bims-proarb Biomed News
on Proteostasis in aging and regenerative biology
Issue of 2022‒06‒05
sixteen papers selected by
Rich Giadone
Harvard University
  1. Critical roles of protein disulfide isomerases in balancing proteostasis in the nervous system.
  2. Minimal Yet Powerful: The Role of Archaeal Small Heat Shock Proteins in Maintaining Protein Homeostasis.
  3. Autophagy Regulation Influences β-Amyloid Toxicity in Transgenic Caenorhabditis elegans.
  4. Intracellular localization of the proteasome in response to stress conditions.
  5. Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional.
  6. Stress routes clients to the proteasome via a BAG2 ubiquitin-independent degradation condensate.
  7. SQSTM1, a protective factor of SOD1-linked motor neuron disease, regulates the accumulation and distribution of ubiquitinated protein aggregates in neuron.
  8. HSP40 overexpression in pacemaker neurons protects against circadian dysfunction in a Drosophila model of Huntington's Disease.
  9. Organization of the autophagy pathway in neurons.
  10. PLAG1 dampens protein synthesis to promote human hematopoietic stem cell self-renewal.
  11. Defective mitophagy and the etiopathogenesis of Alzheimer's disease.
  12. New views of old proteins: clarifying the enigmatic proteome.
  13. Ribosomal protein eL39 is important for maturation of the nascent polypeptide exit tunnel and proper protein folding during translation.
  14. A Small Molecule Stabilizes the Disordered Native State of the Alzheimer's Aβ Peptide.
  15. Fix the process that led to Alzheimer's drug fiasco.
  16. Binding of the HSF-1 DNA-binding domain to multimeric C. elegans consensus HSEs is guided by cooperative interactions.
  1. J Biol Chem. 2022 May 30. pii: S0021-9258(22)00528-2. [Epub ahead of print] 102087
    Critical roles of protein disulfide isomerases in balancing proteostasis in the nervous system.
    Danilo B Medinas, Pablo Rozas, Claudio Hetz.
      Protein disulfide isomerases (PDIs) constitute a family of oxidoreductases promoting redox protein folding and quality control in the endoplasmic reticulum (ER). PDIs catalyze disulfide bond formation, isomerization and reduction, operating in concert with molecular chaperones to fold secretory cargoes in addition to directing misfolded proteins to be refolded or degraded. Importantly, PDIs are emerging as key components of the proteostasis network, integrating protein folding status with central surveillance mechanisms to balance proteostasis according to cellular needs. Recent advances in the field driven by the generation of new mouse models, human genetic studies, and omics methodologies, in addition to interventions using small molecules and gene therapy, have revealed the significance of PDIs to the physiology of the nervous system and their implications in pathologies, ranging from neurodevelopmental conditions to neurodegenerative diseases and traumatic injuries. Here, we review the principles of redox protein folding in the ER with a focus on current evidence linking genetic mutations and biochemical alterations to PDIs in the etiology of neurological conditions.
    Keywords:  endoplasmic reticulum; nervous system; neurodegenerative diseases; neurodevelopmental disorders; protein aggregation; protein disulfide isomerase; proteostasis; redox protein folding
    DOI:  https://doi.org/10.1016/j.jbc.2022.102087
  2. Front Mol Biosci. 2022 ;9 832160
    Minimal Yet Powerful: The Role of Archaeal Small Heat Shock Proteins in Maintaining Protein Homeostasis.
    Mousam Roy, Koustav Bhakta, Abhrajyoti Ghosh.
      Small heat shock proteins (sHsp) are a ubiquitous group of ATP-independent chaperones found in all three domains of life. Although sHsps in bacteria and eukaryotes have been studied extensively, little information was available on their archaeal homologs until recently. Interestingly, archaeal heat shock machinery is strikingly simplified, offering a minimal repertoire of heat shock proteins to mitigate heat stress. sHsps play a crucial role in preventing protein aggregation and holding unfolded protein substrates in a folding-competent form. Besides protein aggregation protection, archaeal sHsps have been shown recently to stabilize membranes and contribute to transferring captured substrate proteins to chaperonin for refolding. Furthermore, recent studies on archaeal sHsps have shown that environment-induced oligomeric plasticity plays a crucial role in maintaining their functional form. Despite being prokaryotes, the archaeal heat shock protein repository shares several features with its highly sophisticated eukaryotic counterpart. The minimal nature of the archaeal heat shock protein repository offers ample scope to explore the function and regulation of heat shock protein(s) to shed light on their evolution. Moreover, similar structural dynamics of archaeal and human sHsps have made the former an excellent system to study different chaperonopathies since archaeal sHsps are more stable under in vitro experiments.
    Keywords:  aggregation protection; holdase; oligomerization; protein folding; small heat shock protein (sHsp)
    DOI:  https://doi.org/10.3389/fmolb.2022.832160
  3. Front Aging Neurosci. 2022 ;14 885145
    Autophagy Regulation Influences β-Amyloid Toxicity in Transgenic Caenorhabditis elegans.
    Hongru Lin, Yehui Gao, Chen Zhang, Botian Ma, Mengchen Wu, Xianghuan Cui, Hongbing Wang.
      Alzheimer's disease (AD) is a progressive, neurodegenerative disease characterized by the accumulation of amyloid-beta (Aβ) proteins in the form of plaques that cause a proteostasis imbalance in the brain. Several studies have identified autophagy deficits in both AD patients and AD animal models. Here, we used transgenic Caenorhabditis elegans to study the relationship between autophagy flux and Aβ. We labeled autophagosomes with an advanced fluorescence reporter system, and used this to observe that human Aβ expression caused autophagosome accumulation in C. elegans muscle. The autophagy-related drugs chloroquine and 3-MA were employed to investigate the relationship between changes in autophagic flux and the toxicity of Aβ expression. We found that reducing autophagosome accumulation delayed Aβ-induced paralysis in the CL4176 strain of C. elegans, and alleviated Aβ-induced toxicity, thus having a neuroprotective effect. Finally, we used RNA-sequencing and proteomics to identify genes whose expression was affected by Aβ aggregation in C. elegans. We identified a series of enriched autophagy-related signal pathways, suggesting that autophagosome accumulation impairs Aβ protein homeostasis in nematodes. Thus, maintaining normal autophagy levels appears to be important in repairing the protein homeostasis imbalance caused by Aβ expression.
    Keywords:  Alzheimer’s disease; Caenorhabditis elegans; RNA-sequencing; autophagy; quantitative proteomics
    DOI:  https://doi.org/10.3389/fnagi.2022.885145
  4. J Biol Chem. 2022 May 27. pii: S0021-9258(22)00524-5. [Epub ahead of print] 102083
    Intracellular localization of the proteasome in response to stress conditions.
    Cordula Enenkel, Ryu Won Kang, Florian Wilfling, Oliver P Ernst.
      The ubiquitin-proteasome-system (UPS) fulfills an essential role in regulating protein homeostasis by spatially and temporally controlling proteolysis in an ATP- and ubiquitin-dependent manner. However, the localization of proteasomes is highly variable under diverse cellular conditions. In yeast, newly synthesized proteasomes are primarily localized to the nucleus during cell proliferation. Yeast proteasomes are transported into the nucleus through the nuclear pore either as immature subcomplexes or as mature enzymes via adaptor proteins Sts1 and Blm10, while in mammalian cells, post-mitotic uptake of proteasomes into the nucleus is mediated by AKIRIN2, an adaptor protein essentially required for nuclear protein degradation. Stressful growth conditions and the reversible halt of proliferation, i.e. quiescence, are associated with a decline in ATP and the re-organization of proteasome localization. Cellular stress leads to proteasome accumulation in membraneless granules either in the nucleus or in the cytoplasm. In quiescence, yeast proteasomes are sequestered in a ubiquitin-dependent manner into motile and reversible proteasome storage granules (PSGs) in the cytoplasm. In cancer cells upon amino acid deprivation, heat shock, osmotic stress, oxidative stress, or the inhibition of either proteasome activity or nuclear export, reversible proteasome foci containing poly-ubiquitinated substrates are formed by liquid-liquid phase separation in the nucleus. In this review, we summarize recent literature revealing new links between nuclear transport, ubiquitin signaling and the intracellular organization of proteasomes during cellular stress conditions.
    Keywords:  liquid-liquid phase separation; nuclear transport; proteasome foci; proteasome storage granule; protein quality control; stress response; ubiquitin-proteasome-system
    DOI:  https://doi.org/10.1016/j.jbc.2022.102083
  5. Nat Commun. 2022 Jun 02. 13(1): 3081
    Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional.
    Daniel A Nissley, Yang Jiang, Fabio Trovato, Ian Sitarik, Karthik B Narayan, Philip To, Yingzi Xia, Stephen D Fried, Edward P O'Brien.
      Some misfolded protein conformations can bypass proteostasis machinery and remain soluble in vivo. This is an unexpected observation, as cellular quality control mechanisms should remove misfolded proteins. Three questions, then, are: how do long-lived, soluble, misfolded proteins bypass proteostasis? How widespread are such misfolded states? And how long do they persist? We address these questions using coarse-grain molecular dynamics simulations of the synthesis, termination, and post-translational dynamics of a representative set of cytosolic E. coli proteins. We predict that half of proteins exhibit misfolded subpopulations that bypass molecular chaperones, avoid aggregation, and will not be rapidly degraded, with some misfolded states persisting for months or longer. The surface properties of these misfolded states are native-like, suggesting they will remain soluble, while self-entanglements make them long-lived kinetic traps. In terms of function, we predict that one-third of proteins can misfold into soluble less-functional states. For the heavily entangled protein glycerol-3-phosphate dehydrogenase, limited-proteolysis mass spectrometry experiments interrogating misfolded conformations of the protein are consistent with the structural changes predicted by our simulations. These results therefore provide an explanation for how proteins can misfold into soluble conformations with reduced functionality that can bypass proteostasis, and indicate, unexpectedly, this may be a wide-spread phenomenon.
    DOI:  https://doi.org/10.1038/s41467-022-30548-5
  6. Nat Commun. 2022 Jun 02. 13(1): 3074
    Stress routes clients to the proteasome via a BAG2 ubiquitin-independent degradation condensate.
    Daniel C Carrettiero, Maria C Almeida, Andrew P Longhini, Jennifer N Rauch, Dasol Han, Xuemei Zhang, Saeed Najafi, Jason E Gestwicki, Kenneth S Kosik.
      The formation of membraneless organelles can be a proteotoxic stress control mechanism that locally condenses a set of components capable of mediating protein degradation decisions. The breadth of mechanisms by which cells respond to stressors and form specific functional types of membraneless organelles, is incompletely understood. We found that Bcl2-associated athanogene 2 (BAG2) marks a distinct phase-separated membraneless organelle, triggered by several forms of stress, particularly hyper-osmotic stress. Distinct from well-known condensates such as stress granules and processing bodies, BAG2-containing granules lack RNA, lack ubiquitin and promote client degradation in a ubiquitin-independent manner via the 20S proteasome. These organelles protect the viability of cells from stress and can traffic to the client protein, in the case of Tau protein, on the microtubule. Components of these ubiquitin-independent degradation organelles include the chaperone HSP-70 and the 20S proteasome activated by members of the PA28 (PMSE) family. BAG2 condensates did not co-localize with LAMP-1 or p62/SQSTM1. When the proteasome is inhibited, BAG2 condensates and the autophagy markers traffic to an aggresome-like structure.
    DOI:  https://doi.org/10.1038/s41467-022-30751-4
  7. Neurochem Int. 2022 May 28. pii: S0197-0186(22)00089-4. [Epub ahead of print] 105364
    SQSTM1, a protective factor of SOD1-linked motor neuron disease, regulates the accumulation and distribution of ubiquitinated protein aggregates in neuron.
    Shun Mitsui, Asako Otomo, Kai Sato, Masahito Ishiyama, Kento Shimakura, Chisa Okada-Yamaguchi, Eiji Warabi, Toru Yanagawa, Masashi Aoki, Hui-Fang Shang, Shinji Hadano.
      Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by selective loss of motor neurons in the brain and spinal cord. Recent studies have shown that mutations in SQSTM1 are linked to ALS. It has also been demonstrated that a systemic loss of SQSTM1 exacerbates disease phenotypes in an ALS mouse model. However, it is still unclear whether and how SQSTM1 in the central nervous system (CNS) specifically regulates ALS-associated disease phenotypes. To address this issue, we generated CNS-specific Sqstm1 deficient SOD1H46R transgenic mice, and conducted gross phenotype analyses as well as the immunohistochemical and biochemical examinations of spinal cord tissues using these mice. CNS-specific SQSTM1 deficiency accelerated the disease onset and shortened the lifespan of SOD1H46R mice. The CNS-specific SQSTM1 ablation also resulted in increased number of ubiquitin-positive aggregates, while their size rather became much smaller. Remarkably, ubiquitin-positive aggregates, which were usually present in extracellular space and/or neuropil in SOD1H46R mice, were preferentially localized to soma and neurites of spinal neurons in CNS-specific SQSTM1 deficient SOD1H46R mice. Next, to further clarify the function of SQSTM1 in neurons, we investigated the contribution of SQSTM1 to the accumulation of polyubiquitinated proteins in relation to the ubiquitin proteasome system (UPS) and the autophagy-endolysosomal system (APELS) in primary cultured motor neurons (PMNs). Loss of SQSTM1 in PMNs resulted in decreased accumulation of insoluble polyubiquitinated proteins, which was induced by simultaneous treatment with proteasome and lysosome inhibitors, suggesting a pivotal role of SQSTM1 in the formation of insoluble protein aggregates. However, SQSTM1 silencing had a limited impact on the susceptibility to proteasome and/or lysosome inhibitor-induced apoptosis in PMNs. Taken together, neuronal SQSTM1, whose functions are associated with both the UPS and APELS, might primarily regulate the distribution and accumulation of misfolded protein aggregates in the CNS, thereby protecting neurons from degeneration in mice.
    Keywords:  Amyotrophic lateral sclerosis; Protein aggregation; SOD1; SQSTM1; Ubiquitin
    DOI:  https://doi.org/10.1016/j.neuint.2022.105364
  8. Dis Model Mech. 2022 May 30. pii: dmm.049447. [Epub ahead of print]
    HSP40 overexpression in pacemaker neurons protects against circadian dysfunction in a Drosophila model of Huntington's Disease.
    Pavitra Prakash, Arpit Kumar Pradhan, Vasu Sheeba.
      Circadian disturbances are early features of neurodegenerative diseases, including Huntington's Disease (HD). Emerging evidence suggests that circadian decline feeds into neurodegenerative symptoms, exacerbating them. Therefore, we asked whether known neurotoxic modifiers can suppress circadian dysfunction. We performed a screen of neurotoxicity-modifier genes to suppress circadian behavioural arrhythmicity in a Drosophila circadian HD model. The molecular chaperones HSP40 and HSP70 (Heat Shock Protein) emerged as significant suppressors in the circadian context, with HSP40 being the more potent mitigator. Upon HSP40 overexpression in the Drosophila circadian ventrolateral neurons (LNv), the behavioural rescue was associated with neuronal rescue of loss of circadian proteins from small LNv soma. Specifically, there was a restoration of the molecular clock protein Period and its oscillations in young flies and a long-lasting rescue of the output neuropeptide Pigment Dispersing Factor. Significantly, there was a reduction in the expanded Huntingtin inclusion load, concomitant with the appearance of a spot-like Huntingtin form. Thus, we provide evidence implicating the neuroprotective chaperone HSP40 in circadian rehabilitation. The involvement of molecular chaperones in circadian maintenance has broader therapeutic implications for neurodegenerative diseases.
    Keywords:  Circadian; Drosophila; HSP40; Heat Shock Protein; Huntington's Disease; neurodegeneration
    DOI:  https://doi.org/10.1242/dmm.049447
  9. Curr Opin Neurobiol. 2022 May 29. pii: S0959-4388(22)00048-4. [Epub ahead of print]75 102554
    Organization of the autophagy pathway in neurons.
    David K Sidibe, Maria C Vogel, Sandra Maday.
      Macroautophagy (hereafter referred to as autophagy) is an essential quality-control pathway in neurons, which face unique functional and morphological challenges in maintaining the integrity of organelles and the proteome. To overcome these challenges, neurons have developed compartment-specific pathways for autophagy. In this review, we discuss the organization of the autophagy pathway, from autophagosome biogenesis, trafficking, to clearance, in the neuron. We dissect the compartment-specific mechanisms and functions of autophagy in axons, dendrites, and the soma. Furthermore, we highlight examples of how steps along the autophagy pathway are impaired in the context of aging and neurodegenerative disease, which underscore the critical importance of autophagy in maintaining neuronal function and survival.
    DOI:  https://doi.org/10.1016/j.conb.2022.102554
  10. Blood. 2022 May 31. pii: blood.2021014698. [Epub ahead of print]
    PLAG1 dampens protein synthesis to promote human hematopoietic stem cell self-renewal.
    Ava Keyvani Chahi, Muluken S Belew, Joshua Xu, He Tian Tony Chen, Stefan Rentas, Veronique Voisin, Gabriela Krivdova, Eric R Lechman, Sajid A Marhon, Daniel De Carvalho, John E Dick, Gary D Bader, Kristin Hope.
      Hematopoietic stem cell (HSC) dormancy is understood as supportive of HSC function and their long-term integrity. While regulation of stress responses incurred as a result of HSC activation is recognized as important in maintaining stem cell function, little is understood of the preventative machinery present in human HSCs that may serve to resist their activation and promote HSC self-renewal. We demonstrate that the transcription factor PLAG1 is essential for long-term HSC function and when overexpressed endows a 15.6-fold enhancement in the frequency of functional HSC in stimulatory conditions. Genome-wide measures of chromatin occupancy and PLAG1-directed gene expression changes combined with functional measures reveal that PLAG1 dampens protein synthesis, restrains cell growth and division, and enhances survival, with the primitive cell advantages it imparts being attenuated by addition of the potent translation activator, c-MYC. We find PLAG1 capitalizes on multiple regulatory factors to ensure protective diminished protein synthesis including 4EBP1 and translation-targeting miR-127, and does so independently of stress response signaling. Overall, our study identifies PLAG1 as an enforcer of human HSC dormancy and self-renewal through its highly context-specific regulation of protein biosynthesis, and classifies PLAG1 among a rare set of bona fide regulators of mRNA translation in these cells. Our findings showcase the importance of regulated translation control underlying human HSC physiology, its dysregulation under activating demands, and the potential if its targeting for therapeutic benefit.
    DOI:  https://doi.org/10.1182/blood.2021014698
  11. Transl Neurodegener. 2022 Jun 03. 11(1): 32
    Defective mitophagy and the etiopathogenesis of Alzheimer's disease.
    Kuan Zeng, Xuan Yu, Yacoubou Abdoul Razak Mahaman, Jian-Zhi Wang, Rong Liu, Yi Li, Xiaochuan Wang.
      Accumulation of impaired mitochondria and energy metabolism disorders are non-negligible features of both aging and age-related neurodegeneration, including Alzheimer's disease (AD). A growing number of studies suggest that mitophagy disorders play an important role in AD occurrence and development. The interaction between mitophagy deficits and Aβ or Tau pathology may form a vicious cycle and cause neuronal damage and death. Elucidating the molecular mechanism of mitophagy and its role in AD may provide insights into the etiology and mechanisms of AD. Defective mitophagy is a potential target for AD prevention and treatment.
    Keywords:  Alzheimer’s disease; Aβ; Mitophagy; PINK1; Tau
    DOI:  https://doi.org/10.1186/s40035-022-00305-1
  12. Mol Cell Proteomics. 2022 May 30. pii: S1535-9476(22)00062-7. [Epub ahead of print] 100254
    New views of old proteins: clarifying the enigmatic proteome.
    Kristin E Burnum-Johnson, Thomas P Conrads, Richard R Drake, Amy E Herr, Ravi Iyengar, Ryan T Kelly, Emma Lundberg, Michael J MacCoss, Alexandra Naba, Garry P Nolan, Pavel A Pevzner, Karin D Rodland, Salvatore Sechi, Nikolai Slavov, Jeffrey M Spraggins, Jennifer E Van Eyk, Marc Vidal, Christine Vogel, David R Walt, Neil L Kelleher.
      All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 year projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
    Keywords:  biotechnology; proteins; proteomics; single molecule sequencing; single-cell biology
    DOI:  https://doi.org/10.1016/j.mcpro.2022.100254
  13. Nucleic Acids Res. 2022 May 27. pii: gkac366. [Epub ahead of print]
    Ribosomal protein eL39 is important for maturation of the nascent polypeptide exit tunnel and proper protein folding during translation.
    Jelena Micic, Olga Rodríguez-Galán, Reyes Babiano, Fiona Fitzgerald, José Fernández-Fernández, Yunyang Zhang, Ning Gao, John L Woolford, Jesús de la Cruz.
      During translation, nascent polypeptide chains travel from the peptidyl transferase center through the nascent polypeptide exit tunnel (NPET) to emerge from 60S subunits. The NPET includes portions of five of the six 25S/5.8S rRNA domains and ribosomal proteins uL4, uL22, and eL39. Internal loops of uL4 and uL22 form the constriction sites of the NPET and are important for both assembly and function of ribosomes. Here, we investigated the roles of eL39 in tunnel construction, 60S biogenesis, and protein synthesis. We show that eL39 is important for proper protein folding during translation. Consistent with a delay in processing of 27S and 7S pre-rRNAs, eL39 functions in pre-60S assembly during middle nucleolar stages. Our biochemical assays suggest the presence of eL39 in particles at these stages, although it is not visualized in them by cryo-electron microscopy. This indicates that eL39 takes part in assembly even when it is not fully accommodated into the body of pre-60S particles. eL39 is also important for later steps of assembly, rotation of the 5S ribonucleoprotein complex, likely through long range rRNA interactions. Finally, our data strongly suggest the presence of alternative pathways of ribosome assembly, previously observed in the biogenesis of bacterial ribosomal subunits.
    DOI:  https://doi.org/10.1093/nar/gkac366
  14. ACS Chem Neurosci. 2022 Jun 01.
    A Small Molecule Stabilizes the Disordered Native State of the Alzheimer's Aβ Peptide.
    Thomas Löhr, Kai Kohlhoff, Gabriella T Heller, Carlo Camilloni, Michele Vendruscolo.
      The stabilization of native states of proteins is a powerful drug discovery strategy. It is still unclear, however, whether this approach can be applied to intrinsically disordered proteins. Here, we report a small molecule that stabilizes the native state of the Aβ42 peptide, an intrinsically disordered protein fragment associated with Alzheimer's disease. We show that this stabilization takes place by a disordered binding mechanism, in which both the small molecule and the Aβ42 peptide remain disordered. This disordered binding mechanism involves enthalpically favorable local π-stacking interactions coupled with entropically advantageous global effects. These results indicate that small molecules can stabilize disordered proteins in their native states through transient non-specific interactions that provide enthalpic gain while simultaneously increasing the conformational entropy of the proteins.
    Keywords:  Alzheimer’s disease; Aβ42 peptide; native state; small molecule
    DOI:  https://doi.org/10.1021/acschemneuro.2c00116
  15. Nature. 2022 06;606(7912): 9
    Fix the process that led to Alzheimer's drug fiasco.
    Jason Karlawish.
      
    Keywords:  Medical research; Policy
    DOI:  https://doi.org/10.1038/d41586-022-01507-3
  16. Sci Rep. 2022 May 28. 12(1): 8984
    Binding of the HSF-1 DNA-binding domain to multimeric C. elegans consensus HSEs is guided by cooperative interactions.
    Lukas Schmauder, Siyuan Sima, Amira Ben Hadj, Ricardo Cesar, Klaus Richter.
      The protein HSF-1 is the controlling transcription factor of the heat-shock response (HSR). Its binding to the heat-shock elements (HSEs) induces the strong upregulation of conserved heat-shock proteins, including Hsp70s, Hsp40s and small HSPs. Next to these commonly known HSPs, more than 4000 other HSEs are found in the promoter regions of C. elegans genes. In microarray experiments, few of the HSE-containing genes are specifically upregulated during the heat-shock response. Most of the 4000 HSE-containing genes instead are unaffected by elevated temperatures and coexpress with genes unrelated to the HSR. This is also the case for several genes related to the HSP chaperone system, like dnj-12, dnj-13, and hsp-1. Interestingly, several promoters of the dedicated HSR-genes, like F44E5.4p, hsp-16.48p or hsp-16.2p, contain extended HSEs in their promoter region, composed of four or five HSE-elements instead of the common trimeric HSEs. We here aim at understanding how HSF-1 interacts with the different promoter regions. To this end we purify the nematode HSF-1 DBD and investigate the interaction with DNA sequences containing these regions. EMSA assays suggest that the HSF-1 DBD interacts with most of these HSE-containing dsDNAs, but with different characteristics. We employ sedimentation analytical ultracentrifugation (SV-AUC) to determine stoichiometry, affinity, and cooperativity of HSF-1 DBD binding to these HSEs. Interestingly, most HSEs show cooperative binding of the HSF-1 DBD with up to five DBDs being bound. In most cases binding to the HSEs of inducible promoters is stronger, even though the consensus scores are not always higher. The observed high affinity of HSF-1 DBD to the non-inducible HSEs of dnj-12, suggests that constitutive expression may be supported from some promoter regions, a fact that is evident for this transcription factor, that is essential also under non-stress conditions.
    DOI:  https://doi.org/10.1038/s41598-022-12736-x
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