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Global profile changes in transcripts induced with a phosphate analogue: implications for gene regulation

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Abstract

Previous work has shown that thiophosphate, a phosphate analogue, leads to a global shift in the distribution of cellular proteins in a variety of organisms. Thiophosphate, when added to culture media, gets incorporated into the nucleic acids of cells resulting in nuclease-resistant phosphorothioate linkages. Using Escherichia coli, as a model organism, it was found that the global changes in protein expression induced with thiophosphate could be accounted for by significant changes in the absolute transcription levels of more than 1500 genes detected via RNA seq analysis. In fact, 58% of transcripts detected in RNA seq studies using total RNA were increased an average of 44 × fold while the remaining 42% were decreased an average of 20 × fold in thiophosphate-treated cells. Furthermore, microarray results showed no correlation between the transcriptional changes observed and the known stability of the corresponding mRNAs measured. Overall, the total amount of non-ribosomal RNA accumulated in TP-treated cells was increased relative to rRNA ~ 4 × fold (1.5–6 ×). The results further indicated that metabolic changes may play a role in inducing the transcriptional profiles observed with thiophosphate. Indeed, pathway analysis of transcripts showed an increase in routes for phosphoribosyl pyrophosphate (PRPP) synthesis and related derivatives, presumably due to a reduction in RNA turnover. These results raise the possibility that the energy savings with reduced RNA turnover could lead to an increased energy charge in the cell that induces transcriptional changes leading to an increase in biosynthetic processes.

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Abbreviations

TP:

Thiophosphate

NT:

Nucleotide

PRPP:

Phosphoribosyl pyrophosphate

LB:

Luria broth

AICAR:

5-Aminoimidazole-4-carboxamide ribonucleotide

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Acknowledgements

I wish to thank Yuriy Alekseyev, Ph.D., Director, Boston University Microarray and Sequencing Resource at BUSM for assistance with the microarray study and the CTSA grant#1UL1TR001430 which helps to fund the BUSM facility. I also wish to thank Wenzhi Li, M.D. of Omega Bioservices for help with the RNA Seq study. Finally, I wish to acknowledge a research grant from the University of Phoenix, in partial support of this work. Thiophosphate was prepared by Frayne Consultants.

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  1. College of General Studies, University of Phoenix, Phoenix, AZ, USA

    Elizabeth G. Frayne

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Correspondence to Elizabeth G. Frayne.

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Frayne, E.G. Global profile changes in transcripts induced with a phosphate analogue: implications for gene regulation. Mol Cell Biochem 468, 111–120 (2020). https://doi.org/10.1007/s11010-020-03715-9

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