Insights Into the Peroxisomal Protein Inventory of Zebrafish

Abstract

Peroxisomes are ubiquitous, oxidative subcellular organelles with important functions in cellular lipid metabolism and redox homeostasis. Loss of peroxisomal functions causes severe disorders with developmental and neurological abnormalities. Zebrafish are emerging as an attractive vertebrate model to study peroxisomal disorders as well as cellular lipid metabolism. Here, we combined bioinformatics analyses with molecular cell biology and reveal the first comprehensive inventory of Danio rerio peroxisomal proteins, which we systematically compared with those of human peroxisomes. Through bioinformatics analysis of all PTS1-carrying proteins, we demonstrate that D. rerio lacks two well-known mammalian peroxisomal proteins (BAAT and ZADH2/PTGR3), but possesses a putative peroxisomal malate synthase (Mlsl) and verified differences in the presence of purine degrading enzymes. Furthermore, we revealed novel candidate peroxisomal proteins in D. rerio, whose function and localisation is discussed. Our findings confirm the suitability of zebrafish as a vertebrate model for peroxisome research and open possibilities for the study of novel peroxisomal candidate proteins in zebrafish and humans.

OrganelX web server for sub-peroxisomal and sub-mitochondrial protein localization and peroxisomal target signal detection

“…The Is-PTS1 algorithm first searches putative PTS1 signals by matching a regular expression [ASCNPHTGEQ][RKHQNSL][LAMIVF] in the C-terminal part of the sequence (last 3 amino acids) [21] , [26] .…”

“…These tools offered online through the OrganelX server facilitate research on peroxisomes and mitochondria by making the prediction of protein sub-cellular localisation easy to perform (only the upload of protein FASTA sequences is needed). OrganelX can be used without the need for programming skills and significantly reduces the number of bioinformatic steps that should have been otherwise performed to extract relevant information from the protein sequences of interest [21] .…”

Navigating sex and sex roles: deciphering sex-biased gene expression in a species with sex-role reversal ( Syngnathus typhle )

“…In the head kidney, female-biased genes, irrespective of age, exhibited a notable enrichment primarily in the peroxisome pathway. These membrane-bound organelles play pivotal roles in lipid metabolism within cells, maintaining cellular oxidative equilibrium [ 79 ]. Given the energy investment in processes like oocyte development by female pipefish, the heightened peroxisomal pathway enrichment suggests an augmented demand for lipid metabolism to fuel these activities.…”

Navigating sex and sex roles: deciphering sex-biased gene expression in a species with sex-role reversal (Syngnathus typhle)

“…On a similar note, in the head kidney, female-biased genes, irrespective of age, exhibited a notable enrichment primarily in the peroxisome pathway. These membrane-bound organelles play pivotal roles in lipid metabolism within cells, maintaining cellular oxidative equilibrium (61). Given the energy investment in processes like oocyte development by female pipefish, the heightened peroxisomal pathway enrichment suggests an augmented demand for lipid metabolism to fuel these activities.…”