Dinucleoside polyphosphates act as 5′-RNA caps in bacteria

Oldřich Hudeček, Roberto Benoni, Paul E. Reyes-Gutierrez, Martin Culka, Hana Šanderová, Martin Hubálek, Lubomír Rulíšek, Josef Cvačka, Libor Krásný and Hana Cahová ()
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Oldřich Hudeček: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Roberto Benoni: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Paul E. Reyes-Gutierrez: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Martin Culka: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Hana Šanderová: Institute of Microbiology of the Czech Academy of Sciences
Martin Hubálek: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Lubomír Rulíšek: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Josef Cvačka: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Libor Krásný: Institute of Microbiology of the Czech Academy of Sciences
Hana Cahová: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract It has been more than 50 years since the discovery of dinucleoside polyphosphates (NpnNs) and yet their roles and mechanisms of action remain unclear. Here, we show that both methylated and non-methylated NpnNs serve as RNA caps in Escherichia coli. NpnNs are excellent substrates for T7 and E. coli RNA polymerases (RNAPs) and efficiently initiate transcription. We demonstrate, that the E. coli enzymes RNA 5′-pyrophosphohydrolase (RppH) and bis(5′-nucleosyl)-tetraphosphatase (ApaH) are able to remove the NpnN-caps from RNA. ApaH is able to cleave all NpnN-caps, while RppH is unable to cleave the methylated forms suggesting that the methylation adds an additional layer to RNA stability regulation. Our work introduces a different perspective on the chemical structure of RNA in prokaryotes and on the role of RNA caps. We bring evidence that small molecules, such as NpnNs are incorporated into RNA and may thus influence the cellular metabolism and RNA turnover.

Date: 2020
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DOI: 10.1038/s41467-020-14896-8

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