The Uso1 globular head interacts with SNAREs to maintain viability even in the absence of the coiled-coil domain
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This paper reports a detailed functional analysis of the Rab1 effector Uso1, and it provides a fundamental advance in our understanding of how ER-derived vesicles deliver their cargo. The authors provide compelling evidence that the key function of Uso1 is promoting SNARE complex formation rather than tethering vesicles as generally assumed. These insights will be of interest to cell and structural biologists who study membrane traffic.
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Abstract
Uso1/p115 and RAB1 tether ER-derived vesicles to the Golgi. Uso1/p115 contains a globular-head-domain (GHD), a coiled-coil (CC) mediating dimerization/tethering, and a C-terminal region (CTR) interacting with golgins. Uso1/p115 is recruited to vesicles by RAB1. Genetic studies placed Uso1 paradoxically acting upstream of, or in conjunction with RAB1 (Sapperstein et al., 1996). We selected two missense mutations in uso1 resulting in E6K and G540S in the GHD that rescued lethality of rab1 -deficient Aspergillus nidulans . The mutations are phenotypically additive, their combination suppressing the complete absence of RAB1, which emphasizes the key physiological role of the GHD. In living hyphae Uso1 recurs on puncta (60 s half-life) colocalizing partially with the Golgi markers RAB1, Sed5, and GeaA/Gea1/Gea2, and totally with the retrograde cargo receptor Rer1, consistent with Uso1 dwelling in a very early Golgi compartment from which ER residents reaching the Golgi recycle back to the ER. Localization of Uso1, but not of Uso1 E6K/G540S , to puncta is abolished by compromising RAB1 function, indicating that E6K/G540S creates interactions bypassing RAB1. That Uso1 delocalization correlates with a decrease in the number of Gea1 cisternae supports that Uso1-and-Rer1-containing puncta are where the protein exerts its physiological role. In S-tag-coprecipitation experiments, Uso1 is an associate of the Sed5/Bos1/Bet1/Sec22 SNARE complex zippering vesicles with the Golgi, with Uso1 E6K/G540S showing a stronger association. Using purified proteins, we show that Bos1 and Bet1 bind the Uso1 GHD directly. However, Bet1 is a strong E6K/G540S-independent binder, whereas Bos1 is weaker but becomes as strong as Bet1 when the GHD carries E6K/G540S. G540S alone markedly increases GHD binding to Bos1, whereas E6K causes a weaker effect, correlating with their phenotypic contributions. AlphaFold2 predicts that G540S increases the binding of the GHD to the Bos1 Habc domain. In contrast, E6K lies in an N-terminal, potentially alpha-helical, region that sensitive genetic tests indicate as required for full Uso1 function. Remarkably, this region is at the end of the GHD basket opposite to the end predicted to interact with Bos1. We show that, unlike dimeric full-length and CTR∆ Uso1 proteins, the GHD lacking the CC/CTR dimerization domain, whether originating from bacteria or Aspergillus extracts and irrespective of whether it carries or not E6K/G540S, would appear to be monomeric. With the finding that overexpression of E6K/G540S and wild-type GHD complement uso1∆ , our data indicate that the GHD monomer is capable of providing, at least partially, the essential Uso1 functions, and that long-range tethering activity is dispensable. Rather, these findings strongly suggest that the essential role of Uso1 involves the regulation of SNAREs.
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eLife assessment
This paper reports a detailed functional analysis of the Rab1 effector Uso1, and it provides a fundamental advance in our understanding of how ER-derived vesicles deliver their cargo. The authors provide compelling evidence that the key function of Uso1 is promoting SNARE complex formation rather than tethering vesicles as generally assumed. These insights will be of interest to cell and structural biologists who study membrane traffic.
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Reviewer #1 (Public Review):
The authors carried out a clever and systematic analysis. Most SNARE complex assembly reactions are thought to involve multi-subunit tethers, and it now seems possible that Uso1/p115 plays this role in the case of the ER-to-Golgi SNARE complex. In addition to documenting the main conclusions of the paper, they characterized Uso1 in various ways, including an analysis of how the different domains of Uso1 contribute to the higher-order structure of the protein and to interactions with other components.
I have only one significant comment about the presentation. The concept that the mutant Uso1 rescues the loss of Rab1 by binding more tightly to SNAREs is reasonable and likely but is not formally proven by the data. Instead, the data show that the mutant binds better to Golgi membranes in the absence of Rab1 …
Reviewer #1 (Public Review):
The authors carried out a clever and systematic analysis. Most SNARE complex assembly reactions are thought to involve multi-subunit tethers, and it now seems possible that Uso1/p115 plays this role in the case of the ER-to-Golgi SNARE complex. In addition to documenting the main conclusions of the paper, they characterized Uso1 in various ways, including an analysis of how the different domains of Uso1 contribute to the higher-order structure of the protein and to interactions with other components.
I have only one significant comment about the presentation. The concept that the mutant Uso1 rescues the loss of Rab1 by binding more tightly to SNAREs is reasonable and likely but is not formally proven by the data. Instead, the data show that the mutant binds better to Golgi membranes in the absence of Rab1 and also binds better to Bos1. It should be acknowledged that this correlation is merely suggestive.
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Reviewer #2 (Public Review):
This is a very dense and thorough analysis of the role of Uso1 in Aspergillus using genetics, pulldown assays, and modelling.
Uso1 has been established as an essential tethering factor that acts in conjunction with Rab1 to deliver ER-derived vesicles to the Golgi. The current picture is that Uso1 is a Rab1 effector, but the authors challenge this interpretation using a combination of genetics experiments, biochemical analysis of protein-protein interactions, and alphafold2 prediction.While Rab1 is essential, they identify strains of Aspergillus that bypass the need for Rab1, which carry two mutations in Uso1. They go on to show that Uso1 binds directly to the Bos1 and Bet1 components of the SNARE complex and that the rescue mutations cause tighter binding of the Uso1 globular head domain to Bos1 and …
Reviewer #2 (Public Review):
This is a very dense and thorough analysis of the role of Uso1 in Aspergillus using genetics, pulldown assays, and modelling.
Uso1 has been established as an essential tethering factor that acts in conjunction with Rab1 to deliver ER-derived vesicles to the Golgi. The current picture is that Uso1 is a Rab1 effector, but the authors challenge this interpretation using a combination of genetics experiments, biochemical analysis of protein-protein interactions, and alphafold2 prediction.While Rab1 is essential, they identify strains of Aspergillus that bypass the need for Rab1, which carry two mutations in Uso1. They go on to show that Uso1 binds directly to the Bos1 and Bet1 components of the SNARE complex and that the rescue mutations cause tighter binding of the Uso1 globular head domain to Bos1 and (hypothetically) to the membrane. They support their genetics and biochemical analysis by doing structure predictions with alphafold2 and suggesting how these mutants might act. They also show that an overexpressed mutated monomeric globular domain of Uso1 (without the coiled-coil 'tether' that causes dimerisation) rescues growth defects of delta Uso1, suggesting the essential activity of Uso1 is not the tethering but its being part of the SNARE complex.
The data is solid, and the interpretation is convincing, showing Uso1 is not 'merely' a tethering factor. It has multiple roles, and this study opens up new questions regarding what exactly is Uso1's function as part of the SNARE bundle, and also in which way the Rab1-mediated tethering and the SNARE complex aspects of Uso1 are linked and/or regulated.
However, there are some aspects of this work that need to be strengthened/clarified including some of the modelling and the interpretation of the role of Uso1 dimerisation. Also, given the availability of models for all homologues, it would be interesting to test whether analogous Uso1 mutant in S.cerevisiae can also rescue rab1- lethality. This would suggest the new proposed role of Uso1 is a general feature, at least for fungi, rather than a particularity of Aspergillus.
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Reviewer #3 (Public Review):
The manuscript by Bravo-Plaza et al. identifies and characterizes new mutations (E6K and G540S) in the Uso1 globular head domain that suppress the loss of function mutations in Rab1. Further experiments show that the combined E6K/G540S mutant restores apparent Golgi-localization of Uso1 in Rab1 deficient cells, that this mutant preferentially co-purifies with ER/Golgi SNARE proteins, that monomeric E6K/G540S globular head-domain binds more avidly to purified Bos1 SNARE protein than wild type head-domain, and that overexpression of E6K/G540S or wild type head-domain alone is sufficient for viability. Based on these findings the authors propose that long-distance tethering by Uso1 is dispensable and that the head domain provides an essential function to directly regulate ER/Golgi SNARE-dependent membrane fusion.
Reviewer #3 (Public Review):
The manuscript by Bravo-Plaza et al. identifies and characterizes new mutations (E6K and G540S) in the Uso1 globular head domain that suppress the loss of function mutations in Rab1. Further experiments show that the combined E6K/G540S mutant restores apparent Golgi-localization of Uso1 in Rab1 deficient cells, that this mutant preferentially co-purifies with ER/Golgi SNARE proteins, that monomeric E6K/G540S globular head-domain binds more avidly to purified Bos1 SNARE protein than wild type head-domain, and that overexpression of E6K/G540S or wild type head-domain alone is sufficient for viability. Based on these findings the authors propose that long-distance tethering by Uso1 is dispensable and that the head domain provides an essential function to directly regulate ER/Golgi SNARE-dependent membrane fusion.
Strengths of the study are that an unbiased screen was used to identify new Rab1 suppresser mutations that land in the Uso1 globular head domain. Characterization of these suppressor mutants reveals that SNARE binding activity of Uso1 resides in the head domain and that elevated expression of the Uso1 head domain is sufficient for viability. Imaging experiments document the localization and dynamics of Uso1 on Golgi compartments and biochemical studies show the properties and binding activity of Uso1 domain mutants. These are new findings and the conclusion that monomeric globular head-domain interacts with specific SNAREs to maintain viability is justified.
Weaknesses are that it is well documented that both Rab1 and Uso1 activity can be bypassed by activation of ER/Golgi SNARE machinery either by overexpression of SNARE proteins or by the single copy SLY1-20 allele. Therefore, it was not surprising that tethering by the Uso1 coiled-coil domain is dispensable. The proposal that the E6K mutation in the head domain of Uso1 promotes membrane targeting was not well supported by experimental evidence. And while the AlphaFold modeling of Uso1 with the ER/Golgi fusion machinery was intriguing, the proposed molecular models remain speculative until further tested.
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