scholarly journals The Autophagy Machinery in Human-Parasitic Protists; Diverse Functions for Universally Conserved Proteins

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1258
Author(s):  
Hirokazu Sakamoto ◽  
Kumiko Nakada-Tsukui ◽  
Sébastien Besteiro
Keyword(s):  
Membrane Vesicle ◽  
Model Organisms ◽  
Unicellular Eukaryotes ◽  
Current State ◽  
Important Challenge ◽  
Molecular Machinery ◽  
Cellular Machinery ◽  
Apparent Reduction ◽  
Related Proteins ◽  
Genome Projects

Autophagy is a eukaryotic cellular machinery that is able to degrade large intracellular components, including organelles, and plays a pivotal role in cellular homeostasis. Target materials are enclosed by a double membrane vesicle called autophagosome, whose formation is coordinated by autophagy-related proteins (ATGs). Studies of yeast and Metazoa have identified approximately 40 ATGs. Genome projects for unicellular eukaryotes revealed that some ATGs are conserved in all eukaryotic supergroups but others have arisen or were lost during evolution in some specific lineages. In spite of an apparent reduction in the ATG molecular machinery found in parasitic protists, it has become clear that ATGs play an important role in stage differentiation or organelle maintenance, sometimes with an original function that is unrelated to canonical degradative autophagy. In this review, we aim to briefly summarize the current state of knowledge in parasitic protists, in the light of the latest important findings from more canonical model organisms. Determining the roles of ATGs and the diversity of their functions in various lineages is an important challenge for understanding the evolutionary background of autophagy.

Genome Projects of Model Organisms

2001 ◽  
pp. 5-40
Author(s):  
Alfred Pühler ◽  
Doris Jording ◽  
Jörn Kalinowski ◽  
Detlev Buttgereit ◽  
Renate Renkawitz‐Pohl ◽  
...  
Keyword(s):  
Model Organisms ◽  
Genome Projects

scholarly journals A Deep Dive into Genome Assemblies of Non-vertebrate Animals

2021 ◽  
Author(s):  
Nadège Guiglielmoni ◽  
Ramón Rivera-Vicéns ◽  
Romain Koszul ◽  
Jean-François Flot
Keyword(s):  
Genome Assembly ◽  
Current Knowledge ◽  
Genome Structure ◽  
Deep Dive ◽  
Sequencing Technologies ◽  
Current State ◽  
Animal Diversity ◽  
And Function ◽  
Genome Assemblies ◽  
Genome Projects

Non-vertebrate species represent about ~95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

scholarly journals Dictyostelium discoideum and autophagy – a perfect pair

2019 ◽  
Vol 63 (8-9-10) ◽  
pp. 485-495 ◽  
Author(s):  
Sarah Fischer ◽  
Ludwig Eichinger
Keyword(s):  
Dictyostelium Discoideum ◽  
Membrane Vesicles ◽  
Model Organisms ◽  
Protein Assemblies ◽  
Large Protein ◽  
Complex Dynamic ◽  
The Social ◽  
Wide Range ◽  
Molecular Machinery ◽  
Chaperone Mediated Autophagy

Autophagy is subdivided into chaperone-mediated autophagy, microautophagy and macroautophagy and is a highly conserved intracellular degradative pathway. It is crucial for cellular homeostasis and also serves as a response to different stresses. Here we focus on macroautophagy, which targets damaged organelles and large protein assemblies, as well as pathogenic intracellular microbes for destruction. During this process, cytosolic material becomes enclosed in newly generated double-membrane vesicles, the so-called autophagosomes. Upon maturation, the autophagosome fuses with the lysosome for degradation of the cargo. The basic molecular machinery that controls macroautophagy works in a sequential order and consists of the ATG1 complex, the PtdIns3K complex, the membrane delivery system, two ubiquitin-like conjugation systems, and autophagy adaptors and receptors. Since the different stages of macroautophagy from initiation to final degradation of cargo are tightly regulated and highly conserved across eukaryotes, simple model organisms in combination with a wide range of techniques contributed significantly to advance our understanding of this complex dynamic process. Here, we present the social amoeba Dictyostelium discoideum as an advantageous and relevant experimental model system for the analysis of macroautophagy.

The molecular machinery of Keilin's respiratory chain

2003 ◽  
Vol 31 (6) ◽  
pp. 1095-1105 ◽  
Author(s):  
P.R. Rich
Keyword(s):  
Respiratory Chain ◽  
Atp Synthesis ◽  
Mitochondrial Respiratory Chain ◽  
New Era ◽  
Current State ◽  
Molecular Machinery ◽  
Tremendous Amount ◽  
Health And Disease ◽  
Level I ◽  
Prosthetic Groups

Keilin's classic paper of 1925 [Keilin (1925) Proc. R. Soc. London Ser. B 100, 129–151], achieved with simple, but elegant, techniques, describes the cytochrome components of the respiratory chain and their roles in intracellular respiration and oxygen consumption. Since that time, a tremendous amount of work has clarified the intricate details of the prosthetic groups, cofactors and proteins that comprise the respiratory chain and associated machinery for ATP synthesis. The work has culminated in advanced crystallographic and spectroscopic methods that provide structural and mechanistic details of this mitochondrial molecular machinery, in many instances to atomic level. I review here the current state of understanding of the mitochondrial respiratory chain in terms of structures and dynamics of the component proteins and their roles in the biological electron and proton transfer processes that result in ATP synthesis. These advances, together with emerging evidence of further diverse roles of mitochondria in health and disease, have prompted a new era of interest in mitochondrial function.

scholarly journals Behavioral Tagging: A Translation of the Synaptic Tagging and Capture Hypothesis

2015 ◽  
Vol 2015 ◽  
pp. 1-21 ◽  
Author(s):  
Diego Moncada ◽  
Fabricio Ballarini ◽  
Haydée Viola
Keyword(s):  
Experimental Data ◽  
Memory Consolidation ◽  
Electrical Stimulus ◽  
Memory Formation ◽  
Synaptic Specificity ◽  
Molecular Machinery ◽  
Synaptic Changes ◽  
Plastic Changes ◽  
Synaptic Tagging And Capture ◽  
Related Proteins

Similar molecular machinery is activated in neurons following an electrical stimulus that induces synaptic changes and after learning sessions that trigger memory formation. Then, to achieve perdurability of these processes protein synthesis is required for the reinforcement of the changes induced in the network. The synaptic tagging and capture theory provided a strong framework to explain synaptic specificity and persistence of electrophysiological induced plastic changes. Ten years later, the behavioral tagging hypothesis (BT) made use of the same argument, applying it to learning and memory models. The hypothesis postulates that the formation of lasting memories relies on at least two processes: the setting of a learning tag and the synthesis of plasticity related proteins, which once captured at tagged sites allow memory consolidation. BT explains how weak events, only capable of inducing transient forms of memories, can result in lasting memories when occurring close in time with other behaviorally relevant experiences that provide proteins. In this review, we detail the findings supporting the existence of BT process in rodents, leading to the consolidation, persistence, and interference of a memory. We focus on the molecular machinery taking place in these processes and describe the experimental data supporting the BT in humans.

scholarly journals Conservation and Variability of Synaptonemal Complex Proteins in Phylogenesis of Eukaryotes

2014 ◽  
Vol 2014 ◽  
pp. 1-16 ◽  
Author(s):  
Tatiana M. Grishaeva ◽  
Yuri F. Bogdanov
Keyword(s):  
Synaptonemal Complex ◽  
Protein Interactions ◽  
Phylogenetic Trees ◽  
Flowering Plants ◽  
Model Organisms ◽  
Protein Protein Interactions ◽  
Lateral Element ◽  
Origin And Evolution ◽  
Eukaryotic Proteomes ◽  
Related Proteins

The problems of the origin and evolution of meiosis include the enigmatic variability of the synaptonemal complexes (SCs) which, being morphology similar, consist of different proteins in different eukaryotic phyla. Using bioinformatics methods, we monitored all available eukaryotic proteomes to find proteins similar to known SC proteins of model organisms. We found proteins similar to SC lateral element (LE) proteins and possessing the HORMA domain in the majority of the eukaryotic taxa and assume them the most ancient among all SC proteins. Vertebrate LE proteins SYCP2, SYCP3, and SC65 proved to have related proteins in many invertebrate taxa. Proteins of SC central space are most evolutionarily variable. It means that different protein-protein interactions can exist to connect LEs. Proteins similar to the known SC proteins were not found in Euglenophyta, Chrysophyta, Charophyta, Xanthophyta, Dinoflagellata, and primitive Coelomata. We conclude that different proteins whose common feature is the presence of domains with a certain conformation are involved in the formation of the SC in different eukaryotic phyla. This permits a targeted search for orthologs of the SC proteins using phylogenetic trees. Here we consider example of phylogenetic trees for protozoans, fungi, algae, mosses, and flowering plants.

scholarly journals The conserved oligomeric Golgi complex is involved in double-membrane vesicle formation during autophagy

2010 ◽  
Vol 188 (1) ◽  
pp. 101-114 ◽  
Author(s):  
Wei-Lien Yen ◽  
Takahiro Shintani ◽  
Usha Nair ◽  
Yang Cao ◽  
Brian C. Richardson ◽  
...  
Keyword(s):  
Membrane Vesicle ◽  
Autophagosome Formation ◽  
Double Membrane ◽  
Complex Part ◽  
Cog Complex ◽  
Conserved Oligomeric Golgi Complex ◽  
Conserved Oligomeric Golgi ◽  
Critical Components ◽  
Molecular Components ◽  
Related Proteins

Macroautophagy is a catabolic pathway used for the turnover of long-lived proteins and organelles in eukaryotic cells. The morphological hallmark of this process is the formation of double-membrane autophagosomes that sequester cytoplasm. Autophagosome formation is the most complex part of macroautophagy, and it is a dynamic event that likely involves vesicle fusion to expand the initial sequestering membrane, the phagophore; however, essentially nothing is known about this process including the molecular components involved in vesicle tethering and fusion. In this study, we provide evidence that the subunits of the conserved oligomeric Golgi (COG) complex are required for double-membrane cytoplasm to vacuole targeting vesicle and autophagosome formation. COG subunits localized to the phagophore assembly site and interacted with Atg (autophagy related) proteins. In addition, mutations in the COG genes resulted in the mislocalization of Atg8 and Atg9, which are critical components involved in autophagosome formation.

Platelets from Munc18c heterozygous mice exhibit normal stimulus-induced release

2004 ◽  
Vol 92 (10) ◽  
pp. 829-837 ◽  
Author(s):  
Todd Schraw ◽  
Garland Crawford ◽  
Qiansheng Ren ◽  
Wangsun Choi ◽  
C. Debbie ◽  
...  
Keyword(s):  
Dense Core ◽  
Critical Aspect ◽  
Platelet Factor ◽  
Normal Morphology ◽  
Binding Partner ◽  
Molecular Machinery ◽  
Apparent Reduction ◽  
Dense Core Granules ◽  
Platelet Exocytosis ◽  
Platelet Secretion

SummaryA critical aspect of hemostasis is the release of clot-forming components from the three intra-platelet stores: dense core granules, α-granules and lysosomes. Exocytosis from these granules is mediated by soluble (SNAPs and NSF) and integralmembrane proteins (v- and t-SNAREs).Three SM (Sec1/Munc18) proteins are present in mouse platelets (Munc18a, 18b and 18c) and each potentially regulates exocytosis via modulation of their cognate syntaxin binding partner. To define the molecular machinery required for platelet exocytosis, we analyzed platelets from Munc18c heterozygous knockout mice. These platelets show a decrease in Munc18c but no apparent reduction in other secretory machinery components. No differences in the rates of aggregation or of secretion of [3H]-5HT (dense core granules), platelet factor 4 (α-granules), or hexosaminidase (lysosomes) were detected between platelets from Munc18c heterozygous knockout or wild-type mice. The platelets also show normal morphology. Contrary to a predicted requirement for Munc18c in platelet secretion, data reported here show that reducing Munc18c levels does not substantially alter platelet function. These data show that despite Munc18c’s role in platelet secretion, the lack of a secretion defect may be attributed to compensation by other Munc18 isoforms or that one allele is sufficient to maintain secretion under standard conditions.

Targeting DNA Repair Systems in Antitubercular Drug Development

2019 ◽  
Vol 26 (8) ◽  
pp. 1494-1505 ◽  
Author(s):  
Alina Minias ◽  
Anna Brzostek ◽  
Jarosław Dziadek
Keyword(s):  
Dna Repair ◽  
Protein Crystal ◽  
Model Organisms ◽  
Dna Repair Genes ◽  
Associated Proteins ◽  
Related Proteins ◽  
Repair Genes

Infections with Mycobacterium tuberculosis, the causative agent of tuberculosis, are difficult to treat using currently available chemotherapeutics. Clinicians agree on the urgent need for novel drugs to treat tuberculosis. In this mini review, we summarize data that prompts the consideration of DNA repair-associated proteins as targets for the development of new antitubercular compounds. We discuss data, including gene expression data, that highlight the importance of DNA repair genes during the pathogenic cycle as well as after exposure to antimicrobials currently in use. Specifically, we report experiments on determining the essentiality of DNA repair-related genes. We report the availability of protein crystal structures and summarize discovered protein inhibitors. Further, we describe phenotypes of available gene mutants of M. tuberculosis and model organisms Mycobacterium bovis and Mycobacterium smegmatis. We summarize experiments regarding the role of DNA repair-related proteins in pathogenesis and virulence performed both in vitro and in vivo during the infection of macrophages and animals. We detail the role of DNA repair genes in acquiring mutations, which influence the rate of drug resistance acquisition.

Genome Projects of Model Organisms

Biotechnology ◽  
2008 ◽  
pp. 4-39
Author(s):  
Alfred Pühler ◽  
Doris Jording ◽  
Jörn Kalinowski ◽  
Detlev Buttgereit ◽  
Renate Renkawitz-Pohl ◽  
...  
Keyword(s):  
Model Organisms ◽  
Genome Projects
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