Novosphingobium aromaticivorans LigR coordinates transcription of genes involved in metabolism of multiple types of aromatics

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ABSTRACT Aromatic compounds are a ubiquitous and diverse family of chemicals with functions as biomolecules, natural products, industrial chemicals, and pollutants. Novosphingobium aromaticivorans DSM 12444 uses multiple inducible pathways to catabolize H-, G-, and S-type aromatics that contain zero, one, or two methoxy groups, respectively. Here, we obtain a systems-level view of the transcriptional control of its aromatic metabolic pathways. Several in vitro analyses found that a N. aromaticivorans homolog of the Sphingobium lignivoran s SYK-6 transcription factor LigR bound genomic DNA upstream of genes involved in metabolism of multiple aromatic types. We found that a ΔLigR mutant had growth defects on all three types of aromatics as sole carbon sources. Transcriptomic analysis revealed that LigR was required to increase expression of gene products that function in metabolism of all three aromatic types. We also found that, in media containing both glucose and an aromatic carbon source, the ΔLigR mutant directed intermediates through alternative aromatic metabolic pathways. Protein-DNA binding assays showed that N. aromaticivorans LigR binds immediately upstream of promoters of genes involved in aromatic metabolism. We found that N. aromaticivorans LigR coordinates the expression of enzymes that function in the catabolism of H-, G-, and S-type aromatics, and that there are differences in the role of LigR in N. aromaticivorans and S. lignivorans . A comparative genomic analysis predicted that LigR homologs and the aromatic-metabolizing genes that it directly regulates are often co-localized in the genomes of Sphingomonadales, but often not found in this arrangement in many other known aromatic metabolizing bacteria. IMPORTANCE The abundance and societal importance of aromatics have led to interest in developing biological catalysts that can use them as a renewable source of industrial chemicals. While the synthesis of proteins needed for aromatic metabolism is often regulated, we lack a systems-level understanding of how cells coordinate the use of these pathways. Here, we used DNA affinity purification sequencing, RNA-seq, and targeted metabolite analysis of the bacterium Novosphingobium aromaticivorans to understand the transcriptional regulation of enzymes needed to metabolize different aromatic types. Analysis of a N. aromaticivorans DNA-binding protein, LigR, illustrated how synthesis of enzymes that function in multiple aromatic pathways is controlled. We propose that the insight obtained from this systems-level view of aromatic metabolism could help engineer bacteria to produce industrial chemicals or remove toxic aromatics from the environment.

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