Molecular basis for the recruitment of the Rab effector protein WDR44 by the GTPase Rab11

Thibodeau, Matthew C.; Harris, Noah J; Jenkins, Meredith L.; Parson, Matthew AH; Evans, John T; Scott, Mackenzie K.; Shaw, Alexandria L.; Pokorný, Daniel; Leonard, Thomas A.; Burke, John E.

doi:10.1016/j.jbc.2022.102764

Cited by 5 publications

(7 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As indicated by the Venn diagram (Fig 2B), our analysis identified proteins that were common to multiple datasets including 6 proteins present in both WDR44 datasets and 25 proteins present in both FAM102A datasets (File S2). Notably, RAB11A and RAB11B GTPases were identified in both datasets for WDR44 (Fig 2C ), consistent with findings in the literature demonstrating that these proteins physically interact and function together in membrane trafficking (Mammoto et al, 1999;Thibodeau et al, 2023;Zeng et al, 1999).…”

Section: Affinity Capture Proteomics Implicates Physical Interactions...supporting

confidence: 90%

Pathways that affect anterior morphogenesis inC. elegansembryos

Balasubramaniam

Topalidou

Kelley

et al. 2023

Preprint

View full text Add to dashboard Cite

During embryogenesis the nascent Caenorhabditis elegans epidermis secretes an apical extracellular matrix (aECM) that serves as an external stabilizer, preventing deformation of the epidermis by mechanical forces exerted during morphogenesis. We showed that two conserved proteins linked to this process, SYM-3/FAM102A and SYM-4/WDR44, colocalize to intracellular and membrane-associated puncta and likely function together in a complex. Proteomics data also suggested potential roles for FAM102A and WDR44 family proteins in intracellular trafficking, consistent with their localization patterns. Nonetheless, we found no evidence to support a clear function for SYM-3 or SYM-4 in the apical deposition of two aECM components, FBN-1 and NOAH. Surprisingly, loss of MEC-8/RBPMS2, a conserved splicing factor and regulator of fbn-1, had little effect on the abundance or deposition of FBN-1 to the aECM. Using a focused screening approach, we identified 32 additional proteins that likely contribute to the structure and function of the embryonic aECM. Lastly, we examined morphogenesis defects in embryos lacking mir-51 microRNA family members, which display a related embryonic phenotype to mec-8; sym double mutants. Collectively, our findings add to our knowledge of pathways controlling embryonic morphogenesis.

show abstract

Section: Affinity Capture Proteomics Implicates Physical Interactions...supporting

confidence: 90%

Pathways that affect anterior morphogenesis inC. elegansembryos

Balasubramaniam

Topalidou

Kelley

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Rab8 was shown to be essential for endocytic recycling and ciliogenesis (Dhekne et al, 2018; Hattula et al, 2006; Nachury et al, 2007; Vidal-Quadras et al, 2017) and Rab10 has been implicated in diverse cellular processes, including basolateral protein sorting, macropinocytosis and, especially relevant for this study, ciliogenesis (Dhekne et al, 2018; Liu et al, 2020; Nakamura et al, 2020). To determine if BLTP2-associated tubules are part of the Rab8/Rab10 TEN, we transfected HeLa cells with plasmids encoding GFP-Rab8, GFP-Rab10 and GFP-Rab11, as WDR44 is an effector of Rab11, (Mammoto et al, 2000; Thibodeau et al, 2023; Zeng et al, 1999) and immunostained them to visualize BLTP2 or WDR44 ( Fig. 5A, B, D, E ).…”

Section: Resultsmentioning

confidence: 99%

Bridge-like lipid transfer protein family member 2 suppresses ciliogenesis

Parolek,

Burd

2023

Preprint

View full text Add to dashboard Cite

Bridge-like lipid transfer protein family member 2 (BLTP2) is an evolutionary conserved protein with unknown function(s). The absence of BLTP2 inDrosophila melanogasterresults in impaired cellular secretion and larval death, while in mice (Mus musculus), it causes preweaning lethality. Structural predictions propose that BLTP2 belongs to the repeating β-groove domain-containing (also called the VPS13) protein family, forming a long tube with a hydrophobic core, suggesting that it operates as a lipid transfer protein (LTP). We establishBLTP2as a negative regulator of ciliogenesis in RPE-1 cells based on a strong genetic interaction withWDR44, a gene that also suppresses ciliogenesis. Like WDR44, BLTP2 localizes to membrane contact sites involving the endoplasmic reticulum and the tubular endosome network in HeLa cells and that BLTP2 depletion enhanced ciliogenesis by serum-fed RPE-1 cells, a condition where ciliogenesis is normally suppressed. This study establishes human BLTP2 as a putative lipid transfer protein acting between tubular endosomes and ER that regulates primary cilium biogenesis.Significance statementWe show the involvement of an ER-localized bridge-like lipid transfer protein, BLTP2, in ciliogenesis and establish that BLTP2 is enriched at organelle-organelle membrane contact sites involving the endoplasmic reticulum (ER) and the tubular endosome network (TEN). These results implicate, for the first time, the involvement of bulk lipid transfer between the ER and TEN in regulating ciliogenesis.

show abstract

“…Structure predictions obtained by either AF2 or AF2-Multimer can also be used in combination with hydrogen-deuterium exchange mass spectrometry (HDX-MS) data to predict or validate models of protein–protein complexes, as HDX-MS is very efficient to identify protein regions involved in protein–protein interactions. , …”

Section: The Impact Of Ai-generated Models Beyond Molecular Replacementmentioning

confidence: 99%

“…Structure predictions obtained by either AF2 or AF2-Multimer can also be used in combination with hydrogendeuterium exchange mass spectrometry (HDX-MS) data to predict or validate models of protein−protein complexes, as HDX-MS is very efficient to identify protein regions involved in protein−protein interactions. 100,101 AF2 and RF should also prove very useful in combination with low-dimensionality structural methods, facilitating their interpretation, for example, with force spectroscopy, 102 CD 103 and SAXS 104−107 or FRET. Given the degeneracy associated with low-dimensionality methods, it is recommended to maximize the number of independent validations (see above).…”

Section: Molecular Biology and Construct Designmentioning

confidence: 99%

Best Practices of Using AI-Based Models in Crystallography and Their Impact in Structural Biology

Graille

Sacquin-Mora

Taly

2023

J. Chem. Inf. Model.

View full text Add to dashboard Cite

The recent breakthrough made in the field of three-dimensional (3D) structure prediction by artificial intelligence softwares, such as initially AlphaFold2 (AF2) and RosettaFold (RF) and more recently large Language Models (LLM), has revolutionized the field of structural biology in particular and also biology as a whole. These models have clearly generated great enthusiasm within the scientific community, and different applications of these 3D predictions are regularly described in scientific articles, demonstrating the impact of these high-quality models. Despite the acknowledged high accuracy of these models in general, it seems important to make users of these models aware of the wealth of information they offer and to encourage them to make the best use of them. Here, we focus on the impact of these models in a specific application by structural biologists using X-ray crystallography. We propose guidelines to prepare models to be used for molecular replacement trials to solve the phase problem. We also encourage colleagues to share as much detail as possible about how they use these models in their research, where the models did not yield correct molecular replacement solutions, and how these predictions fit with their experimental 3D structure. We feel this is important to improve the pipelines using these models and also to get feedback on their overall quality.

show abstract

Molecular basis for the recruitment of the Rab effector protein WDR44 by the GTPase Rab11

Cited by 5 publications

References 46 publications

Pathways that affect anterior morphogenesis inC. elegansembryos

Pathways that affect anterior morphogenesis inC. elegansembryos

Bridge-like lipid transfer protein family member 2 suppresses ciliogenesis

Best Practices of Using AI-Based Models in Crystallography and Their Impact in Structural Biology

Contact Info

Product

Resources

About