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Taniura H, Soeda S, Ohta T, Oki M, Tsuboi R. Sir2D, a Sirtuin family protein, regulates adenylate cyclase A expression through interaction with the MybB transcription factor early in Dictyostelium development upon starvation. Heliyon 2019; 5:e01301. [PMID: 31016257 PMCID: PMC6475656 DOI: 10.1016/j.heliyon.2019.e01301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/07/2019] [Accepted: 02/27/2019] [Indexed: 10/28/2022] Open
Abstract
Sirtuin interacts with many regulatory proteins involved in energy homeostasis, DNA repair, cell survival, and lifespan extension. We investigated the functional roles of Sir2D during early Dictyostelium development upon starvation. We found that ectopic expression of Sir2D accelerated development among three Sirtuins containing highly homologous catalytic domain sequences to mouse Sirt1. Sir2D expression upregulated adenylate cyclase A (aca) mRNA expression 2, 4 and 6 h after starvation. We have previously reported that nicotinamide, a Sirt1 inhibitor, treatment delayed the development and decreased the expression of aca at 4 h after starvation. Sir2D expressing cells showed resistance against the nicotinamide effect. RNAi-mediated Sir2D knockdown cells were generated, and their development was also delayed. Aca expression was decreased 4 h after starvation. Sir2D expression restored the developmental impairment of Sir2D knockdown cells. The induction of aca upon starvation starts with transcriptional activation of MybB. The ectopic expression of MybB accelerated the development and increased the expression of aca 2 and 4 h after starvation but did not restore the phenotype of Sir2D knockdown cells. Sir2D expression had no effects on MybB-null mutant cells during early development. Thus, MybB is necessary for the upregulation of aca by Sir2D, and Sir2D is necessary for the full induction of aca after 4 h by MybB. MybB was coimmunoprecipitated with Sir2D, suggesting an interaction between MybB and Sir2D. These results suggest that Sir2D regulates aca expression through interaction with the MybB transcription factor early in Dictyostelium development upon starvation.
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Affiliation(s)
- Hideo Taniura
- Laboratory of Neurochemistry, College of Pharmacy, Ritsumeikan University, Shiga, Japan
| | - Shuhei Soeda
- Laboratory of Neurochemistry, College of Pharmacy, Ritsumeikan University, Shiga, Japan
| | - Tomoko Ohta
- Laboratory of Neurochemistry, College of Pharmacy, Ritsumeikan University, Shiga, Japan
| | - Maya Oki
- Laboratory of Neurochemistry, College of Pharmacy, Ritsumeikan University, Shiga, Japan
| | - Risako Tsuboi
- Laboratory of Neurochemistry, College of Pharmacy, Ritsumeikan University, Shiga, Japan
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Katoh-Kurasawa M, Santhanam B, Shaulsky G. The GATA transcription factor gene gtaG is required for terminal differentiation in Dictyostelium. J Cell Sci 2016; 129:1722-1733. [PMID: 26962009 DOI: 10.1242/jcs.181545] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The GATA transcription factor GtaG is conserved in Dictyostelids and essential for terminal differentiation in Dictyostelium discoideum, but its function is not well understood. Here we show that gtaG is expressed in prestalk cells at the anterior region of fingers and in the extending stalk during culmination. The gtaG- phenotype is cell-autonomous in prestalk cells and non-cell-autonomous in prespore cells. Transcriptome analyses reveal that GtaG regulates prestalk gene expression during cell differentiation before culmination and is required for progression into culmination. GtaG-dependent genes include genetic suppressors of the Dd-STATa-defective phenotype as well as Dd-STATa target-genes, including extra cellular matrix genes. We show that GtaG may be involved in the production of two culmination-signaling molecules, cyclic di-GMP and the spore differentiation factor SDF-1 and that addition of c-di-GMP rescues the gtaG- culmination and spore formation deficiencies. We propose that GtaG is a regulator of terminal differentiation that functions in concert with Dd-STATa and controls culmination through regulating c-di-GMP and SDF-1 production in prestalk cells.
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Affiliation(s)
- Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Balaji Santhanam
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA
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Li R, Wu F, Ruonala R, Sapkota D, Hu Z, Mu X. Isl1 and Pou4f2 form a complex to regulate target genes in developing retinal ganglion cells. PLoS One 2014; 9:e92105. [PMID: 24643061 PMCID: PMC3958441 DOI: 10.1371/journal.pone.0092105] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/17/2014] [Indexed: 02/01/2023] Open
Abstract
Precise regulation of gene expression during biological processes, including development, is often achieved by combinatorial action of multiple transcription factors. The mechanisms by which these factors collaborate are largely not known. We have shown previously that Isl1, a Lim-Homeodomain transcription factor, and Pou4f2, a class IV POU domain transcription factor, co-regulate a set of genes required for retinal ganglion cell (RGC) differentiation. Here we further explore how these two factors interact to precisely regulate gene expression during RGC development. By GST pulldown assays, co-immunoprecipitation, and electrophoretic mobility shift assays, we show that Isl1 and Pou4f2 form a complex in vitro and in vivo, and identify the domains within these two proteins that are responsible for this interaction. By luciferase assay, in situ hybridization, and RNA-seq, we further demonstrate that the two factors contribute quantitatively to gene expression in the developing RGCs. Although each factor alone can activate gene expression, both factors are required to achieve optimal expression levels. Finally, we discover that Isl1 and Pou4f2 can interact with other POU and Lim-Homeodomain factors respectively, indicating the interactions between these two classes of transcription factors are prevalent in development and other biological processes.
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Affiliation(s)
- Renzhong Li
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
| | - Raili Ruonala
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
| | - Darshan Sapkota
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Department of Biochemistry, University of Buffalo, Buffalo, New York, United States of America
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
| | - Zihua Hu
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Department of Biostatistics, University of Buffalo, Buffalo, New York, United States of America
- Department of Medicine, University of Buffalo, Buffalo, New York, United States of America
- Center of Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- Department of Biochemistry, University of Buffalo, Buffalo, New York, United States of America
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University of Buffalo, Buffalo, New York, United States of America
- SUNY Eye Institute, University of Buffalo, Buffalo, New York, United States of America
- CCSG Cancer Genetics Program, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- * E-mail:
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Miranda ER, Zhuchenko O, Toplak M, Santhanam B, Zupan B, Kuspa A, Shaulsky G. ABC transporters in Dictyostelium discoideum development. PLoS One 2013; 8:e70040. [PMID: 23967067 PMCID: PMC3743828 DOI: 10.1371/journal.pone.0070040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/13/2013] [Indexed: 12/15/2022] Open
Abstract
ATP-binding cassette (ABC) transporters can translocate a broad spectrum of molecules across the cell membrane including physiological cargo and toxins. ABC transporters are known for the role they play in resistance towards anticancer agents in chemotherapy of cancer patients. There are 68 ABC transporters annotated in the genome of the social amoeba Dictyostelium discoideum. We have characterized more than half of these ABC transporters through a systematic study of mutations in their genes. We have analyzed morphological and transcriptional phenotypes for these mutants during growth and development and found that most of the mutants exhibited rather subtle phenotypes. A few of the genes may share physiological functions, as reflected in their transcriptional phenotypes. Since most of the abc-transporter mutants showed subtle morphological phenotypes, we utilized these transcriptional phenotypes to identify genes that are important for development by looking for transcripts whose abundance was unperturbed in most of the mutants. We found a set of 668 genes that includes many validated D. discoideum developmental genes. We have also found that abcG6 and abcG18 may have potential roles in intercellular signaling during terminal differentiation of spores and stalks.
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Affiliation(s)
- Edward Roshan Miranda
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Olga Zhuchenko
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Marko Toplak
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Balaji Santhanam
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Blaz Zupan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Adam Kuspa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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Garciandia A, Suarez T. The NMRA/NMRAL1 homologue PadA modulates the expression of extracellular cAMP relay genes during aggregation in Dictyostelium discoideum. Dev Biol 2013; 381:411-22. [PMID: 23773804 DOI: 10.1016/j.ydbio.2013.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/04/2013] [Accepted: 06/07/2013] [Indexed: 02/08/2023]
Abstract
NMRA-like proteins belong to a class of conserved transcriptional regulators that function as direct sensors of the metabolic state of the cell and link basic metabolism to changes in gene expression. PadA was the first NMRA-like protein described in Dictyostelium discoideum and was shown to be necessary for prestalk cell differentiation and correct development. We describe and characterize padA(-) mutant phenotype during the onset of development, which results in the formation of abnormally small territories and impairment of cAMP responses. Transcriptional analysis shows that cAMP-induced gene expression is downregulated in padA(-), particularly the genes that establish the extracellular cAMP relay. The mutant phenotype can be rescued with the constitutive expression of one of these genes, carA, encoding the cAMP receptor. Transcriptional analysis of padA(-)/A15::carA showed that carA maximum mRNA levels were not reached during aggregation. Our data support a regulatory role for PadA on the regulation of extracellular cAMP relay genes during aggregation and suggest that PadA is required to achieve carA full induction.
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Affiliation(s)
- Ane Garciandia
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
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Parikh A, Huang E, Dinh C, Zupan B, Kuspa A, Subramanian D, Shaulsky G. New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data. BMC Bioinformatics 2010; 11:163. [PMID: 20356373 PMCID: PMC2873529 DOI: 10.1186/1471-2105-11-163] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 03/31/2010] [Indexed: 11/30/2022] Open
Abstract
Background Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant information about genetic networks, but mining the data is not a trivial task. Algorithms that infer Bayesian networks from expression data are powerful tools for learning complex genetic networks, since they can incorporate prior knowledge and uncover higher-order dependencies among genes. However, these algorithms are computationally demanding, so novel techniques that allow targeted exploration for discovering new members of known pathways are essential. Results Here we describe a Bayesian network approach that addresses a specific network within a large dataset to discover new components. Our algorithm draws individual genes from a large gene-expression repository, and ranks them as potential members of a known pathway. We apply this method to discover new components of the cAMP-dependent protein kinase (PKA) pathway, a central regulator of Dictyostelium discoideum development. The PKA network is well studied in D. discoideum but the transcriptional networks that regulate PKA activity and the transcriptional outcomes of PKA function are largely unknown. Most of the genes highly ranked by our method encode either known components of the PKA pathway or are good candidates. We tested 5 uncharacterized highly ranked genes by creating mutant strains and identified a candidate cAMP-response element-binding protein, yet undiscovered in D. discoideum, and a histidine kinase, a candidate upstream regulator of PKA activity. Conclusions The single-gene expansion method is useful in identifying new components of known pathways. The method takes advantage of the Bayesian framework to incorporate prior biological knowledge and discovers higher-order dependencies among genes while greatly reducing the computational resources required to process high-throughput datasets.
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Affiliation(s)
- Anup Parikh
- Graduate Program in Structural Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Brzostowski JA, Parent CA, Kimmel AR. A G alpha-dependent pathway that antagonizes multiple chemoattractant responses that regulate directional cell movement. Genes Dev 2004; 18:805-15. [PMID: 15059962 PMCID: PMC387420 DOI: 10.1101/gad.1173404] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Chemotactic cells, including neutrophils and Dictyostelium discoideum, orient and move directionally in very shallow chemical gradients. As cells polarize, distinct structural and signaling components become spatially constrained to the leading edge or rear of the cell. It has been suggested that complex feedback loops that function downstream of receptor signaling integrate activating and inhibiting pathways to establish cell polarity within such gradients. Much effort has focused on defining activating pathways, whereas inhibitory networks have remained largely unexplored. We have identified a novel signaling function in Dictyostelium involving a Galpha subunit (Galpha9) that antagonizes broad chemotactic response. Mechanistically, Galpha9 functions rapidly following receptor stimulation to negatively regulate PI3K/PTEN, adenylyl cyclase, and guanylyl cyclase pathways. The coordinated activation of these pathways is required to establish the asymmetric mobilization of actin and myosin that typifies polarity and ultimately directs chemotaxis. Most dramatically, cells lacking Galpha9 have extended PI(3,4,5)P(3), cAMP, and cGMP responses and are hyperpolarized. In contrast, cells expressing constitutively activated Galpha9 exhibit a reciprocal phenotype. Their second message pathways are attenuated, and they have lost the ability to suppress lateral pseudopod formation. Potentially, functionally similar Galpha-mediated inhibitory signaling may exist in other eukaryotic cells to regulate chemoattractant response.
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Affiliation(s)
- Joseph A Brzostowski
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive Kidney Diseases, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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