The Experts below are selected from a list of 1908 Experts worldwide ranked by ideXlab platform
Troy A A Harkness - One of the best experts on this subject based on the ideXlab platform.
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rapid nuclear exclusion of hcm1 in aging saccharomyces cerevisiae leads to vacuolar alkalization and replicative senescence
G3: Genes Genomes Genetics, 2018Co-Authors: Ata Ghavidel, Martin Prusinkiewicz, Cynthia L Swan, Zach R Belak, Christopher H Eskiw, Carlos E Carvalho, Kunal Baxi, Troy A A HarknessAbstract:The yeast, Saccharomyces cerevisiae, like other higher eukaryotes, undergo a finite number of cell divisions before exiting the cell cycle due to the effects of aging. Here, we show that yeast aging begins with the nuclear exclusion of Hcm1 in young cells, resulting in loss of acidic vacuoles. Autophagy is required for healthy aging in yeast, with Proteins targeted for turnover by autophagy directed to the vacuole. Consistent with this, vacuolar acidity is necessary for vacuolar function and yeast longevity. Using yeast genetics and immunofluorescence microscopy, we confirm that vacuolar acidity plays a critical role in cell health and lifespan, and is potentially maintained by a series of Forkhead Box (FOX) transcription factors. An interconnected transcriptional network involving the FOX Proteins (Fkh1, Fkh2 and Hcm1) are required for transcription of v-ATPase subunits and vacuolar acidity. As cells age, Hcm1 is rapidly excluded from the nucleus in young cells, blocking the expression of Hcm1 targets (Fkh1 and Fkh2), leading to loss of v-ATPase gene expression, reduced vacuolar acidification, increased α-syn-GFP vacuolar accumulation, and finally, diminished replicative lifespan (RLS). Loss of vacuolar acidity occurs about the same time as Hcm1 nuclear exclusion and is conserved; we have recently demonstrated that lysosomal alkalization similarly contributes to aging in C. elegans following a transition from progeny producing to post-reproductive life. Our data points to a molecular mechanism regulating vacuolar acidity that signals the end of RLS when acidification is lost.
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rapid nuclear exclusion of hcm1 in aging saccharomyces cerevisiae leads to vacuolar alkalization and replicative senescence
bioRxiv, 2018Co-Authors: Troy A A Harkness, Ata Ghavidel, Martin Prusinkiewicz, Cynthia L Swan, Zach R Belak, Christopher H Eskiw, Carlos E Carvalho, Kunal BaxiAbstract:Yeast cells, like other higher eukaryotic cells, undergo a finite number of cell divisions before exiting the cell cycle due to the effects of aging. Here, we show that yeast aging begins with the nuclear exclusion of Hcm1 in young cells, resulting in loss of acidic vacuoles. Autophagy is required for healthy aging in yeast, with Proteins targeted for turnover by autophagy directed to the vacuole. Consistent with this, vacuolar acidity is necessary for vacuolar function and yeast longevity. Using yeast genetics and immunofluorescence microscopy, we confirm that vacuolar acidity plays a critical role in cell health and lifespan, and is potentially maintained by a series of Forkhead Box (FOX) transcription factors. An interconnected transcriptional network involving the FOX Proteins (Fkh1, Fkh2 and Hcm1) are required for transcription of v-ATPase subunits and vacuolar acidity. As cells age, Hcm1 is rapidly excluded from the nucleus in young cells, blocking the expression of Hcm1 targets (Fkh1 and Fkh2), leading to loss of v-ATPase gene expression, reduced vacuolar acidification, increased α-syn-GFP vacuolar accumulation, and finally, diminished replicative lifespan (RLS). Loss of vacuolar acidity occurs about the same time as Hcm1 nuclear exclusion and is conserved; we have recently demonstrated that lysosomal alkalization similarly contributes to aging in C. elegans following a transition from progeny producing to post-reproductive life. Our data points to a molecular mechanism regulating vacuolar acidity that signals the end of RLS when acidification is lost.
Jorge Babul - One of the best experts on this subject based on the ideXlab platform.
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Three-Dimensional Domain Swapping Changes the Folding Mechanism of the Forkhead Domain of FOXP1
Biophysical Journal, 2016Co-Authors: Exequiel Medina, Cristóbal Córdova, Pablo Villalobos, Javiera Reyes, César A. Ramírez-sarmiento, Elizabeth A Komives, Jorge BabulAbstract:Abstract The forkhead family of transcription factors (FOX) controls gene transcription during key processes such as regulation of metabolism, embryogenesis, and immunity. Structurally, FOX Proteins feature a conserved DNA-binding domain known as forkhead. Interestingly, solved forkhead structures of members from the P subfamily (FOXP) show that they can oligomerize by three-dimensional domain swapping, whereby structural elements are exchanged between adjacent subunits, leading to an intertwined dimer. Recent evidence has largely stressed the biological relevance of domain swapping in FOXP, as several disease-causing mutations have been related to impairment of this process. Here, we explore the equilibrium folding and binding mechanism of the forkhead domain of wild-type FOXP1, and of two mutants that hinder DNA-binding (R53H) and domain swapping (A39P), using size-exclusion chromatography, circular dichroism, and hydrogen-deuterium exchange mass spectrometry. Our results show that domain swapping of FOXP1 occurs at micromolar protein concentrations within hours of incubation and is energetically favored, in contrast to classical domain-swapping Proteins. Also, DNA-binding mutations do not significantly affect domain swapping. Remarkably, equilibrium unfolding of dimeric FOXP1 follows a three-state N 2 ↔ 2I ↔ 2U folding mechanism in which dimer dissociation into a monomeric intermediate precedes protein unfolding, in contrast to the typical two-state model described for most domain-swapping Proteins, whereas the A39P mutant follows a two-state N ↔ U folding mechanism consistent with the second transition observed for dimeric FOXP1. Also, the free-energy change of the N ↔ U in A39P FOXP1 is ∼2 kcal⋅mol −1 larger than the I ↔ U transition of both wild-type and R53H FOXP1. Finally, hydrogen-deuterium exchange mass spectrometry reveals that the intermediate strongly resembles the native state. Our results suggest that domain swapping in FOXP1 is at least partially linked to monomer folding stability and follows an unusual three-state folding mechanism, which might proceed via transient structural changes rather than requiring complete protein unfolding as do most domain-swapping Proteins.
Eric Lam - One of the best experts on this subject based on the ideXlab platform.
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forkhead box transcription factors in cancer initiation progression and chemotherapeutic drug response
Frontiers in Oncology, 2014Co-Authors: Eric Lam, Ana R GomesAbstract:Forkhead box (FOX) Proteins are an extensive family of transcription factors, which play a key role in the regulation of crucial biological processes, including cell proliferation, differentiation, metabolism, tissue homeostasis, senescence, survival, apoptosis, and DNA damage repair (1). The unifying feature of FOX Proteins is the “forkhead” box, a sequence of about 100 amino acids that enables binding to specific DNA sequences. The forkhead motif is also known as a “winged-helix” DNA binding domain (DBD) because of its distinct butterfly like appearance. The founding FOX member was first identified in the fruitfly (Drosophilia Melanogaster) over 20 years ago, when mutation of the fork head (fkh) gene in these flies was found to result in fork-patterned embryo heads. To date, over 50 mammalian FOX Proteins have been identified, and further divided into 19 subclasses (FOXA to FOXS) based on their protein sequence homology. These FOX Proteins rely on precise temporal and spatial controls to directly affect crucial cell fate decisions, regulating gene networks involved in cell cycle progression, proliferation, survival, and differentiation. Hence, not unexpectedly, defects in the regulation or deregulation of their activity can lead to profound consequences, such as cancer initiation and progression. The best-studied FOX Proteins involved in cancer are FOXO3a, FOXM1, and FOXA1 (1). There is compelling evidence that FOXO3a and FOXM1 have opposite roles in cancer: while FOXO3a behaves like a typical tumor suppressor, FOXM1 functions as a potent oncogene. FOXA1 is a prominent “pioneer factor” with the ability of initiating transcriptional competency and recruiting other transcription factors to target genes. This pioneer function is of particular importance in gene expression of endocrine-related cancers, including breast and prostate cancers as FOXA1 is a key cooperating factor for the nuclear hormone receptors, estrogen receptor-α (ER), and androgen receptor (AR) (1, 2). With recent advances in next-generation sequencing, novel regulatory mechanisms, functions, and mutations have been uncovered for these FOX Proteins. The present special Research Topic of Frontiers in Oncology is devoted to unveiling this new information, focusing on the role and regulation of FOXA1, FOXO3a, and FOXM1 in cancer initiation, progression, and drug resistance. Apart from cancer initiation, there is convincing evidence that FOXM1 also has a vital role in angiogenesis, invasion, metastasis, DNA damage repair, and the development of chemotherapeutic drug resistance (3). In their review, Alvarez-Fernandez and Medema discuss the recent findings relating to these novel aspects of FOXM1 function (4). Besides FOXM1, the oncogene myc is also negatively regulated by FOXO3a (5, 6), and this regulation may have a key function in the control of cellular metabolism during cancer initiation and progression. In their mini-review, Peck et al. describe the antagonism between FOXO3a and MYC, and its implication in cell metabolism and cancer development (7). There is now ample evidence that the FOXA1 gene is mutated or amplified in some breast and prostate cancers. In their mini-review, Robinson and colleagues consider the accumulated evidence and provide insights into the implications of FOXA1 mutations in the context of breast and prostate cancers (8). Beyond mutations, there are also indications that alternative splicing can produce oncogenic versions of FOX Proteins. The FOXM1 gene is made up of 10 exons, of which exon Va and VIIa are alternatively spliced, giving rise to three distinct isoforms: FOXM1a, FOXM1b, and FOXM1c (3, 9). In their perspective article, Lam et al. present experimental data to support their hypothesis that FOXM1b, which is overexpressed in cancer cells, has a greater oncogenic potential than FOXM1c (10). A thorough understanding of the regulation and role of these FOX Proteins in cancer will allow us to exploit them as biomarkers for cancer diagnosis and targets for treatment (10). Although earlier studies have shown that nuclear translocation of FOXO3a can lead to activation of genes important in cell cycle arrest and cell death, recent studies in cancer patient samples have revealed that sustained nuclear FOXO3a expression is associated with poor prognosis (11, 12). In their commentary, Gong and Koo discuss the implications of nuclear FOXO3a expression and examine the molecular mechanism involved (13). The principal roles played by FOXM1 in different aspects of cancer initiation and progression render it a prime target for pharmaceutical intervention (14). In his perspective article, Teh summarizes the existing information on the role of FOXM1 in cancer initiation, progression, and drug resistance, and explores its usefulness as a biomarker for cancer screening, prognosis, and for monitoring drug treatment (15). The thiazole antibiotics Siomycin A and Thiostrepton have been shown to be able to specifically target cancer cells, while leaving normal cells alone (16). This effect depends on the ability of these antifungal agents to bind the forkhead DNA binding domain of FOXM1 directly (17). In agreement, Gartel comments on the role of Siomycin A and Thiostrepton in blocking the transcriptional activity of FOXM1 and provide future perspectives (18). Together, this collection of articles underscores the importance of FOX Proteins during cancer initiation and development and proposes novel avenues for cancer diagnosis and treatment.
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the emerging roles of forkhead box FOX Proteins in cancer
Nature Reviews Cancer, 2007Co-Authors: Stephen S Myatt, Eric LamAbstract:Forkhead box (FOX) Proteins are a superfamily of evolutionarily conserved transcriptional regulators, which control a wide spectrum of biological processes. As a consequence, a loss or gain of FOX function can alter cell fate and promote tumorigenesis as well as cancer progression. Here we discuss the evidence that the deregulation of FOX family transcription factors has a crucial role in the development and progression of cancer, and evaluate the emerging role of FOX Proteins as direct and indirect targets for therapeutic intervention, as well as biomarkers for predicting and monitoring treatment responses.
Reiner A Veitia - One of the best experts on this subject based on the ideXlab platform.
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forkhead transcription factors in health and disease
Trends in Genetics, 2021Co-Authors: Laetitia Herman, Annelaure Todeschini, Reiner A VeitiaAbstract:Forkhead box (FOX) Proteins belong to an evolutionarily conserved family of transcription factors that has evolved by gene/genome duplication. FOX family members have undergone sequence and regulatory diversification. However, they have retained some degree of functional redundancy, in addition to playing specific roles, both during development and in the adult. Genetic alterations or misregulation of FOX genes underlie human genetic diseases, cancer, and/or aging. In this review, we provide an updated overview of the main characteristics of the members of this family, in terms of breadth of expression, protein domain composition, evolution, and function.
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Insights into the pathogenicity of missense variants in the forkhead domain of FOX Proteins underlying Mendelian disorders
Human Genetics, 2021Co-Authors: Luis Bermúdez-guzmán, Reiner A VeitiaAbstract:Forkhead box (FOX) Proteins are members of a conserved family of transcription factors. Pathogenic variants in FOX genes have been shown to be responsible for several human genetic diseases. Here, we have studied the molecular and structural features of germline pathogenic variants in seven FOX Proteins involved in Mendelian disorders and compared them with those of variants present in the general population (gnomAD). Our study shows that the DNA-binding domain of FOX Proteins is particularly sensitive to damaging variation, although some family members show greater mutational tolerance than others. Next, we set to demonstrate that this tolerance depends on the inheritance mode of FOX-linked disorders. Accordingly, genes whose variants underlie recessive conditions are supposed to have a greater tolerance to variation. This is what we found. As expected, variants responsible for disorders with a dominant inheritance pattern show a higher degree of pathogenicity compared to those segregating in the general population. Moreover, we show that pathogenic and likely pathogenic variants tend to affect mutually exclusive sites with respect to those reported in gnomAD. The former also tend to affect sites with lower solvent exposure and a higher degree of conservation. Our results show the value of using publicly available databases and bioinformatics to gain insights into the molecular and structural bases of disease-causing genetic variation.
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Forkhead transcription factors: key players in health and disease.
Trends in Genetics, 2011Co-Authors: Bérénice A Benayoun, Sandrine Caburet, Reiner A VeitiaAbstract:Forkhead box (FOX) Proteins constitute an evolutionarily conserved family of transcription factors with a central role not only during development, but also in the adult organism. Thus, the misregulation and/or mutation of FOX genes often induce human genetic diseases, promote cancer or deregulate ageing. Indeed, germinal FOX gene mutations cause diseases ranging from infertility to language and/or speech disorders and immunological defects. Moreover, because of their central role in signalling pathways and in the regulation of homeostasis, somatic misregulation and/or mutation of FOX genes are associated with cancer. FOX Proteins have undergone diversification in terms of their sequence, regulation and function. In addition to dedicated roles, evidence suggests that Forkhead factors have retained some functional redundancy. Thus, combinations of slightly defective alleles might induce disease phenotypes in humans, acting as quantitative trait loci. Uncovering such variants would be a big step towards understanding the functional interdependencies of different FOX members and their implications in complex pathologies.
Oscar M. Aparicio - One of the best experts on this subject based on the ideXlab platform.
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Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: A. Zachary Ostrow, Reza Kalhor, Yan Gan, Sandra K. Villwock, Christian Linke, Matteo Barberis, Lin Chen, Oscar M. AparicioAbstract:Forkhead Box (FOX) Proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding Proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which contributes to developmental defects, cancer, and aging. We recently identified Saccharomyces cerevisiae Forkhead 1 (Fkh1) and Forkhead 2 (Fkh2) as required for the clustering of a subset of replication origins in G1 phase and for the early initiation of these origins in the ensuing S phase, suggesting a mechanistic role linking the spatial organization of the origins and their activity. Here, we show that Fkh1 and Fkh2 share a unique structural feature of human FOXP Proteins that enables FOXP2 and FOXP3 to form domain-swapped dimers capable of bridging two DNA molecules in vitro. Accordingly, Fkh1 self-associates in vitro and in vivo in a manner dependent on the conserved domain-swapping region, strongly suggestive of homodimer formation. Fkh1- and Fkh2-domain-swap-minus (dsm) mutations are functional as transcription factors yet are defective in replication origin timing control. Fkh1-dsm binds replication origins in vivo but fails to cluster them, supporting the conclusion that Fkh1 and Fkh2 dimers perform a structural role in the spatial organization of chromosomal elements with functional importance.
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quantitative brdu immunoprecipitation method demonstrates that fkh1 and fkh2 are rate limiting activators of replication origins that reprogram replication timing in g1 phase
Genome Research, 2016Co-Authors: Jared M Peace, Yan Gan, Sandra K. Villwock, John Zeytounian, Oscar M. AparicioAbstract:The Saccharomyces cerevisiae Forkhead Box (FOX) Proteins, Fkh1 and Fkh2, regulate diverse cellular processes including transcription, long-range DNA interactions during homologous recombination, and replication origin timing and long-range origin clustering. We hypothesized that, as stimulators of early origin activation, Fkh1 and Fkh2 abundance limits the rate of origin activation genome-wide. Existing methods, however, are not well-suited to quantitative, genome-wide measurements of origin firing between strains and conditions. To overcome this limitation, we developed qBrdU-seq, a quantitative method for BrdU incorporation analysis of replication dynamics, and applied it to show that overexpression of Fkh1 and Fkh2 advances the initiation timing of many origins throughout the genome resulting in a higher total level of origin initiations in early S phase. The higher initiation rate is accompanied by slower replication fork progression, thereby maintaining a normal length of S phase without causing detectable Rad53 checkpoint kinase activation. The advancement of origin firing time, including that of origins in heterochromatic domains, was established in late G1 phase, indicating that origin timing can be reset subsequently to origin licensing. These results provide novel insights into the mechanisms of origin timing regulation by identifying Fkh1 and Fkh2 as rate-limiting factors for origin firing that determine the ability of replication origins to accrue limiting factors and have the potential to reprogram replication timing late in G1 phase.
