respiratory complex/ respirasome assembly

[ValWood]

Systematic ID	Gene name	Product description	Budding yeast orthologs	Human orthologs	Targets
SPBC115.02c	afg1	AFG1 family mitochondrial ATPase/chaperone Afg1	AFG1	AFG1L
SPBC21D10.07	cmc1	copper-binding protein of the mitochondrial intermembrane space Cmc1	CMC1,CMC2	CMC1,CMC2
SPBC16E9.03c	coa1	cytochrome c oxidase assembly protein Coa1	COA1	COA1
SPAC15A10.17	coa2	cytochrome c oxidase assembly protein Coa2	COA2	NDUFA3
SPAC1B3.21	coa3	cytochrome c oxidase assembly protein Coa3	COA3	COA3
SPCC550.01c	coa4	cytochrome c oxidase assembly protein Coa4	COA4	COA4
SPBC16A3.16	coa5	cytochrome c oxidase assembly protein Coa5	PET191	COA5
SPBC24C6.13	coa6	cytochrome c oxidase assembly protein Coa6	COA6	COA6
SPAC1420.04c	cox1101	cytochrome c oxidase assembly protein Cox1101/ mitochondrial ribosome assembly protein Rsm22 fusion protein	COX11,RSM22	COX11,METTL17
SPAC19B12.13	cox1102	cytochrome c oxidase assembly protein Cox1102/ mitochondrial ribosome assembly protein Rsm2202, fusion protein	COX11,RSM22	COX11,METTL17
SPCC757.15	cox14	cytochrome c oxidase assembly protein Cox14	COX14	COX14
SPBC25H2.18	cox20	cytochrome c oxidase assembly protein Cox20	COX20	COX20
SPBC1604.25	pet117	cytochrome c oxidase assembly protein Pet117	PET117	PET117
SPAC25B8.07c	rcf1	cytochrome c oxidase assembly protein Rcf1	RCF1	HIGD1A,​HIGD1B,​HIGD1C,​HIGD2A,​HIGD2B
SPBC1215.01	shy1	cytochrome c oxidase assembly protein Shy1	SHY1	SURF1
SPCC4B3.20	cmc2	cytochrome c oxidase assembly protein, copper-binding, Cmc2	CMC1,CMC2	CMC1,CMC2
SPAC1565.01	rcf2	cytochrome c oxidase subunit Rcf2	RCF2	HIGD1A,​HIGD1B,​HIGD1C,​HIGD2A,​HIGD2B
SPAC2C4.09		mitochondrial calcium uniporter regulator	FMP32	CCDC90B,MCUR1
SPAC3H1.08c		mitochondrial calcium uniporter regulator	FMP32	CCDC90B,MCUR1
SPBC947.14c	cbp6	mitochondrial complex III assembly protein Cbp6	CBP6	UQCC2
SPAC1486.08	cox16	mitochondrial copper chaperone for cytochrome c oxidase Cox16	COX16	COX16
SPBC26H8.14c	cox17	mitochondrial copper chaperone for cytochrome c oxidase Cox17	COX17	COX17
SPCC1672.04c	cox19	mitochondrial copper chaperone for cytochrome c oxidase Cox19	COX19	COX19
SPBC119.06	sco1	mitochondrial copper chaperone for cytochrome c oxidase Sco1	SCO1,SCO2	SCO1,SCO2
SPAC25B8.04c	mss51	mitochondrial cytochrome C oxidase assembly protein Mss51	MSS51	MSS51
SPAC4G8.11c	atp10	mitochondrial F1-FO ATP synthase chaperone Atp10	ATP10
SPAC3A12.12	atp11	mitochondrial F1-FO ATP synthase chaperone Atp11	ATP11	ATPAF1
SPAC9.12c	atp12	mitochondrial F1-FO ATP synthase chaperone Atp12	ATP12	ATPAF2
SPBC3B8.10	ina17	mitochondrial F1-FO ATP synthase peripheral stalk assembly factor Ina17	INA17
SPAC926.10	ina22	mitochondrial F1-FO ATP synthase peripheral stalk assembly factor Ina22	INA22
SPCC1442.15c	cox18	mitochondrial inner membrane insertase Cox18	COX18	COX18
SPCC320.12	atp23	mitochondrial inner membrane peptidase Atp23	ATP23	ATP23
SPAC1486.11	fmc1	mitochondrial proton-transporting ATP synthase complex assembly factor, LYR family, Fmc1	FMC1	FMC1
SPAC1834.10c		mitochondrial proton-transporting ATP synthase complex assembly protein		TMEM70
SPAC25A8.03c		mitochondrial repliratory complex assembly factro/arginine methyltransferase, human NDUFAF7 ortholog	YKL162C	NDUFAF7
SPBC26H8.16	sdh8	mitochondrial respiratory chain complex II assembly factor 4 Sdh8	SDH8	SDHAF4	sdh1 (chaperone)
SPCC4B3.17	cbp3	mitochondrial respiratory chain complex III assembly protein Cbp3	CBP3	UQCC1
SPBC30D10.21	mzm1	mitochondrial respiratory chain complex III assembly protein, LYR family Mzm1	MZM1	LYRM7
SPBC27B12.14	cbp4	mitochondrial respiratory complex III assembly protein Cbp4	CBP4	UQCC3
SPBC3H7.08c	mra2	mitochondrial respiratory complex/ ATP synthase assembly protein Mra2	MRA1	C15orf48,NDUFA4,NDUFA4L2
SPAPB8E5.10	min8	mitochondrial respiratory complex/ATP synthase complex assembly protein Mra1, meiosis specific splicing in fission yeast	MRA1	C15orf48,NDUFA4,NDUFA4L2
SPAC644.07	bcs1	mitochondrial Rieske ISP assembly ATPase Bcs1	BCS1	BCS1L
SPAC664.12c	sdh6	mitochondrial succinate dehydrogenase assembly factor, LYR family Sdh6	SDH6	SDHAF1	sdh2
SPBP23A10.03c	sdh7	mitochondrial respiratory chain complex II assembly LYR family protein Sdh7	SDH7	SDHAF3	sdh2
SPAC12B10.06c	emi5	succinate dehydrogenase complex assembly protein Emi5	SDH5	SDHAF2
SPBC26H8.01	thi2	thiazole biosynthetic enzyme	THI4

[hattrill]

This is great. I have a rough but incomplete list of assembly factors. I will start putting them in some order. The HGNC have a list, if you want to check it against the human orthos: https://www.genenames.org/data/genegroup/#!/group/645

[ValWood]

need to deal with this too, is it a transferase? (flavination sounds like an activity)

[hattrill]

Google Doc for Assembly Factors

Orthologs via DIOPT. Best calls (Generally best hit in both directions, best scoring and score >3; except where noted) List from GO query of fly annotations, HGNC gene group Mitochondrial respiratory chain complex assembly factors , FlytoCarta list -> Human orthologs -> MitoCarta classification and additional query of list against FB gene groups for any revelant information. 3 genes added that are orthologous to Pombe gene list and not on this set.

Nest step to compare this to general reviews and verifiy/exclude genes.

Would be good to clarify the role of 'accessory' or 'supernumerary' respiratory complex subunits in assembly.

Also, need to think about what is meant by 'mitochondrial respirasome assembly'

FBgn | SYMBOL | NAME | FlytoCarta: Fly ortholog to MitoCarta class | GO evidence | HGNC Gene Group ortholog | FB Gene Group (FB_2024_05) | Assembly GO term annotation | MitoCarta Classification for orthologs | Human Ortholog (best) | S.Pombe | Fly ortholog on PomBase list (NA = no ortholog found, so not applicable as no ortholog found, NOT SEEN means that on fly list but Pombe ortholog not on the Pombe list) -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- FBgn0033209 | CG12107 | - | FlytoCarta | GO |   |   | mitochondrial respirasome assembly | OXPHOS > Respirasome assembly | RAB5IF | No ortholog found | NA FBgn0040529 | COX7A | Cytochrome c oxidase subunit 7A | FlytoCarta | GO | HGNC | MITOCHONDRIAL COMPLEX IV - SUPERNUMERARY SUBUNITS | mitochondrial respirasome assembly | OXPHOS > Respirasome assembly | COX7A1\|COX7A2 | No ortholog found | NA FBgn0033519 | CG11825 | - | FlytoCarta | GO | HGNC |   | mitochondrial respirasome assembly | OXPHOS > Respirasome assembly | HIGD1A\|HIGD1C | SPAC25B8.07c | SPAC25B8.07c FBgn0030743 | CG9921 | - | FlytoCarta | GO | HGNC |   | mitochondrial respirasome assembly | OXPHOS > Respirasome assembly | HIGD2A\|HIGD2B | SPAC25B8.07c | SPAC25B8.07c FBgn0022344 | CG10340 | - | FlytoCarta | GO | HGNC |   | mitochondrial proton-transporting ATP synthase complex assembly | OXPHOS > Complex V > CV assembly factors | ATPAF1 | atp11 | SPAC3A12.12 FBgn0021856 | l(2)k14505 | lethal (2) k14505 | FlytoCarta | GO | HGNC |   | mitochondrial proton-transporting ATP synthase complex assembly | OXPHOS > Complex V > CV assembly factors | ATPAF2 | atp12 | SPAC9.12c FBgn0038871 | CG3337 | - | FlytoCarta |   |   | UNCLASSIFIED PROTEIN-LYSINE N-METHYLTRANSFERASES |   | OXPHOS > Complex V > CV assembly factors | ATPSCKMT | No ortholog found (SPBC3B9.04 eggNOG only) | NA FBgn0032195 | Bcs1 | Bcs1 chaperone | FlytoCarta | GO | HGNC | PROTEIN-TRANSPORTING ATPASES | mitochondrial respiratory chain complex III assembly | OXPHOS > Complex III > CIII assembly factors | BCS1L | SPAC644.07 | SPAC644.07 FBgn0266708 | Cep89 | Centrosomal protein 89kDa | FlytoCarta |   |   |   |   | OXPHOS > Complex IV > CIV assembly factors | CEP89 | No ortholog found | NA FBgn0032595 | CG17996 | - | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > Complex IV > CIV assembly factors | CMC1 | cmc2 | SPCC4B3.20 FBgn0259721 | CG42375 | - | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex assembly | OXPHOS > Complex IV > CIV assembly factors | CMC2 | cmc1 | SPBC21D10.07 FBgn0051913 | CG31913 | - | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex I assembly\|mitochondrial cytochrome c oxidase assembly | OXPHOS > Complex I > CI assembly factors ; OXPHOS > Complex IV > CIV assembly factors | COA1 | No ortholog found | NA FBgn0261353 | Ccdc56 | Coiled-coil domain containing 56 | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > Complex IV > CIV assembly factors | COA3 | tam3 | SPAC1B3.21 FBgn0265083 | CG44194 | - | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex assembly\|mitochondrial cytochrome c oxidase assembly | OXPHOS > Complex IV > CIV assembly factors | COA4 | SPCC550.01c | SPCC550.01c FBgn0040751 | CG13018 | - | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > Complex IV > CIV assembly factors | COA5 | SPBC16A3.16 | SPBC16A3.16 FBgn0259722 | CG42376 | - | FlytoCarta |   | HGNC |   |   | OXPHOS > Complex IV > CIV assembly factors | COA6 | new16 | SPBC24C6.13 FBgn0039965 | Coa7 | Cytochrome c oxidase assembly factor 7 | FlytoCarta |   | HGNC |   |   | OXPHOS > Complex IV > CIV assembly factors | COA7 | No ortholog found | NA FBgn0029594 | Coa8 | Cytochrome c oxidase assembly factor 8 | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > Complex IV > CIV assembly factors | COA8 | No ortholog found | NA FBgn0032222 | Cox10 | Cytochrome c oxidase assembly factor 10 | FlytoCarta |   | HGNC | AROMATIC PRENYLTRANSFERASES |   | OXPHOS > Complex IV > CIV assembly factors | COX10 | cox10 | NOT SEEN FBgn0051648 | Cox11 | Cytochrome c oxidase copper chaperone COX11 | FlytoCarta |   | HGNC |   |   | OXPHOS > Complex IV > CIV assembly factors | COX11 | cox1101/cox1102 | SPAC1420.04c\|SPAC19B12.13 FBgn0034938 | CG3803 | - | FlytoCarta |   | HGNC | NAD(P)H OXIDOREDUCTASES, HEME PROTEIN AS ACCEPTOR |   | OXPHOS > Complex IV > CIV assembly factors | COX15 | etp1 | NOT SEEN FBgn0011476 | l(3)neo43 | lethal (3) neo43 | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > Complex IV > CIV assembly factors | COX16 | SPAC1486.08 | SPAC1486.08 FBgn0030610 | Cox17 | Cytochrome c oxidase copper chaperone COX17 | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > Complex IV > CIV assembly factors | COX17 | cox17 | SPBC26H8.14c FBgn0035960 | CG4942 | - | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > Complex IV > CIV assembly factors | COX18 | cox18 | SPCC1442.15c FBgn0260222 | CG42496 | - | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > Complex IV > CIV assembly factors | COX19 | SPCC1672.04c | SPCC1672.04c FBgn0033093 | CG3270 | - | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | FOXRED1 | No ortholog found | NA FBgn0259832 | CG34229 | - | FlytoCarta | GO |   |   | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | LYRM2 | No ortholog found | NA FBgn0083986 | CG34150 | - | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex III assembly | OXPHOS > Complex III > CIII assembly factors | LYRM7 | new18 | SPBC30D10.21 FBgn0039689 | NdufAF1 | NADH:ubiquinone oxidoreductase complex assembly factor 1 | FlytoCarta | GO | HGNC | MITOCHONDRIAL COMPLEX I INTERMEDIATE ASSEMBLY COMPLEX | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | NDUFAF1 | No ortholog found | NA FBgn0263051 | CG43346 | - | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | NDUFAF2 | No ortholog found | NA FBgn0034919 | NdufAF3 | NADH:ubiquinone oxidoreductase complex assembly factor 3 | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | NDUFAF3 | No ortholog found | NA FBgn0037777 | NdufAF4 | NADH:ubiquinone oxidoreductase complex assembly factor 4 | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | NDUFAF4 | No ortholog found | NA FBgn0033891 | CG8067 | - | FlytoCarta | GO | HGNC | UNCLASSIFIED METHYLTRANSFERASES | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | NDUFAF5 | No ortholog found | NA FBgn0030352 | sicily | severe impairment of CI with lengthened youth | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | NDUFAF6 | No ortholog found | NA FBgn0037880 | CG17726 | - | FlytoCarta | GO | HGNC | PROTEIN ARGININE N-METHYLTRANSFERASES | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | NDUFAF7 | No ortholog found | NA FBgn0259726 | CG42380 | - | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | NDUFAF8 (only called by eggNOG, Panther) | No ortholog found | NA FBgn0032986 | Nubpl | NUBP iron-sulfur cluster assembly factor, mitochondrial | FlytoCarta | GO | HGNC | ATP-DEPENDENT FE-S CLUSTER CHAPERONES | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | NUBPL | SPAC637.08 | NOT SEEN FBgn0034248 | CG14483 | - | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > OXPHOS assembly factors | PET100 | No ortholog found | NA FBgn0031247 | CG11562 | - | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > OXPHOS assembly factors | PET117 | pet117 | SPBC1604.25 FBgn0037024 | tzn | tenzing norgay | FlytoCarta |   | HGNC | UNCLASSIFIED THIOLESTER HYDROLASES |   | OXPHOS > OXPHOS assembly factors | HAGH | SPAC824.07/SPCC13B11.03c | NOT SEEN FBgn0262467 | Scox | Synthesis of cytochrome c oxidase | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > OXPHOS assembly factors | SCO1 | sco1 | SPBC119.06 FBgn0033274 | CG14757 | - | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex II assembly | OXPHOS > Complex II > CII assembly factors | SDHAF2 | SPAC12B10.06c | SPAC12B10.06c FBgn0033523 | CG12895 | - | FlytoCarta | GO |   |   | mitochondrial respiratory chain complex II assembly | OXPHOS > Complex II > CII assembly factors | SDHAF2 | SPAC12B10.06c | SPAC12B10.06c FBgn0038437 | Sdhaf3 | Succinate dehydrogenase assembly factor 3 | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex II assembly | OXPHOS > Complex II > CII assembly factors | SDHAF3 | SPBP23A10.03c | SPBP23A10.03c FBgn0031971 | Sirup | Starvation-upregulated protein | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex II assembly | OXPHOS > Complex II > CII assembly factors | SDHAF4 | SPBC26H8.16 | SPBC26H8.16 FBgn0085271 | CG34242 | - | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly |   | SMIM20 | No ortholog found | NA FBgn0029117 | Surf1 | Surfeit 1 | FlytoCarta | GO | HGNC |   | mitochondrial respirasome assembly\|mitochondrial cytochrome c oxidase assembly | OXPHOS > OXPHOS assembly factors | SURF1 | shy1 | SPBC1215.01 FBgn0032205 | CG4957 | - | FlytoCarta | GO | HGNC |   | mitochondrial cytochrome c oxidase assembly | OXPHOS > OXPHOS assembly factors | TACO1 | SPBC8D2.12c | NOT SEEN FBgn0031708 | CG7382 | - | FlytoCarta |   |   | TIM23[SORT]-SPECIFIC SUBUNITS |   | OXPHOS > OXPHOS assembly factors | TIMM21 | tim21 | NOT SEEN FBgn0010340 | Timmdc1 | Translocase of inner mitochondrial membrane domain containing 1 | FlytoCarta | GO | HGNC | TIMMDC1 FAMILY | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | TIMMDC1 | No ortholog found | NA FBgn0032033 | Tmem126 | Transmembrane protein 126 | FlytoCarta | GO | HGNC | MITOCHONDRIAL COMPLEX I INTERMEDIATE ASSEMBLY COMPLEX | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | TMEM126A | No ortholog found | NA FBgn0053506 | CG33506 | - | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex II assembly | OXPHOS > OXPHOS assembly factors | TMEM177 | No ortholog found | NA FBgn0033808 | Tmem186 | Transmembrane protein 186 | FlytoCarta | GO | HGNC | MITOCHONDRIAL COMPLEX I INTERMEDIATE ASSEMBLY COMPLEX | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | TMEM186 | No ortholog found | NA FBgn0035805 | Tmem70 | Transmembrane protein 70 | FlytoCarta | GO | HGNC |   | mitochondrial proton-transporting ATP synthase complex assembly | OXPHOS > Complex I > CI assembly factors | TMEM70 | SPAC1834.10c (only called by orthoMCL, Panther) | SPAC1834.10c FBgn0032744 | Ttc19 | Tetratricopeptide repeat domain 19 | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex III assembly | OXPHOS > Complex III > CIII assembly factors | TTC19 | No ortholog found | NA FBgn0035722 | Uqcc1 | Ubiquinol-cytochrome c reductase complex assembly factor 1 | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex III assembly | OXPHOS > Complex III > CIII assembly factors | UQCC1 | cbp3 | SPCC4B3.17 FBgn0037018 | Dmac2 | Distal membrane arm assembly component 2 | FlytoCarta | GO | HGNC |   | mitochondrial respiratory chain complex I assembly | OXPHOS > Complex I > CI assembly factors | DMAC2 | No ortholog found | NA FBgn0028436 | ECSIT | ECSIT | FlytoCarta |   |   | MITOCHONDRIAL COMPLEX I INTERMEDIATE ASSEMBLY COMPLEX |   | OXPHOS > Complex I > CI assembly factors | ECSIT | no orthologs found | NA FBgn0083953 | CG34117 | - | FlytoCarta | GO | HGNC |   | mitochondrial proton-transporting ATP synthase complex assembly | OXPHOS > Complex V > CV assembly factors | FMC1 | no orthologs found | NA FBgn0031392 | AIF | Apoptosis inducing factor | GO |   | MITOCHONDRIAL DISULFIDE RELAY SYTEM | mitochondrial respiratory chain complex assembly |   | AIFM1 | aif1 (ony called by eggNOG, Phylome) | NOT SEEN FBgn0033989 | CG7639 | - | GO |   | SORTING AND ASSEMBLY MACHINERY COMPLEX SUBUNITS | mitochondrial respiratory chain complex assembly |   | SAMM50 | sam50 | NOT SEEN FBgn0040634 | CG4186 | - | GO | HGNC |   |   | mitochondrial respiratory chain complex assembly |   | CHCHD7 | no orthologs found | NA FBgn0037579 | COX7AL | Cytochrome c oxidase subunit 7A-like | GO |   | MITOCHONDRIAL COMPLEX IV - SUPERNUMERARY SUBUNITS (Testis) | mitochondrial respirasome assembly |   | COX7A1 | no orthologs found | NA FBgn0037890 | CG17734 | - | GO |   |   |   | mitochondrial respirasome assembly |   | HIGD1A\|HIGD1B\|HIGD1C | SPAC25B8.07c | SPAC25B8.07c FBgn0085201 | COX7AL2 | Cytochrome c oxidase subunit 7A-like 2 | GO |   | MITOCHONDRIAL COMPLEX IV - SUPERNUMERARY SUBUNITS | mitochondrial respirasome assembly |   | COX7A1\|COX7A2L | no orthologs found | NA FBgn0002021 | l(2)37Bb | lethal (2) 37Bb | GO |   |   |   | mitochondrial respiratory chain complex I assembly |   | FOXRED1 | fap2 | NOT SEEN FBgn0011361 | ND-ACP | NADH dehydrogenase (ubiquinone) acyl carrier protein | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFAB1 | SPAC4H3.09 | NOT SEEN FBgn0011455 | ND-SGDH | NADH dehydrogenase (ubiquinone) SGDH subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFB5 | no orthologs found | NA FBgn0017566 | ND-75 | NADH dehydrogenase (ubiquinone) 75 kDa subunit | GO |   | MITOCHONDRIAL COMPLEX I - CORE SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFS1 | no orthologs found | NA FBgn0017567 | ND-23 | NADH dehydrogenase (ubiquinone) 23 kDa subunit | GO |   | MITOCHONDRIAL COMPLEX I - CORE SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFS8 | no orthologs found | NA FBgn0021967 | ND-PDSW | NADH dehydrogenase (ubiquinone) PDSW subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFB10 | no orthologs found | NA FBgn0029868 | ND-B16.6 | NADH dehydrogenase (ubiquinone) B16.6 subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFA13 | no orthologs found | NA FBgn0029888 | ND-ASHI | NADH dehydrogenase (ubiquinone) ASHI subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFB8 | no orthologs found | NA FBgn0029971 | ND-MNLL | NADH dehydrogenase (ubiquinone) MNLL subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFB1 | no orthologs found | NA FBgn0030605 | ND-B18 | NADH dehydrogenase (ubiquinone) B18 subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFB7 | no orthologs found | NA FBgn0030718 | ND-20 | NADH dehydrogenase (ubiquinone) 20 kDa subunit | GO |   | MITOCHONDRIAL COMPLEX I - CORE SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFS7 | no orthologs found | NA FBgn0031021 | ND-18 | NADH dehydrogenase (ubiquinone) 18 kDa subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFS4 | no orthologs found | NA FBgn0031228 | ND-15 | NADH dehydrogenase (ubiquinone) 15 kDa subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFS5 | no orthologs found | NA FBgn0031436 | ND-B17.2 | NADH dehydrogenase (ubiquinone) B17.2 subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFA12 | no orthologs found | NA FBgn0031505 | ND-B14.5B | NADH dehydrogenase (ubiquinone) B14.5 B subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFC2 | no orthologs found | NA FBgn0032511 | ND-B22 | NADH dehydrogenase (ubiquinone) B22 subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFB9 | no orthologs found | NA FBgn0033570 | ND-B14 | NADH dehydrogenase (ubiquinone) B14 subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFA6 | no orthologs found | NA FBgn0033961 | ND-B15 | NADH dehydrogenase (ubiquinone) B15 subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFB4 | no orthologs found | NA FBgn0034576 | ND-B14.7 | NADH dehydrogenase (ubiquinone) B14.7 subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS/NDUFA11 FAMILY | mitochondrial respiratory chain complex I assembly |   | NDUFA11 | no orthologs found | NA FBgn0034578 | CG15653 | - | GO |   |   |   | mitochondrial respiratory chain complex I assembly\|mitochondrial cytochrome c oxidase assembly |   | COA1 | no orthologs found | NA FBgn0034645 | ND-B12 | NADH dehydrogenase (ubiquinone) B12 subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFB3 | no orthologs found | NA FBgn0035046 | ND-19 | NADH dehydrogenase (ubiquinone) 19 kDa subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFA8 | no orthologs found | NA FBgn0037001 | ND-39 | NADH dehydrogenase (ubiquinone) 39 kDa subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFA9 | SPCC1840.09 (only called by eggNOG, Phylome) | NOT SEEN FBgn0039669 | ND-20L | NADH dehydrogenase (ubiquinone) 20 kDa subunit-like | GO |   | MITOCHONDRIAL COMPLEX I - CORE SUBUNITS (Testis) | mitochondrial respiratory chain complex I assembly |   | NDUFS7 | no orthologs found | NA FBgn0040705 | ND-B8 | NADH dehydrogenase (ubiquinone) B8 subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFA2 | mrpl51 | NOT SEEN FBgn0058002 | ND-AGGG | NADH dehydrogenase (ubiquinone) AGGG subunit | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS (Testis) | mitochondrial respiratory chain complex I assembly |   | NDUFB2 | no orthologs found | NA FBgn0085736 | CG40472 | - | GO |   | MITOCHONDRIAL COMPLEX I - ACCESSORY SUBUNITS | mitochondrial respiratory chain complex I assembly |   | NDUFB2 | no orthologs found | NA FBgn0028844 | CG15283 | - | GO |   |   |   | mitochondrial respiratory chain complex II assembly |   | SDHAF4 | SPBC26H8.16 | NOT SEEN FBgn0039576 | UQCR-14L | Ubiquinol-cytochrome c reductase 14 kDa subunit-like | GO |   | MITOCHONDRIAL COMPLEX III - SUPERNUMERARY SUBUNITS (Testis) | mitochondrial respiratory chain complex III assembly |   | UQCRB | qcr7 | NOT SEEN FBgn0040715 | CG15386 | - | GO |   |   |   | mitochondrial respiratory chain complex III assembly |   | no orthologs found | no orthologs found | NA FBgn0050373 | CG30373 | - | GO | HGNC |   |   | mitochondrial respiratory chain complex III assembly |   | C16orf91 | no orthologs found | NA FBgn0052736 | sloth1 | sloth 1 | GO | HGNC |   |   | mitochondrial respiratory chain complex III assembly |   | UQCC5 | no orthologs found | NA FBgn0259204 | sloth2 | sloth 2 | GO | HGNC |   |   | mitochondrial respiratory chain complex III assembly |   | UQCC6 | no orthologs found | NA FBgn0287589 | CG46459 | - | GO | HGNC |   |   | mitochondrial respiratory chain complex III assembly |   | UQCC2 | pyp2 | NOT SEEN FBgn0002354 | l(3)87Df | lethal (3) 87Df | GO | HGNC |   |   | mitochondrial cytochrome c oxidase assembly |   | COX20 | cox20 | SPBC25H2.18 FBgn0031066 | COX6B | Cytochrome c oxidase subunit 6B | GO |   | MITOCHONDRIAL COMPLEX IV - SUPERNUMERARY SUBUNITS | mitochondrial cytochrome c oxidase assembly |   | COX6B1 | cox12 | NOT SEEN FBgn0033547 | CG12935 | - | GO | HGNC |   |   | mitochondrial cytochrome c oxidase assembly |   | TMEM223 | no orthologs found | NA FBgn0027615 | OXA1L | OXA1L mitochondrial inner membrane protein | GO | HGNC | YIDC/ALB3/OXA1 MEMBRANE PROTEIN INSERTASE FAMILY | mitochondrial proton-transporting ATP synthase complex assembly |   | OXA1L | oxa101\|oxa102 | NOT SEEN FBgn0030311 | CG11699 | - | GO | HGNC |   |   | mitochondrial proton-transporting ATP synthase complex assembly |   | TMEM242 | no orthologs found | NA FBgn0032644 | CG5131 | - | GO |   | M76 METALLOENDOPEPTIDASES | mitochondrial proton-transporting ATP synthase complex assembly |   | ATP23 | atp23 | SPCC320.12 FBgn0015582 | dare | defective in the avoidance of repellents |   | HGNC | UNCLASSIFIED OXIDOREDUCTASES |   |   | FDXR | arh1 | NOT SEEN FBgn0011769 | Fdx1 | Ferredoxin 1 |   | HGNC |   |   |   |   | FDX2 | etp1 (only called by eggNOG, Phylome) | NOT SEEN FBgn0038925 | Cchl | Cytochrome c heme lyase |   | HGNC | CARBON-SULFUR LYASES |   |   | HCCS | SPAC24C9.02c | NOT SEEN FBgn0284256 | bsf | bicoid stability factor |   | HGNC |   |   |   |   | LRPPRC | no orthologs found | NA FBgn0034793 | asrij | asrij |   | HGNC |   |   |   |   | OCIAD1 | no orthologs found | NA FBgn0086712 | Egm | Enigma |   |   | MITOCHONDRIAL COMPLEX I INTERMEDIATE ASSEMBLY COMPLEX |   |   | ACAD8\|ACAD9\|ACADL | no orthologs found | NA FBgn0033734 | CG8520 |   |   |   |   |   |   |   |   | SPBC115.02c (from Pombe list) | NA FBgn0036479 | CG13458 |   |   |   |   |   |   |   |   | SPAC25B8.04c (from Pombe list) | NA FBgn0286199 | shps |   |   |   |   |   |   |   |   | SPBC26H8.01 (from Pombe list, only called by OrthoFinder) | NA

[ValWood]

Notes

• anything which is an LRR repeat protein is upstream of assembly. These are all involved in various aspects of gene expression (transcription, translation and splicing), but historically got annotated to complex assembly because the complexes don't for. I see a few of those in there.
• also cox10 protoheme IX farnesyltransferase, catalyzes conversion of protoheme to heme A in heme A, so its required upstream of cyc1, cox1, cyt1 and tim18 (all have heme centres), was originally isolated as an assembly defect in cerevisiae
• • would need to connect up from the ends of this pathway (same applies to etp1) https://amigo.geneontology.org/amigo/model/66c7d41500000841 depending on whether heme b,o, or a
• There do appear to be genes specifically involved in the assembly of supercomplexes (aka respirasomes) i.e The levels of supercomplexes III2IV2 and III2IV were found to be lower in ∆shy1 cells compared to WT cells, while the abundance of COA complexes increased (Fig. 7a), indicating that the formation of supercomplexes involving complex IV is influenced by deletion of shy1. In contrast, the abundance of III2 and V complexes was largely unchanged in ∆shy1 cells (Fig. 7a).
• UQCRB is ubiquinol-cytochrome-c reductase complex subunit 6 (so a respiratory complex III subunit rather than an assembly factor)
• TACO1 is a translational activator, I plan to include in this it in this model http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A67086be200000519
• TIMM21 upstream, import into matrix
• respiratory chain complex IV

[ValWood]

@hattrill should "NOT SEEN" be in the final column for the ones below NDUFAB1 (I am assuming this always means that it isn't in my list?)

[hattrill]

Hi @ValWood there are quite a few that I have doubts about - some are modifiers and protein maturation factors that have made their way onto HGNC, MitoCarta or via GO - IBA, ISS, etc. As this is a mash-up of HGNC calls, MitoCarta calls and what we have in the GO, think there will be a lot of removal from this.

We have COX6B1 as a MITOCHONDRIAL COMPLEX IV - SUPERNUMERARY SUBUNIT gene groups. - I've made a note about those as many of the supernumerary/accessory subunits have assembly GO terms - I think that this is because they are required for complex stability rather than assembly and it's 'cellular phenotype that's been annotated. That's why need to align it against reviews.

"NOT SEEN" means that I found an ortholog via DIOPT for Pombe but not on your list (or I could have missed when I did the cross-search.

Human ATPSCKMT, FDXR, FDX2, HCCS, LRPPRC, OXA1L, SCO1 - come from HGNC or MitoCarta are ones on my current 'dump' list as they seem upstream to assembly.

[ValWood]

"NOT SEEN" means that I found an ortholog via DIOPT for Pombe but not on your list (or I could have missed when I did the cross-search.

I think this is sometimes in the wrong column

[hattrill]

Might have munged the formating - let me update it.

[hattrill]

Hopefully fixed now - some columns got merged a messed the layout up.

I will be removing a lot from the list....just trying to work out where to start - think that ones that are classed as accessory/supernumerary subunits will be first stop there are a lot.

[ValWood]

OK once you have cleaned up, I'll review the pombe ones and make sure all of mine are in your table. I have some definite orthologs for some: COA2 is SPBC16E9.03c(coa2) TTC19 is SPAP27G11.02(mgr3) equivalent complex member FMC1 is SPAC1486.11(fmc1) AIFM1 is SPAC26F1.14c(aif1) SAMM50 is SPAC17C9.06(sam50) pombe has no NDUFA2 (the human ortholog of pombe mrpl51 is human MRPL51) So I will add these (with the evidence once I dig it out).

I'll also have a good look for anything that is missing from pombe (although I am not expecting to find the Complex I assembly - because we don't have it). We do have 3 (I think ) of the subunits but these might really be assembly factors that are also used by other complexes (or something like that).

[hattrill]

This looks like a nice review publication to start with for me: https://doi.org/10.1042/EBC20170098....complex I assembly looks fun! Starting to wish we had no complex I ;-)

[ValWood]

The Wikipedia page isn't half bad, I was looking at it the other week when I found some of the assembly factors in pombe https://en.wikipedia.org/wiki/Respiratory_complex_I

[hattrill]

This is great - I woke up last night thinking I need to find a review with a table - this will do nicely!

[ValWood]

The things which keep us awake ! ;)

[hattrill]

Think I've found the paper that 'poisoned' the complex I assembly well - A lot of annotations originate from PMID:27626371 in which the KO of different accessory CI SUs were examined for their role in assembly. However, although the absence of SUs may impact assembly, I think that this is because they have a structural role in the complex/complex intermediates rather than being factors that assist in the assembly of the complex.

I like this as a definition of assembly "This multistep process involves transiently associated assembly factors that integrate core and accessory/supernumerary subunits as well as cofactors into the final holoenzyme." (PMID: 38086790).

I will have a bit more of a dig and then ask Alex Whitworth as if this works need to get a few places to revise their lists as well as GO.