Decapping by ALPH1 produces ppRNA

The trypanosome mRNA decapping enzyme ALPH1 prefers caps without m7G methylation and produces diphosphate-RNA

Pereira L*, Dzadz DA*, Castaneda Londono PA*, Warminski M, Kowalska J, Seifert N, Braune S, Barbieri Holetz F, Zoltner M, Kramer S, Górna MW.

bioRxiv 2026.01.29.702356 10.64898/2026.01.29.702356

ALPH1 is the atypical enzyme that trypanosomes use for mRNA decapping (in place of the usual decapping enzymes of eukaryotes, Dcp2).

Here, we characterise the enzymatic activity of ALPH1 using several orthogonal assays and reach suprising conclusions:

• ALPH1 prefers RNAs without m7G methylation, despite the heavy methylation of trypanosomal mRNA (cap 4)
• Cleavage by ALPH1 produces a diphosphate RNA (wheras Dcp2 produces pRNA).
• The C-terminal domain of ALPH1 is essential in vivo and increases decapping activity in vitro.

In conclusion, ALPH1 retains some characteristics of its prokaryotic homolog ApaH and is poorly adapted to eukarytic mRNA substrates.

This work was supported mainly by the trilateral DFG/GACR/NCN funding agreement WEAVE:

National Science Centre, Poland [WEAVE UNISONO grant 22022/04/Y/NZ1/00114 to MWG]

Deutsche Forschungsgemeinschaft [KR4017/12-1 to SK], GACR [24-14298L to MZ]