IF 4.5 3区生物学

Traffic Pub Date : 2021-09-01 Epub Date: 2021-07-11 DOI: 10.1111/tra.12808

Lou Fourriere, Paul A Gleeson

引用次数: 9

Sequence-based features that are determinant for tail-anchored membrane protein sorting in eukaryotes. 真核生物中决定尾锚膜蛋白分选的序列特征。

IF 4.5 3区生物学

Traffic Pub Date : 2021-09-01 Epub Date: 2021-08-03 DOI: 10.1111/tra.12809

Michelle Y Fry, Shyam M Saladi, Alexandre Cunha, William M Clemons

{"title":"Sequence-based features that are determinant for tail-anchored membrane protein sorting in eukaryotes.","authors":"Michelle Y Fry, Shyam M Saladi, Alexandre Cunha, William M Clemons","doi":"10.1111/tra.12809","DOIUrl":"10.1111/tra.12809","url":null,"abstract":"The correct targeting and insertion of tail-anchored (TA) integral membrane proteins is critical for cellular homeostasis. TA proteins are defined by a hydrophobic transmembrane domain (TMD) at their C-terminus and are targeted to either the ER or mitochondria. Derived from experimental measurements of a few TA proteins, there has been little examination of the TMD features that determine localization. As a result, the localization of many TA proteins are misclassified by the simple heuristic of overall hydrophobicity. Because ER-directed TMDs favor arrangement of hydrophobic residues to one side, we sought to explore the role of geometric hydrophobic properties. By curating TA proteins with experimentally determined localizations and assessing hypotheses for recognition, we bioinformatically and experimentally verify that a hydrophobic face is the most accurate singular metric for separating ER and mitochondria-destined yeast TA proteins. A metric focusing on an 11 residue segment of the TMD performs well when classifying human TA proteins. The most inclusive predictor uses both hydrophobicity and C-terminal charge in tandem. This work provides context for previous observations and opens the door for more detailed mechanistic experiments to determine the molecular factors driving this recognition.","PeriodicalId":23207,"journal":{"name":"Traffic","volume":"22 9","pages":"306-318"},"PeriodicalIF":4.5,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8380732/pdf/nihms-1726178.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39205172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dynamic, variable oligomerization and the trafficking of variant surface glycoproteins of Trypanosoma brucei. 布鲁氏锥虫动态、可变寡聚化和不同表面糖蛋白的转运。

IF 4.5 3区生物学

Traffic Pub Date : 2021-08-01 Epub Date: 2021-06-29 DOI: 10.1111/tra.12806

Khan Umaer, Francisco Aresta-Branco, Monica Chandra, Monique van Straaten, Johan Zeelen, Karine Lapouge, Brandon Waxman, C Erec Stebbins, James D Bangs

{"title":"Dynamic, variable oligomerization and the trafficking of variant surface glycoproteins of Trypanosoma brucei.","authors":"Khan Umaer, Francisco Aresta-Branco, Monica Chandra, Monique van Straaten, Johan Zeelen, Karine Lapouge, Brandon Waxman, C Erec Stebbins, James D Bangs","doi":"10.1111/tra.12806","DOIUrl":"https://doi.org/10.1111/tra.12806","url":null,"abstract":"African trypanosomes cause disease in humans and livestock, avoiding host immunity by changing the expression of variant surface glycoproteins (VSGs); the major glycosylphosphatidylinositol (GPI) anchored antigens coating the surface of the bloodstream stage. Proper trafficking of VSGs is therefore critical to pathogen survival. The valence model argues that GPI anchors regulate progression and fate in the secretory pathway and that, specifically, a valence of two (VSGs are dimers) is critical for stable cell surface association. However, recent reports that the MITat1.3 (M1.3) VSG N-terminal domain (NTD) behaves as a monomer in solution and in a crystal structure challenge this model. We now show that the behavior of intact M1.3 VSG in standard in vivo trafficking assays is consistent with an oligomer. Nevertheless, Blue Native Gel electrophoresis and size exclusion chromatography-multiangle light scattering chromatography of purified full length M1.3 VSG indicates a monomer in vitro. However, studies with additional VSGs show that multiple oligomeric states are possible, and that for some VSGs oligomerization is concentration dependent. These data argue that individual VSG monomers possess different propensities to self-oligomerize, but that when constrained at high density to the cell surface, oligomeric species predominate. These results resolve the apparent conflict between the valence hypothesis and the M1.3 NTD VSG crystal structure.","PeriodicalId":23207,"journal":{"name":"Traffic","volume":"22 8","pages":"274-283"},"PeriodicalIF":4.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/tra.12806","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39073890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

The ESCRT-III complex contributes to macromitophagy in yeast. ESCRT-III复合体有助于酵母的巨噬细胞。

IF 4.5 3区生物学

Traffic Pub Date : 2021-08-01 Epub Date: 2021-06-16 DOI: 10.1111/tra.12805

Zulin Wu, Haiqian Xu, Junze Liu, Fan Zhou, Yongheng Liang

{"title":"The ESCRT-III complex contributes to macromitophagy in yeast.","authors":"Zulin Wu, Haiqian Xu, Junze Liu, Fan Zhou, Yongheng Liang","doi":"10.1111/tra.12805","DOIUrl":"https://doi.org/10.1111/tra.12805","url":null,"abstract":"Mitochondria play important roles in energy generation and homeostasis maintenance in eukaryotic cells. The damaged or superfluous mitochondria can be nonselectively or selectively removed through the autophagy/lysosome pathway, which was referred as mitophagy. According to the molecular machinery for degrading mitochondria, the selectively removed mitochondria can occur through macromitophagy or micromitophagy. In this study, we show that the endosomal sorting complex required for transport III (ESCRT-III) in budding yeast regulates macromitophagy induced by nitrogen starvation, but not by the post-logarithmic phase growth in lactate medium by monitoring a mitochondrial marker, Om45. Firstly, loss of ESCRT-III subunit Snf7 or Vps4-Vta1 complex subunit Vps4, two representative subunits of the ESCRT complex, suppresses the delivery and degradation of Om45-GFP to vacuoles. Secondly, we show that the mitochondrial marker Om45 and mitophagy receptor Atg32 accumulate on autophagosomes marked with Atg8 (mitophagosomes, MPs) in ESCRT mutants. Moreover, the protease-protection assay indicates that Snf7 and Vps4 are involved in MP closure. Finally, Snf7 interacts with Atg11, which was detected by two ways, glutathione-S-transferase (GST) pulldown and bimolecular fluorescence complementation (BiFC) assay, and this BiFC interaction happens on mitochondrial reticulum. Therefore, we proposed that the ESCRT-III machinery mediates nitrogen starvation-induced macromitophagy by the interaction between Snf7 and Atg11 so that Snf7 is recruited to Atg32-marked MPs by the known Atg11-Atg32 interaction to seal them. These results reveal that the ESCRT-III complex plays a new role in yeast on macromitophagy.","PeriodicalId":23207,"journal":{"name":"Traffic","volume":"22 8","pages":"258-273"},"PeriodicalIF":4.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/tra.12805","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39079307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Legionella pneumophila LegC7 effector protein drives aberrant endoplasmic reticulum:endosome contacts in yeast. 嗜肺军团菌LegC7效应蛋白驱动异常内质网:酵母内体接触。

IF 4.5 3区生物学

Traffic Pub Date : 2021-08-01 Epub Date: 2021-07-07 DOI: 10.1111/tra.12807

Nathan K Glueck, Kevin M O'Brien, Danielle C Seguin, Vincent J Starai

{"title":"Legionella pneumophila LegC7 effector protein drives aberrant endoplasmic reticulum:endosome contacts in yeast.","authors":"Nathan K Glueck, Kevin M O'Brien, Danielle C Seguin, Vincent J Starai","doi":"10.1111/tra.12807","DOIUrl":"https://doi.org/10.1111/tra.12807","url":null,"abstract":"Legionella pneumophila is a facultative intracellular bacterial pathogen, causing the severe form of pneumonia known as Legionnaires' disease. Legionella actively alters host organelle trafficking through the activities of \"effector\" proteins secreted via a type-IVB secretion system, in order to construct the bacteria-laden Legionella-containing vacuole (LCV) and prevent lysosomal degradation. The LCV is created with membrane derived from host endoplasmic reticulum (ER), secretory vesicles and phagosomes, although the precise molecular mechanisms that drive its synthesis remain poorly understood. In an effort to characterize the in vivo activity of the LegC7/YlfA SNARE-like effector protein from Legionella in the context of eukaryotic membrane trafficking in yeast, we find that LegC7 interacts with the Emp46p/Emp47p ER-to-Golgi glycoprotein cargo adapter complex, alters ER morphology and induces aberrant ER:endosome interactions, as measured by visualization of ER cargo degradation, reconstitution of split-GFP proteins and enhanced oxidation of the ER lumen. LegC7-dependent toxicity, disruption of ER morphology and ER:endosome fusion events were dependent upon endosomal VPS class C tethering complexes and the endosomal t-SNARE, Pep12p. This work establishes a model in which LegC7 functions to recruit host ER material to the bacterial phagosome during infection by driving ER:endosome contacts, potentially through interaction with host membrane tethering complexes and/or cargo adapters.","PeriodicalId":23207,"journal":{"name":"Traffic","volume":"22 8","pages":"284-302"},"PeriodicalIF":4.5,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/tra.12807","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39037682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Deep learning for automatic segmentation of the nuclear envelope in electron microscopy data, trained with volunteer segmentations. 电子显微镜数据中核膜自动分割的深度学习，与志愿者分割训练。

IF 4.5 3区生物学

Traffic Pub Date : 2021-07-01 DOI: 10.1111/tra.12789

Helen Spiers, Harry Songhurst, Luke Nightingale, Joost de Folter, Roger Hutchings, Christopher J Peddie, Anne Weston, Amy Strange, Steve Hindmarsh, Chris Lintott, Lucy M Collinson, Martin L Jones

{"title":"Deep learning for automatic segmentation of the nuclear envelope in electron microscopy data, trained with volunteer segmentations.","authors":"Helen Spiers, Harry Songhurst, Luke Nightingale, Joost de Folter, Roger Hutchings, Christopher J Peddie, Anne Weston, Amy Strange, Steve Hindmarsh, Chris Lintott, Lucy M Collinson, Martin L Jones","doi":"10.1111/tra.12789","DOIUrl":"https://doi.org/10.1111/tra.12789","url":null,"abstract":"Advancements in volume electron microscopy mean it is now possible to generate thousands of serial images at nanometre resolution overnight, yet the gold standard approach for data analysis remains manual segmentation by an expert microscopist, resulting in a critical research bottleneck. Although some machine learning approaches exist in this domain, we remain far from realizing the aspiration of a highly accurate, yet generic, automated analysis approach, with a major obstacle being lack of sufficient high-quality ground-truth data. To address this, we developed a novel citizen science project, Etch a Cell, to enable volunteers to manually segment the nuclear envelope (NE) of HeLa cells imaged with serial blockface scanning electron microscopy. We present our approach for aggregating multiple volunteer annotations to generate a high-quality consensus segmentation and demonstrate that data produced exclusively by volunteers can be used to train a highly accurate machine learning algorithm for automatic segmentation of the NE, which we share here, in addition to our archived benchmark data.","PeriodicalId":23207,"journal":{"name":"Traffic","volume":"22 7","pages":"240-253"},"PeriodicalIF":4.5,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/tra.12789","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10055982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 37

Transfer of mitochondria and endosomes between cells by gap junction internalization. 通过间隙连接内化在细胞间传递线粒体和核内体。

IF 4.5 3区生物学

Traffic Pub Date : 2021-06-01 Epub Date: 2021-04-14 DOI: 10.1111/tra.12786

Rachael P Norris

引用次数: 22

Ca_V β controls the endocytic turnover of Ca_V 1.2 L-type calcium channel. CaV β控制CaV 1.2 l型钙通道的内吞转换。

IF 4.5 3区生物学

Traffic Pub Date : 2021-06-01 Epub Date: 2021-05-05 DOI: 10.1111/tra.12788

Rachel Conrad, Daniel Kortzak, Gustavo A Guzman, Erick Miranda-Laferte, Patricia Hidalgo

{"title":"CaV β controls the endocytic turnover of CaV 1.2 L-type calcium channel.","authors":"Rachel Conrad, Daniel Kortzak, Gustavo A Guzman, Erick Miranda-Laferte, Patricia Hidalgo","doi":"10.1111/tra.12788","DOIUrl":"https://doi.org/10.1111/tra.12788","url":null,"abstract":"Membrane depolarization activates the multisubunit CaV 1.2 L-type calcium channel initiating various excitation coupling responses. Intracellular trafficking into and out of the plasma membrane regulates the channel's surface expression and stability, and thus, the strength of CaV 1.2-mediated Ca2+ signals. The mechanisms regulating the residency time of the channel at the cell membrane are unclear. Here, we coexpressed the channel core complex CaV 1.2α1 pore-forming and auxiliary CaV β subunits and analyzed their trafficking dynamics from single-particle-tracking trajectories. Speed histograms obtained for each subunit were best fitted to a sum of diffusive and directed motion terms. The same mean speed for the highest-mobility state underlying directed motion was found for all subunits. The frequency of this component increased by covalent linkage of CaV β to CaV 1.2α1 suggesting that high-speed transport occurs in association with CaV β. Selective tracking of CaV 1.2α1 along the postendocytic pathway failed to show the highly mobile state, implying CaV β-independent retrograde transport. Retrograde speeds of CaV 1.2α1 are compatible with myosin VI-mediated backward transport. Moreover, residency time at the cell surface was significantly prolonged when CaV 1.2α1 was covalently linked to CaV β. Thus, CaV β promotes fast transport speed along anterograde trafficking and acts as a molecular switch controlling the endocytic turnover of L-type calcium channels.","PeriodicalId":23207,"journal":{"name":"Traffic","volume":"22 6","pages":"180-193"},"PeriodicalIF":4.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/tra.12788","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38901206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Implicating extracellular vesicles in Plasmodium falciparum artemisinin resistance development. 恶性疟原虫的细胞外囊泡与青蒿素耐药性的关系。

IF 4.5 3区生物学

Traffic Pub Date : 2021-06-01 Epub Date: 2021-04-24 DOI: 10.1111/tra.12787

Kwesi Z Tandoh, Michael D Wilson, Neils B Quashie, Nancy O Duah-Quashie

引用次数: 5

Versatile allosteric properties in Pex5-like tetratricopeptide repeat proteins to induce diverse downstream function. pex5样四肽重复蛋白的多种变构特性诱导多种下游功能。

IF 4.5 3区生物学

Traffic Pub Date : 2021-05-01 Epub Date: 2021-02-26 DOI: 10.1111/tra.12785

Jérôme Bürgi, Lakhan Ekal, Matthias Wilmanns

{"title":"Versatile allosteric properties in Pex5-like tetratricopeptide repeat proteins to induce diverse downstream function.","authors":"Jérôme Bürgi, Lakhan Ekal, Matthias Wilmanns","doi":"10.1111/tra.12785","DOIUrl":"https://doi.org/10.1111/tra.12785","url":null,"abstract":"Proteins composed of tetratricopeptide repeat (TPR) arrays belong to the α-solenoid tandem-repeat family that have unique properties in terms of their overall conformational flexibility and ability to bind to multiple protein ligands. The peroxisomal matrix protein import receptor Pex5 comprises two TPR triplets that recognize protein cargos with a specific C-terminal Peroxisomal Targeting Signal (PTS) 1 motif. Import of PTS1-containing protein cargos into peroxisomes through a transient pore is mainly driven by allosteric binding, coupling and release mechanisms, without a need for external energy. A very similar TPR architecture is found in the functionally unrelated TRIP8b, a regulator of the hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channel. TRIP8b binds to the HCN ion channel via a C-terminal sequence motif that is nearly identical to the PTS1 motif of Pex5 receptor cargos. Pex5, Pex5-related Pex9, and TRIP8b also share a less conserved N-terminal domain. This domain provides a second protein cargo-binding site and plays a distinct role in allosteric coupling of initial cargo loading by PTS1 motif-mediated interactions and different downstream functional readouts. The data reviewed here highlight the overarching role of molecular allostery in driving the diverse functions of TPR array proteins, which could form a model for other α-solenoid tandem-repeat proteins involved in translocation processes across membranes.","PeriodicalId":23207,"journal":{"name":"Traffic","volume":"22 5","pages":"140-152"},"PeriodicalIF":4.5,"publicationDate":"2021-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1111/tra.12785","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25368177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

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