scholarly journals Autophagosome biogenesis: From membrane growth to closure

2020 ◽  
Vol 219 (6) ◽  
Author(s):  
Thomas J. Melia ◽  
Alf H. Lystad ◽  
Anne Simonsen
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Membrane Vesicle ◽  
Double Membrane ◽  
The Core ◽  
Membrane Modeling ◽  
Membrane Growth ◽  
Initial Discovery ◽  
Insight Into ◽  
Key Questions

Autophagosome biogenesis involves de novo formation of a membrane that elongates to sequester cytoplasmic cargo and closes to form a double-membrane vesicle (an autophagosome). This process has remained enigmatic since its initial discovery >50 yr ago, but our understanding of the mechanisms involved in autophagosome biogenesis has increased substantially during the last 20 yr. Several key questions do remain open, however, including, What determines the site of autophagosome nucleation? What is the origin and lipid composition of the autophagosome membrane? How is cargo sequestration regulated under nonselective and selective types of autophagy? This review provides key insight into the core molecular mechanisms underlying autophagosome biogenesis, with a specific emphasis on membrane modeling events, and highlights recent conceptual advances in the field.

scholarly journals A molecular pore spans the double membrane of the coronavirus replication organelle

Science ◽  
2020 ◽  
Vol 369 (6509) ◽  
pp. 1395-1398 ◽  
Author(s):  
Georg Wolff ◽  
Ronald W. A. L. Limpens ◽  
Jessika C. Zevenhoven-Dobbe ◽  
Ulrike Laugks ◽  
Shawn Zheng ◽  
...  
Keyword(s):  
Drug Target ◽  
Rna Synthesis ◽  
Transmembrane Protein ◽  
Membrane Vesicle ◽  
Membrane Vesicles ◽  
Genome Replication ◽  
Messenger Rnas ◽  
Double Membrane ◽  
The Core ◽  
Cryo Electron Microscopy

Coronavirus genome replication is associated with virus-induced cytosolic double-membrane vesicles, which may provide a tailored microenvironment for viral RNA synthesis in the infected cell. However, it is unclear how newly synthesized genomes and messenger RNAs can travel from these sealed replication compartments to the cytosol to ensure their translation and the assembly of progeny virions. In this study, we used cellular cryo–electron microscopy to visualize a molecular pore complex that spans both membranes of the double-membrane vesicle and would allow export of RNA to the cytosol. A hexameric assembly of a large viral transmembrane protein was found to form the core of the crown-shaped complex. This coronavirus-specific structure likely plays a key role in coronavirus replication and thus constitutes a potential drug target.

scholarly journals An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis

2010 ◽  
Vol 190 (6) ◽  
pp. 1005-1022 ◽  
Author(s):  
Muriel Mari ◽  
Janice Griffith ◽  
Ester Rieter ◽  
Lakshmi Krishnappa ◽  
Daniel J. Klionsky ◽  
...  
Keyword(s):  
Secretory Pathway ◽  
De Novo ◽  
En Bloc ◽  
Genetic Analyses ◽  
Double Membrane ◽  
Precise Nature ◽  
Phagophore Assembly Site ◽  
Assembly Site ◽  
Key Questions ◽  
Phosphatidylinositol 3

Eukaryotes use the process of autophagy, in which structures targeted for lysosomal/vacuolar degradation are sequestered into double-membrane autophagosomes, in numerous physiological and pathological situations. The key questions in the field relate to the origin of the membranes as well as the precise nature of the rearrangements that lead to the formation of autophagosomes. We found that yeast Atg9 concentrates in a novel compartment comprising clusters of vesicles and tubules, which are derived from the secretory pathway and are often adjacent to mitochondria. We show that these clusters translocate en bloc next to the vacuole to form the phagophore assembly site (PAS), where they become the autophagosome precursor, the phagophore. In addition, genetic analyses indicate that Atg1, Atg13, and phosphatidylinositol-3-phosphate are involved in the further rearrangement of these initial membranes. Thus, our data reveal that the Atg9-positive compartments are important for the de novo formation of the PAS and the sequestering vesicle that are the hallmarks of autophagy.

scholarly journals Structures of collagen IV globular domains: insight into associated pathologies, folding and network assembly

IUCrJ ◽  
2018 ◽  
Vol 5 (6) ◽  
pp. 765-779 ◽  
Author(s):  
Patricia Casino ◽  
Roberto Gozalbo-Rovira ◽  
Jesús Rodríguez-Díaz ◽  
Sreedatta Banerjee ◽  
Ariel Boutaud ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Self Assembly ◽  
Molecular Mechanisms ◽  
Collagen Iv ◽  
Basement Membranes ◽  
Missense Mutations ◽  
The Core ◽  
Extracellular Structures ◽  
Insight Into

Basement membranes are extracellular structures of epithelia and endothelia that have collagen IV scaffolds of triple α-chain helical protomers that associate end-to-end, forming networks. The molecular mechanisms by which the noncollagenous C-terminal domains of α-chains direct the selection and assembly of the α1α2α1 and α3α4α5 hetero-oligomers found in vivo remain obscure. Autoantibodies against the noncollagenous domains of the α3α4α5 hexamer or mutations therein cause Goodpasture's or Alport's syndromes, respectively. To gain further insight into oligomer-assembly mechanisms as well as into Goodpasture's and Alport's syndromes, crystal structures of noncollagenous domains produced by recombinant methods were determined. The spontaneous formation of canonical homohexamers (dimers of trimers) of these domains of the α1, α3 and α5 chains was shown and the components of the Goodpasture's disease epitopes were viewed. Crystal structures of the α2 and α4 noncollagenous domains generated by recombinant methods were also determined. These domains spontaneously form homo-oligomers that deviate from the canonical architectures since they have a higher number of subunits (dimers of tetramers and of hexamers, respectively). Six flexible structural motifs largely explain the architectural variations. These findings provide insight into noncollagenous domain folding, while supporting the in vivo operation of extrinsic mechanisms for restricting the self-assembly of noncollagenous domains. Intriguingly, Alport's syndrome missense mutations concentrate within the core that nucleates the folding of the noncollagenous domain, suggesting that this syndrome, when owing to missense changes, is a folding disorder that is potentially amenable to pharmacochaperone therapy.

scholarly journals Identification of the Core MicroRNAs and Potential Molecular Mechanismsin Sarcoidosis Using Bioinformatics Analysis

2021 ◽  
Vol 8 ◽  
Author(s):  
Yuan Cao ◽  
Hua Zhang ◽  
Lulu Zheng ◽  
Qiao Li
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Hub Genes ◽  
The Core ◽  
Ppi Networks ◽  
Go Enrichment ◽  
Mirnas Expression ◽  
Go Enrichment Analysis ◽  
Insight Into

Sarcoidosis is a systemic heterogeneous inflammatory disease; however, the etiology and pathogenesis of sarcoidosis are still unknown. Herein, we investigated the core microRNAs and potential molecular mechanisms in sarcoidosis. The DE-miRNAs were diagnosed using the LIMMA software package. DIANA-mirPath was employed to perform pathway and GO enrichment analysis of the DE-miRNAs. PPI networks and miRNA-target gene regulatory networks were used to obtain insight into the actions of DE-miRNAs. Expression of the hub genes along with miRNAs was validated in clinical specimens. Overall, 266 DE-miRNAs were screened. Among these DE-miRNAs, hsa-miR-144, hsa-miR-126, as well as hsa-miR-106a were the upmost upregulated miRNAs; hsa-miR-151-3p, hsa-miR-320d, and hsa-miR-324-3p were the top downregulated miRNAs. NR3C1, ZBTB7A, NUFIP2, BZW1, ERGIC2, and VEGFA were mapped as the most targeted hub genes in the upregulation of miRNAs, and MCL1 and SAE1 were the most targeted hub genes in the downregulation of miRNA. VEGFA and NR3C1 were selected and potentially modulated by hsa-miR-20b, hsa-miR-126, and hsa-miR-106a. In sarcoidosis pathological tissue, hsa-miR-126 was highly expressed, and VEGFA and NR3C1 were overexpressed. In conclusion, our results revealed the dysregulation of hsa-miR-126 and a potential regulatory mechanism for pathogenesis in sarcoidosis.

scholarly journals Comparative analysis of whole flower transcriptomes in the Zingiberales

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5490 ◽  
Author(s):  
Ana Maria R. Almeida ◽  
Alma Piñeyro-Nelson ◽  
Roxana B. Yockteng ◽  
Chelsea D. Specht
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Model Organisms ◽  
Comparative Approach ◽  
Careful Study ◽  
Sequencing Technologies ◽  
Outgroup Species ◽  
Floral Diversification ◽  
Genomic Scale ◽  
Insight Into

The advancement of next generation sequencing technologies (NGS) has revolutionized our ability to generate large quantities of data at a genomic scale. Despite great challenges, these new sequencing technologies have empowered scientists to explore various relevant biological questions on non-model organisms, even in the absence of a complete sequenced reference genome. Here, we analyzed whole flower transcriptome libraries from exemplar species across the monocot order Zingiberales, using a comparative approach in order to gain insight into the evolution of the molecular mechanisms underlying flower development in the group. We identified 4,153 coding genes shared by all floral transcriptomes analyzed, and 1,748 genes that are only retrieved in the Zingiberales. We also identified 666 genes that are unique to the ginger lineage, and 2,001 that are only found in the banana group, while in the outgroup species Dichorisandra thyrsiflora J.C. Mikan (Commelinaceae) we retrieved 2,686 unique genes. It is possible that some of these genes underlie lineage-specific molecular mechanisms of floral diversification. We further discuss the nature of these lineage-specific datasets, emphasizing conserved and unique molecular processes with special emphasis in the Zingiberales. We also briefly discuss the strengths and shortcomings of de novo assembly for the study of developmental processes across divergent taxa from a particular order. Although this comparison is based exclusively on coding genes, with particular emphasis in transcription factors, we believe that the careful study of other regulatory mechanisms, such as non-coding RNAs, might reveal new levels of complexity, which were not explored in this work.

scholarly journals De novo transcriptome assembly of the Italian white truffle (Tuber magnatum Pico)

2018 ◽  
Author(s):  
Federico Vita ◽  
Amedeo Alpi ◽  
Edoardo Bertolini
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Rna Seq ◽  
Genetic Studies ◽  
Protein Coding ◽  
Important Species ◽  
White Truffle ◽  
Tuber Magnatum ◽  
Insight Into

AbstractThe Italian white truffle (Tuber magnatum Pico) is a gastronomic delicacy that dominates the worldwide truffle market. Despite its importance, the genomic resources currently available for this species are still limited. Here we present the first de novo transcriptome assembly of T. magnatum. Illumina RNA-seq data were assembled using a single-k-mer approach into 22,932 transcripts with N50 of 1,524 bp. Our approach allowed to predict and annotate 12,367 putative protein coding sequences, reunited in 6,723 loci. In addition, we identified 2,581 gene-based SSR markers. This work provides the first publicly available reference transcriptome for genomics and genetic studies providing insight into the molecular mechanisms underlying the biology of this important species.

scholarly journals Mechanisms and Pathophysiological Roles of the ATG8 Conjugation Machinery

Cells ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 973 ◽  
Author(s):  
Lystad ◽  
Simonsen
Keyword(s):  
Molecular Mechanisms ◽  
Genetic Manipulation ◽  
Model Organisms ◽  
Selective Degradation ◽  
Cytoplasmic Material ◽  
Associated Proteins ◽  
Initial Discovery ◽  
Protein Lipidation ◽  
Insight Into

Since their initial discovery around two decades ago, the yeast autophagy-related (Atg)8 protein and its mammalian homologues of the light chain 3 (LC3) and γ-aminobutyric acid receptor associated proteins (GABARAP) families have been key for the tremendous expansion of our knowledge about autophagy, a process in which cytoplasmic material become targeted for lysosomal degradation. These proteins are ubiquitin-like proteins that become directly conjugated to a lipid in the autophagy membrane upon induction of autophagy, thus providing a marker of the pathway, allowing studies of autophagosome biogenesis and maturation. Moreover, the ATG8 proteins function to recruit components of the core autophagy machinery as well as cargo for selective degradation. Importantly, comprehensive structural and biochemical in vitro studies of the machinery required for ATG8 protein lipidation, as well as their genetic manipulation in various model organisms, have provided novel insight into the molecular mechanisms and pathophysiological roles of the mATG8 proteins. Recently, it has become evident that the ATG8 proteins and their conjugation machinery are also involved in intracellular pathways and processes not related to autophagy. This review focuses on the molecular functions of ATG8 proteins and their conjugation machinery in autophagy and other pathways, as well as their links to disease.

scholarly journals Meiotic Cellular Rejuvenation is Coupled to Nuclear Remodeling in Budding Yeast

2019 ◽  
Author(s):  
Grant A. King ◽  
Jay S. Goodman ◽  
Keerthana Chetlapalli ◽  
Jennifer G. Schick ◽  
Danielle M. Jorgens ◽  
...  
Keyword(s):  
Quality Control ◽  
De Novo ◽  
Budding Yeast ◽  
Time Lapse ◽  
Cellular Damage ◽  
Nuclear Pore ◽  
The Core ◽  
Nucleolar Material ◽  
Nuclear Remodeling ◽  
Insight Into

ABSTRACTProduction of healthy gametes in meiosis relies on the quality control and proper distribution of both nuclear and cytoplasmic contents. Meiotic differentiation naturally eliminates age-induced cellular damage by an unknown mechanism. Using time-lapse fluorescence microscopy in budding yeast, we found that nuclear senescence factors – including protein aggregates, extrachromosomal ribosomal DNA circles, and abnormal nucleolar material – are sequestered away from chromosomes during meiosis II and subsequently eliminated. A similar sequestration and elimination process occurs for the core subunits of the nuclear pore complex in both young and old cells. Nuclear envelope remodeling drives the formation of a membranous compartment containing the sequestered material. Importantly,de novogeneration of plasma membrane is required for the sequestration event, preventing the inheritance of long-lived nucleoporins and senescence factors into the newly formed gametes. Our study uncovers a new mechanism of nuclear quality control and provides insight into its function in meiotic cellular rejuvenation.

scholarly journals New Insight into the Octamer of Thymidylate Synthetase Stabilized by Intermolecular Cys43-Disulfide

2018 ◽  
Author(s):  
Dan Xie ◽  
Lulu Wang ◽  
Qi Xiao ◽  
Xiaoyan Wu ◽  
Lin Zhang ◽  
...  
Keyword(s):  
Drug Targets ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Physical Structure ◽  
Size Exclusion ◽  
Primary Target ◽  
Sds Page ◽  
Exclusion Chromatography ◽  
Essential Enzyme ◽  
Insight Into

Thymidylate synthase (TYMS) is an essential enzyme for the de novo synthesis of dTMP and has been a primary target for cancer chemotherapy. Although the physical structure of TYMS and the molecular mechanisms of TYMS catalyzing the conversion of dUMP to dTMP have been conducted thorough studies, oligomeric structure remains unclear. Here, we show that human TYMS not only exists in dimer but also octamer by intermolecular Cys43-disulfide formation. We optimize the expression condition of recombinant human TYMS using Escherichia coli system. Using HPLC-MS/MS, we show that purified TYMS has catalytic activity for producing dTMP. In the absence of reductant β-mercaptoethanol, SDS-PAGE and size exclusion chromatography (SEC) showed size of TYMS protein is about 35 KDa, 70 KDa, and 280 KDa. While the Cys43 was mutated to Gly, the band of ~280 KDa and the peak of octamer disappeared. Therefore, TYMS was determined to form octamer, dependent on the presence of Cys43-disulfide. By measuring Steady-State Parameters for monomer, dimer and octamer, we found the kcat of octamer is increased slightly than monomer. On the basis of these findings, we suggest that octamer in the active state might have a potential influence on the design of new drug targets.

scholarly journals A molecular pore spans the double membrane of the coronavirus replication organelle

2020 ◽  
Author(s):  
Georg Wolff ◽  
Ronald W.A.L. Limpens ◽  
Jessika C. Zevenhoven-Dobbe ◽  
Ulrike Laugks ◽  
Shawn Zheng ◽  
...  
Keyword(s):  
Drug Target ◽  
Rna Synthesis ◽  
Transmembrane Protein ◽  
Membrane Vesicle ◽  
Critical Role ◽  
Membrane Vesicles ◽  
Genome Replication ◽  
Double Membrane ◽  
The Core ◽  
Novel Drug

Coronavirus genome replication is associated with virus-induced cytosolic double-membrane vesicles, which may provide a tailored micro-environment for viral RNA synthesis in the infected cell. However, it is unclear how newly synthesized genomes and mRNAs can travel from these sealed replication compartments to the cytosol to ensure their translation and the assembly of progeny virions. Here, using cellular electron cryo-microscopy, we unveiled a molecular pore complex that spans both membranes of the double-membrane vesicle and would allow export of RNA to the cytosol. A hexameric assembly of a large viral transmembrane protein was found to form the core of the crown-shaped complex. This coronavirus-specific structure likely plays a critical role in coronavirus replication and thus constitutes a novel drug target

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