Circular representation of the zebrafish and human mitochondrial genomes: Both genomes share the same synteny, and the number of genes and are nearly identical in size.

Zebrafish Marriott mitochondrial mutant collection: Schematic representation of various mitochondrial resident pathways for which zebrafish mutants were generated. The nuclear-encoded mitochondrial proteins have been illustrated according to the function they are involved in mitochondrial maintenance and homeostasis. Mutants generated by TALE gene editing are depicted as blue, whereas those generated by the GBT system are depicted in pink.

A depiction of homology of the mutants created for proteins involved in different mitochondrial resident pathways: (A,B): Complex 1 of mitochondrial respiratory chain; (A): NADH: ubiquinone oxidoreductase complex assembly factor 6 (Ndufaf6); (B): NADH: ubiquinone oxidoreductase subunit S4 (Ndufs4); (C): Complex 2 of mitochondrial respiratory chain; (C): Succinate dehydrogenase complex flavoprotein subunit A (Sdha); D-E: Biosynthesis of coenzyme Q; (D): Coenzyme Q2, polyprenyltransferase (Coq2) (E): Decaprenyl-diphosphate synthase subunit 2 (Pdss2); (F): Complex 3 of mitochondrial respiratory chain; (F): Ubiquinol–cytochrome c reductase complex III subunit VIII (Uqcrq); (G,H): Complex 4 of mitochondrial respiratory chain; (G): SURF1 cytochrome C oxidase assembly factor (Surf1); (H): Cytochrome C oxidase assembly factor heme A:farnesyltransferase COX10 (Cox10); (I,J): Complex 5 of mitochondrial respiratory chain; (I): Transmembrane protein 70 (Tmem70); (J): ATP synthase F1 subunit epsilon (Atp5f1e); (K–N): Mitochondrial calcium homeostasis; (K): Mitochondrial calcium uniporter (Mcu) generated by TALEN and (L); by GBT; (M): Mitochondrial calcium uptake 1 (Micu1); (N): Calsequestrin 1 (Casq1a); (O): Mitochondrial protein import; (O): Translocase of inner mitochondrial membrane 50 (Timm50); (P): Stress response; (P): DAP3 binding cell death enhancer 1 (Dele1) (GBT insertion site is in the putative promoter region, site is depicted upstream of exons of dele1 gene in chromosome 14; (Q–U): Mitochondrial genome maintenance; (Q): Leucine-rich pentatricopeptide repeat containing (Lrpprc); (R): NOP2/Sun RNA methyltransferase 2 (Nsun2) ^#candidate line; (S): Mitochondrial methionyl-tRNA formyltransferase (Mtfmt); (T): Mitochondrial ribosomal protein S18B (Mrps18b); (U): Leucine aminopeptidase 3 (Lap3) ^#candidate line; (V–X): Mitochondrial metabolite synthesis; (V): Isocitrate dehydrogenase (NADP(+)) 2, mitochondrial (Idh2); (W): Oxoglutarate dehydrogenase b (Ogdhb); (X): D-2-hydroxyglutarate dehydrogenase (D2hgdh).

A depiction of homology of the mutants created for proteins involved in different mitochondrial resident pathways: (A,B): Complex 1 of mitochondrial respiratory chain; (A): NADH: ubiquinone oxidoreductase complex assembly factor 6 (Ndufaf6); (B): NADH: ubiquinone oxidoreductase subunit S4 (Ndufs4); (C): Complex 2 of mitochondrial respiratory chain; (C): Succinate dehydrogenase complex flavoprotein subunit A (Sdha); D-E: Biosynthesis of coenzyme Q; (D): Coenzyme Q2, polyprenyltransferase (Coq2) (E): Decaprenyl-diphosphate synthase subunit 2 (Pdss2); (F): Complex 3 of mitochondrial respiratory chain; (F): Ubiquinol–cytochrome c reductase complex III subunit VIII (Uqcrq); (G,H): Complex 4 of mitochondrial respiratory chain; (G): SURF1 cytochrome C oxidase assembly factor (Surf1); (H): Cytochrome C oxidase assembly factor heme A:farnesyltransferase COX10 (Cox10); (I,J): Complex 5 of mitochondrial respiratory chain; (I): Transmembrane protein 70 (Tmem70); (J): ATP synthase F1 subunit epsilon (Atp5f1e); (K–N): Mitochondrial calcium homeostasis; (K): Mitochondrial calcium uniporter (Mcu) generated by TALEN and (L); by GBT; (M): Mitochondrial calcium uptake 1 (Micu1); (N): Calsequestrin 1 (Casq1a); (O): Mitochondrial protein import; (O): Translocase of inner mitochondrial membrane 50 (Timm50); (P): Stress response; (P): DAP3 binding cell death enhancer 1 (Dele1) (GBT insertion site is in the putative promoter region, site is depicted upstream of exons of dele1 gene in chromosome 14; (Q–U): Mitochondrial genome maintenance; (Q): Leucine-rich pentatricopeptide repeat containing (Lrpprc); (R): NOP2/Sun RNA methyltransferase 2 (Nsun2) ^#candidate line; (S): Mitochondrial methionyl-tRNA formyltransferase (Mtfmt); (T): Mitochondrial ribosomal protein S18B (Mrps18b); (U): Leucine aminopeptidase 3 (Lap3) ^#candidate line; (V–X): Mitochondrial metabolite synthesis; (V): Isocitrate dehydrogenase (NADP(+)) 2, mitochondrial (Idh2); (W): Oxoglutarate dehydrogenase b (Ogdhb); (X): D-2-hydroxyglutarate dehydrogenase (D2hgdh).

RNAseq analysis of coq2 mutants: (A): Heat map visualization of expression of zebrafish orthologs for human MitoCarta genes. The gradient color scale represents the log₂CPM value obtained for each of the zebrafish mitochondrial orthologs in the two datasets. (B,C): PANTHER classification for all the differentially expressed genes in the homozygous mutant according to protein class (B) and biological process (C). Each histogram represents the percentage of genes falling in each of the categories.

RNAseq analysis of uqcrq mutants: (A): Differential expression of zebrafish orthologs for human mitochondrial resident proteins; MitoCarta is represented as a heat map. The gradient color scale represents the log₂CPM value obtained for each of the zebrafish mitochondrial orthologs in the two datasets. (B,C): Differentially expressed genes classified according to protein class (B) and biological processes (C). Each histogram represents the percentage of genes falling in each of the categories.

RNAseq analysis of mcu mutants: (A): Heat map representation of zebrafish orthologs for human mitochondrial localized proteins (MitoCarta). The gradient color scale represents the log₂CPM value obtained for each of the zebrafish mitochondrial orthologs in the two datasets. (B,C): Classification by PANTHER system for all the differentially expressed genes in the homozygous mutant according to protein class (B) and biological process (C). Each histogram represents the percentage of genes falling in each of the categories.