Multiplexed fitness profiling by RB-TnSeq elucidates pathways for lignin-related aromatic catabolism in Sphingobium sp. SYK-6

Bleem, Alissa; Kato, Ryo; Kellermyer, Zoe A.; Katahira, Rui; Miyamoto, Masahiro; Niinuma, Koh; Kamimura, Naofumi; Masai, Eiji; Beckham, Gregg T.

doi:10.1016/j.celrep.2023.112847

Multiplexed fitness profiling by RB-TnSeq elucidates pathways for lignin-related aromatic catabolism in Sphingobium sp. SYK-6

Journal Article · Fri Jul 28 00:00:00 EDT 2023 · Cell Reports

DOI:https://doi.org/10.1016/j.celrep.2023.112847· OSTI ID:1995017

Bleem, Alissa ^[1]; Kato, Ryo ^[2]; Kellermyer, Zoe A. ^[1]; Katahira, Rui ^[1]; Miyamoto, Masahiro ^[2]; Niinuma, Koh ^[2]; Kamimura, Naofumi ^[2]; Masai, Eiji ^[2]; ^[1]

National Renewable Energy Laboratory (NREL), Golden, CO (United States)
Nagaoka University of Technology, Niigita (Japan)

Bioconversion of lignin-related aromatic compounds relies on robust catabolic pathways in microbes. Sphingobium sp. SYK-6 (SYK-6) is a well-characterized aromatic catabolic organism that has served as a model for microbial lignin conversion, and its utility as a biocatalyst could potentially be further improved by genome-wide metabolic analyses. To this end, we generate a randomly barcoded transposon insertion mutant (RB-TnSeq) library to study gene function in SYK-6. The library is enriched under dozens of enrichment conditions to quantify gene fitness. Several known aromatic catabolic pathways are confirmed, and RB-TnSeq affords additional detail on the genome-wide effects of each enrichment condition. Selected genes are further examined in SYK-6 or Pseudomonas putida KT2440, leading to the identification of new gene functions. The findings from this study further elucidate the metabolism of SYK-6, while also providing targets for future metabolic engineering in this organism or other hosts for the biological valorization of lignin.

View Accepted Manuscript (DOE)

Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office

Grant/Contract Number:: AC36-08GO28308

OSTI ID:: 1995017

Report Number(s):: NREL/JA-2A00-84889; MainId:85662; UUID:5adb5bf7-9673-4e46-a5e1-9be4a423d52a; MainAdminID:70194

Journal Information:: Cell Reports, Journal Name: Cell Reports Journal Issue: 8 Vol. 42; ISSN 2211-1247

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Characterization of ligV Essential for Catabolism of Vanillin by Sphingomonas paucimobilis SYK-6 Masai, Eiji; Yamamoto, Yuko; Inoue, Tomohiko Bioscience, Biotechnology, and Biochemistry, Vol. 71, Issue 10 https://doi.org/10.1271/bbb.70267	journal	October 2007
Bacterial Transformation of Aromatic Monomers in Softwood Black Liquor Navas, Laura E.; Dexter, Gara; Liu, Jie Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.735000	journal	September 2021
Changes in the genetic requirements for microbial interactions with increasing community complexity Morin, Manon; Pierce, Emily C.; Dutton, Rachel J. eLife, Vol. 7 https://doi.org/10.7554/eLife.37072	journal	September 2018
Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator Jahn, Michael; Crang, Nick; Janasch, Markus eLife, Vol. 10 https://doi.org/10.7554/eLife.69019	journal	November 2021

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