Using HHsearch to tackle proteins of unknown function – a pilot study with PH domains
ABSTRACT
Advances in membrane cell biology are hampered by the relatively high proportion of proteins with no known function. Such proteins are largely or entirely devoid of structurally significant domain annotations. Structural bioinformaticians have developed profile‐profile tools such as HHsearch (online version called HHpred), which can detect remote homologies that are missed by tools used to annotate databases. Here we have applied HHsearch to study a single structural fold in a single model organism as proof of principle. In the entire clan of protein domains sharing the pleckstrin homology domain fold in yeast, ...
Source: Traffic - August 31, 2016 Category: Research Authors: David R. Fidler, Sarah E. Murphy, Katherine Courtis, Pantelis Antonoudiou, Rana El ‐Tohamy, Jonathan Ient, Timothy P. Levine Tags: Toolbox Source Type: research
Distinct roles of the two VPS33 proteins in the endolysosomal system in Caenorhabditis elegans
ABSTRACT
Sec1/Munc‐18 (SM) family proteins are essential regulators in intracellular transport in eukaryotic cells. The SM protein Vps33 functions as a core subunit of two tethering complexes, class C core vacuole/endosome tethering (CORVET) and homotypic fusion and vacuole protein sorting (HOPS) in the endocytic pathway in yeast. Metazoan cells possess two Vps33 proteins, VPS33A and VPS33B, but their precise roles remain unknown. Here, we present a comparative analysis of Caenorhabditis elegans null mutants for these proteins. We found that the vps‐33.1 (VPS33A) mutants exhibited severe defects in both endocytic funct...
Source: Traffic - August 25, 2016 Category: Research Authors: Keiko Gengyo ‐Ando, Eriko Kage‐Nakadai, Sawako Yoshina, Muneyoshi Ohtori, Yuko Kagawa‐Nagamura, Junichi Nakai, Shohei Mitani Tags: Original Article Source Type: research
Rab24 interacts with the Rab7/RILP complex to regulate endosomal degradation
Abstract
Endocytosis is a multistep process engaged in extracellular molecules internalization. Several proteins including the Rab GTPases family coordinate the endocytic pathway. The small GTPase Rab7 is present in late endosome (LE) compartments being a marker of endosome maturation. The Rab interacting lysosomal protein (RILP) is a downstream effector of Rab7 that recruits the functional dynein/dynactin motor complex to late compartments. In the present study, we have found Rab24 as a component of the endosome‐lysosome degradative pathway. Rab24 is an atypical protein of the Rab GTPase family, which has been attribute...
Source: Traffic - August 23, 2016 Category: Research Authors: Celina Amaya, Rodrigo D. Militello, Sebasti án D. Calligaris, María I. Colombo Tags: Original Article Source Type: research
Issue Information
(Source: Traffic)
Source: Traffic - August 9, 2016 Category: Research Tags: Issue Information Source Type: research
Issue Cover (September 2016)
Cover legend: Macrophages phagocytosing RFP‐labeled E.coli. GFP‐APPL2 labels the phagosomal membrane. Image produced by N. Condon. See Yeo et al. Traffic 2016; 17(9):1014‐1026.
Read the full article on doi:10.1111/tra.12415 (Source: Traffic)
Source: Traffic - August 9, 2016 Category: Research Tags: Issue Cover Source Type: research
Tracking adenovirus genomes identifies morphologically distinct late DNA replication compartments
In conclusion, our work demonstrates the formation of previously uncharacterized viral DNA replication compartments specific for late phases of infection that produce progeny viral genomes accumulating in ViPR bodies.
The spatial relationship between early adenoviral genome replication and subsequent viral gene expression has been established. In contrast when and where newly replicated genomes are linked to progeny virion production remains unclear. Using direct genome‐labeling techniques, we show the formation of a novel subnuclear compartment late in infection, which we named ViPR body that functions as a reservoir ...
Source: Traffic - July 31, 2016 Category: Research Authors: Tetsuro Komatsu, Derrick R. Robinson, Miharu Hisaoka, Shuhei Ueshima, Mitsuru Okuwaki, Kyosuke Nagata, Harald Wodrich Tags: Original Article Source Type: research
KIF1A mediates axonal transport of BACE1 and identification of independently moving cargoes in living SCG neurons
Abstract
Neurons rely heavily on axonal transport to deliver materials from the sites of synthesis to the axon terminals over distances that can be many centimetres long. KIF1A is the neuron‐specific kinesin with the fastest reported anterograde motor activity. Previous studies have shown that KIF1A transports a subset of synaptic proteins, neurofilaments and dense‐core vesicles. Using two‐colour live imaging, we showed that BACE1‐mCherry moves together with KIF1A‐GFP in both the anterograde and retrograde directions in SCG neurons. We confirmed that KIF1A is functionally required for BACE1 transport by using KIF...
Source: Traffic - July 31, 2016 Category: Research Authors: Christy O.Y. Hung, Michael P. Coleman Tags: Original Article Source Type: research
Vesicles are persistent features of different plastids
Abstract
Peripheral vesicles in plastids have been observed repeatedly, primarily in proplastids and developing chloroplasts, in which they are suggested to function in thylakoid biogenesis. Previous observations of vesicles in mature chloroplasts have mainly concerned low temperature pre‐treated plants occasionally treated with inhibitors blocking vesicle fusion. Here we show that such vesicle‐like structures occur not only in chloroplasts and proplastids but also in etio‐, etio‐chloro‐, leuco‐, chromo‐ and even transforming desiccoplasts without any specific pre‐treatment. Observations are made both in C3...
Source: Traffic - July 14, 2016 Category: Research Authors: Emelie Lindquist, Katalin Solymosi, Henrik Aronsson Tags: Original Article Source Type: research
The HOPS/Class C Vps Complex Tethers High ‐Curvature Membranes via a Direct Protein–Membrane Interaction
Membrane tethering is a physical association of two membranes before their fusion. Many membrane tethering factors have been identified, but the interactions that mediate inter‐membrane associations remain largely a matter of conjecture. Previously, we reported that the homotypic fusion and protein sorting/Class C vacuolar protein sorting (HOPS/Class C Vps) complex, which has two binding sites for the yeast vacuolar Rab GTPase Ypt7p, can tether two low‐curvature liposomes when both membranes bear Ypt7p. Here, we show that HOPS tethers highly curved liposomes to Ypt7p‐bearing low‐curvature liposomes even when the hi...
Source: Traffic - July 14, 2016 Category: Research Authors: Ruoya Ho, Christopher Stroupe Tags: Original Article Source Type: research
The HOPS/Class C Vps Complex Tethers High‐Curvature Membranes via a Direct Protein–Membrane Interaction
Membrane tethering is a physical association of two membranes before their fusion. Many membrane tethering factors have been identified, but the interactions that mediate inter‐membrane associations remain largely a matter of conjecture. Previously, we reported that the homotypic fusion and protein sorting/Class C vacuolar protein sorting (HOPS/Class C Vps) complex, which has two binding sites for the yeast vacuolar Rab GTPase Ypt7p, can tether two low‐curvature liposomes when both membranes bear Ypt7p. Here, we show that HOPS tethers highly curved liposomes to Ypt7p‐bearing low‐curvature liposomes even when the hi...
Source: Traffic - July 14, 2016 Category: Research Authors: Ruoya Ho, Christopher Stroupe Tags: Original Article Source Type: research
Rab35 GTPase: A Central Regulator of Phosphoinositides and F ‐actin in Endocytic Recycling and Beyond
Rab35 is one of the first discovered members of the large Rab GTPase family, yet it received little attention for 10 years being considered merely as a Rab1‐like GTPase. In 2006, Rab35 was recognized as a unique Rab GTPase localized both at the plasma membrane and on endosomes, playing essential roles in endocytic recycling and cytokinesis. Since then, Rab35 has become one of the most studied Rabs involved in a growing number of cellular functions, including endosomal trafficking, exosome release, phagocytosis, cell migration, immunological synapse formation and neurite outgrowth. Recently, Rab35 has been acknowledged ...
Source: Traffic - July 13, 2016 Category: Research Authors: Kerstin Klinkert, Arnaud Echard Tags: Review Source Type: research
Erratum
(Source: Traffic)
Source: Traffic - July 12, 2016 Category: Research Tags: Erratum Source Type: research
Issue Information
(Source: Traffic)
Source: Traffic - July 12, 2016 Category: Research Tags: Issue Information Source Type: research
Issue Cover (August 2016)
Cover legend: Absence of the novel endolysosomal trafficking regulator WDR81 (green) induces the accumulation of tetherin (red) in enlarged early endosomes. WDR81 knock‐out HeLa cells were genetically complemented with an HA‐tagged WDR81 construct and imaged by confocal immunofluorescence microscopy. The original image was processed with photo editing software and overlaid with artistic effects. See Rapiteanu et al. Traffic 2016; 17(8):940–958.
Read the full article on doi: 10.1111/tra.12409 (Source: Traffic)
Source: Traffic - July 12, 2016 Category: Research Tags: Issue Cover Source Type: research
Ikarugamycin: a natural product inhibitor of clathrin ‐mediated endocytosis
Abstract
Ikarugamycin (IKA) is a previously discovered antibiotic, which has been shown to inhibit the uptake of oxidized low‐density lipoproteins in macrophages. Furthermore, several groups have previously used IKA to inhibit clathrin‐mediated endocytosis (CME) in plant cell lines. However, detailed characterization of IKA has yet to be done. Consequently, we performed biochemistry and microscopy experiments to further characterize the effects of IKA on CME. We show that IKA has an IC50 of 2.7 μM in H1299 cells and acutely inhibits CME, but not other endocytic pathways, in a panel of cell lines. Although long‐ter...
Source: Traffic - July 7, 2016 Category: Research Authors: Sarah R. Elkin, Nathaniel W. Oswald, Dana Kim Reed, Marcel Mettlen, John B. McMillan, Sandra L. Schmid Tags: Toolbox Source Type: research
