Meeting at the DNA: Specifying Cytokinin Responses Through Transcription Factor Complex Formation
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Design Principles for Regulator Gene Expression in a Repressible Gene
Design of Repressible Gene Circuits: M.E. Wall et al. 1 Design Principles for Regulator Gene Expression in a Repressible Gene Circuit Michael E. Wall1,2, William S. Hlavacek3* and Michael A. Savageau4+ 1Computer and Computational Sciences Division and 2Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA 3Theoretical Biology and Biophysics Group (T-10), Theoretical Division, Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA 4Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI 48109-0620, USA +Current address: Department of Biomedical Engineering, One Shields Avenue, University of California, Davis, CA 95616, USA. *Corresponding author Tel.: +1-505 665 1355 Fax: +1-505 665 3493 E-mail address of the corresponding author: [email protected] Design of Repressible Gene Circuits: M.E. Wall et al. 2 Summary We consider the design of a type of repressible gene circuit that is common in bacteria. In this type of circuit, a regulator protein acts to coordinately repress the expression of effector genes when a signal molecule with which it interacts is present. The regulator protein can also independently influence the expression of its own gene, such that regulator gene expression is repressible (like effector genes), constitutive, or inducible. Thus, a signal-directed change in the activity of the regulator protein can result in one of three patterns of coupled regulator and effector gene expression: direct coupling, in which regulator and effector gene expression change in the same direction; uncoupling, in which regulator gene expression remains constant while effector gene expression changes; or inverse coupling, in which regulator and effector gene expression change in opposite directions. -
Auxins and Cytokinins in Plant Development 2018
International Journal of Molecular Sciences Meeting Report Auxins and Cytokinins in Plant Development 2018 Jan Petrasek 1, Klara Hoyerova 1, Vaclav Motyka 1 , Jan Hejatko 2 , Petre Dobrev 1, Miroslav Kaminek 1 and Radomira Vankova 1,* 1 Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojova 263, 16502 Prague 6, Czech Republic; [email protected] (J.P.); [email protected] (K.H.); [email protected] (V.M.); [email protected] (P.D.); [email protected] (M.K.) 2 CEITEC–Central European Institute of Technology and Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] * Correspondence: [email protected]; Tel.: +420-225-106-427 Received: 15 February 2019; Accepted: 18 February 2019; Published: 20 February 2019 Abstract: The international symposium “Auxins and Cytokinins in Plant Development” (ACPD), which is held every 4–5 years in Prague, Czech Republic, is a meeting of scientists interested in the elucidation of the action of two important plant hormones—auxins and cytokinins. It is organized by a group of researchers from the Laboratory of Hormonal Regulations in Plants at the Institute of Experimental Botany, the Czech Academy of Sciences. The symposia already have a long tradition, having started in 1972. Thanks to the central role of auxins and cytokinins in plant development, the ACPD 2018 symposium was again attended by numerous experts who presented their results in the opening, two plenary lectures, and six regular sessions, including two poster sessions. Due to the open character of the research community, which is traditionally very well displayed during the meeting, a lot of unpublished data were presented and discussed. -
The Janus-Like Role of Proline Metabolism in Cancer Lynsey Burke1,Innaguterman1, Raquel Palacios Gallego1, Robert G
Burke et al. Cell Death Discovery (2020) 6:104 https://doi.org/10.1038/s41420-020-00341-8 Cell Death Discovery REVIEW ARTICLE Open Access The Janus-like role of proline metabolism in cancer Lynsey Burke1,InnaGuterman1, Raquel Palacios Gallego1, Robert G. Britton1, Daniel Burschowsky2, Cristina Tufarelli1 and Alessandro Rufini1 Abstract The metabolism of the non-essential amino acid L-proline is emerging as a key pathway in the metabolic rewiring that sustains cancer cells proliferation, survival and metastatic spread. Pyrroline-5-carboxylate reductase (PYCR) and proline dehydrogenase (PRODH) enzymes, which catalyze the last step in proline biosynthesis and the first step of its catabolism, respectively, have been extensively associated with the progression of several malignancies, and have been exposed as potential targets for anticancer drug development. As investigations into the links between proline metabolism and cancer accumulate, the complexity, and sometimes contradictory nature of this interaction emerge. It is clear that the role of proline metabolism enzymes in cancer depends on tumor type, with different cancers and cancer-related phenotypes displaying different dependencies on these enzymes. Unexpectedly, the outcome of rewiring proline metabolism also differs between conditions of nutrient and oxygen limitation. Here, we provide a comprehensive review of proline metabolism in cancer; we collate the experimental evidence that links proline metabolism with the different aspects of cancer progression and critically discuss the potential mechanisms involved. ● How is the rewiring of proline metabolism regulated Facts depending on cancer type and cancer subtype? 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; ● Is it possible to develop successful pharmacological ● Proline metabolism is widely rewired during cancer inhibitor of proline metabolism enzymes for development. -
Controlled Transcription of Regulator Gene Cars by Tet-On Or by a Strong Promoter Confirms Its Role As a Repressor of Carotenoid Biosynthesis in Fusarium Fujikuroi
microorganisms Article Controlled Transcription of Regulator Gene carS by Tet-on or by a Strong Promoter Confirms Its Role as a Repressor of Carotenoid Biosynthesis in Fusarium fujikuroi Julia Marente , Javier Avalos and M. Carmen Limón * Department of Genetics, Faculty of Biology, University of Seville, 41012 Seville, Spain; [email protected] (J.M.); [email protected] (J.A.) * Correspondence: [email protected]; Tel.: +34-954-555-947 Abstract: Carotenoid biosynthesis is a frequent trait in fungi. In the ascomycete Fusarium fujikuroi, the synthesis of the carboxylic xanthophyll neurosporaxanthin (NX) is stimulated by light. However, the mutants of the carS gene, encoding a protein of the RING finger family, accumulate large NX amounts regardless of illumination, indicating the role of CarS as a negative regulator. To confirm CarS function, we used the Tet-on system to control carS expression in this fungus. The system was first set up with a reporter mluc gene, which showed a positive correlation between the inducer doxycycline and luminescence. Once the system was improved, the carS gene was expressed using Tet-on in the wild strain and in a carS mutant. In both cases, increased carS transcription provoked a downregulation of the structural genes of the pathway and albino phenotypes even under light. Similarly, when the carS gene was constitutively overexpressed under the control of a gpdA promoter, total downregulation of the NX pathway was observed. The results confirmed the role of CarS as a repressor of carotenogenesis in F. fujikuroi and revealed that its expression must be regulated in the wild strain to allow appropriate NX biosynthesis in response to illumination. -
Transcriptional Regulation of Cancer Immune Checkpoints: Emerging Strategies for Immunotherapy
Review Transcriptional Regulation of Cancer Immune Checkpoints: Emerging Strategies for Immunotherapy Simran Venkatraman 1 , Jarek Meller 2,3, Suradej Hongeng 4, Rutaiwan Tohtong 1,5,* and Somchai Chutipongtanate 6,7,* 1 Graduate Program in Molecular Medicine, Faculty of Science Joint Program Faculty of Medicine Ramathibodi Hospital, Faculty of Medicine Siriraj Hospital, Faculty of Dentistry, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; [email protected] 2 Departments of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; [email protected] 3 Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45267, USA 4 Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; [email protected] 5 Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand 6 Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand 7 Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand * Correspondence: [email protected] (R.T.); [email protected] (S.C.) Received: 30 October 2020; Accepted: 2 December 2020; Published: 4 December 2020 Abstract: The study of immune evasion has gained a well-deserved eminence in cancer research by successfully developing a new class of therapeutics, immune checkpoint inhibitors, such as pembrolizumab and nivolumab, anti-PD-1 antibodies. By aiming at the immune checkpoint blockade (ICB), these new therapeutics have advanced cancer treatment with notable increases in overall survival and tumor remission. -
Genome-Wide Identification, Classification, and Analysis of Two-Component Signal System Genes in Maize
Genome-wide identification, classification, and analysis of two-component signal system genes in maize Z.X. Chu*, Q. Ma*, Y.X. Lin, X.L. Tang, Y.Q. Zhou, S.W. Zhu, J. Fan and B.J. Cheng Anhui Province Key Laboratory of Crop Biology, School of Life Science, Anhui Agricultural University, Hefei, China *These authors contributed equally to this study. Corresponding authors: B.J. Cheng / J. Fan E-mail: [email protected] / [email protected] Genet. Mol. Res. 10 (4): 3316-3330 (2011) Received March 23, 2011 Accepted August 31, 2011 Published December 8, 2011 DOI http://dx.doi.org/10.4238/2011.December.8.3 ABSTRACT. Cytokinins play many vital roles in plant development and physiology. In plants, cytokinin signals are sensed and transduced by the two-component signal system. This signaling cascade is typically com- posed of three proteins: a sensory histidine kinase, a histidine phosphotrans- fer protein, and a response regulator. Through a comprehensive genome- wide analysis of the maize (Zea mays) genome, 48 genes were identified, including 11 ZmHKs, 9 ZmHPs, and 28 ZmRRs (21 A-type ZmRRs and 7 B-type ZmRRs). Using maize genome sequence databases, we analyzed conserved protein motifs and established phylogenetic relationships based on gene structure, homology, and chromosomal location. The duplication of these two-component system genes in the maize genome corresponded to the clusters of these genes in the phylogenetic trees. Sequence analysis of the duplicate genes demonstrated that one gene may be in gene duplica- tion, and that there was significant variation in the evolutionary history of the different gene families. -
Regulatory Region of the Heat Shock-Inducible Capr (Lon) Gene: DNA and Protein Sequences
JOURNAL OF BACTERIOLOGY, Apr. 1985, p. 271-275 Vol. 162, No. 1 0021-9193/85/040271-05$02.00/0 Copyright© 1985, American Society for Microbiology Regulatory Region of the Heat Shock-Inducible capR (Lon) Gene: DNA and Protein Sequences RANDALL C. GAYDA,1t PAUL E. STEPHENS,2 RODNEY HEWICK,3; JOYCE M. SCHOEMAKER,2§ WILLIAM J. DREYER,3 AND ALVIN MARKOVITzt. Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 606371,- Department of Molecular Genetics, Celltech Ltd., Slough SLJ 4DY, Englan~; and Division of Biology, California Institute of Technology, Pasadena, California 911093 Received 22 August 1984/Accepted 4 January 1985 The CapR protein is an ATP hydrolysis-dependent protease as well as a DNA-stimulated ATPase and a nucleic acid-binding PI.'Otein. The sequences of the 5' end of the capR (ion) gene DNA and N-terminal end of the CapR protein were determined. The sequence of DNA that specifies the N-terminal portion of the CapR protein was identified by comparing the amino acid sequence of the CapR protein with the sequence predicted from the DNA. The DNA and protein sequences established that the mature protein is not processed from a precursor form. No sequence corresponding to an SOS box was found in the 5' sequence of DNA. There were sequences that corresponded to a putative -35 and -10 region for RNA polymerase binding. The capR (ion) gene was recently identified as one Qf 17 heat shock genes in Escherichia coli that are positively regulated by the product of the htpR gene. A comparison of the 5' DNA region of the capR gene with that of several other heat shock genes revealed possible consensus sequences. -
Endogenous Levels of Cytokinins, Indole-3-Acetic Acid And
www.nature.com/scientificreports OPEN Endogenous levels of cytokinins, indole-3-acetic acid and abscisic acid in in vitro grown potato: A contribution to potato hormonomics Martin Raspor 1,6*, Václav Motyka 2,6, Slavica Ninković 1, Petre I. Dobrev 2, Jiří Malbeck 3, Tatjana Ćosić 1, Aleksandar Cingel 1, Jelena Savić 1, Vojin Tadić 4 & Ivana Č. Dragićević 5 A number of scientifc reports published to date contain data on endogenous levels of various phytohormones in potato (Solanum tuberosum L.) but a complete cytokinin profle of potato tissues, that would include data on all particular molecular forms of cytokinin, has still been missing. In this work, endogenous levels of all analytically detectable isoprenoid cytokinins, as well as the auxin indole- 3-acetic acid (IAA), and abscisic acid (ABA) have been determined in shoots and roots of 30 day old in vitro grown potato (cv. Désirée). The results presented here are generally similar to other data reported for in vitro grown potato plants, whereas greenhouse-grown plants typically contain lower levels of ABA, possibly indicating that in vitro grown potato is exposed to chronic stress. Cytokinin N-glucosides, particularly N7-glucosides, are the dominant cytokinin forms in both shoots and roots of potato, whereas nucleobases, as the bioactive forms of cytokinins, comprise a low proportion of cytokinin levels in tissues of potato. Diferences in phytohormone composition between shoots and roots of potato suggest specifc patterns of transport and/or diferences in tissue-specifc metabolism of plant hormones. These results represent a contribution to understanding the hormonomics of potato, a crop species of extraordinary economic importance. -
Auxins Cytokinins and Gibberellins TD-I Date: 3/4/2019 Cell Enlargement in Young Leaves, Tissue Differentiation, Flowering, Fruiting, and Delay of Aging in Leaves
Informational TD-I Revision 2.0 Creation Date: 7/3/2014 Revision Date: 3/4/2019 Auxins, Cytokinins and Gibberellins Isolation of the first Cytokinin Growing cells in a tissue culture medium composed in part of coconut milk led to the realization that some substance in coconut milk promotes cell division. The “milk’ of the coconut is actually a liquid endosperm containing large numbers of nuclei. It was from kernels of corn, however, that the substance was first isolated in 1964, twenty years after its presence in coconut milk was known. The substance obtained from corn is called zeatin, and it is one of many cytokinins. What is a Growth Regulator? Plant Cell Growth regulators (e.g. Auxins, Cytokinins and Gibberellins) - Plant hormones play an important role in growth and differentiation of cultured cells and tissues. There are many classes of plant growth regulators used in culture media involves namely: Auxins, Cytokinins, Gibberellins, Abscisic acid, Ethylene, 6 BAP (6 Benzyladenine), IAA (Indole Acetic Acid), IBA (Indole-3-Butyric Acid), Zeatin and trans Zeatin Riboside. The Auxins facilitate cell division and root differentiation. Auxins induce cell division, cell elongation, and formation of callus in cultures. For example, 2,4-dichlorophenoxy acetic acid is one of the most commonly added auxins in plant cell cultures. The Cytokinins induce cell division and differentiation. Cytokinins promote RNA synthesis and stimulate protein and enzyme activities in tissues. Kinetin and benzyl-aminopurine are the most frequently used cytokinins in plant cell cultures. The Gibberellins is mainly used to induce plantlet formation from adventive embryos formed in culture. -
Structure and Function of the Archaeal Response Regulator Chey
Structure and function of the archaeal response PNAS PLUS regulator CheY Tessa E. F. Quaxa, Florian Altegoerb, Fernando Rossia, Zhengqun Lia, Marta Rodriguez-Francoc, Florian Krausd, Gert Bangeb,1, and Sonja-Verena Albersa,1 aMolecular Biology of Archaea, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; bLandes-Offensive zur Entwicklung Wissenschaftlich- ökonomischer Exzellenz Center for Synthetic Microbiology & Faculty of Chemistry, Philipps-University-Marburg, 35043 Marburg, Germany; cCell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; and dFaculty of Chemistry, Philipps-University-Marburg, 35043 Marburg, Germany Edited by Norman R. Pace, University of Colorado at Boulder, Boulder, CO, and approved December 13, 2017 (received for review October 2, 2017) Motility is a central feature of many microorganisms and provides display different swimming mechanisms. Counterclockwise ro- an efficient strategy to respond to environmental changes. Bacteria tation results in smooth swimming in well-characterized peritri- and archaea have developed fundamentally different rotary motors chously flagellated bacteria such as Escherichia coli, whereas enabling their motility, termed flagellum and archaellum, respec- rotation in the opposite direction results in tumbling. In contrast, tively. Bacterial motility along chemical gradients, called chemo- in other bacteria (i.e., Vibrio alginolyticus) and haloarchaea, taxis, critically relies on the response regulator CheY, which, when clockwise rotation results -
A Genetic Framework for Regulation and Seasonal Adaptation of Shoot Architecture in Hybrid Aspen
A genetic framework for regulation and seasonal adaptation of shoot architecture in hybrid aspen Jay P. Mauryaa,b, Pal C. Miskolczia, Sanatkumar Mishraa, Rajesh Kumar Singha, and Rishikesh P. Bhaleraoa,1 aUmeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 87 Umeå, Sweden; and bDepartment of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India Edited by Ronald R. Sederoff, North Carolina State University, Raleigh, NC, and approved April 14, 2020 (received for review March 14, 2020) Shoot architecture is critical for optimizing plant adaptation and time–related transcription factor RAV1 has been validated in productivity. In contrast with annuals, branching in perennials branching in trees (17–19). However, information on branching native to temperate and boreal regions must be coordinated with control in perennials is fragmented, and there is a significant gap seasonal growth cycles. How branching is coordinated with in our knowledge of how branching is controlled and integrated seasonal growth is poorly understood. We identified key compo- with seasonal growth cycles in perennial trees (20). Therefore, nents of the genetic network that controls branching and its using functional genetic approaches, we elucidated the genetic regulation by seasonal cues in the model tree hybrid aspen. network that mediates control of branching and its regulation by Our results demonstrate that branching and its control by sea- seasonal cues in the model tree hybrid aspen. These studies re- sonal cues is mediated by mutually antagonistic action of aspen veal the key role played by the mutually antagonistic action of orthologs of the flowering regulators TERMINAL FLOWER 1 LAP1 and TFL1 in mediating control of branching and its re- (TFL1)andAPETALA1 (LIKE APETALA 1/LAP1). -
Adenovirus-Mediated Gene Transfer of P16INK4/CDKN2 Into Bax-Negative
Cancer Gene Therapy (2002) 9, 641 – 650 D 2002 Nature Publishing Group All rights reserved 0929-1903/02 $25.00 www.nature.com/cgt Adenovirus-mediated gene transfer of P16INK4/CDKN2 into bax-negative colon cancer cells induces apoptosis and tumor regression in vivo Ingo Tamm,1,2 Axel Schumacher,3 Leonid Karawajew,2 Velia Ruppert,2 Wolfgang Arnold,4 Andreas K Nu¨ssler,5 Peter Neuhaus,5 Bernd Do¨rken,1,2 and Gerhard Wolff 2,4 1Department of Hematology and Oncology, Charite´, Campus Virchow, Humboldt University of Berlin, Berlin, Germany; 2Department of Hematology, Oncology and Tumor Immunology, Robert-Ro¨ssle-Klinik, University Medical Center Charite´, Humboldt University of Berlin, Berlin, Germany; 3Department of Cell Biology, Institute of Biology, Humboldt University of Berlin, Berlin, Germany; 4Max Delbru¨ck Center for Molecular Medicine, Berlin, Germany; and 5Department of General, Visceral, and Transplantation Surgery, Charite´, Campus Virchow, Humboldt University of Berlin, Berlin, Germany. The tumor-suppressor gene p16INK4/CDKN2 (p16) is a cyclin-dependent kinase (cdk) inhibitor and important cell cycle regulator. Here, we show that adenovirus-mediated gene transfer of p16 (AdCMV.p16) into colon cancer cells induces uncoupling of S phase and mitosis and subsequently apoptosis. Flow cytometric analysis revealed that cells infected with AdCMV.p16 showed an initial G2-like arrest followed by S phase without intervening mitosis (DNA >4N). Using microscopic analysis, deformed polyploid cells were detectable only in cells infected with AdCMV.p16 but not in control-infected cells. Subsequently, AdCMV.p16-infected polyploid cells underwent apoptosis, as assessed by AnnexinV staining and DNA fragmentation, suggesting that cell cycle dysregulation is upstream of the onset of apoptosis.