scholarly journals Molecular architecture of the human tRNA ligase complex

2021 ◽  
Author(s):  
Alena Kroupova ◽  
Fabian Ackle ◽  
Franziska M Boneberg ◽  
Alessia Chui ◽  
Stefan Weitzer ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Strand Break ◽  
Molecular Architecture ◽  
Cellular Processes ◽  
Unfolded Protein ◽  
Terminal Domain ◽  
Structural Framework ◽  
Dna Double Strand Break ◽  
Protein Response ◽  
Intersubunit Interactions

RtcB enzymes are RNA ligases that play essential roles in tRNA splicing, unfolded protein response, and RNA repair. In metazoa, RtcB functions as part of a five-subunit tRNA ligase complex (tRNA-LC) along with Ddx1, Cgi-99, Fam98B and Ashwin. The human tRNA-LC or its individual subunits have been implicated in additional cellular processes including microRNA maturation, viral replication, DNA double-strand break repair and mRNA transport. Here we present a biochemical analysis of the intersubunit interactions within the human tRNA-LC along with crystal structures of the catalytic subunit RTCB and the N-terminal domain of CGI-99. We show that the core of the human tRNA-LC is assembled from RTCB and the C-terminal alpha-helical regions of DDX1, CGI-99, and FAM98B, all of which are required for complex integrity. The N-terminal domain of CGI-99 displays structural homology to calponin-homology domains, and CGI-99 and FAM98B associate via their N-terminal domains to form a stable subcomplex. The crystal structure of GMP-bound RTCB reveals divalent metal coordination geometry in the active site, providing insights into its catalytic mechanism. Collectively, these findings shed light on the molecular architecture and mechanism of the human tRNA ligase complex, and provide a structural framework for understanding its functions in cellular RNA metabolism.

scholarly journals Molecular architecture of the human tRNA ligase complex

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Alena Kroupova ◽  
Fabian Ackle ◽  
Igor Asanović ◽  
Stefan Weitzer ◽  
Franziska M Boneberg ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Strand Break ◽  
Molecular Architecture ◽  
Rna Repair ◽  
Cellular Processes ◽  
Unfolded Protein ◽  
Terminal Domain ◽  
Structural Framework ◽  
Dna Double Strand Break ◽  
Protein Response

RtcB enzymes are RNA ligases that play essential roles in tRNA splicing, unfolded protein response, and RNA repair. In metazoa, RtcB functions as part of a five-subunit tRNA ligase complex (tRNA-LC) along with Ddx1, Cgi-99, Fam98B and Ashwin. The human tRNA-LC or its individual subunits have been implicated in additional cellular processes including microRNA maturation, viral replication, DNA double-strand break repair and mRNA transport. Here we present a biochemical analysis of the inter-subunit interactions within the human tRNA-LC along with crystal structures of the catalytic subunit RTCB and the N-terminal domain of CGI-99. We show that the core of the human tRNA-LC is assembled from RTCB and the C-terminal alpha-helical regions of DDX1, CGI-99, and FAM98B, all of which are required for complex integrity. The N-terminal domain of CGI-99 displays structural homology to calponin-homology domains, and CGI-99 and FAM98B associate via their N-terminal domains to form a stable subcomplex. The crystal structure of GMP-bound RTCB reveals divalent metal coordination geometry in the active site, providing insights into its catalytic mechanism. Collectively, these findings shed light on the molecular architecture and mechanism of the human tRNA ligase complex, and provide a structural framework for understanding its functions in cellular RNA metabolism.

Proteome analysis of protein partners to nucleosomes containing canonical H2A or the variant histones H2A.Z or H2A.X

2012 ◽  
Vol 393 (1-2) ◽  
pp. 47-61 ◽  
Author(s):  
Satoru Fujimoto ◽  
Corrine Seebart ◽  
Tiziana Guastafierro ◽  
Jessica Prenni ◽  
Paola Caiafa ◽  
...  
Keyword(s):  
Regulation Of Gene Expression ◽  
Proteome Analysis ◽  
Strand Break ◽  
Histone Variants ◽  
Histone H2a ◽  
Systematic Analysis ◽  
Cellular Processes ◽  
Nucleosome Structure ◽  
Protein Partners ◽  
Dna Double Strand Break

Abstract Although the existence of histone variants has been known for quite some time, only recently are we grasping the breadth and diversity of the cellular processes in which they are involved. Of particular interest are the two variants of histone H2A, H2A.Z and H2A.X because of their roles in regulation of gene expression and in DNA double-strand break repair, respectively. We hypothesize that nucleosomes containing these variants may perform their distinct functions by interacting with different sets of proteins. Here, we present our proteome analysis aimed at identifying protein partners that interact with nucleosomes containing H2A.Z, H2A.X or their canonical H2A counterpart. Our development of a nucleosome-pull down assay and analysis of the recovered nucleosome-interacting proteins by mass spectrometry allowed us to directly compare nuclear partners of these variant-containing nucleosomes to those containing canonical H2A. To our knowledge, our data represent the first systematic analysis of the H2A.Z and H2A.X interactome in the context of nucleosome structure.

scholarly journals Polo-like kinase 3 regulates CtIP during DNA double-strand break repair in G1

2014 ◽  
Vol 206 (7) ◽  
pp. 877-894 ◽  
Author(s):  
Olivia Barton ◽  
Steffen C. Naumann ◽  
Ronja Diemer-Biehs ◽  
Julia Künzel ◽  
Monika Steinlage ◽  
...  
Keyword(s):  
Large Scale ◽  
Strand Break ◽  
Dna Double Strand Breaks ◽  
End Joining ◽  
Interacting Protein ◽  
Genomic Deletions ◽  
Cellular Processes ◽  
Dna Double Strand Break ◽  
Radiation Induced ◽  
Alternative Nhej

DNA double-strand breaks (DSBs) are repaired by nonhomologous end joining (NHEJ) or homologous recombination (HR). The C terminal binding protein–interacting protein (CtIP) is phosphorylated in G2 by cyclin-dependent kinases to initiate resection and promote HR. CtIP also exerts functions during NHEJ, although the mechanism phosphorylating CtIP in G1 is unknown. In this paper, we identify Plk3 (Polo-like kinase 3) as a novel DSB response factor that phosphorylates CtIP in G1 in a damage-inducible manner and impacts on various cellular processes in G1. First, Plk3 and CtIP enhance the formation of ionizing radiation-induced translocations; second, they promote large-scale genomic deletions from restriction enzyme-induced DSBs; third, they are required for resection and repair of complex DSBs; and finally, they regulate alternative NHEJ processes in Ku−/− mutants. We show that mutating CtIP at S327 or T847 to nonphosphorylatable alanine phenocopies Plk3 or CtIP loss. Plk3 binds to CtIP phosphorylated at S327 via its Polo box domains, which is necessary for robust damage-induced CtIP phosphorylation at S327 and subsequent CtIP phosphorylation at T847.

The histone codes for meiosis

Reproduction ◽  
2017 ◽  
Vol 154 (3) ◽  
pp. R65-R79 ◽  
Author(s):  
Lina Wang ◽  
Zhiliang Xu ◽  
Muhammad Babar Khawar ◽  
Chao Liu ◽  
Wei Li
Keyword(s):  
Chromatin Remodeling ◽  
Strand Break ◽  
Future Trends ◽  
Functional Roles ◽  
Cellular Processes ◽  
Cell Divisions ◽  
Special Events ◽  
Dna Double Strand Break ◽  
Diploid Cells ◽  
Histone Codes

Meiosis is a specialized process that produces haploid gametes from diploid cells by a single round of DNA replication followed by two successive cell divisions. It contains many special events, such as programmed DNA double-strand break (DSB) formation, homologous recombination, crossover formation and resolution. These events are associated with dynamically regulated chromosomal structures, the dynamic transcriptional regulation and chromatin remodeling are mainly modulated by histone modifications, termed ‘histone codes’. The purpose of this review is to summarize the histone codes that are required for meiosis during spermatogenesis and oogenesis, involving meiosis resumption, meiotic asymmetric division and other cellular processes. We not only systematically review the functional roles of histone codes in meiosis but also discuss future trends and perspectives in this field.

scholarly journals Recent advances in signal integration mechanisms in the unfolded protein response

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1840 ◽  
Author(s):  
G. Elif Karagöz ◽  
Tomás Aragón ◽  
Diego Acosta-Alvear
Keyword(s):  
Unfolded Protein Response ◽  
New Developments ◽  
Cellular Processes ◽  
Unfolded Protein ◽  
Integration Mechanisms ◽  
Physiological Demands ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Er Homeostasis ◽  
Made In

Since its discovery more than 25 years ago, great progress has been made in our understanding of the unfolded protein response (UPR), a homeostatic mechanism that adjusts endoplasmic reticulum (ER) function to satisfy the physiological demands of the cell. However, if ER homeostasis is unattainable, the UPR switches to drive cell death to remove defective cells in an effort to protect the health of the organism. This functional dichotomy places the UPR at the crossroads of the adaptation versus apoptosis decision. Here, we focus on new developments in UPR signaling mechanisms, in the interconnectivity among the signaling pathways that make up the UPR in higher eukaryotes, and in the coordination between the UPR and other fundamental cellular processes.

scholarly journals Structure and Function of Mitochondria-Associated Endoplasmic Reticulum Membranes (MAMs) and Their Role in Cardiovascular Diseases

2021 ◽  
Vol 2021 ◽  
pp. 1-19
Author(s):  
Yi Luan ◽  
Ying Luan ◽  
Rui-Xia Yuan ◽  
Qi Feng ◽  
Xing Chen ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Vascular Endothelial Cells ◽  
Mitochondrial Dynamics ◽  
Cellular Functions ◽  
Cellular Processes ◽  
Unfolded Protein ◽  
Associated Proteins ◽  
Apoptosis And Inflammation ◽  
And Function ◽  
Protein Response

Abnormal function of suborganelles such as mitochondria and endoplasmic reticulum often leads to abnormal function of cardiomyocytes or vascular endothelial cells and cardiovascular disease (CVD). Mitochondria-associated membrane (MAM) is involved in several important cellular functions. Increasing evidence shows that MAM is involved in the pathogenesis of CVD. MAM mediates multiple cellular processes, including calcium homeostasis regulation, lipid metabolism, unfolded protein response, ROS, mitochondrial dynamics, autophagy, apoptosis, and inflammation, which are key risk factors for CVD. In this review, we discuss the structure of MAM and MAM-associated proteins, their role in CVD progression, and the potential use of MAM as the therapeutic targets for CVD treatment.

scholarly journals The Cross-Links of Endoplasmic Reticulum Stress, Autophagy, and Nurodegeneration in Parkinson’s Disease

2021 ◽  
Vol 13 ◽  
Author(s):  
Haigang Ren ◽  
Wanqing Zhai ◽  
Xiaojun Lu ◽  
Guanghui Wang
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Endoplasmic Reticulum ◽  
Er Stress ◽  
Substantia Nigra Pars Compacta ◽  
Cellular Processes ◽  
Unfolded Protein ◽  
Cross Links ◽  
Main Component ◽  
Protein Response

Parkinson’s disease (PD) is the most common neurodegenerative movement disorder, and it is characterized by the selective loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc), as well as the presence of intracellular inclusions with α-synuclein as the main component in surviving DA neurons. Emerging evidence suggests that the imbalance of proteostasis is a key pathogenic factor for PD. Endoplasmic reticulum (ER) stress-induced unfolded protein response (UPR) and autophagy, two major pathways for maintaining proteostasis, play important roles in PD pathology and are considered as attractive therapeutic targets for PD treatment. However, although ER stress/UPR and autophagy appear to be independent cellular processes, they are closely related to each other. In this review, we focused on the roles and molecular cross-links between ER stress/UPR and autophagy in PD pathology. We systematically reviewed and summarized the most recent advances in regulation of ER stress/UPR and autophagy, and their cross-linking mechanisms. We also reviewed and discussed the mechanisms of the coexisting ER stress/UPR activation and dysregulated autophagy in the lesion regions of PD patients, and the underlying roles and molecular crosslinks between ER stress/UPR activation and the dysregulated autophagy in DA neurodegeneration induced by PD-associated genetic factors and PD-related neurotoxins. Finally, we indicate that the combined regulation of ER stress/UPR and autophagy would be a more effective treatment for PD rather than regulating one of these conditions alone.

scholarly journals What Is the Sweetest UPR Flavor for the β-cell? That Is the Question

2021 ◽  
Vol 11 ◽  
Author(s):  
Alina Lenghel ◽  
Alina Maria Gheorghita ◽  
Andrei Mircea Vacaru ◽  
Ana-Maria Vacaru
Keyword(s):  
Molecular Mechanisms ◽  
Secretory Cells ◽  
Insulin Production ◽  
Β Cells ◽  
Β Cell ◽  
Cellular Processes ◽  
Unfolded Protein ◽  
Specific Outcome ◽  
A Cell ◽  
Protein Response

Unfolded protein response (UPR) is a process conserved from yeasts to mammals and, based on the generally accepted dogma, helps the secretory performance of a cell, by improving its capacity to cope with a burden in the endoplasmic reticulum (ER). The ER of β-cells, “professional secretory cells”, has to manage tremendous amounts of insulin, which elicits a strong pressure on the ER intrinsic folding capacity. Thus, the constant demand for insulin production results in misfolded proinsulin, triggering a physiological upregulation of UPR to restore homeostasis. Most diabetic disorders are characterized by the loss of functional β-cells, and the pathological side of UPR plays an instrumental role. The transition from a homeostatic to a pathological UPR that ultimately leads to insulin-producing β-cell decay entails complex cellular processes and molecular mechanisms which remain poorly described so far. Here, we summarize important processes that are coupled with or driven by UPR in β-cells, such as proliferation, inflammation and dedifferentiation. We conclude that the UPR comes in different “flavors” and each of them is correlated with a specific outcome for the cell, for survival, differentiation, proliferation as well as cell death. All these greatly depend on the way UPR is triggered, however what exactly is the switch that favors the activation of one UPR as opposed to others is largely unknown. Substantial work needs to be done to progress the knowledge in this important emerging field as this will help in the development of novel and more efficient therapies for diabetes.

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