Recognition of physiological phosphorylation sites by p21-activated kinase 4
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Chetty, Ashwin K. (ORCID:0000000150172159)↗
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CysLT1R receptor complex with Zafirlukast (P21 space group) structure (SFX@LCLS)
This dataset has overall quality of 3.4 Å (CC*=0.5), P21 space group and cell parameters 43.86, 159.43, 73.48, 90.0, 95.1, 90.0. The dataset has not any PDB record associated with it. Data processing scripts are described in detail [here](https://gist.github.com/marinegor/96102c9b7ce87509a0832649d11ba927).
CXI↗
Molecular basis for integrin adhesion receptor binding to p21-activated kinase 4 (PAK4)
Explore the source record for details and available documents.
Ha, Byung Hak↗
CysLT1R receptor complex with Zafirlukast (P21 space group) structure (SFX@LCLS)
This dataset has overall quality of 2.4 Å (CC*=0.5), P1 space group and cell parameters 41.58, 68.56, 87.37, 76.33, 76.69, 81.19. Structure obtained from this data have been deposited under PDB ID 6RZ5. Data processing scripts are described in detail [here](https://gist.github.com/marinegor/96102c9b7ce87509a0832649d11ba927)
CXI↗
Mechanoregulation of Proliferation, Differentiation, Senescence and Survival of Bone Marrow Primary Osteoprecursor Cells
Cell and animal studies conducted onboard the International Space Station and during the Shuttle program have provided extensive data illustrating bone degenerative responses to mechanical unloading in microgravity. Specifically CDKN1a/p21, an inhibitory modulator of cell cycle progression, is upregulated in osteoprecursor cells of the femur during 15-day spaceflight, suggesting that microgravity can block stem cell-based tissue regenerative process at the level of progenitor proliferation and differentiation. To study a potential role for CDKN1a/p21 in regulating osteogenic mechanosensitivity, we cultured primary bone marrow osteoprogenitor cells from CDKN1a/p21-null (p21-null) and wildtype mice with and without mechanical stimulation, and compared their morphological, proliferative, and in-vitro mineralization responses. Structural cell alterations due to mechanical stimulation were assessed by florescence labeling of f-actin cytoskeleton and focal adhesions. Mechanical stimulation of p21-null cells resulted in more pronounced cytoskeletal alignment with the axis of stretch than for wildtype cells. In addition, p21-null cells subjected to stretch loading also formed significantly more focal adhesions than wildtype cells. Combined these findings suggest that p21-null cells are structurally more responsive to stretch stimulation than the wildtype cells. Because osteoprogenitor cells are well known to respond to mechanical stimulation with increased proliferation, we also tested this response in p21-null cells. Results from those experiments show the proliferative capacity of mechanically stimulated p21-null cells far exceeded that of wildtype controls. Specifically, cell counts from 14, and 21 days post mechanical stimulation, show that p21- null cells to have a 4-fold increase in proliferation compared to wildtype. When the p21-null cell differentiation response to mechanical stimulation was evaluated, the p21-null cultuers elicited more extensive mineralization at earlier assessed timepoints than control cultures. Specifically, Von Kossa staining for mineralized matrix showed that the p21-null cells produced more than twice the mineralized surface area of wildtype cells, and at an earlier 7-day time point in culture. Taken together these results suggest that CDKN1a/p21 normally plays a role in negatively regulating osteoprogenitor proliferation and differentiation responses to mechanostimulation in bone. Findings of CDKN1a/p21's increased expression during spaceflight in microgravity also suggest not only a potential molecular mechanism for arresting regenerative bone growth in space, but potentially also a reduced impact for bone-formation-promoting exercise mechanostimulation. The findings described here constitute a novel role for p21 as a regulator of tissue regeneration in response to mechanical load stimulation, and also suggest a new promising molecular target to promote regenerative health in disuse conditions.
gravity↗
Age-associated expression of p21and p53 during human wound healing
In mice, cellular senescence and senescence-associated secretory phenotype (SASP) positively contribute to cutaneous wound healing. In this proof-of-concept study, we investigated the expressions of p16, p21, and other senescence-associated biomarkers during human wound healing in 24 healthy subjects using a double-biopsy experimental design. The first punch biopsy created the wound and established the baseline. The second biopsy, concentric to the first and taken several days after wounding, was used to probe for expression of biomarkers by immunohistochemistry and RNA FISH. To assess the effects of age, we recruited 12 sex-matched younger (30.2 ± 1.3 years) and 12 sex-matched older (75.6 ± 1.8 years) subjects. We found that p21 and p53, but not p16, were induced during healing in younger, but not older subjects. A role for Notch signaling in p21 expression was inferred from the inducible activation of HES1. Further, other SASP biomarkers such as dipeptidyl peptidase-4 (DPP4) were significantly induced upon wounding in both younger and older groups, whereas matrix metallopeptidase 9 (MMP9) was induced only in the younger group. Senescence-associated β-galactosidase (SA-β-gal) was not detectable before or after wounding. This pilot study suggests the possibility that human cutaneous wound healing is characterized by differential expression of p21 and p53 between younger and older subjects.
59 BASIC BIOLOGICAL SCIENCES↗
Cyclin E-p27 opposition and regulation of the G1 phase of the cell cycle in the murine neocortical PVE: a quantitative analysis of mRNA in situ hybridization
We have analyzed the expression patterns of mRNAs of five cell cycle related proteins in the ventricular zone of the neocortical cerebral wall over the course of the neuronogenetic interval in the mouse. One set of mRNAs (cyclin E and p21) are initially expressed at high levels but expression then falls to a low asymptote. A second set (p27, cyclin B and cdk2) are initially expressed at low levels but ascend to peak levels only to decline again. These patterns divide the overall neuronogenetic interval into three phases. In phase 1 cyclin E and p21 levels of mRNA expression are high, while those of mRNAs of p27, cdk2 and cyclin B are low. In this phase the fraction of cells leaving the cycle after each mitosis, Q, is low and the duration of the G1 phase, TG1, is short. In phase 2 levels of expression of cyclin E and p21 fall to asymptote while levels of expression of mRNA of the other three proteins reach their peaks. Q increases to approach 0.5 and TG1 increases even more rapidly to approach its maximum length. In phase 3 levels of expression of cyclin E and p21 mRNAs remain low and those of the mRNAs of the other three proteins fall. TG1 becomes maximum and Q rapidly increases to 1.0. The character of these phases can be understood in part as consequences of the reciprocal regulatory influence of p27 and cyclin E and of the rate limiting functions of p27 at the restriction point and of cyclin E at the G1 to S transition.
NASA Discipline Cell Biology↗
The Role of CDKN1a/p21 in Cellular Senescence of Bone Marrow Stem Cells Under Spaceflight Stressors
Spaceflight environments and their associated conditions, such as microgravity and space radiation, cause many biological functions formerly considered to be standard to behave in nonstandard ways. Exposure to microgravity has shown to induce deleterious effects in stem cell-based tissue regeneration, leading to immune system and healing response impairments as well as muscle and bone density loss. Such risks must be mitigated in order for long-term human space exploration to proceed. Thus, our work seeks to explore mechanisms of stem cell-based tissue regeneration that experience changes in spaceflight environments. Cellular senescence is a process of inducing cell cycle arrest that can be initiated by various stimuli. This function is influenced by two major pathways, controlled by p53 and pRB tumor suppressor proteins. p53 activity targets the cyclin-dependent kinase inhibitor gene p21Cdkn1a in osteogenic cell cycle arrest. Under conditions of mechanical unloading, stem cell-based tissue regeneration has shown to be decreased in both proliferation and differentiation, as many cells are arrested in progenitor states. p21 has shown upregulation in expression under conditions of microgravity, suggesting its role in regenerative bone formation arrest in space. p21 levels are found to be elevated independent of p53, suggesting a decrease in proliferation and regeneration without apoptosis, but rather through cell cycle arrest alone. Thus, we hypothesize that p21 is a mediator of cellular senescence in bone marrow stem cells. Culturing of bone marrow stem cells from wild type and p21 knockout mice under osteoblastogenic conditions will be completed to explore the role of p21Cdkn1a in stem cell proliferation and maturation. We believe that decreases in somatic stem cell differentiation may occur after spaceflight due to signal pathway alterations that result in downstream inhibition of genes involved in differentiation, preventing tissue from repairing and regenerating normally.
Stem Cells↗
Dual Genes of Muscle Cell Senescence: Unraveling the Radiation-Induced Roles of HDAC4 and MORC2a
As the human race ventures further into space and plans missions to explore the Moon and the expanse that lies ahead, addressing health challenges that may hinder exploration becomes an imperative task. However, limited research exists on the molecular mechanisms within skeletal muscle cells in response to long-term radiation-induced oxidative stress. Upon analyzing GLDS-426 from the GeneLab Repository, upregulation of the DNA damage response gene HDAC4 in space radiation conditions with 1G was observed, where radiation-induced oxidative stress increased DNA damage. DNA damage response gene MORC2a was found to be downregulated in space radiation conditions in 1G with a culture treatment of nanoceria, an antioxidant that alleviates the effects of oxidative stress and causes less DNA damage. Literature review further indicated that MORC2a recruits HDAC4 at the promoter to prevent the transcription of p21. Upregulation of p21 has been linked to cell senescence and muscle atrophy on Earth, but no research has studied its changes in radiation conditions. To address the knowledge gap regarding the HDAC4/MORC2a pathway impact on p21 expression in radiation, our experiment aims to silence HDAC4 and MORC2a in the Mus musculus C2C12 cell culture line. These cultures will be exposed to radiation to assess the effects on cellular senescence (Aim 1). Additionally, we will silence p21 and subject the cell cultures to radiation to measure muscle cell proliferation (Aim 2). Muscle atrophy in future long-term space missions can contribute to the risk of degenerative diseases and hinder the completion of tasks in space. Furthermore, exploring the impact of these genes on muscle atrophy may provide therapeutic insights for individuals experiencing skeletal muscle degeneration and elderly individuals affected by sarcopenia.
GL4HS↗
Cdkn1a transcript variant 2 is a marker of aging and cellular senescence
Cellular senescence is a cell fate response characterized by a permanent cell cycle arrest driven primarily the by cell cycle inhibitor and tumor suppressor proteins p16 Ink4a and p21 Cip1/Waf1 . In mice, the p21 Cip1/Waf1 encoding locus, Cdkn1a , is known to generate two transcripts that produce identical proteins, but one of these transcript variants is poorly characterized. We show that the Cdkn1a transcript variant 2, but not the better-studied variant 1, is selectively elevated during natural aging across multiple mouse tissues. Importantly, mouse cells induced to senescence in culture by genotoxic stress (ionizing radiation or doxorubicin) upregulated both transcripts, but with different temporal dynamics: variant 1 responded nearly immediately to genotoxic stress, whereas variant 2 increased much more slowly as cells acquired senescent characteristics. Upon treating mice systemically with doxorubicin, which induces widespread cellular senescence in vivo , variant 2 increased to a larger extent than variant 1. Variant 2 levels were also more sensitive to the senolytic drug ABT-263 in naturally aged mice. Thus, variant 2 is a novel and more sensitive marker than variant 1 or total p21 Cip1/Waf1 protein for assessing the senescent cell burden and clearance in mice.
60 APPLIED LIFE SCIENCES↗
The influence of SV40 immortalization of human fibroblasts on p53-dependent radiation responses
The simian virus 40 large tumor antigen (SV40 Tag) has been ascribed many functions critical to viral propagation, including binding to the mammalian tumor suppressor p53. Recent studies have demonstrated that SV40-transformed murine cells have functional p53. The status of p53 in SV40-immortalized human cells, however, has not been characterized. We have found that in response to ionizing radiation, p53-dependent p21 transactivation activity is present, albeit reduced, in SV40-immortalized cells and that this activity can be further reduced with either dominant negative p53 expression or higher SV40 Tag expression. Furthermore, overexpression of p53 in SV40-immortalized ataxia-telangiectasia (A-T) cells restores p53-dependent p21 induction to typical A-T levels. All SV40-immortalized cell lines exhibited an absence of G1 arrest. Moreover, all SV40-immortalized cell lines exhibited increased apoptosis relative to primary cells in response to ionizing radiation, suggesting that SV40 immortalization results in a unique phenotype with regard to DNA damage responses. Copyright 1999 Academic Press.
NASA Discipline Radiation Health↗
Activation of polycystin-1 signaling by binding of stalk-derived peptide agonists
Polycystin-1 (PC1) is the protein product of thePKD1gene whose mutation causes autosomal dominant Polycystic Kidney Disease (ADPKD). PC1 is an atypical G protein-coupled receptor (GPCR) with an autocatalytic GAIN domain that cleaves PC1 into extracellular N-terminal and membrane-embedded C-terminal (CTF) fragments. Recently, activation of PC1 CTF signaling was shown to be regulated by a stalk tethered agonist (TA), resembling the mechanism observed for adhesion GPCRs. Here, synthetic peptides of the first 9- (p9), 17- (p17), and 21-residues (p21) of the PC1 stalk TA were shown to re-activate signaling by a stalkless CTF mutant in human cell culture assays. Novel Peptide Gaussian accelerated molecular dynamics (Pep-GaMD) simulations elucidated binding conformations of p9, p17, and p21 and revealed multiple specific binding regions to the stalkless CTF. Peptide agonists binding to the TOP domain of PC1 induced close TOP-putative pore loop interactions, a characteristic feature of stalk TA-mediated PC1 CTF activation. Additional sequence coevolution analyses showed the peptide binding regions were consistent with covarying residue pairs identified between the TOP domain and the stalk TA. These insights into the structural dynamic mechanism of PC1 activation by TA peptide agonists provide an in-depth understanding that will facilitate the development of therapeutics targeting PC1 for ADPKD treatment.
Life Sciences & Biomedicine - Other Topics↗
The tonotopic map in the embryonic chicken cochlea
The purpose of the present study was to determine the tonotopic map in the chicken cochlea at 19 days of incubation (E19) by obtaining characteristic frequencies (CFs) for primary afferents, labeling the characterized neurons, and documenting their projections to the papilla. The lowest and highest CFs recorded were 188 and 1623 Hz respectively. The embryonic tonotopic map coincided with maps reported for post-hatch chicks. There were no evidence that neurons selective to low frequencies project inappropriately to more basal locations of the embryonic papilla. Linear regression was used to estimate the frequency gradient (b = 0.037 +/- 0.012 In Hz/% [b +/- SEb]) and intercept (In C, where C = 111 Hz) of the semilog plot of frequency versus cochlear position (in % distance from apex). From these estimates the octave distribution was calculated to be 18.7%/octave or 0.58 mm/octave. These quantities were not significantly different from those found in post hatch chickens. We conclude that the tonotopic map of the avian cochlea for CFs between 100 and 1700 Hz is stable and relatively mature from age E19 to post-hatch day 21 (P21). The most striking sign of immaturity in the E19 embryo is the limited range of high CFs. We offer the hypothesis that, between the ages of E19 and P21, improvements in middle ear admittance alone or in combination with functional maturation of the cochlear base may be the principal factors responsible for the appearance of adult-like high CF limits and not an apically shifting tonotopic map.
NASA Discipline Neuroscience↗
LxCxD motif of the APC/C coactivator subunit FZR1 is critical for interaction with the retinoblastoma protein
Highlights: • Several oncogenic viral proteins bind to tumor suppressor pRB via LxCxE motif. • LxCxE present in many cellular proteins that interact with pRB. • APC/C interacts with pRB via this motif in its FZR1 subunit. • FZR1 LxCxE-like LxCxD critical for FZR1-pRB direct binding and SKP2 ubiquitylation. • Mutation of FZR1 LxCxD alters cell cycle. Retinoblastoma protein (pRB) regulates cell cycle by utilizing different regions of its pocket domain for interacting with E2F family of transcription factors and with cellular and viral proteins containing an LxCxE motif. An LxCxE-like motif, LxCxD, is present in FZR1, an adaptor protein of the multi-subunit E3 ligase complex anaphase-promoting complex/cyclosome (APC/C). The APC/C{sup FZR1} complex regulates the timely degradation of multiple cell cycle proteins for mitotic exit and maintains G1 state. We report that FZR1 interacts with pRB via its LxCxD motif. By using point mutations, we found that the cysteine residue in the FZR1 LxCxD motif is critical for direct interaction with pRb. The direct binding of the LxCxD motif of FZR1 to the pRB LxCxE binding pocket is confirmed by using human papillomavirus protein E7 as a competitor, both in vitro and in vivo. While mutation of the cysteine residue significantly disrupts FZR1 interaction with pRB, this motif does not affect FZR1 and core APC/C association. Expression of the FZR1 point mutant results in accumulation of S-phase kinase-associated protein 2 (SKP2) and Polo-like kinase 1 (PLK1), while p27{sup Kip1} and p21{sup Cip1} proteins are downregulated, indicating a G1 cell cycle defect. Consistently, cells containing point mutant FZR1 enter the S phase prematurely. Together our results suggest that the LxCxD motif of FZR1 is a critical determinant for the interaction between FZR1 and pRB and is important for G1 restriction.
60 APPLIED LIFE SCIENCES↗
PDRG1 predicts a poor prognosis and facilitates the proliferation and metastasis of colorectal cancer
Highlights: • PDRG1 is overexpressed in colorectal cancer tissues and is associated with poor prognosis of colorectal cancer patients. • PDRG1 regulates the proliferation, apoptosis, cell cycle progression and metastasis of colorectal cancer cells. • PDRG1 promotes the proliferation, migration and invasion of colorectal cancer via p21-mediated cell cycle progression. The incidence and mortality of colorectal cancer (CRC) is increasing yearly and CRC patients are becoming younger in global. Evidences have revealed the carcinogenic effect of p53 and DNA damage-regulated gene 1 (PDRG1) in several types of tumors. However, its biological function is yet to be investigated in CRC. This study aimed to unveil the prooncogenic role of PDRG1 in CRC.
60 APPLIED LIFE SCIENCES↗
Crystal structure of active CDK4-cyclin D and mechanistic basis for abemaciclib efficacy
Despite the biological and therapeutic relevance of CDK4/6 for the treatment of HR+, HER2- advanced breast cancer, the detailed mode of action of CDK4/6 inhibitors is not completely understood. Of particular interest, phosphorylation of CDK4 at T172 (pT172) is critical for generating the active conformation, yet no such crystal structure has been reported to date. We describe here the x-ray structure of active CDK4-cyclin D3 bound to the CDK4/6 inhibitor abemaciclib and discuss the key aspects of the catalytically-competent complex. Furthermore, the effect of CDK4/6 inhibitors on CDK4 T172 phosphorylation has not been explored, despite its role as a potential biomarker of CDK4/6 inhibitor response. We show mechanistically that CDK4/6i stabilize primed (pT172) CDK4-cyclin D complex and selectively displace p21 in responsive tumor cells. Stabilization of active CDK4-cyclin D1 complex can lead to pathway reactivation following alternate dosing regimen. Consequently, sustained binding of abemaciclib to CDK4 leads to potent cell cycle inhibition in breast cancer cell lines and prevents rebound activation of downstream signaling. Overall, our study provides key insights demonstrating that prolonged treatment with CDK4/6 inhibitors and composition of the CDK4/6-cyclin D complex are both critical determinants of abemaciclib efficacy, with implications for this class of anticancer therapy.
60 APPLIED LIFE SCIENCES↗
Polymorphism and phase transitions in Na 2 U 2 O 7 from density functional perturbation theory
Polymorphism and phase transitions in sodium diuranate, Na 2 U 2 O 7 , are investigated with density functional perturbation theory (DFPT). Thermal properties of crystalline α-, β- and γ-Na 2 U 2 O 7 polymorphs are predicted from DFPT phonon calculations, i.e., the first time for the high-temperature γ-Na 2 U 2 O 7 phase (R$\bar{3}$ with combining macron]m symmetry). The standard molar isochoric heat capacities predicted within the quasi-harmonic approximation are C p (298.15K)= 219.4 and 220.9 J K -1 mol -1 mfor P21/a α-Na 2 U 2 O 7 and C2/m β-Na 2 U 2 O 7 , respectively. Gibbs free energy calculations reveal that α-Na 2 U 2 O 7 (P2 1 /a) and β-Na 2 U 2 O 7 (C2/m) are almost energetically degenerate at low temperature, with β-Na 2 U 2 O 7 becoming slightly more stable than α-Na 2 U 2 O 7 as temperature increases. Here these findings are consistent with XRD data showing a mixture of α and β phases after cooling of γ-Na 2 U 2 O 7 to room temperature and the observation of a sluggish α → β phase transition above ca. 600 K. A recently observed α-Na 2 U 2 O 7 structure with P21 symmetry is also shown to be metastable at low temperature. Based on Gibbs free energy, no direct β → γ solid-solid phase transition is predicted at high temperature, although some experiments reported the existence of such phase transition around 1348 K. This, along with recent experiments, suggests the occurrence of a multi-step process consisting of initial β-phase decomposition, followed by recrystallization into γ-phase as temperature increases.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Mechanistic Evaluation of Black Cohosh Extract-Induced Genotoxicity in Human Cells
Abstract Black cohosh extract (BCE) is marketed to women as an alternative to hormone replacement therapy for alleviating menopausal symptoms. Previous studies by the National Toxicology Program revealed that BCE induced micronuclei (MN) and a nonregenerative macrocytic anemia in rats and mice, likely caused by disruption of the folate metabolism pathway. Additional work using TK6 cells showed that BCE induced aneugenicity by destabilizing microtubules. In the present study, BCE-induced MN were confirmed in TK6 and HepG2 cells. We then evaluated BCE-induced DNA damage using the comet assay at multiple time points (0.5–24 h). Following a 0.5-h exposure, BCE induced significant, concentration-dependent increases in %tail DNA in TK6 cells only. Although DNA damage decreased in TK6 cells over time, likely due to repair, small but statistically significant levels of DNA damage were observed after 2 and 4 h exposures to 250 µg/ml BCE. A G1/S arrest in TK6 cells exposed to 125 µg/ml BCE (24 h) was accompanied by apoptosis and increased expression of γH2A.X, p-Chk1, p-Chk2, p53, and p21. Conditioning TK6 cells to physiological levels of folic acid (120 nM) did not increase the sensitivity of cells to BCE-induced DNA damage. BCE did not alter global DNA methylation in TK6 and HepG2 cells cultured in standard medium. Our results suggest that BCE induces acute DNA strand breaks which are quickly repaired in TK6 cells, whereas DNA damage seen at 4 and 24 h may reflect apoptosis. The present study supports that BCE is genotoxic mainly by inducing MN with an aneugenic mode of action.
Seo, Ji-Eun↗