scholarly journals Animal evolution coincides with a novel degree of freedom in exocytic transport processes

2019 ◽  
Author(s):  
Martin Kollmar ◽  
Tobias Welz ◽  
Felix Straub ◽  
Noura Alzahofi ◽  
Klas Hatje ◽  
...  
Keyword(s):  
Protein Function ◽  
Tissue Expression ◽  
Transport Processes ◽  
Degree Of Freedom ◽  
Rab Gtpase ◽  
Animal Evolution ◽  
Protein Activation ◽  
Vesicle Membranes ◽  
Genome Duplications ◽  
Membrane Tethering

AbstractExocytic transport of transmembrane receptors and secreted ligands provides the basis for cellular communication in animals. The RAB8/RAB3/RAB27 trafficking regulators function in transport processes towards the cell membrane. The small G-proteins recruit a diversity of effectors that mediate transport along microtubule and actin tracks, as well as membrane tethering and fusion. SPIRE actin nucleators organise local actin networks at exocytic vesicle membranes. By complex formation with class-5 myosins, vesicle transport track generation and motor protein activation are coordinated. Our phylogenetic analysis traced the onset of SPIRE function back to the origin of the Holozoa. We have identified SPIRE in the closest unicellular relatives of animals, the choanoflagellates, and the more distantly related ichthyosporeans. The discovery of a SPIRE-like protein encoding a KIND and tandem-WH2 domains in the amoebozoanPhysarum polycephalumsuggests that the SPIRE-type actin nucleation mechanism originated even earlier. Choanoflagellate SPIRE interacts with RAB8, the sole choanoflagellate representative of the metazoan RAB8/RAB3/RAB27 family. Major interactions including MYO5, FMN-subgroup formins and vesicle membranes are conserved between the choanoflagellate and mammalian SPIRE proteins and the choanoflagellateMonosiga brevicollisSPIRE protein can rescue mouse SPIRE1/2 function in melanosome transport. Genome duplications generated two mammalianSPIREgenes (SPIRE1andSPIRE2) and allowed for the separation of SPIRE protein function in terms of tissue expression and RAB GTPase binding. SPIRE1 is highest expressed in the nervous system and interacts with RAB27 and RAB8. SPIRE2 shows high expression in the digestive tract and specifically interacts with RAB8. We propose that at the dawn of the animal kingdom a new transport mechanism came into existence, which bridges microtubule tracks, detached vesicles and the cellular actin cytoskeleton by organising actin/myosin forces directly at exocytic vesicle membranes. The new degree of freedom in transport may reflect the increased demands of the sophisticated cellular communications in animals.

scholarly journals Yeast vacuolar HOPS, regulated by its kinase, exploits affinities for acidic lipids and Rab:GTP for membrane binding and to catalyze tethering and fusion

2015 ◽  
Vol 26 (2) ◽  
pp. 305-315 ◽  
Author(s):  
Amy Orr ◽  
William Wickner ◽  
Scott F. Rusin ◽  
Arminja N. Kettenbach ◽  
Michael Zick
Keyword(s):  
Protein Sorting ◽  
Rab Gtpase ◽  
Attachment Protein ◽  
Functional Relationships ◽  
Sensitive Factor ◽  
Protein Receptors ◽  
Membrane Tethering ◽  
Rab Effector ◽  
Supporting Membrane ◽  
Acidic Lipids

Fusion of yeast vacuoles requires the Rab GTPase Ypt7p, four SNAREs (soluble N-ethylmaleimide–sensitive factor attachment protein receptors), the SNARE disassembly chaperones Sec17p/Sec18p, vacuolar lipids, and the Rab-effector complex HOPS (homotypic fusion and vacuole protein sorting). Two HOPS subunits have direct affinity for Ypt7p. Although vacuolar fusion has been reconstituted with purified components, the functional relationships between individual lipids and Ypt7p:GTP have remained unclear. We now report that acidic lipids function with Ypt7p as coreceptors for HOPS, supporting membrane tethering and fusion. After phosphorylation by the vacuolar kinase Yck3p, phospho-HOPS needs both Ypt7p:GTP and acidic lipids to support fusion.

LRRK2 and Rab GTPases

2018 ◽  
Vol 46 (6) ◽  
pp. 1707-1712 ◽  
Author(s):  
Suzanne R. Pfeffer
Keyword(s):  
Membrane Trafficking ◽  
Protein Function ◽  
Short Review ◽  
Rab Gtpase ◽  
Rab Gtpases ◽  
Rab Protein ◽  
Complex Interactions ◽  
Preferential Binding ◽  
Bona Fide ◽  
Mutant Lrrk2

Leucine-rich repeat kinase 2 (LRRK2) is mutated in familial Parkinson's disease, and pathogenic mutations activate the kinase activity. A tour de force screen by Mann and Alessi and co-workers identified a subset of Rab GTPases as bona fide LRRK2 substrates. Rab GTPases are master regulators of membrane trafficking and this short review will summarize what we know about the connection between LRRK2 and this family of regulatory proteins. While, in most cases, Rab GTPase phosphorylation is predicted to interfere with Rab protein function, the discovery of proteins that show preferential binding to phosphorylated Rabs suggests that more complex interactions may also contribute to mutant LRRK2-mediated pathology.

scholarly journals Sub-Diffusive Dynamics Lead to Depleted Particle Densities Near Cellular Borders

2018 ◽  
Author(s):  
William R. Holmes
Keyword(s):  
Particle Density ◽  
Specific Model ◽  
Transport Processes ◽  
Generalized Langevin Equation ◽  
Diffusive Motion ◽  
Protein Activation ◽  
Cellular Environment ◽  
Anomalous Particle ◽  
Canonical Type ◽  
Different Characteristics

AbstractIt has long been known that the complex cellular environment leads to anomalous motion of intracellular particles. At a gross level, this is characterized by mean squared displacements that deviate from the standard linear profile. Statistical analysis of particle trajectories has helped further elucidate how different characteristics of the cellular environment can introduce different types of anomalousness. A significant majority of this literature has however focused on characterizing the properties of trajectories that do not interact with cell borders (e.g. cell membrane or nucleus). Numerous biological processes ranging from protein activation to exocytosis however require particles to be near a membrane. This study investigates the consequences of a canonical type of sub-diffusive motion, Fractional Brownian Motion (FBM), and its physical analogue Generalized Langevin Equation (GLE) Dynamics, on the spatial localization of particles near reflecting boundaries. Results show that this type of sub-diffusive motion leads to the formation of significant zones of depleted particle density near boundaries, and that this effect is independent of the specific model details encoding those dynamics. Rather these depletion layers are a natural and robust consequence of the anti-correlated nature of motion increments that is at the core of FBM / GLE dynamics. If such depletion zones are present, it would be of profound importance given the wide array of signaling and transport processes that occur near membranes. If not, that would suggest our understanding of this type of anomalous motion may be flawed. Either way, this result points to the need to further investigate the consequences of anomalous particle motions near cell borders from both theoretical and experimental perspectives.

scholarly journals Recent advances in user-friendly computational tools to engineer protein function

2020 ◽  
Author(s):  
Carlos Eduardo Sequeiros-Borja ◽  
Bartłomiej Surpeta ◽  
Jan Brezovsky
Keyword(s):  
Protein Engineering ◽  
Protein Design ◽  
Protein Function ◽  
Transport Processes ◽  
Allosteric Communication ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions ◽  
User Friendly ◽  
Ligand Transport ◽  
Further Development

Abstract Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein–protein and protein–nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.

Role of G proteins in stimulation of Na-H exchange by cell shrinkage

1992 ◽  
Vol 262 (2) ◽  
pp. C533-C536 ◽  
Author(s):  
B. A. Davis ◽  
E. M. Hogan ◽  
W. F. Boron
Keyword(s):  
G Protein ◽  
G Proteins ◽  
Transport Processes ◽  
Cell Shrinkage ◽  
Protein Activation ◽  
Kinase C ◽  
G Protein Activation ◽  
Barnacle Muscle Fibers ◽  
Stimulation Of

Many cells respond to shrinkage by stimulating specific ion transport processes (e.g., Na-H exchange). However, it is not known how the cell senses this volume change, nor how this signal is transduced to an ion transporter. We have studied the activation of Na-H exchange in internally dialyzed barnacle muscle fibers, measuring intracellular pH (pHi) with glass microelectrodes. When cells are dialyzed to a pHi of approximately 7.2, Na-H exchange is active only in shrunken cells. We found that the shrinkage-induced stimulation of Na-H exchange, elicited by increasing medium osmolality from 975 to 1,600 mosmol/kgH2O, is inhibited approximately 72% by including in the dialysis fluid 1 mM guanosine 5'-O-(2-thiodiphosphate). The latter is an antagonist of G protein activation. Even in unshrunken cells, Na-H exchange is activated by dialyzing the cell with 1 mM guanosine 5'-O-(3-thiotriphosphate), which causes the prolonged activation of G proteins. Activation of Na-H exchange is also elicited in unshrunken cells by injecting cholera toxin, which activates certain G proteins. Neither exposing cells to 100 nM phorbol 12-myristate 13-acetate nor dialyzing them with a solution containing 20 microM adenosine 3',5'-cyclic monophosphate (cAMP) (or 50 microM dibutyryl cAMP) plus 0.5 mM 3-isobutyl-1-methylxanthine substantially stimulates the exchanger. Thus our data suggest that a G protein plays a key role in the transduction of the shrinkage signal to the Na-H exchanger via a pathway that involves neither protein kinase C nor cAMP.

scholarly journals Dynamics of proteins in solution

2019 ◽  
Vol 52 ◽  
Author(s):  
Marco Grimaldo ◽  
Felix Roosen-Runge ◽  
Fajun Zhang ◽  
Frank Schreiber ◽  
Tilo Seydel
Keyword(s):  
Protein Dynamics ◽  
Protein Function ◽  
Center Of Mass ◽  
Mass Diffusion ◽  
Transport Processes ◽  
Side Chain ◽  
Neutron Spectroscopy ◽  
Length Scales ◽  
Comprehensive Picture ◽  
Mechanistic Understanding

AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

scholarly journals Multiple large-scale gene and genome duplications during the evolution of hexapods

2018 ◽  
Vol 115 (18) ◽  
pp. 4713-4718 ◽  
Author(s):  
Zheng Li ◽  
George P. Tiley ◽  
Sally R. Galuska ◽  
Chris R. Reardon ◽  
Thomas I. Kidder ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Large Scale ◽  
Plant Evolution ◽  
Minor Role ◽  
Animal Evolution ◽  
Gene Retention ◽  
Insect Phylogeny ◽  
Genome Duplications ◽  
History Of ◽  
Gene Age

Polyploidy or whole genome duplication (WGD) is a major contributor to genome evolution and diversity. Although polyploidy is recognized as an important component of plant evolution, it is generally considered to play a relatively minor role in animal evolution. Ancient polyploidy is found in the ancestry of some animals, especially fishes, but there is little evidence for ancient WGDs in other metazoan lineages. Here we use recently published transcriptomes and genomes from more than 150 species across the insect phylogeny to investigate whether ancient WGDs occurred during the evolution of Hexapoda, the most diverse clade of animals. Using gene age distributions and phylogenomics, we found evidence for 18 ancient WGDs and six other large-scale bursts of gene duplication during insect evolution. These bursts of gene duplication occurred in the history of lineages such as the Lepidoptera, Trichoptera, and Odonata. To further corroborate the nature of these duplications, we evaluated the pattern of gene retention from putative WGDs observed in the gene age distributions. We found a relatively strong signal of convergent gene retention across many of the putative insect WGDs. Considering the phylogenetic breadth and depth of the insect phylogeny, this observation is consistent with polyploidy as we expect dosage balance to drive the parallel retention of genes. Together with recent research on plant evolution, our hexapod results suggest that genome duplications contributed to the evolution of two of the most diverse lineages of eukaryotes on Earth.

scholarly journals Comparable Rates of Gene Loss and Functional Divergence After Genome Duplications Early in Vertebrate Evolution

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1259-1266 ◽  
Author(s):  
Joseph H Nadeau ◽  
David Sankoff
Keyword(s):  
Gene Family ◽  
Protein Function ◽  
Gene Loss ◽  
Functional Divergence ◽  
Gene Families ◽  
High Rate ◽  
Vertebrate Evolution ◽  
Duplicated Genes ◽  
Apparent Contradiction ◽  
Genome Duplications

Duplicated genes are an important source of new protein functions and novel developmental and physiological pathways. Whereas most models for fate of duplicated genes show that they tend to be rapidly lost, models for pathway evolution suggest that many duplicated genes rapidly acquire novel functions. Little empirical evidence is available, however, for the relative rates of gene loss vs. divergence to help resolve these contradictory expectations. Gene families resulting from genome duplications provide an opportunity to address this apparent contradiction. With genome duplication, the number of duplicated genes in a gene family is at most 2n, where n is the number of duplications. The size of each gene family, e.g., 1, 2, 3,..., 2n, reflects the patterns of gene loss vs. functional divergence after duplication. We focused on gene families in humans and mice that arose from genome duplications in early vertebrate evolution and we analyzed the frequency distribution of gene family size, i.e., the number of families with two, three or four members. All the models that we evaluated showed that duplicated genes are almost as likely to acquire a new and essential function as to be lost through acquisition of mutations that compromise protein function. An explanation for the unexpectedly high rate of functional divergence is that duplication allows genes to accumulate more neutral than disadvantageous mutations, thereby providing more opportunities to acquire diversified functions and pathways.

scholarly journals An Autoactive Mutant of the M Flax Rust Resistance Protein Has a Preference for Binding ATP, Whereas Wild-Type M Protein Binds ADP

2011 ◽  
Vol 24 (8) ◽  
pp. 897-906 ◽  
Author(s):  
Simon J. Williams ◽  
Pradeep Sornaraj ◽  
Emma deCourcy-Ireland ◽  
R. Ian Menz ◽  
Bostjan Kobe ◽  
...  
Keyword(s):  
Protein Function ◽  
Pathogen Detection ◽  
Biochemical Study ◽  
Expression System ◽  
M Protein ◽  
Wild Type ◽  
Hypersensitive Cell Death ◽  
Yeast Expression System ◽  
Protein Activation ◽  
Key Residues

Resistance (R) proteins are key regulators of the plant innate immune system and are capable of pathogen detection and activation of the hypersensitive cell death immune response. To understand the molecular mechanism of R protein activation, we undertook a phenotypic and biochemical study of the flax nucleotide binding (NB)-ARC leucine-rich repeat protein, M. Using Agrobacterium-mediated transient expression in flax cotyledons, site-directed mutations of key residues within the P-loop, kinase 2, and MHD motifs within the NB-ARC domain of M were shown to affect R protein function. When purified using a yeast expression system and assayed for ATP and ADP, these mutated proteins exhibited marked differences in the quantity and identity of the bound nucleotide. ADP was bound to recombinant wild-type M protein, while the nonfunctional P-loop mutant did not have any nucleotides bound. In contrast, ATP was bound to an autoactive M protein mutated in the highly conserved MHD motif. These data provide direct evidence supporting a model of R protein function in which the “off” R protein binds ADP and activation of R protein defense signaling involves the exchange of ADP for ATP.

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