Table 1.

List of proteins cited in this review, with their localization, function, and main interactors

Protein	Localization	Function	Known interactors	References
β-galactosidase	Lysosome	Catalyzes the hydrolysis of a terminal β-linked galactose residue from ganglioside substrates and other glycoconjugates	Protective protein cathepsi A (PPCA), neuraminidase 1 (NEU1)	126, 127
Cathepsin D	Lysosome	Aspartic-type endopeptidase activity		80
Palmitoyl-protein thioesterase 1, PPT1	Lysosome	Removes thioester-linked fatty acyl groups such as palmitate from cysteine residues	CLN5	80
Tripeptidyl peptidase 1, TPP1	Lysososome	Cleaves N-terminal tripeptides from substrates, and has weaker endopeptidase activity	CLN5	80
PSS1	ER face of the MAMs	Phosphatidylserine synthase 1		128
PSS2	ER face of the MAMs	Phosphatidylserine synthase 2		128
PS- decarboxylase	Mitochondrial side of the MAMs	Phosphatidylserine- decarboxylase		59
PE-methyltransferase, PEMT	MAMs	Phosphatidylethanolamine-methyltransferase		62
Mdm10	Mitochondria/MAMs	ERMES complex	Mdm34, Mmm1, Mdm12, Gem1	45, 71
Mdm34	Mitochondria/MAMs	ERMES complex	Mdm10, Mmm1, Mdm12, Gem1	45, 73
Mmm1	ER/MAMs	ERMES complex	Mdm34, Mmm10, Mdm12, Gem1	45, 72
Mdm12	Cytosol/MAMs	ERMES complex	Mdm34, Mmm10, Mdm1, Gem1	45, 73
Lam6	MAMs, vacuole-mitochondria patches, nuclear-vacuole contact sites	ERMES complex, vCLAMP (vacuole and mitochondria patch), and NVJ (nuclear vacuolar junction)	Mdm10, Mmm1, Mdm12, Mdm34, Vps39, Nvj1, Vac8	74, 75
Gem1	MAMs	ERMES complex	Mdm10, Mmm1, Mdm12, Mdm34	70, 72
EMC1	MAMs	EMC, PS transfer, MAMs architecture	TOM5	78
EMC2	MAMs	EMC, PS transfer, MAMs architecture	TOM5	78
EMC3	MAMs	EMC, PS transfer, MAMs architecture	TOM5	78
EMC4	MAMs	EMC, PS transfer, MAMs architecture	TOM5	78
EMC5	MAMs	EMC, PS transfer, MAMs architecture	TOM5	78
EMC6	MAMs	EMC, PS transfer, MAMs architecture	TOM5	78
CLN8	ER integral membrane protein	Transmembrane protein belonging to a family of proteins containing TLC domains, which are postulated to function in lipid synthesis, transport, or sensing.	CLN5	80
Caspase 12	ER	Member of the cysteine-aspartic acid protease family responsible for ER-stress-induced apoptosis		102, 129
PC- cytidyltransferase, CTP	Cytosol, MAMs	Involved in the regulation of phosphatidylcholine biosynthesis		86
Acetyl-CoA:cholesterol acyltransferase, ACAT	MAMs	Catalyzes the reversible formation of acetoacetyl-CoA from two molecules of acetyl-CoA		35, 90
Steroidogenic acute regulatory protein, StaR	MAMs, mitochondria	Plays a key role in the acute regulation of steroid hormone synthesis by enhancing the conversion of cholesterol into pregnenolone	TOMM22, VDAC2	97
Sigma-1 receptor	ER face of the MAMs	Interacts with a variety of psychotomimetic drugs, including cocaine and amphetamines. The receptor is believed to play an important role in the cellular functions of various tissues associated with the endocrine, immune, and nervous systems.	BiP, IP3R3	100
VDAC-1	Mitochondrial side of the MAMs	Facilitates the exchange of metabolites and ions across the outer mitochondrial membrane	Grp75	130
IP3R-1	ER, MAMs	Mediates calcium release from the endoplasmic reticulum following stimulation by inositol 1,4,5-trisphosphate	GRP75	52, 130, 131
GRP75	ER, mitochondria, MAMs	Member of the heat shock protein 70 gene family, functions as scaffold between IP3R-1 and VDAC1	IP3R-1 and VDAC1	52, 130
BiP	ER, MAMs	Involved in the folding and assembly of proteins in the ER	Interacts with many ER proteins	108, 132
Calnexin	ER, MAMs	Ca2+-binding protein that interacts transiently with newly synthesized N-linked glycoproteins, facilitating protein folding and assembly	PACS2, AMBRA1, WIPI1	116, 133
hFis1	Mitochondria	Promotes mitochondrial fission	t-Bid, Bax,, VDAC1	134, 135
t-Bid	Mitochondria	Member of the BCL-2 family of cell death regulators	Eterodimerizes with either agonist BAX or antagonist BCL2, VDAC1	134, 136
Bax	Mitochondria	Member of the BCL-2 family of cell death regulators	BCL2 family members form hetero- or homodimers and act as anti- or pro-apoptotic regulators	134, 137
LC3	Autophagic vacuoles	LC3 (encoded by MAPLC3A and MAPLC3B) is the homolog of the yeast ATG8, an important marker and effector of autophagy	Microtubules, FYCO1, TP53INP1 and TP53INP2, TBC1D25, SQSTM1, ATG4B, MAPK15 and BNIP3, MAPB1, KEAP1, PCM1, OFD1, CEP131, TECPR2,TBC1D5, UBQLN1, UBQLN2, UBQLN4, UBQLN1, ATG13, FAM134A, FAM134B, FAM134C	140–152
AMBRA1	Autophagic vacuoles	Regulates autophagy and development of the nervous system	BECN1, BECN2, BCL2, dynein light chains 1 and 2, WIPI1, calnexin	116, 151, 152
WIPI1	Autophagic vacuoles	Plays an important role in autophagy and in particular starvation- and calcium-mediated autophagy	Interacts with androgen receptor (AR) and the estrogen receptors ESR1, and ESR2, calnexin	116, 153
CHOP	Nucleus	CCAAT-enhancer-binding protein homologous protein		102
JNK2	Cytosol	JNKs (c-Jun N-terminal kinases) are a group of mitogen-activated protein kinases activated by various environmental stresses		102, 154