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PreprintCited by 2Bacterial Genetics and BiotechnologyMicrobial metabolism and enzyme functionMicrobial Metabolic Engineering and Bioproduction

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The interplay between glucose and aromatic compound regulation by two IclR-type transcription factors, LigR1 and LigR2, in Pseudomonas putida KT2440

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Kadriu, Elina, Qin, Sophie, Prezioso, Stephanie, Christendat, Dinesh·2025·Microbiological Research
DOI 10.1101/2025.08.13.670189

Preprint — published as 10.1016/j.micres.2025.128382 · Paper page

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Abstract

The rhizosphere is a hotspot of microbial activity where plants release a diverse array of aromatic compounds, including shikimate pathway intermediates and monolignols. Pseudomonas putida KT2440, renowned for its metabolic versatility in this niche, uses largely uncharacterized regulatory and enzymatic strategies to utilize these compounds. We investigated two IclR-type transcriptional regulators, LigR1 and LigR2, that control expression of the uncharacterized lig1 and lig2 operons. We demonstrate that ligR1 deletion caused growth defects on glucose and 4-hydroxybenzoate accompanied by cell elongation and aggregation. Structural and functional analyses reveal that LigR1 and LigR2 activate the lig1 operon but repress the lig2 operon. LigR1 binding of 4-hydroxybenzoate induced repression by triggering tetramerization and increasing DNA-binding activity. In contrast, LigR2 responded to quinate, protocatechuate and 4-hydroxybenzoate to potently induce lig2 operon expression by relieving repression. While both operons cooperate in metabolizing these compounds, we propose the lig1 operon mediates influx through its major facilitator superfamily (MFS) transporter (PP_2604), whereas the lig2 operon catalyzes breakdown via a protocatechuate intermediate and the meta-cleavage pathway, supplying oxaloacetate to the TCA cycle. Importantly, we show that P. putida repurposes shikimate pathway intermediates for energy production. These findings challenge the canonical biosynthetic view of the shikimate pathway and redefine the metabolic flexibility of soil pseudomonads. We reveal a novel mechanism enabling P. putida to thrive in the chemically complex rhizosphere and open new avenues for exploring alternate roles of the shikimate pathway, emphasizing transcriptional regulators as tools to deconvolute complex metabolic landscapes. Highlights: LigR1 and LigR2 transcriptionally regulate the lig1 and lig2 operons Lig1 operon is required for import of glucose and shikimate-derived compounds Lig2 operon metabolizes shikimate pathway compounds Dysregulated LigR1/LigR2 expression impacts bacterial physiology Graphical Abstract:

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Metadata

Authors
Kadriu, E., Qin, S., Prezioso, S., & Christendat, D.
Affiliations
University of Toronto (CA)
Corresponding author
Christendat, Dinesh
ORCID
Venue
Microbiological Research
Publisher
openRxiv
Published
2025-08-13
Volume
303
Pages
128382-128382
ISSN
0944-5013 (ISSN-L)
DOI
10.1101/2025.08.13.670189
OpenAlex
W4415641608
Cited by
2
References
1
Citations by year
2026: 2
FWCI
1.17
Type
journal article
Language
en
Open access
Licence
Locations
  • Microbiological Research (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
Funders
Natural Sciences and Engineering Research Council of Canada (rgpin-2020-06052)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial metabolism and enzyme function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Keywords
Pseudomonas putida KT2440, aromatic compound metabolism, glucose metabolism, p-hydroxybenzoic acid, quinic acid, protocatechuic acid, shikimate pathway, major facilitator superfamily transporter, protocatechuate pathway, meta-cleavage pathway, TCA cycle, oxaloacetate, soil bacteria, metabolic flexibility, gene expression regulation
MeSH terms
Bacterial Proteins, Glucose, Operon, Parabens, Transcription Factors, Gene Expression Regulation, Bacterial, Pseudomonas putida, Hydroxybenzoates

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