Loading…
Characterization of argonaute nucleases from mesophilic bacteria Pseudobutyrivibrio ruminis
Mesophilic Argonautes (Agos) from microbial resources have received significant attention due to their potential applications in genome editing and molecular diagnostics. This study characterizes a novel Ago from Pseudobutyrivibrio ruminis ( Pr Ago), which can cleave single-stranded DNA using guide...
Saved in:
| Published in: | Bioresources and bioprocessing 2024-10, Vol.11 (1), p.94-13, Article 94 |
|---|---|
| Main Authors: | , , , , , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that this one cites |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | |
|---|---|
| cites | cdi_FETCH-LOGICAL-c523t-2ade7601e0f5b48a96e0b10bb668bd1c130ba41b7e641bf5a6c6b947eb915aac3 |
| container_end_page | 13 |
| container_issue | 1 |
| container_start_page | 94 |
| container_title | Bioresources and bioprocessing |
| container_volume | 11 |
| creator | Xu, Xiaoyi Yang, Hao Dong, Huarong Li, Xiao Liu, Qian Feng, Yan |
| description | Mesophilic Argonautes (Agos) from microbial resources have received significant attention due to their potential applications in genome editing and molecular diagnostics. This study characterizes a novel Ago from
Pseudobutyrivibrio ruminis
(
Pr
Ago), which can cleave single-stranded DNA using guide DNA (gDNA).
Pr
Ago, functioning as a multi-turnover enzyme, effectively cleaves DNA using 5′-phosphate gDNA, 14–30 nucleotides in length, in the presence of both Mn
2+
and Mg
2+
ions.
Pr
Ago demonstrates DNA cleavage activity over a broad pH range (pH 4–12), with optimal activity at pH 11. As a mesophilic enzyme,
Pr
Ago cleaves efficiently DNA at temperatures ranging from 25 to 65 °C, particularly at 65 °C.
Pr
Ago does not show strong preferences for the 5′-nucleotide in gDNA. It shows high tolerance for single-base mismatches, except at positions 13 and 15 of gDNA. Continuous double-nucleotide mismatches at positions 10–16 of gDNA significantly reduce cleavage activity. Furthermore,
Pr
Ago mediates DNA-guided DNA cleavage of AT-rich double stranded DNA at 65 °C. Additionally, molecular dynamic simulations suggest that interactions between the PAZ domain and different nucleic acids strongly influence cleavage efficiency. These findings expand our understanding of Protokaryotic Agos and their potential applications in biotechnology.
Graphical Abstract |
| doi_str_mv | 10.1186/s40643-024-00797-x |
| format | article |
| fullrecord | <record><control><sourceid>proquest_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_466b35e508f640b7b602330dcba4e1c8</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><doaj_id>oai_doaj_org_article_466b35e508f640b7b602330dcba4e1c8</doaj_id><sourcerecordid>3114011665</sourcerecordid><originalsourceid>FETCH-LOGICAL-c523t-2ade7601e0f5b48a96e0b10bb668bd1c130ba41b7e641bf5a6c6b947eb915aac3</originalsourceid><addsrcrecordid>eNp9kk1v1DAQhiMEolXpH-CAInHhEvDEX9kTQqsClSqVA5w4WGNnsutVEi92UrX8erxNKW0PXGzL88w7nvFbFK-BvQdo1IckmBK8YrWoGNMrXV0_K45ryAfBlXz-4HxUnKa0Y4wBFxyEfFkc8RXXvNH8uPi53mJEN1H0v3HyYSxDV2LchBHnicpxdj1holR2MQzlQCnst773rrRLEpbfEs1tsPN0E_2Vt9GHMs6DH316VbzosE90erefFD8-n31ff60uLr-crz9dVE7WfKpqbEkrBsQ6aUWDK0XMArNWqca24IAziwKsJpXXTqJyyq6EJrsCiej4SXG-6LYBd2Yf_YDxxgT05vYixI3BOPnciRFKWS5JsqZTglltFas5Z63LFQhck7U-Llr72Q7UOhqniP0j0ceR0W_NJlwZyJNtGg1Z4d2dQgy_ZkqTGXxy1Pc4UpiT4QBcS8FqmdG3T9BdmOOYZ3WgBANQ6kDVC-ViSClSd_8aYObgBbN4wWQvmFsvmOuc9OZhH_cpf38-A3wBUg6NG4r_av9H9g9vFcIQ</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3114011665</pqid></control><display><type>article</type><title>Characterization of argonaute nucleases from mesophilic bacteria Pseudobutyrivibrio ruminis</title><source>Open Access: PubMed Central</source><source>Springer Nature - SpringerLink Journals - Fully Open Access</source><source>Publicly Available Content (ProQuest)</source><source>Coronavirus Research Database</source><creator>Xu, Xiaoyi ; Yang, Hao ; Dong, Huarong ; Li, Xiao ; Liu, Qian ; Feng, Yan</creator><creatorcontrib>Xu, Xiaoyi ; Yang, Hao ; Dong, Huarong ; Li, Xiao ; Liu, Qian ; Feng, Yan</creatorcontrib><description>Mesophilic Argonautes (Agos) from microbial resources have received significant attention due to their potential applications in genome editing and molecular diagnostics. This study characterizes a novel Ago from
Pseudobutyrivibrio ruminis
(
Pr
Ago), which can cleave single-stranded DNA using guide DNA (gDNA).
Pr
Ago, functioning as a multi-turnover enzyme, effectively cleaves DNA using 5′-phosphate gDNA, 14–30 nucleotides in length, in the presence of both Mn
2+
and Mg
2+
ions.
Pr
Ago demonstrates DNA cleavage activity over a broad pH range (pH 4–12), with optimal activity at pH 11. As a mesophilic enzyme,
Pr
Ago cleaves efficiently DNA at temperatures ranging from 25 to 65 °C, particularly at 65 °C.
Pr
Ago does not show strong preferences for the 5′-nucleotide in gDNA. It shows high tolerance for single-base mismatches, except at positions 13 and 15 of gDNA. Continuous double-nucleotide mismatches at positions 10–16 of gDNA significantly reduce cleavage activity. Furthermore,
Pr
Ago mediates DNA-guided DNA cleavage of AT-rich double stranded DNA at 65 °C. Additionally, molecular dynamic simulations suggest that interactions between the PAZ domain and different nucleic acids strongly influence cleavage efficiency. These findings expand our understanding of Protokaryotic Agos and their potential applications in biotechnology.
Graphical Abstract</description><identifier>ISSN: 2197-4365</identifier><identifier>EISSN: 2197-4365</identifier><identifier>DOI: 10.1186/s40643-024-00797-x</identifier><identifier>PMID: 39373873</identifier><language>eng</language><publisher>Singapore: Springer Nature Singapore</publisher><subject>Biochemical Engineering ; Biotechnology ; Chemistry ; Chemistry and Materials Science ; Cleavage ; Deoxyribonucleic acid ; Discovery and engineering of novel enzymes for synthesis of new moleculars ; DNA ; DNA cleavage ; Endonuclease ; Environmental Engineering/Biotechnology ; Enzymes ; Industrial and Production Engineering ; Magnesium ; Manganese ions ; Mesophilic Argonaute ; Mesophilic bacteria ; Microorganisms ; Molecular dynamics ; Nucleic acids ; Nucleotides ; pH effects ; Prokaryotic Argonaute ; Pseudobutyrivibrio ruminis Argonaute ; Single-stranded DNA</subject><ispartof>Bioresources and bioprocessing, 2024-10, Vol.11 (1), p.94-13, Article 94</ispartof><rights>The Author(s) 2024</rights><rights>2024. The Author(s).</rights><rights>The Author(s) 2024. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>The Author(s) 2024 2024</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c523t-2ade7601e0f5b48a96e0b10bb668bd1c130ba41b7e641bf5a6c6b947eb915aac3</cites><orcidid>0000-0002-2522-2115</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/3114011665/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/3114011665?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,38516,43895,44590,53791,53793,74284,74998</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39373873$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Xu, Xiaoyi</creatorcontrib><creatorcontrib>Yang, Hao</creatorcontrib><creatorcontrib>Dong, Huarong</creatorcontrib><creatorcontrib>Li, Xiao</creatorcontrib><creatorcontrib>Liu, Qian</creatorcontrib><creatorcontrib>Feng, Yan</creatorcontrib><title>Characterization of argonaute nucleases from mesophilic bacteria Pseudobutyrivibrio ruminis</title><title>Bioresources and bioprocessing</title><addtitle>Bioresour. Bioprocess</addtitle><addtitle>Bioresour Bioprocess</addtitle><description>Mesophilic Argonautes (Agos) from microbial resources have received significant attention due to their potential applications in genome editing and molecular diagnostics. This study characterizes a novel Ago from
Pseudobutyrivibrio ruminis
(
Pr
Ago), which can cleave single-stranded DNA using guide DNA (gDNA).
Pr
Ago, functioning as a multi-turnover enzyme, effectively cleaves DNA using 5′-phosphate gDNA, 14–30 nucleotides in length, in the presence of both Mn
2+
and Mg
2+
ions.
Pr
Ago demonstrates DNA cleavage activity over a broad pH range (pH 4–12), with optimal activity at pH 11. As a mesophilic enzyme,
Pr
Ago cleaves efficiently DNA at temperatures ranging from 25 to 65 °C, particularly at 65 °C.
Pr
Ago does not show strong preferences for the 5′-nucleotide in gDNA. It shows high tolerance for single-base mismatches, except at positions 13 and 15 of gDNA. Continuous double-nucleotide mismatches at positions 10–16 of gDNA significantly reduce cleavage activity. Furthermore,
Pr
Ago mediates DNA-guided DNA cleavage of AT-rich double stranded DNA at 65 °C. Additionally, molecular dynamic simulations suggest that interactions between the PAZ domain and different nucleic acids strongly influence cleavage efficiency. These findings expand our understanding of Protokaryotic Agos and their potential applications in biotechnology.
Graphical Abstract</description><subject>Biochemical Engineering</subject><subject>Biotechnology</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Cleavage</subject><subject>Deoxyribonucleic acid</subject><subject>Discovery and engineering of novel enzymes for synthesis of new moleculars</subject><subject>DNA</subject><subject>DNA cleavage</subject><subject>Endonuclease</subject><subject>Environmental Engineering/Biotechnology</subject><subject>Enzymes</subject><subject>Industrial and Production Engineering</subject><subject>Magnesium</subject><subject>Manganese ions</subject><subject>Mesophilic Argonaute</subject><subject>Mesophilic bacteria</subject><subject>Microorganisms</subject><subject>Molecular dynamics</subject><subject>Nucleic acids</subject><subject>Nucleotides</subject><subject>pH effects</subject><subject>Prokaryotic Argonaute</subject><subject>Pseudobutyrivibrio ruminis Argonaute</subject><subject>Single-stranded DNA</subject><issn>2197-4365</issn><issn>2197-4365</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>COVID</sourceid><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNp9kk1v1DAQhiMEolXpH-CAInHhEvDEX9kTQqsClSqVA5w4WGNnsutVEi92UrX8erxNKW0PXGzL88w7nvFbFK-BvQdo1IckmBK8YrWoGNMrXV0_K45ryAfBlXz-4HxUnKa0Y4wBFxyEfFkc8RXXvNH8uPi53mJEN1H0v3HyYSxDV2LchBHnicpxdj1holR2MQzlQCnst773rrRLEpbfEs1tsPN0E_2Vt9GHMs6DH316VbzosE90erefFD8-n31ff60uLr-crz9dVE7WfKpqbEkrBsQ6aUWDK0XMArNWqca24IAziwKsJpXXTqJyyq6EJrsCiej4SXG-6LYBd2Yf_YDxxgT05vYixI3BOPnciRFKWS5JsqZTglltFas5Z63LFQhck7U-Llr72Q7UOhqniP0j0ceR0W_NJlwZyJNtGg1Z4d2dQgy_ZkqTGXxy1Pc4UpiT4QBcS8FqmdG3T9BdmOOYZ3WgBANQ6kDVC-ViSClSd_8aYObgBbN4wWQvmFsvmOuc9OZhH_cpf38-A3wBUg6NG4r_av9H9g9vFcIQ</recordid><startdate>20241007</startdate><enddate>20241007</enddate><creator>Xu, Xiaoyi</creator><creator>Yang, Hao</creator><creator>Dong, Huarong</creator><creator>Li, Xiao</creator><creator>Liu, Qian</creator><creator>Feng, Yan</creator><general>Springer Nature Singapore</general><general>Springer Nature B.V</general><general>SpringerOpen</general><scope>C6C</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>COVID</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>L6V</scope><scope>LK8</scope><scope>M7P</scope><scope>M7S</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-2522-2115</orcidid></search><sort><creationdate>20241007</creationdate><title>Characterization of argonaute nucleases from mesophilic bacteria Pseudobutyrivibrio ruminis</title><author>Xu, Xiaoyi ; Yang, Hao ; Dong, Huarong ; Li, Xiao ; Liu, Qian ; Feng, Yan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c523t-2ade7601e0f5b48a96e0b10bb668bd1c130ba41b7e641bf5a6c6b947eb915aac3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Biochemical Engineering</topic><topic>Biotechnology</topic><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Cleavage</topic><topic>Deoxyribonucleic acid</topic><topic>Discovery and engineering of novel enzymes for synthesis of new moleculars</topic><topic>DNA</topic><topic>DNA cleavage</topic><topic>Endonuclease</topic><topic>Environmental Engineering/Biotechnology</topic><topic>Enzymes</topic><topic>Industrial and Production Engineering</topic><topic>Magnesium</topic><topic>Manganese ions</topic><topic>Mesophilic Argonaute</topic><topic>Mesophilic bacteria</topic><topic>Microorganisms</topic><topic>Molecular dynamics</topic><topic>Nucleic acids</topic><topic>Nucleotides</topic><topic>pH effects</topic><topic>Prokaryotic Argonaute</topic><topic>Pseudobutyrivibrio ruminis Argonaute</topic><topic>Single-stranded DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Xu, Xiaoyi</creatorcontrib><creatorcontrib>Yang, Hao</creatorcontrib><creatorcontrib>Dong, Huarong</creatorcontrib><creatorcontrib>Li, Xiao</creatorcontrib><creatorcontrib>Liu, Qian</creatorcontrib><creatorcontrib>Feng, Yan</creatorcontrib><collection>SpringerOpen</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>Coronavirus Research Database</collection><collection>ProQuest Central</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection (Proquest) (PQ_SDU_P3)</collection><collection>ProQuest Engineering Collection</collection><collection>Biological Sciences</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Publicly Available Content (ProQuest)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Directory of Open Access Journals</collection><jtitle>Bioresources and bioprocessing</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Xu, Xiaoyi</au><au>Yang, Hao</au><au>Dong, Huarong</au><au>Li, Xiao</au><au>Liu, Qian</au><au>Feng, Yan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characterization of argonaute nucleases from mesophilic bacteria Pseudobutyrivibrio ruminis</atitle><jtitle>Bioresources and bioprocessing</jtitle><stitle>Bioresour. Bioprocess</stitle><addtitle>Bioresour Bioprocess</addtitle><date>2024-10-07</date><risdate>2024</risdate><volume>11</volume><issue>1</issue><spage>94</spage><epage>13</epage><pages>94-13</pages><artnum>94</artnum><issn>2197-4365</issn><eissn>2197-4365</eissn><abstract>Mesophilic Argonautes (Agos) from microbial resources have received significant attention due to their potential applications in genome editing and molecular diagnostics. This study characterizes a novel Ago from
Pseudobutyrivibrio ruminis
(
Pr
Ago), which can cleave single-stranded DNA using guide DNA (gDNA).
Pr
Ago, functioning as a multi-turnover enzyme, effectively cleaves DNA using 5′-phosphate gDNA, 14–30 nucleotides in length, in the presence of both Mn
2+
and Mg
2+
ions.
Pr
Ago demonstrates DNA cleavage activity over a broad pH range (pH 4–12), with optimal activity at pH 11. As a mesophilic enzyme,
Pr
Ago cleaves efficiently DNA at temperatures ranging from 25 to 65 °C, particularly at 65 °C.
Pr
Ago does not show strong preferences for the 5′-nucleotide in gDNA. It shows high tolerance for single-base mismatches, except at positions 13 and 15 of gDNA. Continuous double-nucleotide mismatches at positions 10–16 of gDNA significantly reduce cleavage activity. Furthermore,
Pr
Ago mediates DNA-guided DNA cleavage of AT-rich double stranded DNA at 65 °C. Additionally, molecular dynamic simulations suggest that interactions between the PAZ domain and different nucleic acids strongly influence cleavage efficiency. These findings expand our understanding of Protokaryotic Agos and their potential applications in biotechnology.
Graphical Abstract</abstract><cop>Singapore</cop><pub>Springer Nature Singapore</pub><pmid>39373873</pmid><doi>10.1186/s40643-024-00797-x</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0002-2522-2115</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 2197-4365 |
| ispartof | Bioresources and bioprocessing, 2024-10, Vol.11 (1), p.94-13, Article 94 |
| issn | 2197-4365 2197-4365 |
| language | eng |
| recordid | cdi_doaj_primary_oai_doaj_org_article_466b35e508f640b7b602330dcba4e1c8 |
| source | Open Access: PubMed Central; Springer Nature - SpringerLink Journals - Fully Open Access; Publicly Available Content (ProQuest); Coronavirus Research Database |
| subjects | Biochemical Engineering Biotechnology Chemistry Chemistry and Materials Science Cleavage Deoxyribonucleic acid Discovery and engineering of novel enzymes for synthesis of new moleculars DNA DNA cleavage Endonuclease Environmental Engineering/Biotechnology Enzymes Industrial and Production Engineering Magnesium Manganese ions Mesophilic Argonaute Mesophilic bacteria Microorganisms Molecular dynamics Nucleic acids Nucleotides pH effects Prokaryotic Argonaute Pseudobutyrivibrio ruminis Argonaute Single-stranded DNA |
| title | Characterization of argonaute nucleases from mesophilic bacteria Pseudobutyrivibrio ruminis |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-07T21%3A28%3A35IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Characterization%20of%20argonaute%20nucleases%20from%20mesophilic%20bacteria%20Pseudobutyrivibrio%20ruminis&rft.jtitle=Bioresources%20and%20bioprocessing&rft.au=Xu,%20Xiaoyi&rft.date=2024-10-07&rft.volume=11&rft.issue=1&rft.spage=94&rft.epage=13&rft.pages=94-13&rft.artnum=94&rft.issn=2197-4365&rft.eissn=2197-4365&rft_id=info:doi/10.1186/s40643-024-00797-x&rft_dat=%3Cproquest_doaj_%3E3114011665%3C/proquest_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c523t-2ade7601e0f5b48a96e0b10bb668bd1c130ba41b7e641bf5a6c6b947eb915aac3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=3114011665&rft_id=info:pmid/39373873&rfr_iscdi=true |