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9.B.135 The Membrane Trafficking Yip (Yip) Family

The YIP1 family of proteins are small membrane proteins with 5 putative TMSs with roles in membrane trafficking from the ER to the golgi. In yeast they participate in vesicle biogenesis and mediate the association of Rab proteins with membranes. Yeast YIP1 is an essential gene and can be fully complemented by a human counterpart, suggesting that the essential function of Yip1p is evolutionarily conserved (Chen and Collins, 2005).  Prokaryotic homologues are found in family 9.B.29 and possibly family 3.A.1.122, and families 9.B.29 and 9.B.135 may comprise a superfamily.

Human YIPF3 and YIPF4 are localized to the cis-Golgi. YIPF3 is synthesized in the ER as a N-glycosylated form (40 kDa), is then O-glycosylated in the Golgi and finally is cleaved at its C-terminal luminal domain. YIPF3 and YIPF4 form a complex in the Golgi apparatus. The knockdown of YIPF3 or YIPF4 in HeLa cells induced fragmentation of the Golgi apparatus (Tanimoto et al., 2011). Mutation of Yip1 domain family, member 6 (Yipf6), induces spontaneous intestinal inflammation in mice (Brandl et al., 2012). YIPF proteins primarily localise to the Golgi complex and can be grouped into trans-Golgi-localising YIPFs (YIPF1 and YIPF2) and cis-Golgi-localising YIPFs (YIPF3, YIPF4 and YIPF5), with YIPF6 and YIPF7 showing a broader profile being distributed throughout the Golgi stack (Kranjc et al. 2017). YIPF proteins have a long soluble N-terminal region, which is orientated towards the cytosol, followed by 5 closely stacked TMSs, and a C terminus, orientated towards the lumen of the Golgi. A number of specific morphological changes to this organelle on their depletion (Kranjc et al. 2017). Transcriptional regulation analysis of porcine Yip1 domain family member 3 genehas been reported (Ni et al. 2020).

S. cerevisiae contains four YIPFs: Yip1p, Yif1p, Yip4p, and Yip5p. Yip1p and Yif1p bind to each other and play a role in budding of transport vesicles and/or fusion of vesicles to target membranes. Human cells have nine family members that have overlapping functions. These YIPF proteins are divided into two sub-families: YIPFα/Yip1p and YIPFβ/Yif1p. A YIPFα molecule forms a complex with a specific partner YIPFβ molecule. A basic tetrameric complex is formed from two molecules of each partner YIPF protein, and this tetramer forms a higher order oligomer (Shaik et al. 2019). Three distinct YIPF protein complexes are formed from pairs of YIPFα and YIPFβ proteins. These are differently localized in either the early, middle, or late compartments of the Golgi apparatus and are recycled between adjacent compartments. Because a YIPF protein is predicted to have five TMSs, a YIPF tetramer complex is predicted to have 20 TMSs. This high number of TMSs suggests that YIPF complexes function as channels, transporters, or transmembrane receptors (Shaik et al. 2019).

This family belongs to the: YIP Superfamily.

References associated with 9.B.135 family:

Brandl, K., W. Tomisato, X. Li, C. Neppl, E. Pirie, W. Falk, Y. Xia, E.M. Moresco, R. Baccala, A.N. Theofilopoulos, B. Schnabl, and B. Beutler. (2012). Yip1 domain family, member 6 (Yipf6) mutation induces spontaneous intestinal inflammation in mice. Proc. Natl. Acad. Sci. USA 109: 12650-12655. 22802641
Chen, C.Z. and R.N. Collins. (2005). Analysis and properties of the yeast YIP1 family of Ypt-interacting proteins. Methods Enzymol 403: 333-339. 16473599
Kranjc, T., E. Dempsey, G. Cagney, N. Nakamura, D.C. Shields, and J.C. Simpson. (2017). Functional characterisation of the YIPF protein family in mammalian cells. Histochem Cell Biol 147: 439-451. 27999994
Ni, D., X. Huang, Z. Wang, L. Deng, L. Zeng, Y. Zhang, D. Lu, and X. Zou. (2020). Expression characterization and transcription regulation analysis of porcine Yip1 domain family member 3 gene. Asian-Australas J Anim Sci 33: 398-407. 31480180
Shaik, S., H. Pandey, S.K. Thirumalasetti, and N. Nakamura. (2019). Characteristics and Functions of the Yip1 Domain Family (YIPF), Multi-Span Transmembrane Proteins Mainly Localized to the Golgi Apparatus. Front Cell Dev Biol 7: 130. 31417902
Soonthornsit, J., N. Sakai, Y. Sasaki, R. Watanabe, S. Osako, and N. Nakamura. (2017). YIPF1, YIPF2, and YIPF6 are medial-/trans-Golgi and trans-Golgi network-localized Yip domain family proteins, which play a role in the Golgi reassembly and glycan synthesis. Exp Cell Res 353: 100-108. 28286305
Tanimoto, K., K. Suzuki, E. Jokitalo, N. Sakai, T. Sakaguchi, D. Tamura, G. Fujii, K. Aoki, S. Takada, R. Ishida, M. Tanabe, H. Itoh, Y. Yoneda, M. Sohda, Y. Misumi, and N. Nakamura. (2011). Characterization of YIPF3 and YIPF4, cis-Golgi Localizing Yip domain family proteins. Cell Struct Funct 36: 171-185. 21757827