-
Biochimica Et Biophysica Acta. Gene... Feb 2021Transcription initiation is a major regulatory step in eukaryotic gene expression. It involves the assembly of general transcription factors and RNA polymerase II into a... (Review)
Review
Transcription initiation is a major regulatory step in eukaryotic gene expression. It involves the assembly of general transcription factors and RNA polymerase II into a functional pre-initiation complex at core promoters. The degree of chromatin compaction controls the accessibility of the transcription machinery to template DNA. Co-activators have critical roles in this process by actively regulating chromatin accessibility. Many transcriptional coactivators are multisubunit complexes, organized into distinct structural and functional modules and carrying multiple regulatory activities. The first nuclear histone acetyltransferase (HAT) characterized was General Control Non-derepressible 5 (Gcn5). Gcn5 was subsequently identified as a subunit of the HAT module of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex, which is an experimental paradigm for multifunctional co-activators. We know today that Gcn5 is the catalytic subunit of multiple distinct co-activator complexes with specific functions. In this review, we summarize recent advances in the structure of Gcn5-containing co-activator complexes, most notably SAGA, and discuss how these new structural insights contribute to better understand their functions.
Topics: Acetylation; Amino Acid Sequence; Animals; Arabidopsis; Conserved Sequence; Cryoelectron Microscopy; Crystallography; Drosophila melanogaster; Evolution, Molecular; Gene Expression Regulation; Histones; Humans; Multienzyme Complexes; Protein Structure, Quaternary; Saccharomyces cerevisiae; Structure-Activity Relationship; Trans-Activators; p300-CBP Transcription Factors
PubMed: 32739556
DOI: 10.1016/j.bbagrm.2020.194614 -
Trends in Biochemical Sciences Jan 2020Bacterial RNA degradosomes are multienzyme molecular machines that act as hubs for post-transcriptional regulation of gene expression. The ribonuclease activities of... (Review)
Review
Bacterial RNA degradosomes are multienzyme molecular machines that act as hubs for post-transcriptional regulation of gene expression. The ribonuclease activities of these complexes require tight regulation, as they are usually essential for cell survival while potentially destructive. Recent studies have unveiled a wide variety of regulatory mechanisms including autoregulation, post-translational modifications, and protein compartmentalization. Recently, the subcellular organization of bacterial RNA degradosomes was found to present similarities with eukaryotic messenger ribonucleoprotein (mRNP) granules, membraneless compartments that are also involved in mRNA and protein storage and/or mRNA degradation. In this review, we present the current knowledge on the composition and targets of RNA degradosomes, the most recent developments regarding the regulation of these machineries, and their similarities with the eukaryotic mRNP granules.
Topics: Endoribonucleases; Multienzyme Complexes; Polyribonucleotide Nucleotidyltransferase; RNA Helicases; RNA, Bacterial
PubMed: 31679841
DOI: 10.1016/j.tibs.2019.10.002 -
Journal of Molecular Biology Sep 2019Cellular RNA polymerase is a multi-subunit macromolecular assembly responsible for gene transcription, a highly regulated process conserved from bacteria to humans. In... (Review)
Review
Cellular RNA polymerase is a multi-subunit macromolecular assembly responsible for gene transcription, a highly regulated process conserved from bacteria to humans. In bacteria, sigma factors are employed to mediate gene-specific expression in response to a variety of environmental conditions. The major variant σ factor, σ, has a specific role in stress responses. Unlike σ-dependent transcription, which often can spontaneously proceed to initiation, σ-dependent transcription requires an additional ATPase protein for activation. As a result, structures of a number of distinct functional states during the dynamic process of transcription initiation have been captured using the σ system with both x-ray crystallography and cryo electron microscopy, furthering our understanding of σ-dependent transcription initiation and DNA opening. Comparisons with σ and eukaryotic polymerases reveal unique and common features during transcription initiation.
Topics: Adenosine Triphosphatases; Bacteria; Cryoelectron Microscopy; Crystallography, X-Ray; DNA, Bacterial; DNA-Directed RNA Polymerases; Multienzyme Complexes; Promoter Regions, Genetic; Protein Conformation; RNA Polymerase Sigma 54; Transcription Initiation, Genetic
PubMed: 31029702
DOI: 10.1016/j.jmb.2019.04.022 -
Open Biology Jun 2021Herpes simplex virus type 1 (HSV-1) is one of the nine herpesviruses that infect humans. HSV-1 encodes seven proteins to replicate its genome in the hijacked human cell.... (Review)
Review
Herpes simplex virus type 1 (HSV-1) is one of the nine herpesviruses that infect humans. HSV-1 encodes seven proteins to replicate its genome in the hijacked human cell. Among these are the herpes virus DNA helicase and primase that are essential components of its replication machinery. In the HSV-1 replisome, the helicase-primase complex is composed of three components including UL5 (helicase), UL52 (primase) and UL8 (non-catalytic subunit). UL5 and UL52 subunits are functionally interdependent, and the UL8 component is required for the coordination of UL5 and UL52 activities proceeding in opposite directions with respect to the viral replication fork. Anti-viral compounds currently under development target the functions of UL5 and UL52. Here, we review the structural and functional properties of the UL5/UL8/UL52 complex and highlight the gaps in knowledge to be filled to facilitate molecular characterization of the structure and function of the helicase-primase complex for development of alternative anti-viral treatments.
Topics: Animals; Antiviral Agents; DNA Helicases; DNA Primase; Drug Development; Herpes Simplex; Herpesvirus 1, Human; Humans; Models, Molecular; Multienzyme Complexes; Protein Binding; Protein Interaction Domains and Motifs; Protein Subunits; Structure-Activity Relationship; Virus Replication
PubMed: 34102080
DOI: 10.1098/rsob.210011 -
Methods in Molecular Biology (Clifton,... 2020The eukaryotic RNA exosome is a conserved and ubiquitous multiprotein complex that possesses multiple RNase activities and is involved in a diverse array of RNA... (Review)
Review
The eukaryotic RNA exosome is a conserved and ubiquitous multiprotein complex that possesses multiple RNase activities and is involved in a diverse array of RNA degradation and processing events. While much of our current understanding of RNA exosome function has been elucidated using genetics and cell biology based studies of protein functions, in particular in S. cerevisiae, many important contributions in the field have been enabled through use of in vitro reconstituted complexes. Here, we present an overview of our approach to purify exosome components from recombinant sources and reconstitute them into functional complexes. Three chapters following this overview provide detailed protocols for reconstituting exosome complexes from S. cerevisiae, S. pombe, and H. sapiens. We additionally provide insight on some of the drawbacks of these methods and highlight several important discoveries that have been achieved using reconstituted complexes.
Topics: Animals; Exoribonucleases; Exosome Multienzyme Ribonuclease Complex; Exosomes; Humans; RNA Stability; RNA, Fungal; Recombinant Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 31768988
DOI: 10.1007/978-1-4939-9822-7_20 -
Journal of Medicinal Chemistry Jul 2019Proteasomes are multienzyme complexes that maintain protein homeostasis (proteostasis) and important cellular functions through the degradation of misfolded, redundant,... (Review)
Review
Proteasomes are multienzyme complexes that maintain protein homeostasis (proteostasis) and important cellular functions through the degradation of misfolded, redundant, and damaged proteins. It is well established that aging is associated with the accumulation of damaged and misfolded proteins. This phenomenon is paralleled by declined proteasome activity. When the accumulation of redundant proteins exceed degradation, undesirable signaling and/or aggregation occurs and are the hallmarks of neurodegenerative diseases and many cancers. Thus, increasing proteasome activity has been recognized as a new approach to delay the onset or ameliorate the symptoms of neurodegenerative and other proteotoxic disorders. Enhancement of proteasome activity has many therapeutic potentials but is still a relatively unexplored field. In this perspective, we review current approaches, genetic manipulation, posttranslational modification, and small molecule proteasome agonists used to increase proteasome activity, challenges facing the field, and applications beyond aging and neurodegenerative diseases.
Topics: Animals; Drug Discovery; Enzyme Activators; Humans; Molecular Targeted Therapy; Neurodegenerative Diseases; Proteasome Endopeptidase Complex; Protein Processing, Post-Translational; Proteolysis; Proteostasis; Small Molecule Libraries
PubMed: 30839208
DOI: 10.1021/acs.jmedchem.9b00101 -
Bioscience Reports Apr 2021Pyruvate dehydrogenase kinase (PDK) can regulate the catalytic activity of pyruvate decarboxylation oxidation via the mitochondrial pyruvate dehydrogenase complex, and... (Review)
Review
Pyruvate dehydrogenase kinase (PDK) can regulate the catalytic activity of pyruvate decarboxylation oxidation via the mitochondrial pyruvate dehydrogenase complex, and it further links glycolysis with the tricarboxylic acid cycle and ATP generation. This review seeks to elucidate the regulation of PDK activity in different species, mainly mammals, and the role of PDK inhibitors in preventing increased blood glucose, reducing injury caused by myocardial ischemia, and inducing apoptosis of tumor cells. Regulations of PDKs expression or activity represent a very promising approach for treatment of metabolic diseases including diabetes, heart failure, and cancer. The future research and development could be more focused on the biochemical understanding of the diseases, which would help understand the cellular energy metabolism and its regulation by pharmacological effectors of PDKs.
Topics: Animals; Cardiovascular Diseases; Diabetes Mellitus; Humans; Neoplasms; Pyruvate Dehydrogenase Complex
PubMed: 33739396
DOI: 10.1042/BSR20204402 -
Cell Reports Nov 2023The RNA exosome is a versatile ribonuclease. In the nucleoplasm of mammalian cells, it is assisted by its adaptors the nuclear exosome targeting (NEXT) complex and the...
The RNA exosome is a versatile ribonuclease. In the nucleoplasm of mammalian cells, it is assisted by its adaptors the nuclear exosome targeting (NEXT) complex and the poly(A) exosome targeting (PAXT) connection. Via its association with the ARS2 and ZC3H18 proteins, NEXT/exosome is recruited to capped and short unadenylated transcripts. Conversely, PAXT/exosome is considered to target longer and adenylated substrates via their poly(A) tails. Here, mutational analysis of the core PAXT component ZFC3H1 uncovers a separate branch of the PAXT pathway, which targets short adenylated RNAs and relies on a direct ARS2-ZFC3H1 interaction. We further demonstrate that similar acidic-rich short linear motifs of ZFC3H1 and ZC3H18 compete for a common ARS2 epitope. Consequently, while promoting NEXT function, ZC3H18 antagonizes PAXT activity. We suggest that this organization of RNA decay complexes provides co-activation of NEXT and PAXT at loci with abundant production of short exosome substrates.
Topics: Animals; Cell Nucleus; Exosome Multienzyme Ribonuclease Complex; Mammals; RNA Stability; RNA, Messenger; RNA, Nuclear; RNA-Binding Proteins
PubMed: 37889751
DOI: 10.1016/j.celrep.2023.113325 -
Life Science Alliance Feb 2022The accumulation of sphingolipid species in the cell contributes to the development of obesity and neurological disease. However, the subcellular localization of...
The accumulation of sphingolipid species in the cell contributes to the development of obesity and neurological disease. However, the subcellular localization of sphingolipid-synthesizing enzymes is unclear, limiting the understanding of where and how these lipids accumulate inside the cell and why they are toxic. Here, we show that SPTLC2, a subunit of the serine palmitoyltransferase (SPT) complex, catalyzing the first step in de novo sphingolipid synthesis, localizes dually to the ER and the outer mitochondrial membrane. We demonstrate that mitochondrial SPTLC2 interacts and forms a complex in trans with the ER-localized SPT subunit SPTLC1. Loss of SPTLC2 prevents the synthesis of mitochondrial sphingolipids and protects from palmitate-induced mitochondrial toxicity, a process dependent on mitochondrial ceramides. Our results reveal the in trans assembly of an enzymatic complex at an organellar membrane contact site, providing novel insight into the localization of sphingolipid synthesis and the composition and function of ER-mitochondria contact sites.
Topics: Biological Transport; Endoplasmic Reticulum; Mitochondria; Multienzyme Complexes; Serine C-Palmitoyltransferase
PubMed: 34785538
DOI: 10.26508/lsa.202101278 -
Journal of Molecular Biology Sep 2019Prokaryotic transcription is one of the most studied biological systems, with relevance to many fields including the development and use of antibiotics, the construction... (Review)
Review
Prokaryotic transcription is one of the most studied biological systems, with relevance to many fields including the development and use of antibiotics, the construction of synthetic gene networks, and the development of many cutting-edge methodologies. Here, we discuss recent structural, biochemical, and single-molecule biophysical studies targeting the mechanisms of transcription initiation in bacteria, including the formation of the open complex, the reaction of initial transcription, and the promoter escape step that leads to elongation. We specifically focus on the mechanisms employed by the RNA polymerase holoenzyme with the housekeeping sigma factor σ. The recent progress provides answers to long-held questions, identifies intriguing new behaviours, and opens up fresh questions for the field of transcription.
Topics: Bacteria; DNA, Bacterial; DNA-Directed RNA Polymerases; Multienzyme Complexes; Promoter Regions, Genetic; Sigma Factor; Transcription Initiation, Genetic
PubMed: 31082441
DOI: 10.1016/j.jmb.2019.04.046