Pseudomonas pseudoalcaligenes E1205 Genome Harbors Bacterial E3 ubiquitin ligase Homolog: A Bioinformatics Study

Pseudomonas pseudoalcaligenes E1205 Genome Harbors Bacterial E3 ubiquitin ligase Homolog: A Bioinformatics Study | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Pseudomonas pseudoalcaligenes E1205 Genome Harbors Bacterial E3 ubiquitin ligase Homolog: A Bioinformatics Study Kinza Munsif, Muhammad Sufian, Beenish Rafique, Kayinaat Khalid This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3861763/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background Pseudomonas genus is a significant industrial bacteria having wide range of applications. Pseudomonas pseudoalcaligenes (or P. oleovorans ) has applications as bio-implant, bioplastics materials, pharmaceuticals, etc. P. pseudoalcaligenes strain E1205 has a genome size of 5.57 Mb and 5,081 proteins in NCBI database. Its genome harbors many hypothetical proteins and needed to be characterized for their structure and function. Objectives Our research was focused on finding unidentified pathogenicity protein in the P. pseudoalcaligenes genome. Methods Bioinformatics based methods involved in the identification of HP on the basis of sequence similarity were followed by its gene mapping, prediction of family and domain, protein secondary structure, subcellular localization, and transmembrane helices. Results Bacterial E3 ubiquitin ligase family protein (BELs) of P. whenzhouensis (NCBI WP_230925174.1) was the homolog of GIDE (Growth Inhibition and Death E3 Ligase) domain-containing protein, further referred as HP (NCBI WP_119693237.1) of P. oleovorans that shared percent identity of 87.38%. Prediction of secondary structures of both HP and BELs revealed sharing of majority of alpha-helices and beta-sheets, out of which 2 were predicted as transmembrane helices. From CELLO and PSORTb score, it was predicted that the major portion of HP was present in cytoplasm, but still it is considered that HP was membrane-bound. Conclusion The HP of P. pseudoalcaligenes was predicted to be functioning as a BEL (pathogenicity element). Such bacteria when introduced into eukaryotic host cells, the HP will likely to imitate the function of host E3 ubiquitin ligases by ubiquitinating and then degrading a set of targeted proteins. BELs Pseudomonas P. pseudoalcaligenes P. oleovorans Bioinformatics E3 Ubiquitin Ligase Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-3861763","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":267387987,"identity":"f0a45f04-4fab-4b1d-a68b-75b633fc31e4","order_by":0,"name":"Kinza Munsif","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA5ElEQVRIiWNgGAWjYBACCWYYi5nx4QMgxcNHghZmYwOQFjaCWhBMZjMwh6AWyXbewx9+5hzOk29nZqv8mmMnw8bA/PDRDTxapJn5Egx7tx0uNjjMzHZbdlsy0GFsxsY5eLTIMfMYJPBuO5y4gZn/2G3JbcxALTxs0oS0HPwL1DK/mZmtWHJbPWEt0sw8hs0gWxqADmP8uO0wYS2SzTzGzLLb0hM3HGZmlmbcdpyHjZmAXyTOnzH++HabdeL8/sOMH39uq7bnZ29++BifFhTAzAMmiVUOAow/SFE9CkbBKBgFIwYAABtPPo8itrcaAAAAAElFTkSuQmCC","orcid":"","institution":"Mirpur University of Science and Technology (MUST), Mirpur-10250, AJK, Pakistan.","correspondingAuthor":true,"prefix":"","firstName":"Kinza","middleName":"","lastName":"Munsif","suffix":""},{"id":267387988,"identity":"31a66b02-e3f6-418f-b2f8-1ad22e9b2195","order_by":1,"name":"Muhammad Sufian","email":"","orcid":"","institution":"Mirpur University of Science and Technology (MUST), Mirpur-10250, AJK, Pakistan.","correspondingAuthor":false,"prefix":"","firstName":"Muhammad","middleName":"","lastName":"Sufian","suffix":""},{"id":267387989,"identity":"e92f75ba-53ee-4191-9efb-8c34da486150","order_by":2,"name":"Beenish Rafique","email":"","orcid":"","institution":"Mirpur University of Science and Technology (MUST), Mirpur-10250, AJK, Pakistan.","correspondingAuthor":false,"prefix":"","firstName":"Beenish","middleName":"","lastName":"Rafique","suffix":""},{"id":267387991,"identity":"6889d1c1-e33b-44e4-a57e-75ff946becce","order_by":3,"name":"Kayinaat Khalid","email":"","orcid":"","institution":"Mirpur University of Science and Technology (MUST), Mirpur-10250, AJK, Pakistan.","correspondingAuthor":false,"prefix":"","firstName":"Kayinaat","middleName":"","lastName":"Khalid","suffix":""}],"badges":[],"createdAt":"2024-01-14 02:14:10","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3861763/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3861763/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":49839727,"identity":"a6c25ab9-cf44-45b2-8dc6-bbb0f364a15c","added_by":"auto","created_at":"2024-01-18 21:01:09","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":567734,"visible":true,"origin":"","legend":"","description":"","filename":"Pseudomonaspseudoalcaligenes.ABioinformaticsStudy.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3861763/v1_covered_3aa83249-8d31-4a2a-b669-fe6c8f61469c.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Pseudomonas pseudoalcaligenes E1205 Genome Harbors Bacterial E3 ubiquitin ligase Homolog: A Bioinformatics Study","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"BELs, Pseudomonas, P. pseudoalcaligenes, P. oleovorans, Bioinformatics, E3 Ubiquitin Ligase","lastPublishedDoi":"10.21203/rs.3.rs-3861763/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3861763/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003ePseudomonas genus is a significant industrial bacteria having wide range of applications. \u003cem\u003ePseudomonas pseudoalcaligenes\u003c/em\u003e (or \u003cem\u003eP. oleovorans\u003c/em\u003e) has applications as bio-implant, bioplastics materials, pharmaceuticals, etc. \u003cem\u003eP. pseudoalcaligenes\u003c/em\u003e strain E1205 has a genome size of 5.57 Mb and 5,081 proteins in NCBI database. Its genome harbors many hypothetical proteins and needed to be characterized for their structure and function.\u003c/p\u003e\u003ch2\u003eObjectives\u003c/h2\u003e \u003cp\u003eOur research was focused on finding unidentified pathogenicity protein in the \u003cem\u003eP. pseudoalcaligenes\u003c/em\u003e genome.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e \u003cp\u003eBioinformatics based methods involved in the identification of HP on the basis of sequence similarity were followed by its gene mapping, prediction of family and domain, protein secondary structure, subcellular localization, and transmembrane helices.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eBacterial E3 ubiquitin ligase family protein (BELs) of \u003cem\u003eP. whenzhouensis\u003c/em\u003e (NCBI WP_230925174.1) was the homolog of GIDE (Growth Inhibition and Death E3 Ligase) domain-containing protein, further referred as HP (NCBI WP_119693237.1) of \u003cem\u003eP. oleovorans\u003c/em\u003e that shared percent identity of 87.38%. Prediction of secondary structures of both HP and BELs revealed sharing of majority of alpha-helices and beta-sheets, out of which 2 were predicted as transmembrane helices. From CELLO and PSORTb score, it was predicted that the major portion of HP was present in cytoplasm, but still it is considered that HP was membrane-bound.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eThe HP of \u003cem\u003eP. pseudoalcaligenes\u003c/em\u003e was predicted to be functioning as a BEL (pathogenicity element). Such bacteria when introduced into eukaryotic host cells, the HP will likely to imitate the function of host E3 ubiquitin ligases by ubiquitinating and then degrading a set of targeted proteins.\u003c/p\u003e","manuscriptTitle":"Pseudomonas pseudoalcaligenes E1205 Genome Harbors Bacterial E3 ubiquitin ligase Homolog: A Bioinformatics Study","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-01-18 20:36:57","doi":"10.21203/rs.3.rs-3861763/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"ffdbe229-514c-4a1d-b170-2b12c29b964b","owner":[],"postedDate":"January 18th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2024-01-18T20:36:59+00:00","versionOfRecord":[],"versionCreatedAt":"2024-01-18 20:36:57","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-3861763","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3861763","identity":"rs-3861763","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}