Characteristics and Functions of the Yip1 Domain Family (YIPF), Multi-Span Transmembrane Proteins Mainly Localized to the Golgi Apparatus

Shaheena, Shaik; Pandey, Himani; Thirumalasetti, Satish; Nakamura, Nobuhiro

doi:10.3389/fcell.2019.00130

Cited by 19 publications

(21 citation statements)

References 69 publications

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“…Several proteins associated with COP-II are also involved in the STING signaling. Yip1 domain family (YIPF) proteins are multi-spanning membrane proteins ( 29 ). Yeast Yip1p regulates COP-II vesicle biogenesis ( 30 ).…”

Section: Exocytic Membrane Traffic Of Sting From the Ermentioning

confidence: 99%

STING Operation at the ER/Golgi Interface

et al. 2021

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DNA is present in the nucleus and mitochondria of eukaryotic cells. There are, however, certain instances in which DNA emerges in the cytosol. The two major sources of cytosolic DNA are self DNA that is leaked out from the nucleus or mitochondria, and non-self DNA from DNA viruses. The cytosolic DNA triggers the host immune response. Recent studies have identified two key molecules, cyclic GMP-AMP (cGAMP) synthase (cGAS) and stimulator of interferon genes (STING) in this immune response. STING is an endoplasmic reticulum (ER) protein. After STING binding to cGAMP, STING exits the ER and translocates to the Golgi, where STING triggers the type I interferon- and proinflammatory responses through the activation of interferon regulatory factor 3 (IRF3) and nuclear factor-kappa B (NF-κB). STING also activates other cellular responses including cell senescence, autophagy, and cell death. In this review, we focus on emerging issues regarding the regulation of STING by membrane traffic, with a particular focus on the retrograde membrane traffic from the Golgi to the ER. The retrograde membrane traffic is recently shown by us and others to be critical for silencing the STING signaling pathway and the defect in this traffic underlies the pathogenesis of the COPA syndrome, a monogenic autoinflammatory disease caused by missense mutations of coatomer protein complex subunit α (COP-α).

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Section: Exocytic Membrane Traffic Of Sting From the Ermentioning

confidence: 99%

STING Operation at the ER/Golgi Interface

et al. 2021

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“…This was the only protein identified as a receptor. Transporters described with a TCDB identifier may be under-represented as recent work has been published on the sideroflexin ( Kory et al, 2018 ; Rivell et al, 2019 ) as well as YIPF ( Shaik et al, 2019 ) family members.…”

Section: Analysis Resultsmentioning

confidence: 99%

“…Hence, with such a heavy influence on possible functional activities and localization preferences associated with the 5TM architecture, we performed more comprehensive analysis of these families. Additionally, we performed phylogenetic analysis on the sideroflexin family as we were not able to find a current wide ranging evolutionary study on this family while investigations have been published on the tweety and YIPF families ( Matthews et al, 2007 ; Han et al, 2019 ; Shaik et al, 2019 ).…”

Section: The Three Major 5tm Familiesmentioning

confidence: 99%

“…Nine human members make up this family including YIF1A, YIF1B, YIPF1, YIPF2, YIPF3, YIPF4, YIPF5, YIPF6, and YIPF7. These proteins form complexes with each other in specific partner pairs to form oligomers with 20 transmembrane segments ( Shaik et al, 2019 ). All of the proteins except YIPF7 and YIF1A appear to have low tissue specificity and are detected in all the investigated tissues, while YIPF7 is enriched in skeletal muscles and tongue and YIF1A is tissue enhanced in the liver and both are detected in some other tissues.…”

Section: The Three Major 5tm Familiesmentioning

confidence: 99%

“…All of the proteins except YIPF7 and YIF1A appear to have low tissue specificity and are detected in all the investigated tissues, while YIPF7 is enriched in skeletal muscles and tongue and YIF1A is tissue enhanced in the liver and both are detected in some other tissues. All of the YIPF members are expected to localize to the early, middle or late compartments of the Golgi apparatus, depending on the protein complexes that are formed, and transport to and from between other compartments ( Shaik et al, 2019 ). Hence, additional annotations describe YIF1B, YIPF4, YIPF5, and YIPF6 to be found in vesicles, while YIPF1, YIPF3, and YIPF5 have also been found in the nucleoplasm.…”

Section: The Three Major 5tm Familiesmentioning

confidence: 99%

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Characterization of Five Transmembrane Proteins: With Focus on the Tweety, Sideroflexin, and YIP1 Domain Families

Attwood

Schiöth

2021

Front. Cell Dev. Biol.

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Transmembrane proteins are involved in many essential cell processes such as signal transduction, transport, and protein trafficking, and hence many are implicated in different disease pathways. Further, as the structure and function of proteins are correlated, investigating a group of proteins with the same tertiary structure, i.e., the same number of transmembrane regions, may give understanding about their functional roles and potential as therapeutic targets. This analysis investigates the previously unstudied group of proteins with five transmembrane-spanning regions (5TM). More than half of the 58 proteins identified with the 5TM architecture belong to 12 families with two or more members. Interestingly, more than half the proteins in the dataset function in localization activities through movement or tethering of cell components and more than one-third are involved in transport activities, particularly in the mitochondria. Surprisingly, no receptor activity was identified within this dataset in large contrast with other TM groups. The three major 5TM families, which comprise nearly 30% of the dataset, include the tweety family, the sideroflexin family and the Yip1 domain (YIPF) family. We also analyzed the evolutionary origin of these three families. The YIPF family appears to be the most ancient with presence in bacteria and archaea, while the tweety and sideroflexin families are first found in eukaryotes. We found no evidence of common decent for these three families. About 30% of the 5TM proteins have prominent expression in the brain, liver, or testis. Importantly, 60% of these proteins are identified as cancer prognostic markers, where they are associated with clinical outcomes of various tumor types. Nearly 10% of the 5TMs are still not fully characterized and further investigation of their functional activities and expression is warranted. This study provides the first comprehensive analysis of proteins with the 5TM architecture, providing details of their unique characteristics.

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