scholarly journals Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors

2021 ◽  
Author(s):  
Gökçe Senger ◽  
Stefano Santaguida ◽  
Martin H Schaefer
Keyword(s):  
Protein Degradation ◽  
Protein Complex ◽  
Transcriptional Control ◽  
Patient Survival ◽  
Cellular Protein ◽  
The Other ◽  
Compensatory Mechanism ◽  
Proteomic Data ◽  
Chromosome Imbalance ◽  
Chromosome Level

Aneuploidy, a state of chromosome imbalance, is a hallmark of human tumors, but its role in cancer still remains to be fully elucidated. To understand the consequences of whole chromosome-level aneuploidies on the proteome, we integrated aneuploidy, transcriptomic and proteomic data from hundreds of TCGA/CPTAC tumor samples. We found a surprisingly large number of expression changes happened on other, non-aneuploid chromosomes. Moreover, we identified an association between those changes and co-complex members of proteins from aneuploid chromosomes. This co-abundance association is tightly regulated for aggregation-prone aneuploid proteins and those involved in a smaller number of complexes. On the other hand, we observe that complexes of the cellular core machinery are under functional selection to maintain their stoichiometric balance in aneuploid tumors. Ultimately, we provide evidence that those compensatory and functional maintenance mechanisms are established through post-transcriptional control and that the degree of success of a tumor to deal with aneuploidy-induced stoichiometric imbalance impacts the activation of cellular protein degradation programs and patient survival.

scholarly journals Timescale of degradation-driven protein level fluctuation in the yeast Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Bahareh Mahrou ◽  
Azady Pirhanov ◽  
Moluk Hadi Alijanvand ◽  
Yong Ku Cho ◽  
Yong-Jun Shin
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Degradation ◽  
Protein Level ◽  
Transcriptional Control ◽  
Degradation Rate ◽  
Modulation Frequency ◽  
Cellular Protein ◽  
Yeast Saccharomyces Cerevisiae ◽  
Protein Levels ◽  
Protein Degradation Rate

Generating robust, predictable perturbations in cellular protein levels will advance our understanding of protein function and enable control of physiological outcomes in biotechnology applications. Previous studies have shown that controlling RNA transcription achieves perturbations in protein levels over a timescale of several hours. Here, we demonstrate the potential for harnessing the protein degradation machinery to achieve robust, rapid control of a specific protein level in the yeast Saccharomyces cerevisiae. Using a light-driven protein degradation machinery and red fluorescent proteins as reporters, we show that under constant transcriptional induction, repeated triangular fluctuations in protein levels can be generated by controlling the protein degradation rate. Consistent with previous results using transcriptional control, we observed a continuous decrease in the magnitude of fluctuations as the modulation frequency increased, indicating low-pass filtering of input perturbation. However, compared to hour-scale fluctuations observed using transcriptional control, modulating the protein degradation rate enabled five to ten minute-scale fluctuations. Our study demonstrates the potential for repeated control of protein levels by controlling protein degradation rate, at timescales much shorter than that achieved by transcriptional control.

scholarly journals Drosophila COP9 signalosome subunit 7 interacts with multiple genomic loci to regulate development

2014 ◽  
Vol 42 (15) ◽  
pp. 9761-9770 ◽  
Author(s):  
Ruth Singer ◽  
Shimshi Atar ◽  
Osnat Atias ◽  
Efrat Oron ◽  
Daniel Segal ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Protein Degradation ◽  
Protein Complex ◽  
Transcriptional Control ◽  
Regulation Of Gene Expression ◽  
Active Regions ◽  
Cop9 Signalosome ◽  
Drosophila Genome

Abstract The COP9 signalosome protein complex has a central role in the regulation of development of multicellular organisms. While the function of this complex in ubiquitin-mediated protein degradation is well established, results over the past few years have hinted that the COP9 signalosome may function more broadly in the regulation of gene expression. Here, using DamID technology, we show that COP9 signalosome subunit 7 functionally associates with a large number of genomic loci in the Drosophila genome, and show that the expression of many genes within these loci is COP9 signalosome-dependent. This association is likely direct as we show CSN7 binds DNA in vitro. The genes targeted by CSN7 are preferentially enriched for transcriptionally active regions of the genome, and are involved in the regulation of distinct gene ontology groupings including imaginal disc development and cell-cycle control. In accord, loss of CSN7 function leads to cell-cycle delay and altered wing development. These results indicate that CSN7, and by extension the entire COP9 signalosome, functions directly in transcriptional control. While the COP9 signalosome protein complex has long been known to regulate protein degradation, here we expand the role of this complex by showing that subunit 7 binds DNA in vitro and functions directly in vivo in transcriptional control of developmentally important pathways that are relevant for human health.

scholarly journals Atomic Force Microscopy Investigation of the Interactions between the MCM Helicase and DNA

Materials ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 687
Author(s):  
Amna Abdalla Mohammed Khalid ◽  
Pietro Parisse ◽  
Barbara Medagli ◽  
Silvia Onesti ◽  
Loredana Casalis
Keyword(s):  
Atomic Force Microscopy ◽  
Nucleic Acid ◽  
Single Molecule ◽  
Protein Complex ◽  
The Other ◽  
Contour Length ◽  
Force Microscopy ◽  
Atomic Force ◽  
Mcm Complex ◽  
Dna Double Helix

The MCM (minichromosome maintenance) protein complex forms an hexameric ring and has a key role in the replication machinery of Eukaryotes and Archaea, where it functions as the replicative helicase opening up the DNA double helix ahead of the polymerases. Here, we present a study of the interaction between DNA and the archaeal MCM complex from Methanothermobacter thermautotrophicus by means of atomic force microscopy (AFM) single molecule imaging. We first optimized the protocol (surface treatment and buffer conditions) to obtain AFM images of surface-equilibrated DNA molecules before and after the interaction with the protein complex. We discriminated between two modes of interaction, one in which the protein induces a sharp bend in the DNA, and one where there is no bending. We found that the presence of the MCM complex also affects the DNA contour length. A possible interpretation of the observed behavior is that in one case the hexameric ring encircles the dsDNA, while in the other the nucleic acid wraps on the outside of the ring, undergoing a change of direction. We confirmed this topographical assignment by testing two mutants, one affecting the N-terminal β-hairpins projecting towards the central channel, and thus preventing DNA loading, the other lacking an external subdomain and thus preventing wrapping. The statistical analysis of the distribution of the protein complexes between the two modes, together with the dissection of the changes of DNA contour length and binding angle upon interaction, for the wild type and the two mutants, is consistent with the hypothesis. We discuss the results in view of the various modes of nucleic acid interactions that have been proposed for both archaeal and eukaryotic MCM complexes.

scholarly journals In Trypanosoma brucei RNA Editing, TbMP18 (Band VII) Is Critical for Editosome Integrity and for both Insertional and Deletional Cleavages

2006 ◽  
Vol 27 (2) ◽  
pp. 777-787 ◽  
Author(s):  
Julie A. Law ◽  
Sean O'Hearn ◽  
Barbara Sollner-Webb
Keyword(s):  
Rna Interference ◽  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Protein Complex ◽  
Substrate Recognition ◽  
The Other ◽  
Major Protein

ABSTRACT In trypanosome RNA editing, uridylate (U) residues are inserted and deleted at numerous sites within mitochondrial pre-mRNAs by an ∼20S protein complex that catalyzes cycles of cleavage, U addition/U removal, and ligation. We used RNA interference to deplete TbMP18 (band VII), the last unexamined major protein of our purified editing complex, showing it is essential. TbMP18 is critical for the U-deletional and U-insertional cleavages and for integrity of the ∼20S editing complex, whose other major components, TbMP99, TbMP81, TbMP63, TbMP52, TbMP48, TbMP42 (bands I through VI), and TbMP57, instead sediment as ∼10S associations. Additionally, TbMP18 augments editing substrate recognition by the TbMP57 terminal U transferase, possibly aiding the recognition component, TbMP81. The other editing activities and their coordination in precleaved editing remain active in the absence of TbMP18. These data are reminiscent of the data on editing subcomplexes reported by A. Schnaufer et al. (Mol. Cell 12:307-319, 2003) and suggest that these subcomplexes are held together in the ∼20S complex by TbMP18, as was proposed previously. Our data additionally imply that the proteins are less long-lived in these subcomplexes than they are when held in the complete editing complex. The editing endonucleolytic cleavages being lost when the editing complex becomes fragmented, as upon TbMP18 depletion, should be advantageous to the trypanosome, minimizing broken mRNAs.

scholarly journals Compromising the 19S proteasome complex protects cells from reduced flux through the proteasome

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Peter Tsvetkov ◽  
Marc L Mendillo ◽  
Jinghui Zhao ◽  
Jan E Carette ◽  
Parker H Merrill ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Cellular Protein ◽  
Fitness Cost ◽  
Survival Advantage ◽  
Protein Homeostasis ◽  
Proteotoxic Stress ◽  
Genome Wide ◽  
Regulatory Complex ◽  
Modest Reduction ◽  
Specific Inhibitors

Proteasomes are central regulators of protein homeostasis in eukaryotes. Proteasome function is vulnerable to environmental insults, cellular protein imbalance and targeted pharmaceuticals. Yet, mechanisms that cells deploy to counteract inhibition of this central regulator are little understood. To find such mechanisms, we reduced flux through the proteasome to the point of toxicity with specific inhibitors and performed genome-wide screens for mutations that allowed cells to survive. Counter to expectation, reducing expression of individual subunits of the proteasome's 19S regulatory complex increased survival. Strong 19S reduction was cytotoxic but modest reduction protected cells from inhibitors. Protection was accompanied by an increased ratio of 20S to 26S proteasomes, preservation of protein degradation capacity and reduced proteotoxic stress. While compromise of 19S function can have a fitness cost under basal conditions, it provided a powerful survival advantage when proteasome function was impaired. This means of rebalancing proteostasis is conserved from yeast to humans.

scholarly journals Substrate-Specific Effects of Natural Genetic Variation on Proteasome Activity

2021 ◽  
Author(s):  
Mahlon Collins ◽  
Randi R. Avery ◽  
Frank W Albert
Keyword(s):  
Genetic Variation ◽  
Protein Degradation ◽  
Dynamic Control ◽  
Cellular Protein ◽  
Proteasome Activity ◽  
Heritable Variation ◽  
Natural Genetic Variation ◽  
Specific Effects ◽  
Regulatory Particle

The bulk of targeted cellular protein degradation is performed by the proteasome, a multi-subunit complex consisting of the 19S regulatory particle, which binds, unfolds, and translocates substrate proteins, and the 20S core particle, which degrades them. Protein homeostasis requires precise, dynamic control of proteasome activity. To what extent genetic variation creates differences in proteasome activity is almost entirely unknown. Using the ubiquitin-independent degrons of the ornithine decarboxylase and Rpn4 proteins, we developed reporters that provide high-throughput, quantitative measurements of proteasome activity in vivo in genetically diverse cell populations. We used these reporters to characterize the genetic basis of variation in proteasome activity in the yeast Saccharomyces cerevisiae. We found that proteasome activity is a complex, polygenic trait, shaped by variation throughout the genome. Genetic influences on proteasome activity were predominantly substrate-specific, suggesting that they primarily affect the function or activity of the 19S regulatory particle. Our results demonstrate that individual genetic differences create heritable variation in proteasome activity and suggest that genetic effects on proteasomal protein degradation may be an important source of variation in cellular and organismal traits.

scholarly journals Golden Dawn through a psychosocial lens

HISTOREIN ◽  
2016 ◽  
Vol 15 (2) ◽  
pp. 56
Author(s):  
Thalia Dragonas
Keyword(s):  
The Other ◽  
The Political ◽  
Compensatory Mechanism ◽  
False Self ◽  
Psychic Life ◽  
Greek Crisis ◽  
Personal Boundaries ◽  
Negative Feelings ◽  
And Control

The economic and sociopolitical factors related to the current Greek crisis are translated into intrapsychic and interpersonal mechanisms in order to explain the political phenomenon of Golden Dawn. I draw on psychoanalytic concepts to reflect on how the crisis has functioned as a mechanism for the production and control of individual and collective subjectivities. I argue that the crisis has created immense insecurity and has fuelled feelings of desperation, fear and anger. For some, these feelings have been displaced onto a substitute reality offered by a transcendent group represented by Golden Dawn; personal boundaries have loosened, and subjectivities have been absorbed by a large, collective “false self”. At the centre of the notion of this substitute reality is the fantasy of omnipotence, channelled through the mechanism of projection onto the leader of the group. History is used and misused in order to cement the psychic life of the group and as a compensatory mechanism for the felt national shame. Moreover, collective denigration, or even extinction, of immigrants serves to displace negative feelings and impulses onto the “other”. I borrow Freud’s contention that when evil is not condemned, raw and wild impulses are let loose –hence, the assassination of a leftwing rapper that has landed Golden Dawn in court.

Development of Deuterated-leucine Labeling with Immunoprecipitation to Analyze Cellular Protein Complex

2008 ◽  
Vol 01 (06) ◽  
pp. 293-301 ◽  
Author(s):  
Shufang Liang ◽  
Xuejiao Xu ◽  
Haojie Lu ◽  
Pengyuan Yang
Keyword(s):  
Protein Complex ◽  
Cellular Protein

scholarly journals Comparative Integrated Omics Analysis of the Hfq Regulon in Bordetella pertussis

2019 ◽  
Vol 20 (12) ◽  
pp. 3073 ◽  
Author(s):  
Ana Dienstbier ◽  
Fabian Amman ◽  
Daniel Štipl ◽  
Denisa Petráčková ◽  
Branislav Večerek
Keyword(s):  
Gene Expression ◽  
Bordetella Pertussis ◽  
Transcriptional Control ◽  
Whooping Cough ◽  
Expression Profiles ◽  
Bacterial Pathogen ◽  
Gene Expression Profiles ◽  
Control Of Gene Expression ◽  
Proteomic Data

Bordetella pertussis is a Gram-negative strictly human pathogen of the respiratory tract and the etiological agent of whooping cough (pertussis). Previously, we have shown that RNA chaperone Hfq is required for virulence of B. pertussis. Furthermore, microarray analysis revealed that a large number of genes are affected by the lack of Hfq. This study represents the first attempt to characterize the Hfq regulon in bacterial pathogen using an integrative omics approach. Gene expression profiles were analyzed by RNA-seq and protein amounts in cell-associated and cell-free fractions were determined by LC-MS/MS technique. Comparative analysis of transcriptomic and proteomic data revealed solid correlation (r2 = 0.4) considering the role of Hfq in post-transcriptional control of gene expression. Importantly, our study confirms and further enlightens the role of Hfq in pathogenicity of B. pertussis as it shows that Δhfq strain displays strongly impaired secretion of substrates of Type III secretion system (T3SS) and substantially reduced resistance to serum killing. On the other hand, significantly increased production of proteins implicated in transport of important metabolites and essential nutrients observed in the mutant seems to compensate for the physiological defect introduced by the deletion of the hfq gene.

scholarly journals Sec16 influences transitional ER sites by regulating rather than organizing COPII

2013 ◽  
Vol 24 (21) ◽  
pp. 3406-3419 ◽  
Author(s):  
Nike Bharucha ◽  
Yang Liu ◽  
Effrosyni Papanikou ◽  
Conor McMahon ◽  
Masatoshi Esaki ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Coat Protein ◽  
Pichia Pastoris ◽  
Protein Complex ◽  
The Other ◽  
Yeast Pichia Pastoris ◽  
Functional Regions ◽  
Conserved Domain ◽  
Copii Vesicles ◽  
Negative Regulatory Role

During the budding of coat protein complex II (COPII) vesicles from transitional endoplasmic reticulum (tER) sites, Sec16 has been proposed to play two distinct roles: negatively regulating COPII turnover and organizing COPII assembly at tER sites. We tested these ideas using the yeast Pichia pastoris. Redistribution of Sec16 to the cytosol accelerates tER dynamics, supporting a negative regulatory role for Sec16. To evaluate a possible COPII organization role, we dissected the functional regions of Sec16. The central conserved domain, which had been implicated in coordinating COPII assembly, is actually dispensable for normal tER structure. An upstream conserved region (UCR) localizes Sec16 to tER sites. The UCR binds COPII components, and removal of COPII from tER sites also removes Sec16, indicating that COPII recruits Sec16 rather than the other way around. We propose that Sec16 does not in fact organize COPII. Instead, regulation of COPII turnover can account for the influence of Sec16 on tER sites.

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