Multiplexed Fitness Profiling by RB-TnSeq Elucidates Pathways for Lignin-Related Aromatic Catabolism in Sphingobium sp. SYK-6: Article No. 112847

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

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: Article No. 112847

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

Nagaoka University of Technology

Research output: Contribution to journal › Article › peer-review

12 Scopus Citations

Abstract

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.

Original language	American English
Number of pages	20
Journal	Cell Reports
Volume	42
Issue number	8
DOIs	https://doi.org/10.1016/j.celrep.2023.112847
State	Published - 2023

NREL Publication Number

NREL/JA-2A00-84889

Keywords

acid tolerance
aromatic catabolism
bacterial genetics
lignin
Pseudomonas putida
Sphingobium sp. SYK-6
transposon insertion sequencing

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10.1016/j.celrep.2023.112847

https://www.nrel.gov/docs/fy23osti/84889.pdf

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title = "Multiplexed Fitness Profiling by RB-TnSeq Elucidates Pathways for Lignin-Related Aromatic Catabolism in Sphingobium sp. SYK-6: Article No. 112847",

abstract = "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.",

keywords = "acid tolerance, aromatic catabolism, bacterial genetics, lignin, Pseudomonas putida, Sphingobium sp. SYK-6, transposon insertion sequencing",

author = "Alissa Bleem and Ryo Kato and Zoe Kellermyer and Rui Katahira and Masahiro Miyamoto and Koh Niinuma and Naofumi Kamimura and Eiji Masai and Gregg Beckham",

year = "2023",

doi = "10.1016/j.celrep.2023.112847",

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volume = "42",

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AU - Bleem, Alissa

AU - Kato, Ryo

AU - Kellermyer, Zoe

AU - Katahira, Rui

AU - Miyamoto, Masahiro

AU - Niinuma, Koh

AU - Kamimura, Naofumi

AU - Masai, Eiji

AU - Beckham, Gregg

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

KW - acid tolerance

KW - aromatic catabolism

KW - bacterial genetics

KW - lignin

KW - Pseudomonas putida

KW - Sphingobium sp. SYK-6

KW - transposon insertion sequencing

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U2 - 10.1016/j.celrep.2023.112847

DO - 10.1016/j.celrep.2023.112847

M3 - Article

SN - 2211-1247

VL - 42

JO - Cell Reports

JF - Cell Reports

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ER -

Multiplexed Fitness Profiling by RB-TnSeq Elucidates Pathways for Lignin-Related Aromatic Catabolism in Sphingobium sp. SYK-6: Article No. 112847

Abstract

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Keywords

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