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. 2024 Mar;170(3):001449.
doi: 10.1099/mic.0.001449.

Gene expression reprogramming of Pseudomonas alloputida in response to arginine through the transcriptional regulator ArgR

María Antonia Molina-Henares  1 , María Isabel Ramos-González  1 , Serena Rinaldo  2 , Manuel Espinosa-Urgel  1
Affiliations

Gene expression reprogramming of Pseudomonas alloputida in response to arginine through the transcriptional regulator ArgR

María Antonia Molina-Henares et al. Microbiology (Reading). 2024 Mar.

Abstract

Different bacteria change their life styles in response to specific amino acids. In Pseudomonas putida (now alloputida) KT2440, arginine acts both as an environmental and a metabolic indicator that modulates the turnover of the intracellular second messenger c-di-GMP, and expression of biofilm-related genes. The transcriptional regulator ArgR, belonging to the AraC/XylS family, is key for the physiological reprogramming in response to arginine, as it controls transport and metabolism of the amino acid. To further expand our knowledge on the roles of ArgR, a global transcriptomic analysis of KT2440 and a null argR mutant growing in the presence of arginine was carried out. Results indicate that this transcriptional regulator influences a variety of cellular functions beyond arginine metabolism and transport, thus widening its regulatory role. ArgR acts as positive or negative modulator of the expression of several metabolic routes and transport systems, respiratory chain and stress response elements, as well as biofilm-related functions. The partial overlap between the ArgR regulon and those corresponding to the global regulators RoxR and ANR is also discussed.

Keywords: arginine; gene expression; metabolism; redox; regulation.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Fig. 1.
Fig. 1.. Mean difference (MD) plot of the RNA-Seq data corresponding to the ΔargR mutant vs. wild-type strain. Data above log2 fold change=0.5 or below log2 fold change=−0.5 (P-value≤0.05) are shown in red and blue, respectively.
Fig. 2.
Fig. 2.. Functional classification and relative abundance of genes identified as positively or negatively regulated by ArgR in the RNA-Seq analysis (P-value<0.01; log2 fold change >0.8/ <−0.8). Details can be found in Tables S2 and S3.
Fig. 3.
Fig. 3.. Influence of ArgR on arginine metabolism. Blue arrows correspond to the arginine biosynthesis pathway (some details have been omitted for simplicity), and black arrows to the different arginine catabolic pathways, indicated in the grey boxes, and other relevant reactions associated to arginine/glutamate metabolism. Broken arrows indicate compounds feeding into the TCA cycle. Elements positively or negatively regulated by ArgR are shown in green and red, respectively.
Fig. 4.
Fig. 4.. Summary of relevant functions belonging to the ArgR regulon.
Fig. 5.
Fig. 5.. Quantitative RT-PCR of selected genes. The relative expression of the indicated genes in the ΔargR mutant with respect to the wild-type was analysed by qRT-PCR, as described in the Methods section. Fold-change data are presented in logarithmic scale for ease of representation, and correspond to the averages and standard deviations of three biological replicas with three technical repetitions.
Fig. 6.
Fig. 6.. Consensus ARG box in P. alloputida KT2440, created with WebLogo [37] using the sequences indicated in Tables S3 and S4.
See this image and copyright information in PMC

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