scholarly journals Proteasomes: unfoldase-assisted protein degradation machines

2019 ◽  
Vol 401 (1) ◽  
pp. 183-199 ◽  
Author(s):  
Parijat Majumder ◽  
Wolfgang Baumeister
Keyword(s):  
Stress Response ◽  
Molecular Machines ◽  
Molecular Architecture ◽  
Core Particle ◽  
Protein Substrates ◽  
Macromolecular Assemblies ◽  
Current State ◽  
Intracellular Proteins ◽  
Domains Of Life ◽  
Aaa Atpases

Abstract Proteasomes are the principal molecular machines for the regulated degradation of intracellular proteins. These self-compartmentalized macromolecular assemblies selectively degrade misfolded, mistranslated, damaged or otherwise unwanted proteins, and play a pivotal role in the maintenance of cellular proteostasis, in stress response, and numerous other processes of vital importance. Whereas the molecular architecture of the proteasome core particle (CP) is universally conserved, the unfoldase modules vary in overall structure, subunit complexity, and regulatory principles. Proteasomal unfoldases are AAA+ ATPases (ATPases associated with a variety of cellular activities) that unfold protein substrates, and translocate them into the CP for degradation. In this review, we summarize the current state of knowledge about proteasome – unfoldase systems in bacteria, archaea, and eukaryotes, the three domains of life.

scholarly journals Vaccinia-Related Kinase 2 Modulates the Stress Response to Hypoxia Mediated by TAK1

2007 ◽  
Vol 27 (20) ◽  
pp. 7273-7283 ◽  
Author(s):  
Sandra Blanco ◽  
Claudio Santos ◽  
Pedro A. Lazo
Keyword(s):  
Stress Response ◽  
Cellular Response ◽  
Mapk Signaling ◽  
Cellular Stress Response ◽  
Mitogen Activated Protein Kinase ◽  
Stable Complex ◽  
Intracellular Proteins ◽  
Mitogen Activated Protein ◽  
Jnk Activation ◽  
Protein Kinase Kinase

ABSTRACT Hypoxia represents a major stress that requires an immediate cellular response in which different signaling pathways participate. Hypoxia induces an increase in the activity of TAK1, an atypical mitogen-activated protein kinase kinase kinase (MAPKKK), which responds to oxidative stress by triggering cascades leading to the activation of c-Jun N-terminal kinase (JNK). JNK activation by hypoxia requires assembly with the JIP1 scaffold protein, which might also interact with other intracellular proteins that are less well known but that might modulate MAPK signaling. We report that TAK1 is able to form a stable complex with JIP1 and thus regulate the activation of JNK, which in turn determines the cellular stress response to hypoxia. This activation of TAK1-JIP1-JNK is suppressed by vaccinia-related kinase 2 (VRK2). VRK2A is able to interact with TAK1 by its C-terminal region, forming stable complexes. The kinase activity of VRK2 is not necessary for this interaction or the downregulation of AP1-dependent transcription. Furthermore, reduction of the endogenous VRK2 level with short hairpin RNA can increase the response induced by hypoxia, suggesting that the intracellular levels of VRK2 can determine the magnitude of this stress response.

scholarly journals Ammonium ion transport by the AMT/Rh homologue LeAMT1;1

2006 ◽  
Vol 396 (3) ◽  
pp. 431-437 ◽  
Author(s):  
Maria Mayer ◽  
Marek Dynowski ◽  
Uwe Ludewig
Keyword(s):  
Structural Data ◽  
Homology Model ◽  
Ammonium Transporter ◽  
Ammonium Ion ◽  
Molecular Architecture ◽  
Gas Channel ◽  
Domains Of Life ◽  
Single Positive ◽  
Key Residues ◽  
Related Proteins

AMT (ammonium transporter)/Rh (Rhesus) ammonium transporters/channels are identified in all domains of life and fulfil contrasting functions related either to ammonium acquisition or excretion. Based on functional and crystallographic high-resolution structural data, it was recently proposed that the bacterial AmtB (ammonium transporter B) is a gas channel for NH3 [Khademi, O'Connell, III, Remis, Robles-Colmenares, Miercke and Stroud (2004) Science 305, 1587–1594; Zheng, Kostrewa, Berneche, Winkler and Li (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 17090–17095]. Key residues, proposed to be crucial for NH3 conduction, and the hydrophobic, but obstructed, pore were conserved in a homology model of LeAMT1;1 from tomato. Transport by LeAMT1;1 was affected by mutations of residues that were predicted to constitute the aromatic recruitment site for NH4+ at the external pore entrance. Despite the structural similarities, LeAMT1;1 was shown to transport only the ion; each transported 14C-methylammonium molecule carried a single positive elementary charge. Similarly, NH4+ (or H+/NH3) was transported, but NH3 conduction was excluded. It is concluded that related proteins and a similar molecular architecture can apparently support contrasting transport mechanisms.

scholarly journals The C. elegans Hypertonic Stress Response: Big Insights from Shrinking Worms

2020 ◽  
Vol 55 (S1) ◽  
pp. 89-105
Keyword(s):  
Stress Response ◽  
Cell Volume ◽  
Molecular Mechanisms ◽  
Model Organism ◽  
Future Research ◽  
Transcriptional Level ◽  
Molecular Signaling ◽  
Hypertonic Stress ◽  
Macromolecular Assemblies ◽  
C Elegans

Cell volume is one of the most aggressively defended physiological set points in biology. Changes in intracellular ion and water concentrations, which are induced by changes in metabolism or environmental exposures, disrupt protein folding, enzymatic activity, and macromolecular assemblies. To counter these challenges, cells and organisms have evolved multifaceted, evolutionarily conserved molecular mechanisms to restore cell volume and repair stress induced damage. However, many unanswered questions remain regarding the nature of cell volume 'sensing' as well as the molecular signaling pathways involved in activating physiological response mechanisms. Unbiased genetic screening in the model organism C. elegans is providing new and unexpected insights into these questions, particularly questions relating to the hypertonic stress response (HTSR) pathway. One surprising characteristic of the HTSR pathway in C. elegans is that it is under strong negative regulation by proteins involved in protein homeostasis and the extracellular matrix (ECM). The role of the ECM in particular highlights the importance of studying the HTSR in the context of a live organism where native ECM-tissue associations are preserved. A second novel and recently discovered characteristic is that the HTSR is regulated at the post-transcriptional level. The goal of this review is to describe these discoveries, to provide context for their implications, and to raise outstanding questions to guide future research.

Stress responses as master keys to epigenomic changes in transcriptome and metabolome for cancer etiology and therapeutics

2021 ◽  
Author(s):  
Atanu Mondal ◽  
Apoorva Bhattacharya ◽  
Vipin Singh ◽  
Shruti Pandita ◽  
Albino Bacolla ◽  
...  
Keyword(s):  
Stress Response ◽  
Cancer Cells ◽  
Stress Responses ◽  
Current Knowledge ◽  
Cancer Therapeutics ◽  
Molecular Architecture ◽  
Cancer Etiology ◽  
Treatment Scenario ◽  
Anti Cancer ◽  
Novel Therapeutic Strategies

From initiation through progression, cancer cells are subjected to a magnitude of endogenous and exogenous stresses, which aid in their neoplastic transformation. Exposure to these classes of stress induces imbalance in cellular homeostasis and, in response, cancer cells employ informative adaptive mechanisms to rebalance biochemical processes that facilitate survival and maintain their existence. Different kinds of stress stimuli trigger epigenetic alterations in cancer cells, which leads to changes in their transcriptome and metabolome, ultimately resulting in suppression of growth inhibition or induction of apoptosis. Whether cancer cells show a protective response to stress or succumb to cell death depends on the type of stress and duration of exposure. A thorough understanding of epigenetic and molecular architecture of cancer cell stress response pathways can unveil a plethora of information required to develop novel anti-cancer therapeutics. The present view highlights current knowledge about alterations in epigenome and transcriptome of cancer cells as a consequence of exposure to different physicochemical stressful stimuli such as reactive oxygen species (ROS), hypoxia, radiation, hyperthermia, genotoxic agents, and nutrient deprivation. Currently, an anti-cancer treatment scenario involving the imposition of stress on target cancer cells is gaining traction to augment or even replace conventional therapeutic regimens. Therefore, a comprehensive understanding of stress response pathways is crucial for devising and implementing novel therapeutic strategies.

Small proteins in Archaea, a mainly unexplored world

2021 ◽  
Author(s):  
Katrin Weidenbach ◽  
Miriam Gutt ◽  
Liam Cassidy ◽  
Cynthia Chibani ◽  
Ruth A. Schmitz
Keyword(s):  
Evolutionary Conservation ◽  
Tool Development ◽  
Small Proteins ◽  
Current State ◽  
Genome Wide ◽  
Domains Of Life ◽  
Global Identification ◽  
State Of Research ◽  
Eukaryotic Organisms ◽  
Research Show

In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome wide approaches.

scholarly journals Structure and mechanism of the ESCRT pathway AAA+ ATPase Vps4

2019 ◽  
Vol 47 (1) ◽  
pp. 37-45 ◽  
Author(s):  
Han Han ◽  
Christopher P. Hill
Keyword(s):  
Cell Biology ◽  
Cellular Membrane ◽  
Structural Features ◽  
Transport Pathways ◽  
Endosomal Sorting ◽  
Aaa Atpase ◽  
Protein Substrates ◽  
Membrane Fission ◽  
Aaa Atpases ◽  
Equivalent Mechanism

Abstract The progression of ESCRT (Endosomal Sorting Complexes Required for Transport) pathways, which mediate numerous cellular membrane fission events, is driven by the enzyme Vps4. Understanding of Vps4 mechanism is, therefore, of fundamental importance in its own right and, moreover, it is highly relevant to the understanding of many related AAA+ ATPases that function in multiple facets of cell biology. Vps4 unfolds its ESCRT-III protein substrates by translocating them through its central hexameric pore, thereby driving membrane fission and recycling of ESCRT-III subunits. This mini-review focuses on recent advances in Vps4 structure and mechanism, including ideas about how Vps4 translocates and unfolds ESCRT-III subunits. Related AAA+ ATPases that share structural features with Vps4 and likely utilize an equivalent mechanism are also discussed.

scholarly journals Real-Time Interactive Visualisation of Large Macromolecular Assemblies and Molecular Machines at Atomic Resolution

2017 ◽  
Vol 112 (3) ◽  
pp. 178a ◽  
Author(s):  
David Sehnal ◽  
Mandar Deshpande ◽  
Radka Svobodova Varekova ◽  
Saquib Mir ◽  
Karel Berka ◽  
...  
Keyword(s):  
Real Time ◽  
Molecular Machines ◽  
Atomic Resolution ◽  
Macromolecular Assemblies ◽  
Interactive Visualisation

scholarly journals Structure of the Cdc48 segregase in the act of unfolding an authentic substrate

Science ◽  
2019 ◽  
Vol 365 (6452) ◽  
pp. 502-505 ◽  
Author(s):  
Ian Cooney ◽  
Han Han ◽  
Michael G. Stewart ◽  
Richard H. Carson ◽  
Daniel T. Hansen ◽  
...  
Keyword(s):  
Protein Translocation ◽  
Substrate Binding ◽  
Adaptor Protein ◽  
Biological Pathways ◽  
Protein Substrates ◽  
Adenosine Triphosphatases ◽  
Binding Residues ◽  
Aaa Atpases ◽  
Helical Configuration ◽  
Resolution Structure

The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite extensive studies, the mechanism of Cdc48 has remained obscure, and its reported structures are inconsistent with models of substrate translocation proposed for other AAA+ ATPases (adenosine triphosphatases). Here, we report a 3.7-angstrom–resolution structure of Cdc48 in complex with an adaptor protein and a native substrate. Cdc48 engages substrate by adopting a helical configuration of substrate-binding residues that extends through the central pore of both of the ATPase rings. These findings indicate a unified hand-over-hand mechanism of protein translocation by Cdc48 and other AAA+ ATPases.

scholarly journals Role of Cytochrome P450 Enzymes in Plant Stress Response

Antioxidants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 454 ◽  
Author(s):  
Balaji Aravindhan Pandian ◽  
Rajendran Sathishraj ◽  
Maduraimuthu Djanaguiraman ◽  
P.V. Vara Prasad ◽  
Mithila Jugulam
Keyword(s):  
Stress Response ◽  
Stress Responses ◽  
Higher Plants ◽  
Plant Stress ◽  
Cytochrome P450 Enzymes ◽  
Crop Species ◽  
Plant Stress Response ◽  
Biochemical Processes ◽  
Domains Of Life

Cytochrome P450s (CYPs) are the largest enzyme family involved in NADPH- and/or O2-dependent hydroxylation reactions across all the domains of life. In plants and animals, CYPs play a central role in the detoxification of xenobiotics. In addition to this function, CYPs act as versatile catalysts and play a crucial role in the biosynthesis of secondary metabolites, antioxidants, and phytohormones in higher plants. The molecular and biochemical processes catalyzed by CYPs have been well characterized, however, the relationship between the biochemical process catalyzed by CYPs and its effect on several plant functions was not well established. The advent of next-generation sequencing opened new avenues to unravel the involvement of CYPs in several plant functions such as plant stress response. The expression of several CYP genes are regulated in response to environmental stresses, and they also play a prominent role in the crosstalk between abiotic and biotic stress responses. CYPs have an enormous potential to be used as a candidate for engineering crop species resilient to biotic and abiotic stresses. The objective of this review is to summarize the latest research on the role of CYPs in plant stress response.

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