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RNA-seq profiling of Methylotuvimicrobium alcaliphilum 20ZR grown with or without La-supplementation

ABSTRACT: In this study we investigated the steady-state growth of Methylotuvimicrobium alcaliphilum 20ZR in media containing calcium (Ca) or lanthanum (La, a REE element). RNA-seq profiling of Methylomicrobium alcaliphilum strain 20ZR in bioreactor on methane. Sample cultures, La-optimum, La-CH4 limited, Ca-optimum and Ca-CH4 limited, were collected and immediately transferred into tubes containing 5 ml of the stop solution (5% water-equilibrated phenol in ethanol). It was found, that cells supplemented with La show a higher growth rate compared to Ca-cultures; however, the efficiency of carbon conversion, estimated as biomass yield, is higher in cells grown with Ca. The study was financially supported by DOE under FOA DE-FOA-0001085 and by NSF-CBET award 1605031

ORGANISM(S): Methylotuvimicrobium alcaliphilum 20Z

PROVIDER: GSE253414 | GEO | 2024/02/02

REPOSITORIES: GEO

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Project description:Purpose: The goals of this study is to compare the transcriptome (RNA-seq) modulations in Saccharomyces cerevisiae exposed to two rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements, respectively. Methods: mRNA were sequenced from Saccharomyces cerevisiae exposed to two different rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements respectively. The transcriptome of S. cerevisiae was analysed after being exposed for one hour to the EC10 (Effective concentration 10 %) and the EC50 (Effective concentration 50 %) of lanthanum (50 and 160 µM) and ytterbium (6 and 8 µM). The sequence reads were trimmed using Trimmomativ v0.36.1 and FastQC v0.67 used for quality check. Reads passing the quality check were mapped on the reference genome (S288C R64-2-1 of 2015-01-31 from https://www.yeastgenome.org/) of S. cerevisiae using TopHat v2.1.1. Reads that were mapped on the reference genome were quantified using HTSeq-count v0.6.1p1. Finally, differential gene expression analysis between treatments was carried out using DESeq2 v1.14.1. Differentially expressed genes between conditions were obtained and expressed as log2-fold change with adjusted p-values calculated via a Benjamini-Hochberg test. A cut-off adjusted p-value of < 0.01 was applied. Results: The transcription of genes related to several crucial pathways was modulated in response to both REEs, such as oxidative-reduction processes, DNA replication, and carbohydrate metabolism. REE-specific responses involving the cell wall and the pheromone signalling pathways were highlighted, while these were not reported for other metals. REE exposure also modified the expression and abundance of several ion transport systems, for which strong discrepancies were observed between the two contrasted REEs. Conclusions: Our results demonstrate the discrepancies in yeast response to different rare earth elements (light vs heavy rare earth elements). This results are valuable to prioritize key genes and proteins involved in REE detoxification mechanisms that would deserve further characterisation to better understand the REE toxicity on the environment and human health.

Project description:Ever since the discovery of the first rare earth element (REE)-dependent enzyme,the physiological role of lanthanides has become an emerging field of research due to the environmental implications and biotechnological opportunities. In Pseudomonas putida KT2440, the two pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs) PedE and PedH are inversely regulated in response to REE availability. This transcriptional switch is orchestrated by a complex regulatory network that includes the PedR2/PedS2 two-component system and is important for efficient growth on several alcoholic volatiles. To study whether cellular responses beyond the REE switch exist, the differential proteomic responses that occur during growth on various model carbon sources were analyzed. Apart from the Ca2+-dependent enzyme PedE, the differential abundances of most identified proteins were conditional. During growth on glycerol-and concomitant with the proteomic changes-lanthanum (La3+) availability affected different growth parameters, including the onset of logarithmic growth and final optical densities. Studies with mutant strains revealed a novel metabolic route for glycerol utilization, initiated by PedE and/or PedH activity. Upon oxidation to glycerate via glyceraldehyde, phosphorylation by the glycerate kinase GarK most likely yields glycerate-2-phosphate, which is eventually channeled into the central metabolism of the cell. This new route functions in parallel with the main degradation pathway encoded by the glpFKRD operon and provides a growth advantage to the cells by allowing an earlier onset of growth with glycerol as the sole source of carbon and energy.IMPORTANCE The biological role of REEs has long been underestimated, and research has mainly focused on methanotrophic and methylotrophic bacteria. We have recently demonstrated that P. putida, a plant growth-promoting bacterium that thrives in the rhizosphere of various food crops,possesses a REE-dependent alcohol dehydrogenase (PedH), but knowledge about REE-specific effects on physiological traits in nonmethylotrophic bacteria is still scarce. This study demonstrates that the cellular response of P.putida to lanthanum (La3+) is mostly substrate specific and that La3+ availability highly affects the growth of cells on glycerol. Further, a novel route for glycerol metabolism is identified, which is initiated by PedE and/or PedH activity and provides a growth advantage to this biotechnologically relevant organism by allowing a faster onset of growth. Overall, these findings demonstrate that lanthanides can affect physiological traits in nonmethylotrophic bacteria and might influence their competitiveness in various environmental niches.

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RNA-seq profiling of Methylotuvimicrobium alcaliphilum 20ZR grown with or without La-supplementation

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