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Microbiol. 15:1361335. doi: 10.3389/fmicb.2024.1361335 Keywords: Sphingobium baderi SC-1, whole-genome sequencing, 3-phenoxybenzoic acid-degrading gene, resting cells, degradation characteristics Author: Qin Li Creator: LaTeX with hyperref package Producer: pdfTeX-1.40.18 CreationDate: Tue Apr 2 13:59:49 2024 CEST ModDate: Tue Apr 2 14:27:54 2024 CEST Custom Metadata: yes Metadata Stream: yes Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 12 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 2654718 bytes Optimized: no PDF version: 1.5 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- ZWOBVU+MinionPro-Regular Type 1 Custom yes yes no 35 0 RCMHFU+MuseoSans-700 Type 1 Custom yes yes no 36 0 OEZRXC+MuseoSans-300 Type 1 Custom yes yes no 37 0 XIZUJH+HelveticaNeueLTStd-Lt Type 1 Custom yes yes no 42 0 ZLJPRI+MuseoSans-300Italic Type 1 Custom yes yes no 43 0 RIZZLZ+MuseoSans-500 Type 1 Custom yes yes no 44 0 SNUQXY+MuseoSans-500Italic Type 1 Custom yes yes no 45 0 TQJWNX+MTSYN Type 1 Builtin yes yes no 55 0 UBAIOX+MuseoSans-700Italic Type 1 Custom yes yes no 56 0 ECBGHR+MinionPro-It Type 1 Custom yes yes no 159 0 QHWLRN+MTGU Type 1 Builtin yes yes no 167 0 MICLTQ+MinionPro-Bold Type 1 Custom yes yes no 224 0 HODWAH+RBLMI Type 1 Builtin yes yes no 306 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2025-04-12 02:41:42 CEST RepresentationInformation: pmc_11026547.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2025-04-11 05:19:09 CEST Size: 2654718 Format: PDF Version: 1.5 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 826 FreeObjects: 3 IncrementalUpdates: 1 DocumentCatalog: PageLayout: SinglePage PageMode: UseOutlines Outlines: Item: Title: Whole-genome sequencing of Sphingobium baderi SC-1 and identification of a crucial 3-phenoxybenzoic acid-degrading gene Children: Item: Title: 1 Introduction Item: Title: 2 Materials and methods Children: Item: Title: 2.1 Microorganisms and vectors Item: Title: 2.2 DNA extraction and whole-genome sequencing Item: Title: 2.3 Bioinformatics analysis and identification of the 3-PBA dioxygenase gene Item: Title: 2.4 Cloning and validation of dioxygenase genes Item: Title: 2.5 Characterizing 3-PBA degradation in resting cells Children: Item: Title: 2.5.1 Time-course degradation of 3-PBA in resting cells Item: Title: 2.5.2 Metabolite identification Item: Title: 2.5.3 The optimum temperature and pH Item: Title: 2.5.4 Temperature and pH stability Item: Title: 2.5.5 The effect of metal ions Item: Title: 2.5.6 The effect of chemical reagents Item: Title: 2.5.7 Determination of substrate tolerance Item: Title: 2.5.8 The effect of cell concentration Item: Title: 2.5.9 Substrate specificity determination Item: Title: 2.6 Data analysis Item: Title: 3 Results Children: Item: Title: 3.1 Bioinformatics analysis of whole-genome sequences Children: Item: Title: 3.1.1 Quality control analysis of DNA and sequencing data Item: Title: 3.1.2 Genome assembly and evaluation results Item: Title: 3.1.3 Genome analysis and genome function annotation Item: Title: 3.2 Screening and validation of dioxygenase genes Item: Title: 3.3 Assessment of 3-PBA degradation activity across distinct cellular states Item: Title: 3.4 Characterizing 3-PBA degradation in resting cells Children: Item: Title: 3.4.1 Time-course degradation and metabolite identification of 3-PBA in resting cells Item: Title: 3.4.2 The optimum temperature and pH Item: Title: 3.4.3 Temperature and pH stability Item: Title: 3.4.4 The effect of metal ions Item: Title: 3.4.5 The effects of chemical reagents Item: Title: 3.4.6 Determination of substrate tolerance Item: Title: 3.4.7 The effect of cell concentration Item: Title: 3.4.8 Substrate specificity determination Item: Title: 4 Discussion Item: Title: 5 Conclusion Item: Title: Data availability statement Item: Title: Author contributions Item: Title: Funding Item: Title: Conflict of interest Item: Title: Publisher's note Item: Title: Supplementary material Item: Title: References Info: Title: Whole-genome sequencing of Sphingobium baderi SC-1 and identification of a crucial 3-phenoxybenzoic acid-degrading gene Author: Qin Li Subject: Li Q, Zhou Q, Chen Y, Hu K, Sarrà M, Li J, Liu A, Zou L and Liu S (2024) Whole-genome sequencing of Sphingobium baderi SC-1 and identification of a crucial 3-phenoxybenzoic acid-degrading gene. Front. 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Front. Microbiol. 15:1361335. doi: 10.3389/fmicb.2024.1361335 Copyright © 2024 Li, Zhou, Chen, Hu, Sarrà, Li, Liu, Zou and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). Qin Li Qiao Zhou Yuan Chen Kaidi Hu Montserrat Sarrà Jianlong Li Aiping Liu Likou Zou Shuliang Liu 2024-04-02T17:29:49+05:30 Sphingobium baderi SC-1 whole-genome sequencing 3-phenoxybenzoic acid-degrading gene resting cells degradation characteristics 2024-04-02T17:29:49+05:30 2024-04-02T17:57:54+05:30 2024-04-02T17:57:54+05:30 LaTeX with hyperref package uuid:59059b1d-7a82-4620-a39b-620a3ea3ea3e uuid:18b2d19e-80d4-42ba-a048-4b52a4de8034 Pages: Page: Sequence: 1 Annotations: Annotation: Subtype: Link Rect: 48, 791, 235, 807 Annotation: Subtype: Link Rect: 433, 798, 514, 807 Annotation: Subtype: Link Rect: 433, 789, 518, 798 Annotation: Subtype: Link Rect: 433, 779, 547, 789 Annotation: Subtype: Link Rect: 48, 704, 126, 721 Annotation: Subtype: Link Rect: 62, 421, 157, 428 Annotation: Subtype: Link Rect: 158, 380, 186, 387 Annotation: Subtype: Link Rect: 48, 371, 84, 378 Annotation: Subtype: Link Rect: 84, 371, 120, 378 Annotation: Subtype: Link Rect: 120, 371, 146, 378 Annotation: 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