Arf Proteins and Their Regulators: At the Interface Between Membrane Lipids and the Protein Trafficking Machinery

Jackson, Catherine

doi:10.1007/978-3-319-07761-1_8

Cited by 6 publications

(4 citation statements)

References 158 publications

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“…While Arf4 and Arf6 seem to duplicate only sporadically, Arf1 is often present in more than one copy, suggesting a high propensity for duplication; this tendency is in fact seen for eukaryote lineage in general (Supplementary table 2). Phylogenetic analyses usually do not recover Arf1 and Arf4 as supported monophyletic clades (e.g., Figure 4), which is probably a result of their high sequence similarity reflected also in partial functional overlap of Arf1 and Arf4 (Jackson, 2014;Jackson and Bouvet, 2014). However, their separation is obvious from the comparison of the exon-intron structures of the respective genes (Supplementary figure 11).…”

Section: Expansion Of the Arf Family In Holozoamentioning

confidence: 99%

“…Phylogenetic analyses usually do not recover Arf1 and Arf4 as supported monophyletic clades (e.g., fig. 4), which is probably a result of their high sequence similarity reflected also in partial functional overlap of Arf1 and Arf4 (Jackson 2014;Jackson and Bouvet 2014). However, their separation is obvious from the comparison of the exon-intron structures of the respective genes (supplementary fig, 11, Supplementary…”

Section: Expansion Of the Arf Family In Holozoamentioning

confidence: 99%

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A eukaryote-wide perspective on the diversity and evolution of the ARF GTPase protein family

Vargová

Wideman

Derelle

et al. 2020

Preprint

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ARF family GTPases act in diverse cellular processes, critical for organellar function today and understanding eukaryotic origins. However, our understanding of ARF family evolution is limited. Our phylogenetically comprehensive in silico analyses of ARF family members here doubles the set of ancestral eukaryotic paralogs and challenges existing norms for small GTPases, with examples of non-standard modes of membrane association and novel protein architectures. Evidence for the pan-eukaryotic and ancestral origin of Arf6, Arl13 and Arl16 is presented for the first time, while three newly described ancient sub-families are absent from well-studied model organisms, leaving their functions completely unexplored. Evolutionary analysis of metazoa-specific ARF family GTPases also uncovered several new proteins in animals. Delving back to eukaryogenesis, the relationship within the ARF GTPases sets boundaries for scenarios of vesicle coat origins. Finally, we report the discovery of the archaeal proteins from which the entire eukaryotic ARF family is derived.

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Section: Expansion Of the Arf Family In Holozoamentioning

confidence: 99%

Section: Expansion Of the Arf Family In Holozoamentioning

confidence: 99%

A eukaryote-wide perspective on the diversity and evolution of the ARF GTPase protein family

Vargová

Wideman

Derelle

et al. 2020

Preprint

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“…GBF1 is an activator of small GTPases of the Arf family and activated Arfs recruit to membranes multiple Arf effector proteins that establish a biochemically distinct local membrane environment (119, 120). The Arf activating function of GBF1 is essential for the enterovirus replication, and all Arf isoforms massively associate with the replication organelles (54, 82, 83).…”

Section: Discussionmentioning

confidence: 99%

A Proximity Biotinylation Assay with a Host Protein Bait Reveals Multiple Factors Modulating Enterovirus Replication

Moghimi

Viktorova

Gabaglio

et al. 2022

Preprint

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As ultimate parasites, viruses depend on host factors for every step of their life cycle. On the other hand, cells evolved multiple mechanisms of detecting and interfering with viral replication. Yet, our understanding of the complex ensembles of pro- and anti-viral factors is very limited in virtually every virus-cell system. Here we investigated the proteins recruited to the replication organelles of poliovirus, a representative of the genus Enterovirus of the Picornaviridae family. We took advantage of a strict dependence of enterovirus replication on a host protein GBF1, and established a stable cell line expressing a truncated GBF1 fused to APEX2 peroxidase that effectively supported viral replication upon inhibition of the endogenous GBF1. This construct biotinylated multiple host and viral proteins on the replication organelles. Among the viral proteins, the polyprotein cleavage intermediates were overrepresented, arguing that the GBF1 environment is linked to the viral polyprotein processing. The proteomics characterization of biotinylated host proteins identified those previously associated with the enterovirus replication, as well as more than 200 new factors recruited to the replication organelles. RNA metabolism proteins many of which normally localize in the nucleus constituted the largest group, underscoring the massive release of nuclear factors in the cytoplasm of infected cells and their involvement in the viral replication. Analysis of several newly identified proteins revealed both pro- and anti-viral factors, including a novel component of infection-induced stress granules. Depletion of these proteins similarly affected the replication of diverse enteroviruses indicating broad conservation of the replication mechanisms. Thus, our data significantly increase the knowledge about the organization of enterovirus replication organelles and may provide new targets for anti-viral interventions.

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“…There are six mammalian Arf proteins (humans have five: Arf1, Arf3, Arf4, Arf5 and Arf6), which are separated into three classes on the basis of sequence homology [69]. Class I consists of Arf1, Arf2 and Arf3 and is found in all eukaryotes, while classes II (Arf4 and Arf5) and III (Arf6) are less conserved [70]. In yeast, simultaneous deletion of Arf1 and Arf2 results in a lack of viability suggesting an overlapping function of these two proteins not provided by Arf3 [71].…”

Section: Regulation Of Copi Vesicle Formation By Arf Family Gtpasesmentioning

confidence: 99%

The structure of COPI vesicles and regulation of vesicle turnover

2022

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Edited by Jacqueline Cherfils COPI-coated vesicles mediate transport between Golgi stacks and retrograde transport from the Golgi to the endoplasmic reticulum. The COPI coat exists as a stable heptameric complex in the cytosol termed coatomer and is recruited en bloc to the membrane for vesicle formation. Recruitment of COPI onto membranes is mediated by the Arf family of small GTPases, which, in their GTP-bound state, bind both membrane and coatomer. Arf GTPases also influence cargo selection, vesicle scission and vesicle uncoating. Guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) regulate nucleotide binding by Arf GTPases. To understand the mechanism of COPI-coated vesicle trafficking, it is necessary to characterize the interplay between coatomer and Arf GTPases and their effectors. It is also necessary to understand interactions between coatomer and cargo, cargo adaptors/receptors and tethers facilitating binding to the target membrane. Here, we summarize current knowledge of COPI coat protein structure; we describe how structural and biochemical studies contributed to this knowledge; we review mechanistic insights into COPI vesicle biogenesis and disassembly; and we discuss the potential to answer open questions in the field.

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Arf Proteins and Their Regulators: At the Interface Between Membrane Lipids and the Protein Trafficking Machinery

Cited by 6 publications

References 158 publications

A eukaryote-wide perspective on the diversity and evolution of the ARF GTPase protein family

A eukaryote-wide perspective on the diversity and evolution of the ARF GTPase protein family

A Proximity Biotinylation Assay with a Host Protein Bait Reveals Multiple Factors Modulating Enterovirus Replication

The structure of COPI vesicles and regulation of vesicle turnover

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