PUMPKIN, the Sole Plastid UMP Kinase, Associates with Group II Introns and Alters Their Metabolism

Abstract

The chloroplast hosts photosynthesis and a variety of metabolic pathways that are essential for plant viability and acclimation processes. In this study, we show that the sole plastid UMP kinase (PUMPKIN) in Arabidopsis (Arabidopsis thaliana) associates specifically with the introns of the plastid transcripts trnG-UCC, trnV-UAC, petB, petD, and ndhA in vivo, as revealed by RNA immunoprecipitation coupled with deep sequencing (RIP-Seq); and that PUMPKIN can bind RNA efficiently in vitro. Analyses of target transcripts showed that PUMPKIN affects their metabolism. Null alleles and knockdowns of pumpkin were viable but clearly affected in growth, plastid translation, and photosynthetic performance. In pumpkin mutants, the levels of many plastid transcripts were reduced, while the amounts of others were increased, as revealed by RNA-Seq analysis. PUMPKIN is a homomultimeric, plastid-localized protein that forms in vivo RNA-containing megadalton-sized complexes and catalyzes the ATP-dependent conversion of UMP to UDP in vitro with properties characteristic of known essential eubacterial UMP kinases. A moonlighting function of PUMPKIN combining RNA and pyrimidine metabolism is discussed. 1 This research was supported by the German Science Foundation, Deutsche Forschungsgemeinschaft (ME 1794/6 to J.M.; MO 1032/4-1 to T.M.; TRR 175 D01 to J.M.M; A05 to D.L.; and A03 to J.M.).

Nucleotide Metabolism in Plants

“…Interestingly, the enzyme binds certain plastidic transcripts and is involved in plastid RNA metabolism, which may not require its enzymatic function. Mutants are small and compromised in plastid translation and photosynthetic performance (Schmid et al, 2019). The orthologous enzyme in rice is localized in chloroplasts and participates in RNA metabolism, and the corresponding loss-of-function mutants are pale green (Zhu et al, 2016;Chen et al, 2018a).…”

On the move: redox-dependent protein relocation in plants

“…Akter et al applied DYn-2 is Arabidopsis cultures (Akter et al, 2015), identifying 226 sulfenylation events in response to oxidative stress, and, more recently, in plants (Akter et al, 2017). (Schmid et al, 2019)…”

UMP Pyrophosphorylase: A Moonlighting Protein with Essential Functions in Chloroplast Development and Photosynthesis Establishment

“…These results indicate that UPP plays a vital role in the establishment of photosynthesis, but that this role is independent of the protein's UPRT activity. Interestingly, the two enzymes downstream of UPP in the plastidic uracil salvage pathway, UMP kinase (EC 2.7.1.14) and nucleoside diphosphate kinase 2 (EC 2.7.4.6), are also moonlighting proteins that function in photosynthetic mechanisms (Dorion and Rivoal, 2015;Schmid et al, 2019). These findings not only reveal a crucial role for UPP in establishing photosynthetic capacity, but also Figure 1.…”