NuA4 and SWR1-C: two chromatin-modifying complexes with overlapping functions and componentsThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal's usual peer review process.

2009 ◽  
Vol 87 (5) ◽  
pp. 799-815 ◽  
Author(s):  
Phoebe Y.T. Lu ◽  
Nancy Lévesque ◽  
Michael S. Kobor
Keyword(s):  
Chromatin Structure ◽  
Protein Complexes ◽  
Peer Review Process ◽  
Histone Variant ◽  
Chromatin Remodelling ◽  
Cellular Processes ◽  
Evolutionarily Conserved ◽  
And Function ◽  
Histone Deposition ◽  
Chemical Groups

Chromatin structure is important for the compaction of eukaryotic genomes, thus chromatin modifications play a fundamental role in regulating many cellular processes. The coordinated activities of various chromatin-remodelling and -modifying complexes are crucial in maintaining distinct chromatin neighbourhoods, which in turn ensure appropriate gene expression, as well as DNA replication, repair, and recombination. SWR1-C is an ATP-dependent histone deposition complex for the histone variant H2A.Z, whereas NuA4 is a histone acetyltransferase for histones H4, H2A, and H2A.Z. Together the NuA4 and SWR1-C chromatin-modifying complexes alter the chromatin structure through 3 distinct modifications in yeast: post-translational addition of chemical groups, ATP-dependent chromatin remodelling, and histone variant incorporation. These 2 multi-protein complexes share 4 subunits and function together to regulate the circuitry of H2A.Z biology. The components and functions of both multi-protein complexes are evolutionarily conserved and play important roles in multi-cellular development and cellular differentiation in higher eukaryotes. This review will summarize recent findings about NuA4 and SWR1-C and will focus on the connection between these complexes by investigating their physical and functional interactions through eukaryotic evolution.

scholarly journals Chromatin architectural proteins regulate flowering time by precluding gene looping

2021 ◽  
Vol 7 (24) ◽  
pp. eabg3097
Author(s):  
Bo Zhao ◽  
Yanpeng Xi ◽  
Junghyun Kim ◽  
Sibum Sung
Keyword(s):  
Chromatin Structure ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionarily Conserved ◽  
Architectural Proteins ◽  
Floral Repressor ◽  
Flanking Regions ◽  
Genome Wide Study

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

The roles of peptidyl-proline isomerases in gene regulation1This review is part of Special Issue entitled Asilomar Chromatin and has undergone the Journal’s usual peer review process.

2012 ◽  
Vol 90 (1) ◽  
pp. 55-69 ◽  
Author(s):  
David Dilworth ◽  
Geoff Gudavicius ◽  
Andrew Leung ◽  
Christopher J. Nelson
Keyword(s):  
Protein Function ◽  
Peer Review Process ◽  
Post Translational Modification ◽  
Multiple Control ◽  
Proline Isomerization ◽  
Evolutionarily Conserved ◽  
Covalent Modifications ◽  
And Function ◽  
Fk506 Binding Proteins ◽  
Substrate Proteins

The post-translational modification of proteins and enzymes provides a dynamic and reversible means to control protein function and transmit biological signals. While covalent modifications such as phosphorylation and acetylation have drawn much attention, in the past decade the involvement of peptidyl-proline isomerases (PPIs) in signaling and post-translational modification of protein function has become increasingly apparent. Three distinct families of PPI enzymes (parvulins, cyclophilins, and FK506-binding proteins (FKBPs)) each have the capacity to catalyze cis–trans proline isomerization in substrate proteins, and this modification can regulate both structure and function. In eukaryotic cells, a subset of these enzymes is localized to the nucleus, where they regulate gene expression at multiple control points. Here we summarize this body of work that together establishes a clear role of these enzymes as evolutionarily conserved players in the control of both transcription of mRNAs and the assembly of chromatin.

scholarly journals Post-translational modifications of Hsp90 and translating the chaperone code

2020 ◽  
Vol 295 (32) ◽  
pp. 11099-11117 ◽  
Author(s):  
Sarah J. Backe ◽  
Rebecca A. Sager ◽  
Mark R. Woodford ◽  
Alan M. Makedon ◽  
Mehdi Mollapour
Keyword(s):  
Protein Complexes ◽  
Cell Cycle Control ◽  
Heat Shock Protein 90 ◽  
Post Translational Modifications ◽  
Cellular Processes ◽  
Chaperone Function ◽  
Short Period ◽  
Evolutionarily Conserved ◽  
Hsp90 Chaperone ◽  
The Stability

Cells have a remarkable ability to synthesize large amounts of protein in a very short period of time. Under these conditions, many hydrophobic surfaces on proteins may be transiently exposed, and the likelihood of deleterious interactions is quite high. To counter this threat to cell viability, molecular chaperones have evolved to help nascent polypeptides fold correctly and multimeric protein complexes assemble productively, while minimizing the danger of protein aggregation. Heat shock protein 90 (Hsp90) is an evolutionarily conserved molecular chaperone that is involved in the stability and activation of at least 300 proteins, also known as clients, under normal cellular conditions. The Hsp90 clients participate in the full breadth of cellular processes, including cell growth and cell cycle control, signal transduction, DNA repair, transcription, and many others. Hsp90 chaperone function is coupled to its ability to bind and hydrolyze ATP, which is tightly regulated both by co-chaperone proteins and post-translational modifications (PTMs). Many reported PTMs of Hsp90 alter chaperone function and consequently affect myriad cellular processes. Here, we review the contributions of PTMs, such as phosphorylation, acetylation, SUMOylation, methylation, O-GlcNAcylation, ubiquitination, and others, toward regulation of Hsp90 function. We also discuss how the Hsp90 modification state affects cellular sensitivity to Hsp90-targeted therapeutics that specifically bind and inhibit its chaperone activity. The ultimate challenge is to decipher the comprehensive and combinatorial array of PTMs that modulate Hsp90 chaperone function, a phenomenon termed the “chaperone code.”

Connection between histone H2A variants and chromatin remodeling complexesThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 35-50 ◽  
Author(s):  
Mohammed Altaf ◽  
Andréanne Auger ◽  
Marcela Covic ◽  
Jacques Côté
Keyword(s):  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Cellular Response ◽  
Peer Review Process ◽  
Histone Variants ◽  
Histone H2a ◽  
Chromatin Dynamics ◽  
Recent Developments ◽  
Chromatin Remodeling Complexes ◽  
And Function

The organization of the eukaryotic genome into chromatin makes it inaccessible to the factors required for gene transcription and DNA replication, recombination, and repair. In addition to histone-modifying enzymes and ATP-dependent chromatin remodeling complexes, which play key roles in regulating many nuclear processes by altering the chromatin structure, cells have developed a mechanism of modulating chromatin structure by incorporating histone variants. These variants are incorporated into specific regions of the genome throughout the cell cycle. H2A.Z, which is an evolutionarily conserved H2A variant, performs several seemingly unrelated and even contrary functions. Another H2A variant, H2A.X, plays a very important role in the cellular response to DNA damage. This review summarizes the recent developments in our understanding of the role of H2A.Z and H2A.X in the regulation of chromatin structure and function, focusing on their functional links with chromatin modifying and remodeling complexes.

scholarly journals The formation of a fuzzy complex in the negative arm regulates the robustness of the circadian clock.

2022 ◽  
Author(s):  
Meaghan S. Jankowski ◽  
Daniel Griffith ◽  
Divya G. Shastry ◽  
Jacqueline F. Pelham ◽  
Garrett M. Ginell ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Electrostatic Interactions ◽  
Motif Discovery ◽  
Rational Design ◽  
Protein Complexes ◽  
Linear Motif ◽  
Cellular Processes ◽  
Evolutionarily Conserved ◽  
Positively Charged ◽  
Clock Protein

The circadian clock times cellular processes to the day/night cycle via a Transcription-Translation negative Feedback Loop (TTFL). However, a mechanistic understanding of the negative arm in both the timing of the TTFL and its control of output is lacking. We posited that the formation of negative-arm protein complexes was fundamental to clock regulation stemming from the negative arm. Using a modified peptide microarray approach termed Linear motif discovery using rational design (LOCATE), we characterized the interaction of the disordered negative-arm clock protein FREQUENCY to its partner protein FREQUENCY-Interacting RNA helicase. LOCATE identified a specific Short Linear Motif (SLiM) and interaction hotspot as well as positively charged islands that mediate electrostatic interactions, suggesting a model where negative arm proteins form a fuzzy complex essential for clock timing and robustness. Further analysis revealed that the positively charged islands were an evolutionarily conserved feature in higher eukaryotes and contributed to proper clock function.

scholarly journals Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Hiroaki Tachiwana ◽  
Mariko Dacher ◽  
Kazumitsu Maehara ◽  
Akihito Harada ◽  
Yosuke Seto ◽  
...  
Keyword(s):  
Dna Replication ◽  
Chromatin Structure ◽  
Histone Variant ◽  
Condensed Chromatin ◽  
Deposition Mechanism ◽  
Permeabilized Cells ◽  
Genome Wide ◽  
A Genome ◽  
Histone Deposition ◽  
Epigenetic Feature

In eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, the RhIP (Reconstituted histone complex Incorporation into chromatin of Permeabilized cell) assay, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. Using this method, we found that H3.1 and H3.3 were incorporated into chromatin in replication-dependent and -independent manners, respectively. We further found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition to maintain the epigenetic chromatin states.

scholarly journals Cdc48: A Swiss Army Knife of Cell Biology

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Guem Hee Baek ◽  
Haili Cheng ◽  
Vitnary Choe ◽  
Xin Bao ◽  
Jia Shao ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Atpase Activity ◽  
Cell Biology ◽  
Protein Complexes ◽  
Biological Functions ◽  
Cellular Processes ◽  
Broad Array ◽  
And Function ◽  
Regulatory Functions ◽  
Lateral Sclerosis

Cdc48 (also called VCP and p97) is an abundant protein that plays essential regulatory functions in a broad array of cellular processes. Working with various cofactors, Cdc48 utilizes its ATPase activity to promote the assembly and disassembly of protein complexes. Here, we review key biological functions and regulation of Cdc48 in ubiquitin-related events. Given the broad employment of Cdc48 in cell biology and its intimate ties to human diseases (e.g., amyotrophic lateral sclerosis), studies of Cdc48 will bring significant insights into the mechanism and function of ubiquitin in health and diseases.

scholarly journals Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay

2019 ◽  
Author(s):  
Hiroaki Tachiwana ◽  
Mariko Dacher ◽  
Kazumitsu Maehara ◽  
Akihito Harada ◽  
Yasuyuki Ohkawa ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Histone Variant ◽  
Condensed Chromatin ◽  
Deposition Mechanism ◽  
Permeabilized Cells ◽  
Genome Wide ◽  
A Genome ◽  
Essential Region ◽  
Histone Deposition ◽  
Epigenetic Feature

AbstractIn eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. We found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that the condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. This led to the recapitulation of the pre-existing chromatin structure: the genome-wide even distribution of H2A and the exclusion of H2A.Z from the closed chromatin. Intriguingly, an H2A.Z mutant with mutations in the developmentally essential region was incorporated into closed chromatin. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition for maintaining the epigenetic chromatin states.

scholarly journals Two novel heteropolymer-forming proteins maintain multicellular shape of the cyanobacteriumAnabaenasp. PCC 7120

2019 ◽  
Author(s):  
Benjamin L. Springstein ◽  
Dennis J. Nürnberg ◽  
Christian Woehle ◽  
Julia Weissenbach ◽  
Marius L. Theune ◽  
...  
Keyword(s):  
Double Mutant ◽  
Protein Complexes ◽  
Coiled Coil ◽  
Filamentous Structure ◽  
Cellular Processes ◽  
Junction Protein ◽  
And Function ◽  
Pcc 7120

AbstractPolymerizing and filament-forming proteins are instrumental for numerous cellular processes such as cell division and growth. Their function in stabilization and localization of protein complexes and replicons is achieved by a filamentous structure. Known filamentous proteins assemble into homopolymers consisting of single subunits – e.g. MreB and FtsZ in bacteria – or heteropolymers that are composed of two subunits, e.g. keratin and α/β tubulin in eukaryotes. Here, we describe two novel coiled-coil-rich proteins (CCRPs) in the filament forming cyanobacteriumAnabaenasp. PCC 7120 (hereafterAnabaena) that assemble into a heteropolymer and function in the maintenance of theAnabaenamulticellular shape (termed trichome). The two CCRPs – Alr4504 and Alr4505 (named ZicK and ZacK) – are strictly interdependent for the assembly of protein filamentsin vivoand polymerize nucleotide-independentlyin vitro, similar to known intermediate filament (IF) proteins. A ΔzicKΔzacK double mutant is characterized by a zigzagged cell arrangement and hence a loss of the typical linearAnabaenatrichome shape. ZicK and ZacK interact with themselves, with each other, with the elongasome protein MreB, the septal junction protein SepJ and the divisome associate septal protein SepI. Our results suggest that ZicK and ZacK function in cooperation with SepJ and MreB to stabilize theAnabaenatrichome and are likely essential for the manifestation of the multicellular shape inAnabaena. Our study reveals the presence of filament-forming IF-like proteins whose function is achieved through the formation of heteropolymers in cyanobacteria.

Ca2+-Activated K+ Channels: From Protein Complexes to Function

2010 ◽  
Vol 90 (4) ◽  
pp. 1437-1459 ◽  
Author(s):  
Henrike Berkefeld ◽  
Bernd Fakler ◽  
Uwe Schulte
Keyword(s):  
Protein Interactions ◽  
Muscle Tone ◽  
Protein Complexes ◽  
Neuronal Firing ◽  
Protein Protein Interactions ◽  
Cellular Processes ◽  
And Function ◽  
And Control ◽  
Proteomic Research ◽  
Partner Proteins

Molecular research on ion channels has demonstrated that many of these integral membrane proteins associate with partner proteins, often versatile in their function, or even assemble into stable macromolecular complexes that ensure specificity and proper rate of the channel-mediated signal transduction. Calcium-activated potassium (KCa) channels that link excitability and intracellular calcium concentration are responsible for a wide variety of cellular processes ranging from regulation of smooth muscle tone to modulation of neurotransmission and control of neuronal firing pattern. Most of these functions are brought about by interaction of the channels' pore-forming subunits with distinct partner proteins. In this review we summarize recent insights into protein complexes associated with KCa channels as revealed by proteomic research and discuss the results available on structure and function of these complexes and on the underlying protein-protein interactions. Finally, the results are related to their significance for the function of KCa channels under cellular conditions.

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