Cold Regulation of Genes Encoding Ion Transport Systems in the Oligotrophic Bacterium Caulobacter crescentus.

Hugo L De Araújo,Alan P R Lorenzetti,Bianca P Martins,Marilis V Marques,Tie Koide,Alexandre M Vicente,Jeffrey A Gralnick

doi:10.1128/spectrum.00710-21

Hugo L De Araújo, Alan P R Lorenzetti + Show 5 more

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https://doi.org/10.1128/spectrum.00710-21

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Abstract

ABSTRACTIn this study, we characterize the response of the free-living oligotrophic alphaproteobacterium Caulobacter crescentus to low temperatures by global transcriptomic analysis. Our results showed that 656 genes were upregulated and 619 were downregulated at least 2-fold after a temperature downshift. The identified differentially expressed genes (DEG) belong to several functional categories, notably inorganic ion transport and metabolism, and a subset of these genes had their expression confirmed by reverse transcription quantitative real-time PCR (RT-qPCR). Several genes belonging to the ferric uptake regulator (Fur) regulon were downregulated, indicating that iron homeostasis is relevant for adaptation to cold. Several upregulated genes encode proteins that interact with nucleic acids, particularly RNA: cspA, cspB, and the DEAD box RNA helicases rhlE, dbpA, and rhlB. Moreover, 31 small regulatory RNAs (sRNAs), including the cell cycle-regulated noncoding RNA (ncRNA) CcnA, were upregulated, indicating that posttranscriptional regulation is important for the cold stress response. Interestingly, several genes related to transport were upregulated under cold stress, including three AcrB-like cation/multidrug efflux pumps, the nitrate/nitrite transport system, and the potassium transport genes kdpFABC. Further characterization showed that kdpA is upregulated in a potassium-limited medium and at a low temperature in a SigT-independent way. kdpA mRNA is less stable in rho and rhlE mutant strains, but while the expression is positively regulated by RhlE, it is negatively regulated by Rho. A kdpA-deleted strain was generated, and its viability in response to osmotic, acidic, or cold stresses was determined. The implications of such variation in the gene expression for cold adaptation are discussed.IMPORTANCE Low-temperature stress is an important factor for nucleic acid stability and must be circumvented in order to maintain the basic cell processes, such as transcription and translation. The oligotrophic lifestyle presents further challenges to ensure the proper nutrient uptake and osmotic balance in an environment of slow nutrient flow. Here, we show that in Caulobacter crescentus, the expression of the genes involved in cation transport and homeostasis is altered in response to cold, which could lead to a decrease in iron uptake and an increase in nitrogen and high-affinity potassium transport by the Kdp system. This previously uncharacterized regulation of the Kdp transporter has revealed a new mechanism for adaptation to low temperatures that may be relevant for oligotrophic bacteria.

Highlights

In this study, we characterize the response of the free-living oligotrophic alphaproteobacterium Caulobacter crescentus to low temperatures by global transcriptomic analysis
To identify the genes differentially expressed in response to cold stress, we compared the transcriptome of the wild-type C. crescentus strain NA1000 under optimal growth conditions (30°C) and after 2 h under cold stress (10°C)
The study of how bacteria cope with the physiological alterations caused by low temperature stress is of significance for understanding the different strategies used for each group

Summary

Introduction

We characterize the response of the free-living oligotrophic alphaproteobacterium Caulobacter crescentus to low temperatures by global transcriptomic analysis. We show that in Caulobacter crescentus, the expression of the genes involved in cation transport and homeostasis is altered in response to cold, which could lead to a decrease in iron uptake and an increase in nitrogen and highaffinity potassium transport by the Kdp system This previously uncharacterized regulation of the Kdp transporter has revealed a new mechanism for adaptation to low temperatures that may be relevant for oligotrophic bacteria. CSPs possess a conserved cold shock domain, composed of two nucleic acid-binding motifs in tandem that bind to RNA and prevent the formation of secondary structures [18,19,20,21] These proteins have been shown to participate in many cellular processes, such as transcription antitermination and the initiation of translation [22, 23]. The DEAD box RNA helicases unwind the RNA:RNA bonds in the RNA secondary structures and are frequently found associated with the RNA degradosome complex, where they play a role in RNA decay and are important for the correct assembly of the rRNA-protein complexes [24,25,26,27,28]

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