInstitute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, RussiaSkolkovo Institute of Science and Technology, Moscow, RussiaSkolkovo Institute of Science and Technology, Moscow, RussiaInstitute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, RussiaWaksman University for Microbiology, Rutgers, New Jersey, USADivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USAInstitute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, RussiaABSTRACT Prokaryotic Argonaute (pAgo) proteins are guide-dependent nucleases that function in host defense against invaders. Recently, it was shown that TtAgo from Thermus thermophilus also participates in the completion of DNA replication by decatenating chromosomal DNA. Here, we show that two pAgos from cyanobacteria Synechococcus elongatus (SeAgo) and Limnothrix rosea (LrAgo) are active in heterologous Escherichia coli and aid cell division in the presence of the gyrase inhibitor ciprofloxacin, depending on the host double-strand break repair machinery. Both pAgos are preferentially loaded with small guide DNAs (smDNAs) derived from the sites of replication termination. Ciprofloxacin increases the amounts of smDNAs from the termination region and from the sites of genomic DNA cleavage by gyrase, suggesting that smDNA biogenesis depends on DNA replication and is stimulated by gyrase inhibition. Ciprofloxacin enhances asymmetry in the distribution of smDNAs around Chi sites, indicating that it induces double-strand breaks that serve as a source of smDNA during their processing by RecBCD. While active in E. coli, SeAgo does not protect its native host S. elongatus from ciprofloxacin. These results suggest that pAgo nucleases may help to complete replication of chromosomal DNA by promoting chromosome decatenation or participating in the processing of gyrase cleavage sites, and may switch their functional activities depending on the host species. IMPORTANCE Prokaryotic Argonautes (pAgos) are programmable nucleases with incompletely understood functions in vivo. In contrast to eukaryotic Argonautes, most studied pAgos recognize DNA targets. Recent studies suggested that pAgos can protect bacteria from invader DNA and counteract phage infection and may also have other functions including possible roles in DNA replication, repair, and gene regulation. Here, we have demonstrated that two cyanobacterial pAgos, SeAgo and LrAgo, can assist DNA replication and facilitate cell division in the presence of topoisomerase inhibitors in Escherichia coli. They are specifically loaded with small guide DNAs from the region of replication termination and protect the cells from the action of the gyrase inhibitor ciprofloxacin, suggesting that they help to complete DNA replication and/or repair gyrase-induced breaks. The results show that pAgo proteins may serve as a backup to topoisomerases under conditions unfavorable for DNA replication and may modulate the resistance of host bacterial strains to antibiotics.https://journals.asm.org/doi/10.1128/spectrum.04146-22prokaryotic ArgonautesgyraseDNA replicationter sitescell divisionDNA gyrase |
| spellingShingle | Anna Olina Aleksei Agapov Denis Yudin Dmitry Sutormin Alina Galivondzhyan Anton Kuzmenko Konstantin Severinov Alexei A. Aravin Andrey Kulbachinskiy Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli Microbiology Spectrum prokaryotic Argonautes gyrase DNA replication ter sites cell division DNA gyrase |
| title | Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli |
| title_full | Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli |
| title_fullStr | Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli |
| title_full_unstemmed | Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli |
| title_short | Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli |
| title_sort | bacterial argonaute proteins aid cell division in the presence of topoisomerase inhibitors in escherichia coli |
| topic | prokaryotic Argonautes gyrase DNA replication ter sites cell division DNA gyrase |
| url | https://journals.asm.org/doi/10.1128/spectrum.04146-22 |
| work_keys_str_mv | AT annaolina bacterialargonauteproteinsaidcelldivisioninthepresenceoftopoisomeraseinhibitorsinescherichiacoli AT alekseiagapov bacterialargonauteproteinsaidcelldivisioninthepresenceoftopoisomeraseinhibitorsinescherichiacoli AT denisyudin bacterialargonauteproteinsaidcelldivisioninthepresenceoftopoisomeraseinhibitorsinescherichiacoli AT dmitrysutormin bacterialargonauteproteinsaidcelldivisioninthepresenceoftopoisomeraseinhibitorsinescherichiacoli AT alinagalivondzhyan bacterialargonauteproteinsaidcelldivisioninthepresenceoftopoisomeraseinhibitorsinescherichiacoli AT antonkuzmenko bacterialargonauteproteinsaidcelldivisioninthepresenceoftopoisomeraseinhibitorsinescherichiacoli AT konstantinseverinov bacterialargonauteproteinsaidcelldivisioninthepresenceoftopoisomeraseinhibitorsinescherichiacoli AT alexeiaaravin bacterialargonauteproteinsaidcelldivisioninthepresenceoftopoisomeraseinhibitorsinescherichiacoli AT andreykulbachinskiy bacterialargonauteproteinsaidcelldivisioninthepresenceoftopoisomeraseinhibitorsinescherichiacoli |