Cryptic peroxisomal targeting via alternative splicing and stop codon read-through in fungi

Abstract

Peroxisomes are eukaryotic organelles important for the metabolism of long-chain fatty acids. Here we show that in numerous fungal species, several core enzymes of glycolysis, including glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and 3-phosphoglycerate kinase (PGK), reside in both the cytoplasm and peroxisomes. We detected in these enzymes cryptic type 1 peroxisomal targeting signals (PTS1), which are activated by post-transcriptional processes. Notably, the molecular mechanisms that generate the peroxisomal isoforms vary considerably among different species. In the basidiomycete plant pathogen Ustilago maydis, peroxisomal targeting of Pgk1 results from ribosomal read-through, whereas alternative splicing generates the PTS1 of Gapdh. In the filamentous ascomycete Aspergillus nidulans, peroxisomal targeting of these enzymes is achieved by exactly the opposite mechanisms. We also detected PTS1 motifs in the glycolytic enzymes triose-phosphate isomerase and fructose-bisphosphate aldolase. U. maydis mutants lacking the peroxisomal isoforms of Gapdh or Pgk1 showed reduced virulence. In addition, mutational analysis suggests that GAPDH, together with other peroxisomal NADH-dependent dehydrogenases, has a role in redox homeostasis. Owing to its hidden nature, partial peroxisomal targeting of well-studied cytoplasmic enzymes has remained undetected. Thus, we anticipate that further bona fide cytoplasmic proteins exhibit similar dual targeting.

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

“…A systematic survey of RNA-seq data identified 246 cases of genes whose alternative isoforms differentially include or exclude amino-terminal signal-peptide-encoding regions (three of which were verified by RT-PCR), suggesting that alternative splicing has a role in the generation of proteins targeted to different subcellular compartments (below). Alternative splicing has recently been shown to mediate dual targeting of glycolytic enzymes to the cytosol and peroxisome in fungi 13 .…”

Origin of Spliceosomal Introns and Alternative Splicing

“…This may be achieved by on/off protein switches (Bingham et al 1988), or by coupling missense AS to NMD (Lewis et al 2003;Lareau et al 2007;Yap et al 2012), leading to transcript degradation before translation. Third, inclusion of alternative sequences may lead to differences in intracellular transport, either at the mRNA (Buckley et al 2011) or protein level (Freitag et al 2012;Kabran et al 2012). Nevertheless, despite a plethora of described examples of each kind, a major unanswered question is still to what extent AS is functional or simply splicing "noise" (Sorek et al 2004;Irimia et al 2008;Roy and Irimia 2008).…”

Differential remodelling of peroxisome function underpins the environmental and metabolic adaptability of diplonemids and kinetoplastids

“…Glycolysis takes place in the cytosol, but glycolytic enzymes have also been associated with the plasma membrane of erythrocytes [2] and with mitochondria [3,4]. In addition, enzyme isoforms with non-glycolytic roles are found to locate to other compartments [5].…”