Loading…

Computational Analysis of the Tripartite Interaction of Phasins -DNA of IAzospirillum brasilense/I Sp7

Azospirillum brasilense Sp7 produces PHB, which is covered by granule-associated proteins (GAPs). Phasins are the main GAPs. Previous studies have shown phasins can regulate PHB synthesis. When A. brasilense grows under stress conditions, it uses sigma factors to transcribe genes for survival. One o...

Full description

Saved in:
Bibliographic Details
Published in:Polymers 2024-02, Vol.16 (5)
Main Authors: Aguilar-Carrillo, Yovani, Soto-Urzúa, Lucía, Martínez-Martínez, María De Los Ángeles, Becerril-Ramírez, Mirian, Martínez-Morales, Luis Javier
Format: Article
Language:English
Subjects:
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by
cites
container_end_page
container_issue 5
container_start_page
container_title Polymers
container_volume 16
creator Aguilar-Carrillo, Yovani
Soto-Urzúa, Lucía
Martínez-Martínez, María De Los Ángeles
Becerril-Ramírez, Mirian
Martínez-Morales, Luis Javier
description Azospirillum brasilense Sp7 produces PHB, which is covered by granule-associated proteins (GAPs). Phasins are the main GAPs. Previous studies have shown phasins can regulate PHB synthesis. When A. brasilense grows under stress conditions, it uses sigma factors to transcribe genes for survival. One of these factors is the σ[sup.24] factor. This study determined the possible interaction between phasins and the σ[sup.24] factor or phasin-σ[sup.24] factor complex and DNA. Three-dimensional structures of phasins and σ[sup.24] factor structures were predicted using the I-TASSER and SWISS-Model servers, respectively. Subsequently, a molecular docking between phasins and the σ[sup.24] factor was performed using the ClusPro 2.0 server, followed by molecular docking between protein complexes and DNA using the HDOCK server. Evaluation of the types of ligand–receptor interactions was performed using the BIOVIA Discovery Visualizer for three-dimensional diagrams, as well as the LigPlot server to obtain bi-dimensional diagrams. The results showed the phasins (Pha4[sub.Abs7] or Pha5[sub.Abs7] )-σ[sup.24] factor complex was bound near the −35 box of the promoter region of the phaC gene. However, in the individual interaction of PhaP5[sub.Abs7] and the σ[sup.24] factor, with DNA, both proteins were bound to the −35 box. This did not occur with PhaP4[sub.Abs7] , which was bound to the −10 box. This change could affect the transcription level of the phaC gene and possibly affect PHB synthesis.
doi_str_mv 10.3390/polym16050611
format article
fullrecord <record><control><sourceid>gale</sourceid><recordid>TN_cdi_gale_infotracmisc_A786438896</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A786438896</galeid><sourcerecordid>A786438896</sourcerecordid><originalsourceid>FETCH-LOGICAL-g676-ac5965c7a6d0ce60787ae0a20e43d60786e3f123ec80a124b82dcad59b20ef0c3</originalsourceid><addsrcrecordid>eNptTj1rwzAQFaWFhjRjd0FnJ5JlS_Zo0i9DaAv1HmT5lKjIlrGUIf31lWmHDL2Du3u8946H0D0la8ZKshmdPfeUk5xwSq_QIiWCJRnj5PrivkUr779IrCznnIoF0lvXj6cgg3GDtLiK4-yNx07jcATcTGaUUzABcD0EmKSahTP7cZTeDB4nj2_VjOvq2_nRTMbaU4_bKbIWBg-bGn-O4g7daGk9rP72EjXPT832Ndm9v9TbapccuOCJVHnJcyUk74gCTkQhJBCZEshYN0MOTNOUgSqIpGnWFmmnZJeXbZRootgSPfy-PUgLezNoF2Lk3ni1r6I7Y0VR8qha_6OK3UFvlBtAx-iXhh80Emke</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>Computational Analysis of the Tripartite Interaction of Phasins -DNA of IAzospirillum brasilense/I Sp7</title><source>PubMed Central (Open Access)</source><source>Publicly Available Content (ProQuest)</source><creator>Aguilar-Carrillo, Yovani ; Soto-Urzúa, Lucía ; Martínez-Martínez, María De Los Ángeles ; Becerril-Ramírez, Mirian ; Martínez-Morales, Luis Javier</creator><creatorcontrib>Aguilar-Carrillo, Yovani ; Soto-Urzúa, Lucía ; Martínez-Martínez, María De Los Ángeles ; Becerril-Ramírez, Mirian ; Martínez-Morales, Luis Javier</creatorcontrib><description>Azospirillum brasilense Sp7 produces PHB, which is covered by granule-associated proteins (GAPs). Phasins are the main GAPs. Previous studies have shown phasins can regulate PHB synthesis. When A. brasilense grows under stress conditions, it uses sigma factors to transcribe genes for survival. One of these factors is the σ[sup.24] factor. This study determined the possible interaction between phasins and the σ[sup.24] factor or phasin-σ[sup.24] factor complex and DNA. Three-dimensional structures of phasins and σ[sup.24] factor structures were predicted using the I-TASSER and SWISS-Model servers, respectively. Subsequently, a molecular docking between phasins and the σ[sup.24] factor was performed using the ClusPro 2.0 server, followed by molecular docking between protein complexes and DNA using the HDOCK server. Evaluation of the types of ligand–receptor interactions was performed using the BIOVIA Discovery Visualizer for three-dimensional diagrams, as well as the LigPlot server to obtain bi-dimensional diagrams. The results showed the phasins (Pha4[sub.Abs7] or Pha5[sub.Abs7] )-σ[sup.24] factor complex was bound near the −35 box of the promoter region of the phaC gene. However, in the individual interaction of PhaP5[sub.Abs7] and the σ[sup.24] factor, with DNA, both proteins were bound to the −35 box. This did not occur with PhaP4[sub.Abs7] , which was bound to the −10 box. This change could affect the transcription level of the phaC gene and possibly affect PHB synthesis.</description><identifier>ISSN: 2073-4360</identifier><identifier>EISSN: 2073-4360</identifier><identifier>DOI: 10.3390/polym16050611</identifier><language>eng</language><publisher>MDPI AG</publisher><subject>Analysis ; DNA ; Genetic transcription ; Identification and classification ; Polyhydroxyalkanoates ; Properties ; Structure</subject><ispartof>Polymers, 2024-02, Vol.16 (5)</ispartof><rights>COPYRIGHT 2024 MDPI AG</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,777,781,27905,27906</link.rule.ids></links><search><creatorcontrib>Aguilar-Carrillo, Yovani</creatorcontrib><creatorcontrib>Soto-Urzúa, Lucía</creatorcontrib><creatorcontrib>Martínez-Martínez, María De Los Ángeles</creatorcontrib><creatorcontrib>Becerril-Ramírez, Mirian</creatorcontrib><creatorcontrib>Martínez-Morales, Luis Javier</creatorcontrib><title>Computational Analysis of the Tripartite Interaction of Phasins -DNA of IAzospirillum brasilense/I Sp7</title><title>Polymers</title><description>Azospirillum brasilense Sp7 produces PHB, which is covered by granule-associated proteins (GAPs). Phasins are the main GAPs. Previous studies have shown phasins can regulate PHB synthesis. When A. brasilense grows under stress conditions, it uses sigma factors to transcribe genes for survival. One of these factors is the σ[sup.24] factor. This study determined the possible interaction between phasins and the σ[sup.24] factor or phasin-σ[sup.24] factor complex and DNA. Three-dimensional structures of phasins and σ[sup.24] factor structures were predicted using the I-TASSER and SWISS-Model servers, respectively. Subsequently, a molecular docking between phasins and the σ[sup.24] factor was performed using the ClusPro 2.0 server, followed by molecular docking between protein complexes and DNA using the HDOCK server. Evaluation of the types of ligand–receptor interactions was performed using the BIOVIA Discovery Visualizer for three-dimensional diagrams, as well as the LigPlot server to obtain bi-dimensional diagrams. The results showed the phasins (Pha4[sub.Abs7] or Pha5[sub.Abs7] )-σ[sup.24] factor complex was bound near the −35 box of the promoter region of the phaC gene. However, in the individual interaction of PhaP5[sub.Abs7] and the σ[sup.24] factor, with DNA, both proteins were bound to the −35 box. This did not occur with PhaP4[sub.Abs7] , which was bound to the −10 box. This change could affect the transcription level of the phaC gene and possibly affect PHB synthesis.</description><subject>Analysis</subject><subject>DNA</subject><subject>Genetic transcription</subject><subject>Identification and classification</subject><subject>Polyhydroxyalkanoates</subject><subject>Properties</subject><subject>Structure</subject><issn>2073-4360</issn><issn>2073-4360</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid/><recordid>eNptTj1rwzAQFaWFhjRjd0FnJ5JlS_Zo0i9DaAv1HmT5lKjIlrGUIf31lWmHDL2Du3u8946H0D0la8ZKshmdPfeUk5xwSq_QIiWCJRnj5PrivkUr779IrCznnIoF0lvXj6cgg3GDtLiK4-yNx07jcATcTGaUUzABcD0EmKSahTP7cZTeDB4nj2_VjOvq2_nRTMbaU4_bKbIWBg-bGn-O4g7daGk9rP72EjXPT832Ndm9v9TbapccuOCJVHnJcyUk74gCTkQhJBCZEshYN0MOTNOUgSqIpGnWFmmnZJeXbZRootgSPfy-PUgLezNoF2Lk3ni1r6I7Y0VR8qha_6OK3UFvlBtAx-iXhh80Emke</recordid><startdate>20240201</startdate><enddate>20240201</enddate><creator>Aguilar-Carrillo, Yovani</creator><creator>Soto-Urzúa, Lucía</creator><creator>Martínez-Martínez, María De Los Ángeles</creator><creator>Becerril-Ramírez, Mirian</creator><creator>Martínez-Morales, Luis Javier</creator><general>MDPI AG</general><scope/></search><sort><creationdate>20240201</creationdate><title>Computational Analysis of the Tripartite Interaction of Phasins -DNA of IAzospirillum brasilense/I Sp7</title><author>Aguilar-Carrillo, Yovani ; Soto-Urzúa, Lucía ; Martínez-Martínez, María De Los Ángeles ; Becerril-Ramírez, Mirian ; Martínez-Morales, Luis Javier</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-g676-ac5965c7a6d0ce60787ae0a20e43d60786e3f123ec80a124b82dcad59b20ef0c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Analysis</topic><topic>DNA</topic><topic>Genetic transcription</topic><topic>Identification and classification</topic><topic>Polyhydroxyalkanoates</topic><topic>Properties</topic><topic>Structure</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Aguilar-Carrillo, Yovani</creatorcontrib><creatorcontrib>Soto-Urzúa, Lucía</creatorcontrib><creatorcontrib>Martínez-Martínez, María De Los Ángeles</creatorcontrib><creatorcontrib>Becerril-Ramírez, Mirian</creatorcontrib><creatorcontrib>Martínez-Morales, Luis Javier</creatorcontrib><jtitle>Polymers</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Aguilar-Carrillo, Yovani</au><au>Soto-Urzúa, Lucía</au><au>Martínez-Martínez, María De Los Ángeles</au><au>Becerril-Ramírez, Mirian</au><au>Martínez-Morales, Luis Javier</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Computational Analysis of the Tripartite Interaction of Phasins -DNA of IAzospirillum brasilense/I Sp7</atitle><jtitle>Polymers</jtitle><date>2024-02-01</date><risdate>2024</risdate><volume>16</volume><issue>5</issue><issn>2073-4360</issn><eissn>2073-4360</eissn><abstract>Azospirillum brasilense Sp7 produces PHB, which is covered by granule-associated proteins (GAPs). Phasins are the main GAPs. Previous studies have shown phasins can regulate PHB synthesis. When A. brasilense grows under stress conditions, it uses sigma factors to transcribe genes for survival. One of these factors is the σ[sup.24] factor. This study determined the possible interaction between phasins and the σ[sup.24] factor or phasin-σ[sup.24] factor complex and DNA. Three-dimensional structures of phasins and σ[sup.24] factor structures were predicted using the I-TASSER and SWISS-Model servers, respectively. Subsequently, a molecular docking between phasins and the σ[sup.24] factor was performed using the ClusPro 2.0 server, followed by molecular docking between protein complexes and DNA using the HDOCK server. Evaluation of the types of ligand–receptor interactions was performed using the BIOVIA Discovery Visualizer for three-dimensional diagrams, as well as the LigPlot server to obtain bi-dimensional diagrams. The results showed the phasins (Pha4[sub.Abs7] or Pha5[sub.Abs7] )-σ[sup.24] factor complex was bound near the −35 box of the promoter region of the phaC gene. However, in the individual interaction of PhaP5[sub.Abs7] and the σ[sup.24] factor, with DNA, both proteins were bound to the −35 box. This did not occur with PhaP4[sub.Abs7] , which was bound to the −10 box. This change could affect the transcription level of the phaC gene and possibly affect PHB synthesis.</abstract><pub>MDPI AG</pub><doi>10.3390/polym16050611</doi></addata></record>
fulltext fulltext
identifier ISSN: 2073-4360
ispartof Polymers, 2024-02, Vol.16 (5)
issn 2073-4360
2073-4360
language eng
recordid cdi_gale_infotracmisc_A786438896
source PubMed Central (Open Access); Publicly Available Content (ProQuest)
subjects Analysis
DNA
Genetic transcription
Identification and classification
Polyhydroxyalkanoates
Properties
Structure
title Computational Analysis of the Tripartite Interaction of Phasins -DNA of IAzospirillum brasilense/I Sp7
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-17T15%3A11%3A01IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Computational%20Analysis%20of%20the%20Tripartite%20Interaction%20of%20Phasins%20-DNA%20of%20IAzospirillum%20brasilense/I%20Sp7&rft.jtitle=Polymers&rft.au=Aguilar-Carrillo,%20Yovani&rft.date=2024-02-01&rft.volume=16&rft.issue=5&rft.issn=2073-4360&rft.eissn=2073-4360&rft_id=info:doi/10.3390/polym16050611&rft_dat=%3Cgale%3EA786438896%3C/gale%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-g676-ac5965c7a6d0ce60787ae0a20e43d60786e3f123ec80a124b82dcad59b20ef0c3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_id=info:pmid/&rft_galeid=A786438896&rfr_iscdi=true