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Wang S, Fang R, Wang H, Li X, Xing J, Li Z, Song N. The role of transcriptional regulators in metal ion homeostasis of Mycobacterium tuberculosis. Front Cell Infect Microbiol 2024; 14:1360880. [PMID: 38529472 PMCID: PMC10961391 DOI: 10.3389/fcimb.2024.1360880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
Metal ions are essential trace elements for all living organisms and play critical catalytic, structural, and allosteric roles in many enzymes and transcription factors. Mycobacterium tuberculosis (MTB), as an intracellular pathogen, is usually found in host macrophages, where the bacterium can survive and replicate. One of the reasons why Tuberculosis (TB) is so difficult to eradicate is the continuous adaptation of its pathogen. It is capable of adapting to a wide range of harsh environmental stresses, including metal ion toxicity in the host macrophages. Altering the concentration of metal ions is the common host strategy to limit MTB replication and persistence. This review mainly focuses on transcriptional regulatory proteins in MTB that are involved in the regulation of metal ions such as iron, copper and zinc. The aim is to offer novel insights and strategies for screening targets for TB treatment, as well as for the development and design of new therapeutic interventions.
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Affiliation(s)
- Shuxian Wang
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Ren Fang
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Hui Wang
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Xiaotian Li
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Jiayin Xing
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Zhaoli Li
- Drug Innovation Research Center, SAFE Pharmaceutical Technology Co. Ltd., Beijing, China
| | - Ningning Song
- Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
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2
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Shen J, Ying L, Wu J, Fang Y, Zhou W, Qi C, Gu L, Mou S, Yan Y, Tian M, Ni Z, Che X. Integrative ATAC-seq and RNA-seq analysis associated with diabetic nephropathy and identification of novel targets for treatment by dapagliflozin. Cell Biochem Funct 2024; 42:e3943. [PMID: 38379015 DOI: 10.1002/cbf.3943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 12/01/2023] [Accepted: 01/12/2024] [Indexed: 02/22/2024]
Abstract
Dapagliflozin (DAPA) are clinically effective in improving diabetic nephropathy (DN). However, whether and how chromatin accessibility changed by DN responds to DAPA treatment is unclear. Therefore, we performed ATAC-seq, RNA-seq, and weighted gene correlation network analysis to identify the chromatin accessibility, the messenger RNA (mRNA) expression, and the correlation between clinical phenotypes and mRNA expression using kidney from three mouse groups: db/m mice (Controls), db/db mice (case group), and those treated with DAPA (treatment group). RNA-Seq and ATAC-seq conjoint analysis revealed many overlapping pathways and networks suggesting that the transcriptional changes of DN and DAPA intervention largely occured dependently on chromatin remodeling. Specifically, the results showed that some key signal transduction pathways, such as immune dysfunction, glucolipid metabolism, oxidative stress and xenobiotic and endobiotic metabolism, were repeatedly enriched in the analysis of the RNA-seq data alone, as well as combined analysis with ATAC-seq data. Furthermore, we identified some candidate genes (UDP glucuronosyltransferase 1 family, Dock2, Tbc1d10c, etc.) and transcriptional regulators (KLF6 and GFI1) that might be associated with DN and DAPA restoration. These reversed genes and regulators confirmed that pathways related to immune response and metabolism pathways were critically involved in DN progression.
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Affiliation(s)
- Jianxiao Shen
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Ying
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiajia Wu
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Fang
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenyan Zhou
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaojun Qi
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leyi Gu
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shan Mou
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuru Yan
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Tian
- Department of Burn, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaohui Ni
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiajing Che
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Bagchi S, Sharma AK, Ghosh A, Saha S, Basu J, Kundu M. RegX3-dependent transcriptional activation of kdpDE and repression of rv0500A are linked to potassium homeostasis in Mycobacterium tuberculosis. FEBS J 2024. [PMID: 38414198 DOI: 10.1111/febs.17100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/18/2024] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
Ionic homeostasis is essential for the survival and replication of Mycobacterium tuberculosis within its host. Low potassium ion concentrations trigger a transition of M. tuberculosis into dormancy. Our current knowledge of the transcriptional regulation mechanisms governing genes involved in potassium homeostasis remains limited. Potassium transport is regulated by the constitutive Trk system and the inducible Kdp system in M. tuberculosis. The two-component system KdpDE (also known as KdpD/KdpE) activates expression of the kdpFABC operon, encoding the four protein subunits of the Kdp potassium uptake system (KdpFABC). We show that, under potassium deficiency, expression of the two-component system senX3/regX3 is upregulated, and bacterial survival is compromised in a regX3-inactivated mutant, ΔregX3. Electrophoretic mobility shift assays (EMSAs), promoter reporter assays and chromatin immunoprecipitation (ChIP) show that RegX3 binds to the kdpDE promoter and activates it under potassium deficiency, whereas RegX3 (K204A), a DNA binding-deficient mutant, fails to bind to the promoter. Mutation of the RegX3 binding motifs on the kdpDE promoter abrogates RegX3 binding. In addition, EMSAs and ChIP assays show that RegX3 represses Rv0500A, a repressor of kdpFABC, by binding to consensus RegX3 binding motifs on the rv0500A promoter. Our findings provide important insight into two converging pathways regulated by RegX3; one in which it activates an activator of kdpFABC, and the other in which it represses a repressor of kdpFABC, during potassium insufficiency. This culminates in increased expression of the potassium uptake system encoded by kdpFABC, enabling bacterial survival. These results further expand the growing transcriptional network in which RegX3 serves as a central node to enable bacterial survival under stress.
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Affiliation(s)
- Shreya Bagchi
- Department of Chemical Sciences, Bose Institute, Kolkata, India
| | | | - Abhirupa Ghosh
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Sudipto Saha
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Joyoti Basu
- Department of Chemical Sciences, Bose Institute, Kolkata, India
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4
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Saikia M, Cheung N, Singh AK, Kapoor V. Role of Midkine in Cancer Drug Resistance: Regulators of Its Expression and Its Molecular Targeting. Int J Mol Sci 2023; 24:ijms24108739. [PMID: 37240085 DOI: 10.3390/ijms24108739] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/06/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Molecules involved in drug resistance can be targeted for better therapeutic efficacies. Research on midkine (MDK) has escalated in the last few decades, which affirms a positive correlation between disease progression and MDK expression in most cancers and indicates its association with multi-drug resistance in cancer. MDK, a secretory cytokine found in blood, can be exploited as a potent biomarker for the non-invasive detection of drug resistance expressed in various cancers and, thereby, can be targeted. We summarize the current information on the involvement of MDK in drug resistance, and transcriptional regulators of its expression and highlight its potential as a cancer therapeutic target.
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Affiliation(s)
- Minakshi Saikia
- Department of Radiation Oncology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Nathan Cheung
- Department of Radiation Oncology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Abhay Kumar Singh
- Department of Radiation Oncology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Vaishali Kapoor
- Department of Radiation Oncology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
- Siteman Cancer Center, St. Louis, MO 63108, USA
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White LJ, Russell AJ, Pizzey AR, Dasmahapatra KK, Pownall ME. The Presence of Two MyoD Genes in a Subset of Acanthopterygii Fish Is Associated with a Polyserine Insert in MyoD1. J Dev Biol 2023; 11:jdb11020019. [PMID: 37218813 DOI: 10.3390/jdb11020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023] Open
Abstract
The MyoD gene was duplicated during the teleost whole genome duplication and, while a second MyoD gene (MyoD2) was subsequently lost from the genomes of some lineages (including zebrafish), many fish lineages (including Alcolapia species) have retained both MyoD paralogues. Here we reveal the expression patterns of the two MyoD genes in Oreochromis (Alcolapia) alcalica using in situ hybridisation. We report our analysis of MyoD1 and MyoD2 protein sequences from 54 teleost species, and show that O. alcalica, along with some other teleosts, include a polyserine repeat between the amino terminal transactivation domains (TAD) and the cysteine-histidine rich region (H/C) in MyoD1. The evolutionary history of MyoD1 and MyoD2 is compared to the presence of this polyserine region using phylogenetics, and its functional relevance is tested using overexpression in a heterologous system to investigate subcellular localisation, stability, and activity of MyoD proteins that include and do not include the polyserine region.
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Affiliation(s)
- Lewis J White
- Biology Department, University of York, York YO10 5DD, UK
| | | | | | | | - Mary E Pownall
- Biology Department, University of York, York YO10 5DD, UK
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6
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Di Marzo M, Babolin N, Viana VE, de Oliveira AC, Gugi B, Caporali E, Herrera-Ubaldo H, Martínez-Estrada E, Driouich A, de Folter S, Colombo L, Ezquer I. The Genetic Control of SEEDSTICK and LEUNIG-HOMOLOG in Seed and Fruit Development: New Insights into Cell Wall Control. Plants (Basel) 2022; 11:3146. [PMID: 36432874 PMCID: PMC9698089 DOI: 10.3390/plants11223146] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Although much is known about seed and fruit development at the molecular level, many gaps remain in our understanding of how cell wall modifications can impact developmental processes in plants, as well as how biomechanical alterations influence seed and fruit growth. Mutants of Arabidopsis thaliana constitute an excellent tool to study the function of gene families devoted to cell wall biogenesis. We have characterized a collection of lines carrying mutations in representative cell wall-related genes for seed and fruit size developmental defects, as well as altered germination rates. We have linked these studies to cell wall composition and structure. Interestingly, we have found that disruption of genes involved in pectin maturation and hemicellulose deposition strongly influence germination dynamics. Finally, we focused on two transcriptional regulators, SEEDSTICK (STK) and LEUNIG-HOMOLOG (LUH), which positively regulate seed growth. Herein, we demonstrate that these factors regulate specific aspects of cell wall properties such as pectin distribution. We propose a model wherein changes in seed coat structure due to alterations in the xyloglucan-cellulose matrix deposition and pectin maturation are critical for organ growth and germination. The results demonstrate the importance of cell wall properties and remodeling of polysaccharides as major factors responsible for seed development.
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Affiliation(s)
- Maurizio Di Marzo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Nicola Babolin
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Vívian Ebeling Viana
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
- Plant Genomics and Breeding Center, Federal University of Pelotas, Capão do Leão 96010-610, RS, Brazil
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Federal University of Pelotas, Capão do Leão 96010-610, RS, Brazil
| | - Bruno Gugi
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale EA4358, UNIROUEN—Universitè de Rouen Normandie, 76000 Rouen, France
| | - Elisabetta Caporali
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato 36824, Guanajuato, Mexico
| | - Eduardo Martínez-Estrada
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato 36824, Guanajuato, Mexico
| | - Azeddine Driouich
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale EA4358, UNIROUEN—Universitè de Rouen Normandie, 76000 Rouen, France
- Fédération de Recherche “NORVEGE”-FED 4277, 76000 Rouen, France
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato 36824, Guanajuato, Mexico
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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Hojo H, Saito T, He X, Guo Q, Onodera S, Azuma T, Koebis M, Nakao K, Aiba A, Seki M, Suzuki Y, Okada H, Tanaka S, Chung UI, McMahon AP, Ohba S. Runx2 regulates chromatin accessibility to direct the osteoblast program at neonatal stages. Cell Rep 2022; 40:111315. [PMID: 36070691 PMCID: PMC9510047 DOI: 10.1016/j.celrep.2022.111315] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/31/2022] [Accepted: 08/15/2022] [Indexed: 12/12/2022] Open
Abstract
The transcriptional regulator Runx2 (runt-related transcription factor 2) has essential but distinct roles in osteoblasts and chondrocytes in skeletal development. However, Runx2-mediated regulatory mechanisms underlying the distinctive programming of osteoblasts and chondrocytes are not well understood. Here, we perform an integrative analysis to investigate Runx2-DNA binding and chromatin accessibility ex vivo using neonatal osteoblasts and chondrocytes. We find that Runx2 engages with cell-type-distinct chromatin-accessible regions, potentially interacting with different combinations of transcriptional regulators, forming cell-type-specific hotspots, and potentiating chromatin accessibility. Genetic analysis and direct cellular reprogramming studies suggest that Runx2 is essential for establishment of chromatin accessibility in osteoblasts. Functional enhancer studies identify an Sp7 distal enhancer driven by Runx2-dependent binding and osteoblast-specific chromatin accessibility, contributing to normal osteoblast differentiation. Our findings provide a framework for understanding the regulatory landscape encompassing Runx2-mediated and cell-type-distinct enhancer networks that underlie the specification of osteoblasts. Hojo et al. investigate the gene-regulatory landscape underlying specification of skeletal cell types in neonatal mice. Runx2, an osteoblast determinant, engages with cell-type-distinct chromatin-accessible regions and is essential for establishment of chromatin accessibility in osteoblasts. The study provides insights into enhancer networks in skeletal development.
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Affiliation(s)
- Hironori Hojo
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Taku Saito
- Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Xinjun He
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Shoko Onodera
- Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Toshifumi Azuma
- Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Michinori Koebis
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kazuki Nakao
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Atsu Aiba
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Hiroyuki Okada
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Sakae Tanaka
- Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ung-Il Chung
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Shinsuke Ohba
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan; Department of Oral Anatomy and Developmental Biology, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan.
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Liang Z, Rybtke M, Kragh KN, Johnson O, Schicketanz M, Zhang YE, Andersen JB, Tolker-Nielsen T. Transcription of the Alginate Operon in Pseudomonas aeruginosa Is Regulated by c-di-GMP. Microbiol Spectr 2022; 10:e0067522. [PMID: 35862969 PMCID: PMC9431422 DOI: 10.1128/spectrum.00675-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/19/2022] [Indexed: 02/03/2023] Open
Abstract
Overproduction of the exopolysaccharide alginate contributes to the pathogenicity and antibiotic tolerance of Pseudomonas aeruginosa in chronic infections. The second messenger, c-di-GMP, is a positive regulator of the production of various biofilm matrix components and is known to regulate alginate synthesis at the posttranslational level in P. aeruginosa. We provide evidence that c-di-GMP also regulates transcription of the alginate operon in P. aeruginosa. Previous work has shown that transcription of the alginate operon is regulated by nine different proteins, AmrZ, AlgP, IHFα, IHFβ, CysB, Vfr, AlgR, AlgB, and AlgQ, and we investigated if some of these proteins function as a c-di-GMP effector. We found that deletion of algP, algQ, IHFα, and IHFβ had only a marginal effect on the transcription of the alginate operon. Deletion of vfr and cysB led to decreased transcription of the alginate operon, and the dependence of the c-di-GMP level was less pronounced, indicating that Vfr and CysB could be partially required for c-di-GMP-mediated regulation of alginate operon transcription. Our experiments indicated that the AmrZ, AlgR, and AlgB proteins are absolutely required for transcription of the alginate operon. However, differential radial capillary action of ligand assay (DRaCALA) and site-directed mutagenesis indicated that c-di-GMP does not bind to any of the AmrZ, AlgR, and AlgB proteins. IMPORTANCE The proliferation of alginate-overproducing P. aeruginosa variants in the lungs of cystic fibrosis patients often leads to chronic infection. The alginate functions as a biofilm matrix that protects the bacteria against host immune defenses and antibiotic treatment. Knowledge about the regulation of alginate synthesis is important in order to identify drug targets for the development of medicine against chronic P. aeruginosa infections. We provide evidence that c-di-GMP positively regulates transcription of the alginate operon in P. aeruginosa. Moreover, we revisited the role of the known alginate regulators, AmrZ, AlgP, IHFα, IHFβ, CysB, Vfr, AlgR, AlgB, and AlgQ, and found that their effect on transcription of the alginate operon is highly varied. Deletion of algP, algQ, IHFα, or IHFβ only had a marginal effect on transcription of the alginate operon, whereas deletion of vfr or cysB led to decreased transcription and deletion of amrZ, algR, or algB abrogated transcription.
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Affiliation(s)
- Ziwei Liang
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Nørskov Kragh
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Owen Johnson
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Muriel Schicketanz
- Department of Biology, Copenhagen Biocenter, University of Copenhagen, Copenhagen, Denmark
| | - Yong Everett Zhang
- Department of Biology, Copenhagen Biocenter, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bo Andersen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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Abstract
T-lymphocytes play crucial roles for maintaining immune homeostasis by fighting against various pathogenic microorganisms and establishing self-antigen tolerance. They will go through several stages and checkpoints in the thymus from progenitors to mature T cells, from CD4-CD8- double negative (DN) cells to CD4+CD8+ double positive (DP) cells, finally become CD4+ or CD8+ single positive (SP) cells. The mature SP cells then emigrate out of the thymus and further differentiate into distinct subsets under different environment signals to perform specific functions. Each step is regulated by various transcriptional regulators downstream of T cell receptors (TCRs) that have been extensively studied both in vivo and vitro via multiple mouse models and advanced techniques, such as single cell RNA sequencing (scRNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). This review will summarize the transcriptional regulators participating in the early stage of T cell development reported in the past decade, trying to figure out cascade networks in each process and provide possible research directions in the future.
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Affiliation(s)
- Xueyang Bao
- Department of Pathogenic Biology and Immunology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Yingyu Qin
- Department of Pathogenic Biology and Immunology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Linrong Lu
- Shanghai Immune Therapy Institute, Renji Hospital, Jiao Tong University School of Medicine, Shanghai, China.,Institute of Immunology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Mingzhu Zheng
- Department of Pathogenic Biology and Immunology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
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10
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Pis Diez CM, Juncos MJ, Villarruel Dujovne M, Capdevila DA. Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization. Int J Mol Sci 2022; 23:2179. [PMID: 35216300 DOI: 10.3390/ijms23042179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
The different niches through which bacteria move during their life cycle require a fast response to the many environmental queues they encounter. The sensing of these stimuli and their correct response is driven primarily by transcriptional regulators. This kind of protein is involved in sensing a wide array of chemical species, a process that ultimately leads to the regulation of gene transcription. The allosteric-coupling mechanism of sensing and regulation is a central aspect of biological systems and has become an important field of research during the last decades. In this review, we summarize the state-of-the-art techniques applied to unravel these complex mechanisms. We introduce a roadmap that may serve for experimental design, depending on the answers we seek and the initial information we have about the system of study. We also provide information on databases containing available structural information on each family of transcriptional regulators. Finally, we discuss the recent results of research about the allosteric mechanisms of sensing and regulation involving many transcriptional regulators of interest, highlighting multipronged strategies and novel experimental techniques. The aim of the experiments discussed here was to provide a better understanding at a molecular level of how bacteria adapt to the different environmental threats they face.
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11
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Sharma V, Hardy A, Luthe T, Frunzke J. Phylogenetic Distribution of WhiB- and Lsr2-Type Regulators in Actinobacteriophage Genomes. Microbiol Spectr 2021; 9:e0072721. [PMID: 34817283 DOI: 10.1128/Spectrum.00727-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses that infect different actinobacterial host species are known as actinobacteriophages. They are composed of highly divergent and mosaic genomes due to frequent gene exchange between their bacterial hosts and related viral species. This is also reflected by the adaptive incorporation of host transcription factors (TFs) into phage regulatory networks. Previous studies discovered Lsr2-type and WhiB-type regulators encoded by actinobacteriophage genomes. However, limited information is available about their distribution, evolution, and impact on host species. In this study, we computationally screened the distribution of known bacterial and phage TFs inside 2951 complete actinobacteriophage genomes and identified 13 different TF domains. Among those, WhiB, Lsr2, MerR, and Cro/CI-like proteins were widespread and found in more than 10% of the analyzed actinobacteriophage genomes. Neighboring genomic context analysis of the whiB and lsr2 loci showed group-specific conservation of gene synteny and potential involvement of these genes in diverse regulatory functions. Both genes were significantly enriched in temperate phages, and the Lsr2-encoding genomes featured an overall lower GC content. Phylogenetic analysis of WhiB and Lsr2 proteins showed the grouping of phage sequences within bacterial clades, suggesting gene acquisition by phages from their bacterial host species or by multiple, independent acquisition events. Overall, our study reports the global distribution of actinobacteriophage regulatory proteins and sheds light on their origin and evolution. IMPORTANCE Actinobacteriophages are viruses that infect bacterial species of the diverse phylum of Actinobacteria. Phages engage in a close relationship with their bacterial host. This is also reflected by the adoption of genetic material from their host and its incorporation into phage regulatory circuits. In this study, we systematically searched the genomes of actinobacteriophages for the presence of transcription factor domains. We show that proteins belonging to the regulator families of WhiB and Lsr2 belong to the most abundant regulatory proteins encoded by actinobacteriophages. Further phylogenetic analysis shed light on their origin and evolution. Altogether, this study provides an important basis for further experimental investigation of their role in the coordination of the phage life cycle and their interaction with the host regulatory network in this important bacterial phylum.
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12
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Abstract
Chromatinopathies can be defined as a class of neurodevelopmental disorders caused by mutations affecting proteins responsible for chromatin remodeling and transcriptional regulation. The resulting dysregulation of gene expression favors the onset of a series of clinical features such as developmental delay, intellectual disability, facial dysmorphism, and behavioral disturbances. Cornelia de Lange syndrome (CdLS) is a prime example of a chromatinopathy. It is caused by mutations affecting subunits or regulators of the cohesin complex, a multisubunit protein complex involved in various molecular mechanisms such as sister chromatid cohesion, transcriptional regulation and formation of topologically associated domains. However, disease-causing variants in non-cohesin genes with overlapping functions have also been described in association with CdLS. Notably, the majority of these genes had been previously found responsible for distinct neurodevelopmental disorders that also fall within the category of chromatinopathies and are frequently considered as differential diagnosis for CdLS. In this review, we provide a systematic overview of the current literature to summarize all mutations in non-cohesin genes identified in association with CdLS phenotypes and discuss about the interconnection of proteins belonging to the chromatinopathies network.
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Affiliation(s)
- Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany
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13
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Hanley SE, Willis SD, Cooper KF. Snx4-assisted vacuolar targeting of transcription factors defines a new autophagy pathway for controlling ATG expression. Autophagy 2021; 17:3547-3565. [PMID: 33678121 PMCID: PMC8632336 DOI: 10.1080/15548627.2021.1877934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
Autophagy, in part, is controlled by the repression and activation of autophagy-related (ATG) genes. Here, we describe a new selective autophagy pathway that targets functional transcriptional regulators to control their activity. This pathway is activated in response to nitrogen starvation and recycles transcriptional activators (Msn2 and Rim15) and a repressor (Ssn2/Med13) of ATG expression. Further analysis of Ssn2/Med13 vacuolar proteolysis revealed that this pathway utilizes the core autophagic machinery. However, it is independent of known nucleophagy mechanisms, receptor proteins, and the scaffold protein Atg11. Instead, Ssn2/Med13 exits the nucleus through the nuclear pore complex (NPC) and associates with the cytoplasmic nucleoporin Gle1, a member of the RNA remodeling complex. Dbp5 and Nup159, that act in concert with Gle1, are also required for Ssn2/Med13 clearance. Ssn2/Med13 is retrieved from the nuclear periphery and degraded by Atg17-initiated phagophores anchored to the vacuole. Efficient transfer to phagophores depends on the sorting nexin heterodimer Snx4/Atg24-Atg20, which binds to Atg17, and relocates to the perinucleus following nitrogen starvation. To conclude, this pathway defines a previously undescribed autophagy mechanism that targets select transcriptional regulators for rapid vacuolar proteolysis, utilizing the RNA remodeling complex, the sorting nexin heterodimer Snx4-Atg20, Atg17, and the core autophagic machinery. It is physiologically relevant as this Snx4-assisted vacuolar targeting pathway permits cells to fine-tune the autophagic response by controlling the turnover of both positive and negative regulators of ATG transcription.Abbreviations: AIM: Atg8 interacting motif; ATG: autophagy-related; CKM: CDK8 kinase module; IDR: intrinsically disordered region; IP6: phosphoinositide inositol hexaphosphate; NPC: nuclear pore complex; PAS: phagophore assembly site; UPS: ubiquitin-proteasomal system.
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Affiliation(s)
- Sara E. Hanley
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Stephen D. Willis
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Katrina F. Cooper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
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14
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Beck C, Gren T, Ortiz-López FJ, Jørgensen TS, Carretero-Molina D, Martín Serrano J, Tormo JR, Oves-Costales D, Kontou EE, Mohite OS, Mingyar E, Stegmann E, Genilloud O, Weber T. Activation and Identification of a Griseusin Cluster in Streptomyces sp. CA-256286 by Employing Transcriptional Regulators and Multi-Omics Methods. Molecules 2021; 26:6580. [PMID: 34770989 PMCID: PMC8588249 DOI: 10.3390/molecules26216580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
Streptomyces are well-known producers of a range of different secondary metabolites, including antibiotics and other bioactive compounds. Recently, it has been demonstrated that "silent" biosynthetic gene clusters (BGCs) can be activated by heterologously expressing transcriptional regulators from other BGCs. Here, we have activated a silent BGC in Streptomyces sp. CA-256286 by overexpression of a set of SARP family transcriptional regulators. The structure of the produced compound was elucidated by NMR and found to be an N-acetyl cysteine adduct of the pyranonaphtoquinone polyketide 3'-O-α-d-forosaminyl-(+)-griseusin A. Employing a combination of multi-omics and metabolic engineering techniques, we identified the responsible BGC. These methods include genome mining, proteomics and transcriptomics analyses, in combination with CRISPR induced gene inactivations and expression of the BGC in a heterologous host strain. This work demonstrates an easy-to-implement workflow of how silent BGCs can be activated, followed by the identification and characterization of the produced compound, the responsible BGC, and hints of its biosynthetic pathway.
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Affiliation(s)
- Charlotte Beck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Daniel Carretero-Molina
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Jesús Martín Serrano
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - José R. Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Eftychia E. Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Omkar S. Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
| | - Erik Mingyar
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (E.S.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Evi Stegmann
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (E.M.); (E.S.)
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Av. Conocimiento, 34, 18016 Granada, Spain; (F.J.O.-L.); (D.C.-M.); (J.M.S.); (J.R.T.); (D.O.-C.)
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark; (C.B.); (T.G.); (T.S.J.); (E.E.K.); (O.S.M.)
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15
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Garcia AA, Koperniku A, Ferreira JCB, Mochly-Rosen D. Treatment strategies for glucose-6-phosphate dehydrogenase deficiency: past and future perspectives. Trends Pharmacol Sci 2021; 42:829-844. [PMID: 34389161 DOI: 10.1016/j.tips.2021.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/19/2021] [Accepted: 07/13/2021] [Indexed: 01/20/2023]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) maintains redox balance in a variety of cell types and is essential for erythrocyte resistance to oxidative stress. G6PD deficiency, caused by mutations in the G6PD gene, is present in ~400 million people worldwide, and can cause acute hemolytic anemia. Currently, there are no therapeutics for G6PD deficiency. We discuss the role of G6PD in hemolytic and nonhemolytic disorders, treatment strategies attempted over the years, and potential reasons for their failure. We also discuss potential pharmacological pathways, including glutathione (GSH) metabolism, compensatory NADPH production routes, transcriptional upregulation of the G6PD gene, highlighting potential drug targets. The needs and opportunities described here may motivate the development of a therapeutic for hematological and other chronic diseases associated with G6PD deficiency.
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Affiliation(s)
- Adriana A Garcia
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Ana Koperniku
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Julio C B Ferreira
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA, USA; Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA, USA.
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16
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Santoso CS, Li Z, Rottenberg JT, Liu X, Shen VX, Fuxman Bass JI. Therapeutic Targeting of Transcription Factors to Control the Cytokine Release Syndrome in COVID-19. Front Pharmacol 2021; 12:673485. [PMID: 34163359 PMCID: PMC8215608 DOI: 10.3389/fphar.2021.673485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/21/2021] [Indexed: 12/15/2022] Open
Abstract
Treatment of the cytokine release syndrome (CRS) has become an important part of rescuing hospitalized COVID-19 patients. Here, we systematically explored the transcriptional regulators of inflammatory cytokines involved in the COVID-19 CRS to identify candidate transcription factors (TFs) for therapeutic targeting using approved drugs. We integrated a resource of TF-cytokine gene interactions with single-cell RNA-seq expression data from bronchoalveolar lavage fluid cells of COVID-19 patients. We found 581 significantly correlated interactions, between 95 TFs and 16 cytokines upregulated in the COVID-19 patients, that may contribute to pathogenesis of the disease. Among these, we identified 19 TFs that are targets of FDA approved drugs. We investigated the potential therapeutic effect of 10 drugs and 25 drugs combinations on inflammatory cytokine production, which revealed two drugs that inhibited cytokine production and numerous combinations that show synergistic efficacy in downregulating cytokine production. Further studies of these candidate repurposable drugs could lead to a therapeutic regimen to treat the CRS in COVID-19 patients.
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Affiliation(s)
| | - Zhaorong Li
- Bioinformatics Program, Boston University, Boston, MA, United States
| | | | - Xing Liu
- Department of Biology, Boston University, Boston, MA, United States
| | - Vivian X. Shen
- Department of Biology, Boston University, Boston, MA, United States
| | - Juan I. Fuxman Bass
- Department of Biology, Boston University, Boston, MA, United States
- Bioinformatics Program, Boston University, Boston, MA, United States
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17
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Mancarella C, Morrione A, Scotlandi K. Novel Regulators of the IGF System in Cancer. Biomolecules 2021; 11:273. [PMID: 33673232 DOI: 10.3390/biom11020273] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
The insulin-like growth factor (IGF) system is a dynamic network of proteins, which includes cognate ligands, membrane receptors, ligand binding proteins and functional downstream effectors. It plays a critical role in regulating several important physiological processes including cell growth, metabolism and differentiation. Importantly, alterations in expression levels or activation of components of the IGF network are implicated in many pathological conditions including diabetes, obesity and cancer initiation and progression. In this review we will initially cover some general aspects of IGF action and regulation in cancer and then focus in particular on the role of transcriptional regulators and novel interacting proteins, which functionally contribute in fine tuning IGF1R signaling in several cancer models. A deeper understanding of the biological relevance of this network of IGF1R modulators might provide novel therapeutic opportunities to block this system in neoplasia.
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18
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Balakrishnan A, Belfiore L, Chu TH, Fleming T, Midha R, Biernaskie J, Schuurmans C. Insights Into the Role and Potential of Schwann Cells for Peripheral Nerve Repair From Studies of Development and Injury. Front Mol Neurosci 2021; 13:608442. [PMID: 33568974 PMCID: PMC7868393 DOI: 10.3389/fnmol.2020.608442] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 12/31/2020] [Indexed: 12/13/2022] Open
Abstract
Peripheral nerve injuries arising from trauma or disease can lead to sensory and motor deficits and neuropathic pain. Despite the purported ability of the peripheral nerve to self-repair, lifelong disability is common. New molecular and cellular insights have begun to reveal why the peripheral nerve has limited repair capacity. The peripheral nerve is primarily comprised of axons and Schwann cells, the supporting glial cells that produce myelin to facilitate the rapid conduction of electrical impulses. Schwann cells are required for successful nerve regeneration; they partially “de-differentiate” in response to injury, re-initiating the expression of developmental genes that support nerve repair. However, Schwann cell dysfunction, which occurs in chronic nerve injury, disease, and aging, limits their capacity to support endogenous repair, worsening patient outcomes. Cell replacement-based therapeutic approaches using exogenous Schwann cells could be curative, but not all Schwann cells have a “repair” phenotype, defined as the ability to promote axonal growth, maintain a proliferative phenotype, and remyelinate axons. Two cell replacement strategies are being championed for peripheral nerve repair: prospective isolation of “repair” Schwann cells for autologous cell transplants, which is hampered by supply challenges, and directed differentiation of pluripotent stem cells or lineage conversion of accessible somatic cells to induced Schwann cells, with the potential of “unlimited” supply. All approaches require a solid understanding of the molecular mechanisms guiding Schwann cell development and the repair phenotype, which we review herein. Together these studies provide essential context for current efforts to design glial cell-based therapies for peripheral nerve regeneration.
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Affiliation(s)
- Anjali Balakrishnan
- Biological Sciences Platform, Sunnybrook Research Institute (SRI), Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Lauren Belfiore
- Biological Sciences Platform, Sunnybrook Research Institute (SRI), Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Tak-Ho Chu
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Taylor Fleming
- Biological Sciences Platform, Sunnybrook Research Institute (SRI), Toronto, ON, Canada
| | - Rajiv Midha
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Carol Schuurmans
- Biological Sciences Platform, Sunnybrook Research Institute (SRI), Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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19
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Teper D, Pandey SS, Wang N. The HrpG/HrpX Regulon of Xanthomonads-An Insight to the Complexity of Regulation of Virulence Traits in Phytopathogenic Bacteria. Microorganisms 2021; 9:187. [PMID: 33467109 DOI: 10.3390/microorganisms9010187] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/05/2022] Open
Abstract
Bacteria of the genus Xanthomonas cause a wide variety of economically important diseases in most crops. The virulence of the majority of Xanthomonas spp. is dependent on secretion and translocation of effectors by the type 3 secretion system (T3SS) that is controlled by two master transcriptional regulators HrpG and HrpX. Since their discovery in the 1990s, the two regulators were the focal point of many studies aiming to decipher the regulatory network that controls pathogenicity in Xanthomonas bacteria. HrpG controls the expression of HrpX, which subsequently controls the expression of T3SS apparatus genes and effectors. The HrpG/HrpX regulon is activated in planta and subjected to tight metabolic and genetic regulation. In this review, we cover the advances made in understanding the regulatory networks that control and are controlled by the HrpG/HrpX regulon and their conservation between different Xanthomonas spp.
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20
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Papathanasiou M, Tsiftsoglou SA, Polyzos AP, Papadopoulou D, Valakos D, Klagkou E, Karagianni P, Pliatska M, Talianidis I, Agelopoulos M, Thanos D. Identification of a dynamic gene regulatory network required for pluripotency factor-induced reprogramming of mouse fibroblasts and hepatocytes. EMBO J 2021; 40:e102236. [PMID: 33034061 PMCID: PMC7780151 DOI: 10.15252/embj.2019102236] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/27/2020] [Accepted: 09/07/2020] [Indexed: 01/04/2023] Open
Abstract
The generation of induced pluripotent stem cells (iPSCs) from somatic cells provides an excellent model to study mechanisms of transcription factor-induced global alterations of the epigenome and genome function. Here, we have investigated the early transcriptional events of cellular reprogramming triggered by the co-expression of Oct4, Sox2, Klf4, and c-Myc (OSKM) in mouse embryonic fibroblasts (MEFs) and mouse hepatocytes (mHeps). In this analysis, we identified a gene regulatory network composed of nine transcriptional regulators (9TR; Cbfa2t3, Gli2, Irf6, Nanog, Ovol1, Rcan1, Taf1c, Tead4, and Tfap4), which are directly targeted by OSKM, in vivo. Functional studies using single and double shRNA knockdowns of any of these factors caused disruption of the network and dramatic reductions in reprogramming efficiency, indicating that this network is essential for the induction and establishment of pluripotency. We demonstrate that the stochastic co-expression of 9TR network components occurs in a remarkably small number of cells, approximating the percentage of terminally reprogrammed cells as a result of dynamic molecular events. Thus, the early DNA-binding patterns of OSKM and the subsequent probabilistic co-expression of essential 9TR components in subpopulations of cells undergoing reprogramming steer the reconstruction of a gene regulatory network marking the transition to pluripotency.
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Affiliation(s)
| | | | | | | | | | | | | | - Maria Pliatska
- Biomedical Research Foundation Academy of AthensAthensGreece
| | | | | | - Dimitris Thanos
- Biomedical Research Foundation Academy of AthensAthensGreece
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21
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Santoso CS, Li Z, Rottenberg JT, Liu X, Shen VX, Bass JIF. In vitro Targeting of Transcription Factors to Control the Cytokine Release Syndrome in COVID-19. bioRxiv 2020:2020.12.29.424728. [PMID: 33398281 PMCID: PMC7781316 DOI: 10.1101/2020.12.29.424728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Treatment of the cytokine release syndrome (CRS) has become an important part of rescuing hospitalized COVID-19 patients. Here, we systematically explored the transcriptional regulators of inflammatory cytokines involved in the COVID-19 CRS to identify candidate transcription factors (TFs) for therapeutic targeting using approved drugs. We integrated a resource of TF-cytokine gene interactions with single-cell RNA-seq expression data from bronchoalveolar lavage fluid cells of COVID-19 patients. We found 581 significantly correlated interactions, between 95 TFs and 16 cytokines upregulated in the COVID-19 patients, that may contribute to pathogenesis of the disease. Among these, we identified 19 TFs that are targets of FDA approved drugs. We investigated the potential therapeutic effect of 10 drugs and 25 drug combinations on inflammatory cytokine production in peripheral blood mononuclear cells, which revealed two drugs that inhibited cytokine production and numerous combinations that show synergistic efficacy in downregulating cytokine production. Further studies of these candidate repurposable drugs could lead to a therapeutic regimen to treat the CRS in COVID-19 patients.
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Affiliation(s)
| | - Zhaorong Li
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | | | - Xing Liu
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Vivian X. Shen
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Juan I. Fuxman Bass
- Department of Biology, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
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Dabrowska D, Mozejko-Ciesielska J, Pokój T, Ciesielski S. Transcriptome Changes in Pseudomonas putida KT2440 during Medium-Chain-Length Polyhydroxyalkanoate Synthesis Induced by Nitrogen Limitation. Int J Mol Sci 2020; 22:ijms22010152. [PMID: 33375721 PMCID: PMC7801951 DOI: 10.3390/ijms22010152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas putida’s versatility and metabolic flexibility make it an ideal biotechnological platform for producing valuable chemicals, such as medium-chain-length polyhydroxyalkanoates (mcl-PHAs), which are considered the next generation bioplastics. This bacterium responds to environmental stimuli by rearranging its metabolism to improve its fitness and increase its chances of survival in harsh environments. Mcl-PHAs play an important role in central metabolism, serving as a reservoir of carbon and energy. Due to the complexity of mcl-PHAs’ metabolism, the manner in which P. putida changes its transcriptome to favor mcl-PHA synthesis in response to environmental stimuli remains unclear. Therefore, our objective was to investigate how the P. putida KT2440 wild type and mutants adjust their transcriptomes to synthesize mcl-PHAs in response to nitrogen limitation when supplied with sodium gluconate as an external carbon source. We found that, under nitrogen limitation, mcl-PHA accumulation is significantly lower in the mutant deficient in the stringent response than in the wild type or the rpoN mutant. Transcriptome analysis revealed that, under N-limiting conditions, 24 genes were downregulated and 21 were upregulated that were common to all three strains. Additionally, potential regulators of these genes were identified: the global anaerobic regulator (Anr, consisting of FnrA, Fnrb, and FnrC), NorR, NasT, the sigma54-dependent transcriptional regulator, and the dual component NtrB/NtrC regulator all appear to play important roles in transcriptome rearrangement under N-limiting conditions. The role of these regulators in mcl-PHA synthesis is discussed.
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Affiliation(s)
- Dorota Dabrowska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (D.D.); (T.P.)
| | - Justyna Mozejko-Ciesielska
- Department of Microbiology and Mycology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Tomasz Pokój
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (D.D.); (T.P.)
| | - Slawomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (D.D.); (T.P.)
- Correspondence: ; Tel.: +48-89-5234162
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Maucourt B, Vuilleumier S, Bringel F. Transcriptional regulation of organohalide pollutant utilisation in bacteria. FEMS Microbiol Rev 2020; 44:189-207. [PMID: 32011697 DOI: 10.1093/femsre/fuaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.
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Affiliation(s)
- Bruno Maucourt
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Stéphane Vuilleumier
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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Ogihara T, Mizoi K, Kamioka H, Yano K. Physiological Roles of ERM Proteins and Transcriptional Regulators in Supporting Membrane Expression of Efflux Transporters as Factors of Drug Resistance in Cancer. Cancers (Basel) 2020; 12:E3352. [PMID: 33198344 PMCID: PMC7696277 DOI: 10.3390/cancers12113352] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/23/2022] Open
Abstract
One factor contributing to the malignancy of cancer cells is the acquisition of drug resistance during chemotherapy via increased expression of efflux transporters, such as P-glycoprotein (P-gp), multidrug resistance-associated proteins (MRPs), and breast cancer resistance protein (BCRP). These transporters operate at the cell membrane, and are anchored in place by the scaffold proteins ezrin (Ezr), radixin (Rdx), and moesin (Msn) (ERM proteins), which regulate their functional activity. The identity of the regulatory scaffold protein(s) differs depending upon the transporter, and also upon the tissue in which it is expressed, even for the same transporter. Another factor contributing to malignancy is metastatic ability. Epithelial-mesenchymal transition (EMT) is the first step in the conversion of primary epithelial cells into mesenchymal cells that can be transported to other organs via the blood. The SNAI family of transcriptional regulators triggers EMT, and SNAI expression is used is an indicator of malignancy. Furthermore, EMT has been suggested to be involved in drug resistance, since drug excretion from cancer cells is promoted during EMT. We showed recently that ERM proteins are induced by a member of the SNAI family, Snail. Here, we first review recent progress in research on the relationship between efflux transporters and scaffold proteins, including the question of tissue specificity. In the second part, we review the relationship between ERM scaffold proteins and the transcriptional regulatory factors that induce their expression.
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Affiliation(s)
- Takuo Ogihara
- Graduate School of Pharmaceutical Sciences, Takasaki University of Health and Welfare, 60, Nakaorui-machi, Takasaki, Gunma 370-0033, Japan;
| | - Kenta Mizoi
- Faculty of Pharmacy, Takasaki University of Health and Welfare, 60, Nakaorui-machi, Takasaki, Gunma 370-0033, Japan; (K.M.); (K.Y.)
| | - Hiroki Kamioka
- Graduate School of Pharmaceutical Sciences, Takasaki University of Health and Welfare, 60, Nakaorui-machi, Takasaki, Gunma 370-0033, Japan;
| | - Kentaro Yano
- Faculty of Pharmacy, Takasaki University of Health and Welfare, 60, Nakaorui-machi, Takasaki, Gunma 370-0033, Japan; (K.M.); (K.Y.)
- Laboratory of Drug Metabolism and Pharmacokinetics, Yokohama University of Pharmacy, 601, Matano-cho, Totsuka-ku, Yokohama, Kanagawa 245-0066, Japan
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25
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Shao X, Xie Y, Zhang Y, Liu J, Ding Y, Wu M, Wang X, Deng X. Novel therapeutic strategies for treating Pseudomonas aeruginosa infection. Expert Opin Drug Discov 2020; 15:1403-1423. [PMID: 32880507 DOI: 10.1080/17460441.2020.1803274] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Persistent infections caused by the superbug Pseudomonas aeruginosa and its resistance to multiple antimicrobial agents are huge threats to patients with cystic fibrosis as well as those with compromised immune systems. Multidrug-resistant P. aeruginosa has posed a major challenge to conventional antibiotics and therapeutic approaches, which show limited efficacy and cause serious side effects. The public demand for new antibiotics is enormous; yet, drug development pipelines have started to run dry with limited targets available for inventing new antibacterial drugs. Consequently, it is important to uncover potential therapeutic targets. AREAS COVERED The authors review the current state of drug development strategies that are promising in terms of the development of novel and potent drugs to treat P. aeruginosa infection. EXPERT OPINION The prevention of P. aeruginosa infection is increasingly challenging. Furthermore, targeting key virulence regulators has great potential for developing novel anti-P. aeruginosa drugs. Additional promising strategies include bacteriophage therapy, immunotherapies, and antimicrobial peptides. Additionally, the authors believe that in the coming years, the overall network of molecular regulatory mechanism of P. aeruginosa virulence will be fully elucidated, which will provide more novel and promising drug targets for treating P. aeruginosa infections.
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Affiliation(s)
- Xiaolong Shao
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Yingpeng Xie
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Yingchao Zhang
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Jingui Liu
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Yiqing Ding
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota , Grand Forks, North Dakota, USA
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China.,Shenzhen Research Institute, City University of Hong Kong , Shenzhen, China
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Grabek J, Straube J, Bywater M, Lane SW. MPN: The Molecular Drivers of Disease Initiation, Progression and Transformation and their Effect on Treatment. Cells 2020; 9:E1901. [PMID: 32823933 DOI: 10.3390/cells9081901] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Myeloproliferative neoplasms (MPNs) constitute a group of disorders identified by an overproduction of cells derived from myeloid lineage. The majority of MPNs have an identifiable driver mutation responsible for cytokine-independent proliferative signalling. The acquisition of coexisting mutations in chromatin modifiers, spliceosome complex components, DNA methylation modifiers, tumour suppressors and transcriptional regulators have been identified as major pathways for disease progression and leukemic transformation. They also confer different sensitivities to therapeutic options. This review will explore the molecular basis of MPN pathogenesis and specifically examine the impact of coexisting mutations on disease biology and therapeutic options.
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Canchi S, Raao B, Masliah D, Rosenthal SB, Sasik R, Fisch KM, De Jager PL, Bennett DA, Rissman RA. Integrating Gene and Protein Expression Reveals Perturbed Functional Networks in Alzheimer's Disease. Cell Rep 2020; 28:1103-1116.e4. [PMID: 31340147 PMCID: PMC7503200 DOI: 10.1016/j.celrep.2019.06.073] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/20/2019] [Accepted: 06/19/2019] [Indexed: 12/23/2022] Open
Abstract
Asymptomatic and symptomatic Alzheimer’s disease (AD) subjects may present with equivalent neuropathological burdens but have significantly different antemortem cognitive decline rates. Using the transcriptome as a proxy for functional state, we selected 414 expression profiles of symptomatic AD subjects and age-matched non-demented controls from a community-based neuropathological study. By combining brain tissue-specific protein interactomes with gene networks, we identified functionally distinct composite clusters of genes that reveal extensive changes in expression levels in AD. Global expression for clusters broadly corresponding to synaptic transmission, metabolism, cell cycle, survival, and immune response were downregulated, while the upregulated cluster included largely uncharacterized processes. We propose that loss of EGR3 regulation mediates synaptic deficits by targeting the synaptic vesicle cycle. Our results highlight the utility of integrating protein interactions with gene perturbations to generate a comprehensive framework for characterizing alterations in the molecular network as applied to AD. Canchi et al. reveal the transcriptomic dynamics of clinically and neuropathologically confirmed Alzheimer’s disease subjects by integrating brain tissue-specific proteome data with gene network analysis. They identify perturbed biological processes and provide insights into the interactions between molecular mechanisms in symptomatic Alzheimer’s disease.
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Affiliation(s)
- Saranya Canchi
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Balaji Raao
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Deborah Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Roman Sasik
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Robert A Rissman
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, San Diego, CA, USA.
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28
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Vaid S, Huttner WB. Transcriptional Regulators and Human-Specific/Primate-Specific Genes in Neocortical Neurogenesis. Int J Mol Sci 2020; 21:ijms21134614. [PMID: 32610533 PMCID: PMC7369782 DOI: 10.3390/ijms21134614] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/09/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022] Open
Abstract
During development, starting from a pool of pluripotent stem cells, tissue-specific genetic programs help to shape and develop functional organs. To understand the development of an organ and its disorders, it is important to understand the spatio-temporal dynamics of the gene expression profiles that occur during its development. Modifications in existing genes, the de-novo appearance of new genes, or, occasionally, even the loss of genes, can greatly affect the gene expression profile of any given tissue and contribute to the evolution of organs or of parts of organs. The neocortex is evolutionarily the most recent part of the brain, it is unique to mammals, and is the seat of our higher cognitive abilities. Progenitors that give rise to this tissue undergo sequential waves of differentiation to produce the complete sets of neurons and glial cells that make up a functional neocortex. We will review herein our understanding of the transcriptional regulators that control the neural precursor cells (NPCs) during the generation of the most abundant class of neocortical neurons, the glutametergic neurons. In addition, we will discuss the roles of recently-identified human- and primate-specific genes in promoting neurogenesis, leading to neocortical expansion.
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Abstract
Gas molecules are ubiquitous in the environment and are used as nutrient and energy sources for living organisms. Many organisms, therefore, have developed gas-sensing systems to respond efficiently to changes in the atmospheric environment. In microorganisms and plants, two-component systems (TCSs) and transcription factors (TFs) are two primary mechanisms to sense gas molecules. In this review, gas-sensing transcriptional regulators, TCSs, and TFs, focusing on protein structures, mechanisms of gas molecule interaction, DNA binding regions of transcriptional regulators, signal transduction mechanisms, and gene expression regulation are discussed. At first, transcriptional regulators that directly sense gas molecules with the help of a prosthetic group is described and then gas-sensing systems that indirectly recognize the presence of gas molecules is explained. Overall, this review provides a comprehensive understanding of gas-sensing transcriptional regulators in microorganisms and plants, and proposes a future perspective on the use of gas-sensing transcriptional regulators.
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Affiliation(s)
- Irisappan Ganesh
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
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30
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Alimadadi A, Aryal S, Manandhar I, Joe B, Cheng X. Identification of Upstream Transcriptional Regulators of Ischemic Cardiomyopathy Using Cardiac RNA-Seq Meta-Analysis. Int J Mol Sci 2020; 21:E3472. [PMID: 32423033 DOI: 10.3390/ijms21103472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/30/2020] [Accepted: 05/08/2020] [Indexed: 12/30/2022] Open
Abstract
Ischemic cardiomyopathy (ICM), characterized by pre-existing myocardial infarction or severe coronary artery disease, is the major cause of heart failure (HF). Identification of novel transcriptional regulators in ischemic HF can provide important biomarkers for developing new diagnostic and therapeutic strategies. In this study, we used four RNA-seq datasets from four different studies, including 41 ICM and 42 non-failing control (NF) samples of human left ventricle tissues, to perform the first RNA-seq meta-analysis in the field of clinical ICM, in order to identify important transcriptional regulators and their targeted genes involved in ICM. Our meta-analysis identified 911 differentially expressed genes (DEGs) with 582 downregulated and 329 upregulated. Interestingly, 54 new DEGs were detected only by meta-analysis but not in individual datasets. Upstream regulator analysis through Ingenuity Pathway Analysis (IPA) identified three key transcriptional regulators. TBX5 was identified as the only inhibited regulator (z-score = -2.89). F2R and SFRP4 were identified as the activated regulators (z-scores = 2.56 and 2.00, respectively). Multiple downstream genes regulated by TBX5, F2R, and SFRP4 were involved in ICM-related diseases such as HF and arrhythmia. Overall, our study is the first to perform an RNA-seq meta-analysis for clinical ICM and provides robust candidate genes, including three key transcriptional regulators, for future diagnostic and therapeutic applications in ischemic heart failure.
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31
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Cordeiro B, Jeon P, Boukhaled GM, Corrado M, Lapohos O, Roy DG, Williams K, Jones RG, Gruenheid S, Sagan SM, Krawczyk CM. MicroRNA-9 Fine-Tunes Dendritic Cell Function by Suppressing Negative Regulators in a Cell-Type-Specific Manner. Cell Rep 2020; 31:107585. [PMID: 32375032 DOI: 10.1016/j.celrep.2020.107585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 08/08/2019] [Accepted: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
Dendritic cells, cells of the innate immune system, are found in a steady state poised to respond to activating stimuli. Once stimulated, they rapidly undergo dynamic changes in gene expression to adopt an activated phenotype capable of stimulating immune responses. We find that the microRNA miR-9 is upregulated in both bone marrow-derived DCs and conventional DC1s but not in conventional DC2s following stimulation. miR-9 expression in BMDCs and conventional DC1s promotes enhanced DC activation and function, including the ability to stimulate T cell activation and control tumor growth. We find that miR-9 regulated the expression of several negative regulators of transcription, including the transcriptional repressor Polycomb group factor 6 (Pcgf6). These findings demonstrate that miR-9 facilitates the transition of DCs from steady state to mature state by regulating the expression of several negative regulators of DC function in a cell-type-specific manner.
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Affiliation(s)
- Brendan Cordeiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Peter Jeon
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Giselle M Boukhaled
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Mario Corrado
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Orsolya Lapohos
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Dominic G Roy
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Kelsey Williams
- Metabolic and Nutritional Programming Group, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
| | - Russell G Jones
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada; Metabolic and Nutritional Programming Group, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
| | - Samantha Gruenheid
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Connie M Krawczyk
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada; Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada; Metabolic and Nutritional Programming Group, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA.
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Willemin MS, Vingerhoets M, Holliger C, Maillard J. Hybrid Transcriptional Regulators for the Screening of Target DNA Motifs in Organohalide-Respiring Bacteria. Front Microbiol 2020; 11:310. [PMID: 32194528 PMCID: PMC7062800 DOI: 10.3389/fmicb.2020.00310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/12/2020] [Indexed: 11/13/2022] Open
Abstract
The bioremediation of persistent organohalide molecules under anoxic conditions mostly relies on the bacterial process called organohalide respiration (OHR). Organohalide-respiring bacteria (OHRB) are phylogenetically diverse anaerobic bacteria that share the capacity to use organohalides as terminal electron acceptors in an energy-conserving process. The reductive dehalogenase (rdh) gene clusters encode for proteins specialized in the respiration of one or a limited number of organohalides. One particular OHRB may harbor up to several dozens of rdh gene clusters suggesting a wide potential for bioremediation. To avoid wasting energy in producing unnecessary proteins, rdh gene clusters often include a transcriptional regulator. In organohalide-respiring Firmicutes, RdhK is a dedicated transcriptional regulator of OHR and represents a subfamily of proteins among the CRP/FNR superfamily of regulators. RdhK proteins are composed of an effector-binding domain (EBD) which recognizes a given organohalide and subsequently controls the interaction of its C-terminal DNA-binding domain (DBD) with a DNA motif (referred to as dehalobox, or DB) located in the promoter region of the target rdh genes. The two binding partners (i.e. an organohalide molecule and a DB sequence) of RdhK proteins are interdependent which impairs the exploration of OHR regulatory networks. Here, we propose a strategy relying on hybrid proteins to efficiently screen the DNA target of a single RdhK protein without prior knowledge on its effector. To demonstrate the potential of the method, two hybrids with alternative fusion points were designed based on RdhK6 EBD and RdhK1 DBD from Desulfitobacterium hafniense. Electrophoretic mobility shift assay was performed with purified hybrids along with the parental proteins and their binding properties were further tested in vivo through a β-galactosidase reporter assay. Along with revealing new RdhK6 features, we show that both hybrids resulted in active regulatory proteins with distinct binding patterns. While Hybrid A was less specific for the DNA motif, Hybrid B successfully mimicked the binding behavior of the parental proteins and thus represents a promising template for the design of new RdhK hybrids to screen yet uncharacterized RdhK proteins and also possibly other members of the CRP/FNR superfamily.
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Affiliation(s)
- Mathilde Stéphanie Willemin
- Laboratory for Environmental Biotechnology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marie Vingerhoets
- Laboratory for Environmental Biotechnology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Ambri F, D’Ambrosio V, Di Blasi R, Maury J, Jacobsen SAB, McCloskey D, Jensen MK, Keasling JD. High-Resolution Scanning of Optimal Biosensor Reporter Promoters in Yeast. ACS Synth Biol 2020; 9:218-226. [PMID: 31935067 DOI: 10.1021/acssynbio.9b00333] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Small-molecule binding allosteric transcription factors (aTFs) derived from bacteria enable real-time monitoring of metabolite abundances, high-throughput screening of genetic designs, and dynamic control of metabolism. Yet, engineering of reporter promoter designs of prokaryotic aTF biosensors in eukaryotic cells is complex. Here we investigate the impact of aTF binding site positions at single-nucleotide resolution in >300 reporter promoter designs in Saccharomyces cerevisiae. From this we identify biosensor output landscapes with transient and distinct aTF binding site position effects for aTF repressors and activators, respectively. Next, we present positions for tunable reporter promoter outputs enabling metabolite-responsive designs for a total of four repressor-type and three activator-type aTF biosensors with dynamic output ranges up to 8- and 26-fold, respectively. This study highlights aTF binding site positions in reporter promoters as key for successful biosensor engineering and that repressor-type aTF biosensors allows for more flexibility in terms of choice of binding site positioning compared to activator-type aTF biosensors.
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Affiliation(s)
- Francesca Ambri
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Vasil D’Ambrosio
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Roberto Di Blasi
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Jerome Maury
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | | | - Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Jay. D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China
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Gladman N, Jiao Y, Lee YK, Zhang L, Chopra R, Regulski M, Burow G, Hayes C, Christensen SA, Dampanaboina L, Chen J, Burke J, Ware D, Xin Z. Fertility of Pedicellate Spikelets in Sorghum Is Controlled by a Jasmonic Acid Regulatory Module. Int J Mol Sci 2019; 20:ijms20194951. [PMID: 31597271 PMCID: PMC6801740 DOI: 10.3390/ijms20194951] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 01/07/2023] Open
Abstract
As in other cereal crops, the panicles of sorghum (Sorghum bicolor (L.) Moench) comprise two types of floral spikelets (grass flowers). Only sessile spikelets (SSs) are capable of producing viable grains, whereas pedicellate spikelets (PSs) cease development after initiation and eventually abort. Consequently, grain number per panicle (GNP) is lower than the total number of flowers produced per panicle. The mechanism underlying this differential fertility is not well understood. To investigate this issue, we isolated a series of ethyl methane sulfonate (EMS)-induced multiseeded (msd) mutants that result in full spikelet fertility, effectively doubling GNP. Previously, we showed that MSD1 is a TCP (Teosinte branched/Cycloidea/PCF) transcription factor that regulates jasmonic acid (JA) biosynthesis, and ultimately floral sex organ development. Here, we show that MSD2 encodes a lipoxygenase (LOX) that catalyzes the first committed step of JA biosynthesis. Further, we demonstrate that MSD1 binds to the promoters of MSD2 and other JA pathway genes. Together, these results show that a JA-induced module regulates sorghum panicle development and spikelet fertility. The findings advance our understanding of inflorescence development and could lead to new strategies for increasing GNP and grain yield in sorghum and other cereal crops.
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Affiliation(s)
- Nicholas Gladman
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Yinping Jiao
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Young Koung Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
- Plasma Technology Research Center, National Fusion Research Institute, 37, Dongjangsan-ro, Gunsan-si, Jeollabuk-do 54004, Korea.
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Ratan Chopra
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
- Current address: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Gloria Burow
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Chad Hayes
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Shawn A Christensen
- Chemistry Research Unit, USDA-ARS, 1700 S.W. 23RD DRIVE, Gainesville, FL 32608, USA.
| | - Lavanya Dampanaboina
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - John Burke
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA.
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
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Gao T, Jernigan J, Raza SA, Dammer EB, Xiao H, Seyfried NT, Levey AI, Rangaraju S. Transcriptional regulation of homeostatic and disease-associated-microglial genes by IRF1, LXRβ, and CEBPα. Glia 2019; 67:1958-1975. [PMID: 31301160 PMCID: PMC7190149 DOI: 10.1002/glia.23678] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/23/2019] [Accepted: 06/25/2019] [Indexed: 01/08/2023]
Abstract
Microglia transform from homeostatic to disease-associated-microglia (DAM) profiles in neurodegeneration. Within DAM, we recently identified distinct pro-inflammatory and anti-inflammatory sub-profiles although transcriptional regulators of homeostatic and distinct DAM profiles remain unclear. Informed by these studies, we nominated CEBPα, IRF1, and LXRβ as likely regulators of homeostatic, pro-inflammatory and anti-inflammatory DAM states and performed in-vitro siRNA studies in primary microglia to identify roles of each transcriptional factor (TF) in regulating microglial activation, using an integrated transcriptomics, bioinformatics and experimental validation approach. Efficient (>70%) silencing of TFs in microglia revealed reciprocal regulation between each TF specifically following pro-inflammatory activation. Neuroinflammatory transcriptomic profiling of microglia coupled with qPCR validation revealed distinct gene clusters with unique patterns of regulation by each TF, which were independent of LPS stimulation. While all three TFs (especially IRF1 and LXRβ) positively regulated core DAM genes (Apoe, Axl, Clec7a, Tyrobp, and Trem2) as well as homeostatic and pro-inflammatory DAM genes, LPS, and IFNγ increased pro-inflammatory DAM but suppressed homeostatic and anti-inflammatory DAM gene expression via an Erk1/2-dependent signaling pathway. IRF1 and LXRβ silencing suppressed microglial phagocytic activity for polystyrene microspheres as well as fAβ42 while IRF1 silencing strongly suppressed production of pro-inflammatory cytokines in response to LPS. Our studies reveal complex transcriptional regulation of homeostatic and DAM profiles whereby IRF1, LXRβ, and CEBPα positively regulate both pro- and anti-inflammatory DAM genes while activating stimuli independently augment pro-inflammatory DAM responses and suppress homeostatic and anti-inflammatory responses via Erk signaling. This framework can guide development of therapeutic immuno-modulatory strategies for neurodegeneration.
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Affiliation(s)
- Tianwen Gao
- Department of Neurology, Emory University, Atlanta, GA, USA
- Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | | | - Syed Ali Raza
- Department of Neurology, Emory University, Atlanta, GA, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University, Atlanta, Georgia
| | - Hailian Xiao
- Department of Neurology, Emory University, Atlanta, GA, USA
| | | | - Allan I Levey
- Department of Neurology, Emory University, Atlanta, GA, USA
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Abstract
The mammary gland is a highly dynamic organ that undergoes profound changes within its epithelium during puberty and the reproductive cycle. These changes are fueled by dedicated stem and progenitor cells. Both short- and long-lived lineage-restricted progenitors have been identified in adult tissue as well as a small pool of multipotent mammary stem cells (MaSCs), reflecting intrinsic complexity within the epithelial hierarchy. While unipotent progenitor cells predominantly execute day-to-day homeostasis and postnatal morphogenesis during puberty and pregnancy, multipotent MaSCs have been implicated in coordinating alveologenesis and long-term ductal maintenance. Nonetheless, the multipotency of stem cells in the adult remains controversial. The advent of large-scale single-cell molecular profiling has revealed striking changes in the gene expression landscape through ontogeny and the presence of transient intermediate populations. An increasing number of lineage cell-fate determination factors and potential niche regulators have now been mapped along the hierarchy, with many implicated in breast carcinogenesis. The emerging diversity among stem and progenitor populations of the mammary epithelium is likely to underpin the heterogeneity that characterizes breast cancer.
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Affiliation(s)
- Nai Yang Fu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore; Tumour-Host Interaction Laboratory, Francis Crick Institute, London, United Kingdom; Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia; Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; and Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Emma Nolan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore; Tumour-Host Interaction Laboratory, Francis Crick Institute, London, United Kingdom; Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia; Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; and Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Geoffrey J Lindeman
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore; Tumour-Host Interaction Laboratory, Francis Crick Institute, London, United Kingdom; Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia; Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; and Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jane E Visvader
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore; Tumour-Host Interaction Laboratory, Francis Crick Institute, London, United Kingdom; Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia; Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; and Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
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Newman J, Caron K, Nebl T, Peat TS. Structures of the transcriptional regulator BgaR, a lactose sensor. Acta Crystallogr D Struct Biol 2019; 75:639-646. [PMID: 31282473 DOI: 10.1107/s2059798319008131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/06/2019] [Indexed: 11/10/2022]
Abstract
The structure of BgaR, a transcriptional regulator of the lactose operon in Clostridium perfringens, has been solved by SAD phasing using a mercury derivative. BgaR is an exquisite sensor of lactose, with a binding affinity in the low-micromolar range. This sensor and regulator has been captured bound to lactose and to lactulose as well as in a nominal apo form, and was compared with AraC, another saccharide-binding transcriptional regulator. It is shown that the saccharides bind in the N-terminal region of a jelly-roll fold, but that part of the saccharide is exposed to bulk solvent. This differs from the classical AraC saccharide-binding site, which is mostly sequestered from the bulk solvent. The structures of BgaR bound to lactose and to lactulose highlight how specific and nonspecific interactions lead to a higher binding affinity of BgaR for lactose compared with lactulose. Moreover, solving multiple structures of BgaR in different space groups, both bound to saccharides and unbound, verified that the dimer interface along a C-terminal helix is similar to the dimer interface observed in AraC.
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Affiliation(s)
- Janet Newman
- Biomedical Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Karine Caron
- Health and Biosecurity, CSIRO, Clunies Ross Street, Black Mountain, ACT 2601, Australia
| | - Tom Nebl
- Biomedical Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas S Peat
- Biomedical Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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Belvin BR, Musayev FN, Burgner J, Scarsdale JN, Escalante CR, Lewis JP. Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR. Acta Crystallogr D Struct Biol 2019; 75:437-450. [PMID: 30988260 PMCID: PMC6465984 DOI: 10.1107/s205979831900264x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/21/2019] [Indexed: 11/10/2022] Open
Abstract
Although the HcpR regulator plays a vital step in initiation of the nitrosative stress response in many Gram-negative anaerobic bacteria, the molecular mechanisms that it uses to mediate gas sensing are not well understood. Here, a 2.6 Å resolution crystal structure of the N-terminal sensing domain of the anaerobic periodontopathogen Porphyromonas gingivalis HcpR is presented. The protein has classical features of the regulators belonging to the FNR-CRP family and contains a hydrophobic pocket in its N-terminal sensing domain. It is shown that heme bound to HcpR exhibits heme iron as a hexacoordinate system in the absence of nitric oxide (NO) and that upon nitrosylation it transitions to a pentacoordinate system. Finally, small-angle X-ray scattering experiments on full-length HcpR reveal that the C-terminal DNA-binding domain of HcpR has a high degree of interdomain flexibility.
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Affiliation(s)
- B. Ross Belvin
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Faik N. Musayev
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - John Burgner
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - J. Neel Scarsdale
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Institute for Structural Biology, Drug Discovery, and Development, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Carlos R. Escalante
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Janina P. Lewis
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- The Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
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You M, Jogasuria A, Lee K, Wu J, Zhang Y, Lee YK, Sadana P. Signal Transduction Mechanisms of Alcoholic Fatty Liver Disease: Emer ging Role of Lipin-1. Curr Mol Pharmacol 2019; 10:226-236. [PMID: 26278388 DOI: 10.2174/1874467208666150817112109] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 02/06/2023]
Abstract
Lipin-1, a mammalian phosphatidic acid phosphatase (PAP), is a bi-functional molecule involved in various signaling pathways via its function as a PAP enzyme in the triglyceride synthesis pathway and in the nucleus as a transcriptional co-regulator. In the liver, lipin-1 is known to play a vital role in controlling the lipid metabolism and inflammation process at multiple regulatory levels. Alcoholic fatty liver disease (AFLD) is one of the earliest forms of liver injury and approximately 8-20% of patients with simple steatosis can develop into more severe forms of liver injury, including steatohepatitis, fibrosis/ cirrhosis, and eventually hepatocellular carcinoma (HCC). The signal transduction mechanisms for alcohol-induced detrimental effects in liver involves alteration of complex and multiple signaling pathways largely governed by a central and upstream signaling system, namely, sirtuin 1 (SIRT1)-AMP activated kinase (AMPK) axis. Emerging evidence suggests a pivotal role of lipin-1 as a crucial downstream regulator of SIRT1-AMPK signaling system that is likely to be ultimately responsible for development and progression of AFLD. Several lines of evidence demonstrate that ethanol exposure significantly induces lipin-1 gene and protein expression levels in cultured hepatocytes and in the livers of rodents, induces lipin-1-PAP activity, impairs the functional activity of nuclear lipin-1, disrupts lipin-1 mRNA alternative splicing and induces lipin-1 nucleocytoplasmic shuttling. Such impairment in response to ethanol leads to derangement of hepatic lipid metabolism, and excessive production of inflammatory cytokines in the livers of the rodents and human alcoholics. This review summarizes current knowledge about the role of lipin-1 in the pathogenesis of AFLD and its potential signal transduction mechanisms.
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Affiliation(s)
- Min You
- 4209 State Route 44, Rootstown OH 44272. United States
| | | | | | - Jiashin Wu
- Department of Pharmaceutical Sciences. 0
| | - Yanqiao Zhang
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, College of Pharmacy and College of Medicine, Rootstown OH 44272. United States
| | - Yoon Kwang Lee
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, College of Pharmacy and College of Medicine, Rootstown OH 44272. United States
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Karki AB, Marasini D, Oakey CK, Mar K, Fakhr MK. Campylobacter coli From Retail Liver and Meat Products Is More Aerotolerant Than Campylobacter jejuni. Front Microbiol 2018; 9:2951. [PMID: 30631306 PMCID: PMC6315125 DOI: 10.3389/fmicb.2018.02951] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 11/16/2018] [Indexed: 02/01/2023] Open
Abstract
Aerotolerance in the microaerophilic species Campylobacter was previously reported and could increase bacterial survival and transmission in foods during stressful processing and storage conditions. In this study, 167 Campylobacter isolates (76 C. jejuni and 91 C. coli) were screened for aerotolerance; these strains were previously isolated from retail chicken meat, chicken livers, chicken gizzards, turkey, pork, and beef liver samples. Bacterial cultures were incubated aerobically in Mueller Hinton broth with agitation and viable cell counts were taken at 0, 6, 12, and 24 h. Approximately 47% of the screened Campylobacter isolates were aerotolerant (viable after a 12-h aerobic incubation period), whereas 24% were hyper-aerotolerant (viable after a 24-h aerobic incubation). A greater prevalence of aerotolerant strains (80%) was found among C. coli isolates as compared to C. jejuni isolates (6%). Differences in the oxidative stress response related genes were detected among C. jejuni and C. coli isolates when comparative genomics was used to analyze 17 Whole Genome Sequenced (WGS) strains from our laboratory. Genes encoding putative transcriptional regulator proteins and a catalase-like heme binding protein were found in C. coli genomes, but were absent in the genomes of C. jejuni. PCR screening showed the presence of a catalase-like protein gene in 75% (68/91) of C. coli strains, which was absent in all tested C. jejuni strains. While about 79% (30/38) of the hyper-aerotolerant C. coli strains harbored the catalase-like protein gene, the gene was also present in a number of the aerosensitive strains. The Catalase like protein gene was found to be expressed in both aerobic and microaerobic conditions with a 2-fold higher gene expression detected in aerobic conditions for an aerosensitive strain. However, the exact function of the gene remains unclear and awaits further investigation. In conclusion, aerotolerant Campylobacter strains (especially C. coli) are prevalent in various retail meats. Further studies are needed to investigate whether the genes encoding catalase-like heme binding protein and putative transcriptional regulators in C. coli strains are involved in stress response.
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Affiliation(s)
- Anand B Karki
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Daya Marasini
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Clark K Oakey
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Kaitlin Mar
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Mohamed K Fakhr
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
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Martín-Mora D, Fernández M, Velando F, Ortega Á, Gavira JA, Matilla MA, Krell T. Functional Annotation of Bacterial Signal Transduction Systems: Progress and Challenges. Int J Mol Sci 2018; 19:ijms19123755. [PMID: 30486299 PMCID: PMC6321045 DOI: 10.3390/ijms19123755] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 01/15/2023] Open
Abstract
Bacteria possess a large number of signal transduction systems that sense and respond to different environmental cues. Most frequently these are transcriptional regulators, two-component systems and chemosensory pathways. A major bottleneck in the field of signal transduction is the lack of information on signal molecules that modulate the activity of the large majority of these systems. We review here the progress made in the functional annotation of sensor proteins using high-throughput ligand screening approaches of purified sensor proteins or individual ligand binding domains. In these assays, the alteration in protein thermal stability following ligand binding is monitored using Differential Scanning Fluorimetry. We illustrate on several examples how the identification of the sensor protein ligand has facilitated the elucidation of the molecular mechanism of the regulatory process. We will also discuss the use of virtual ligand screening approaches to identify sensor protein ligands. Both approaches have been successfully applied to functionally annotate a significant number of bacterial sensor proteins but can also be used to study proteins from other kingdoms. The major challenge consists in the study of sensor proteins that do not recognize signal molecules directly, but that are activated by signal molecule-loaded binding proteins.
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Affiliation(s)
- David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology 'B' and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Murcia, Spain.
| | - José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, (CSIC-UGR), Avenida las Palmeras 4, 18100 Armilla, Spain.
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
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Weigend S, Holst SC, Meier J, Brock M, Kohler M, Landolt HP. Prolonged Waking and Recovery Sleep Affect the Serum MicroRNA Expression Profile in Humans. Clocks Sleep 2019; 1:75-86. [PMID: 33089155 DOI: 10.3390/clockssleep1010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/20/2018] [Indexed: 01/28/2023] Open
Abstract
MicroRNAs (miRNAs) are small, abundant, non-coding RNA fragments that regulate gene expression and silencing at the post-transcriptional level. The miRNAs each control various downstream targets and play established roles in different biological processes. Given that miRNAs were recently proposed to contribute to the molecular control of sleep-wake regulation in animal models and narcoleptic patients, we investigated the impact of acute sleep deprivation on blood miRNA expression in healthy adult men of two different age groups. Twenty-two young (mean age: 24 ± 3 years) and nine older (65 ± 1 years) volunteers completed a controlled in-lab study, consisting of 8 h baseline sleep, followed by 40 h of extended wakefulness, and a 10-h recovery sleep opportunity. At the same circadian time in all three conditions (at 4:23 p.m. ± 23 min), qPCR expression profiling of 86 miRNAs was performed in blood serum. Thirteen different miRNAs could be reliably quantified and were analyzed using mixed-model ANOVAs. It was found that miR-30c and miR-127 were reliably affected by previous sleep and wakefulness, such that expression of these miRNAs was upregulated after extended wakefulness and normalized after recovery sleep. Together with previous findings in narcolepsy patients, our preliminary data indicate that miR-30c and its target proteins may provide a biomarker of elevated sleep debt in humans.
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Kehl T, Schneider L, Kattler K, Stöckel D, Wegert J, Gerstner N, Ludwig N, Distler U, Tenzer S, Gessler M, Walter J, Keller A, Graf N, Meese E, Lenhof HP. The role of TCF3 as potential master regulator in blastemal Wilms tumors. Int J Cancer 2018; 144:1432-1443. [PMID: 30155889 DOI: 10.1002/ijc.31834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/05/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
Abstract
Wilms tumors are the most common type of pediatric kidney tumors. While the overall prognosis for patients is favorable, especially tumors that exhibit a blastemal subtype after preoperative chemotherapy have a poor prognosis. For an improved risk assessment and therapy stratification, it is essential to identify the driving factors that are distinctive for this aggressive subtype. In our study, we compared gene expression profiles of 33 tumor biopsies (17 blastemal and 16 other tumors) after neoadjuvant chemotherapy. The analysis of this dataset using the Regulator Gene Association Enrichment algorithm successfully identified several biomarkers and associated molecular mechanisms that distinguish between blastemal and nonblastemal Wilms tumors. Specifically, regulators involved in embryonic development and epigenetic processes like chromatin remodeling and histone modification play an essential role in blastemal tumors. In this context, we especially identified TCF3 as the central regulatory element. Furthermore, the comparison of ChIP-Seq data of Wilms tumor cell cultures from a blastemal mouse xenograft and a stromal tumor provided further evidence that the chromatin states of blastemal cells share characteristics with embryonic stem cells that are not present in the stromal tumor cell line. These stem-cell like characteristics could potentially add to the increased malignancy and chemoresistance of the blastemal subtype. Along with TCF3, we detected several additional biomarkers that are distinctive for blastemal Wilms tumors after neoadjuvant chemotherapy and that may provide leads for new therapeutic regimens.
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Affiliation(s)
- Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Lara Schneider
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Daniel Stöckel
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Würzburg University, Würzburg, Germany
| | - Nico Gerstner
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Nicole Ludwig
- Human Genetics, Saarland University, Homburg, Germany
| | - Ute Distler
- Institute for Immunology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, Würzburg University, Würzburg, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, Medical School, Saarland University, Homburg, Germany
| | - Eckart Meese
- Human Genetics, Saarland University, Homburg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
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Sarmiento‐Villamil JL, Prieto P, Klosterman SJ, García‐Pedrajas MD. Characterization of two homeodomain transcription factors with critical but distinct roles in virulence in the vascular pathogen Verticillium dahliae. Mol Plant Pathol 2018; 19:986-1004. [PMID: 28727279 PMCID: PMC6638091 DOI: 10.1111/mpp.12584] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 05/11/2023]
Abstract
Vascular wilt caused by Verticillium dahliae is a destructive disease that represents a chronic economic problem for crop production worldwide. In this work, we characterized two new regulators of pathogenicity in this species. Vph1 (VDAG_06555) was identified in a candidate gene approach as a putative homologue of the transcription factor Ste12. Vhb1 (VDAG_08786), identified in a forward genetics approach, is similar to the homeobox transcription factor Htf1, reported as a regulator of conidiogenesis in several fungi. Deletion of vph1 did not affect vegetative growth, whereas deletion of vhb1 greatly reduced sporulation rates in liquid medium. Both mutants failed to induce Verticillium wilt symptoms. However, unlike Δvph1, Δvhb1 could be re-isolated from the vascular system of some asymptomatic plants. Confocal microscopy further indicated that Δvph1 and Δvhb1 differed in their behaviour in planta; Δvph1 could not penetrate the root cortex, whereas Δvhb1 was impaired in its ability to colonize the xylem. In agreement with these observations, only Δvhb1 could penetrate cellophane paper. On cellophane, wild-type and Δvhb1 strains produced numerous short branches with swollen tips, resembling the hyphopodia formed on root surfaces, contrasting with Δvph1, which generated unbranched long filaments without swollen tips. A microarray analysis showed that these differences in growth were associated with differences in global transcription patterns, and allowed us to identify a large set of novel genes potentially involved in virulence in V. dahliae. Ste12 homologues are known regulators of invasive growth, but Vhb1 is the first putative Htf1 homologue identified with a critical role in virulence.
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Affiliation(s)
- Jorge L. Sarmiento‐Villamil
- Estación Experimental ‘La Mayora’Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Algarrobo‐CostaMálaga 29750Spain
| | - Pilar Prieto
- Departamento de Mejora Genética, Instituto de Agricultura Sostenible (IAS)Consejo Superior de Investigaciones Científicas (CSIC)Córdoba14004Spain
| | - Steven J. Klosterman
- Agricultural Research ServiceUnited States Department of AgricultureSalinasCA 93905USA
| | - María D. García‐Pedrajas
- Estación Experimental ‘La Mayora’Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM‐UMA‐CSIC)Algarrobo‐CostaMálaga 29750Spain
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Mathlouthi A, Pennacchietti E, De Biase D. Effect of Temperature, pH and Plasmids on In Vitro Biofilm Formation in Escherichia coli. Acta Naturae 2018; 10:129-32. [PMID: 30713773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Acid resistance (AR) in Escherichia coli is an important trait that protects this microorganism from the deleterious effect of low-pH environments. Reports on biofilm formation in E. coli K12 showed that the genes participating in AR were differentially expressed. Herein, we investigated the relationship between AR genes, in particular those coding for specific transcriptional regulators, and their biofilm-forming ability at the phenotypic level. The latter was measured in 96-well plates by staining the bacteria attached to the well, following 24-hour growth under static conditions, with crystal violet. The growth conditions were as follows: Luria Bertani (LB) medium at neutral and acidic pH, at 37°C or 25°C. We observed that the three major transcriptional regulators of the AR genes (gadX, gadE, gadW) only marginally affected biofilm formation in E. coli. However, a striking and novel finding was the different abilities of all the tested E. coli strains to form a biofilm depending on the temperature and pH of the medium: LB, pH 7.4, strongly supported biofilm formation at 25°C, with biofilm being hardly detectable at 37°C. On the contrary, LB, pH 5.5, best supported biofilm formation at 37°C. Moreover, we observed that when E. coli carried a plasmid, the presence of the plasmid itself affected the ability to develop a biofilm, typically by increasing its formation. This phenomenon varies from plasmid to plasmid, depends on growth conditions, and, to the best of our knowledge, remains largely uninvestigated.
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Bocsanczy AM, Huguet-Tapia JC, Norman DJ. Comparative Genomics of Ralstonia solanacearum Identifies Candidate Genes Associated with Cool Virulence. Front Plant Sci 2017; 8:1565. [PMID: 28955357 PMCID: PMC5601409 DOI: 10.3389/fpls.2017.01565] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/28/2017] [Indexed: 06/01/2023]
Abstract
Strains of the Ralstonia solanacearum species complex in the phylotype IIB group are capable of causing Bacterial Wilt disease in potato and tomato at temperatures lower than 24°C. The capability of these strains to survive and to incite infection at temperatures colder than their normally tropical boundaries represents a threat to United States agriculture in temperate regions. In this work, we used a comparative genomics approach to identify orthologous genes linked to the lower temperature virulence phenotype. Six R. solanacearum cool virulent (CV) strains were compared to six strains non-pathogenic at low temperature (NPLT). CV strains can cause Bacterial Wilt symptoms at temperatures below 24°C, while NPLT cannot. Four R. solanacearum strains were sequenced for this work in order to complete the comparison. An orthologous genes comparison identified 44 genes present only in CV strains and 19 genes present only in NPLT strains. Gene annotation revealed a high percentage of genes compared with whole genomes in the transcriptional regulator and transport categories. A single nucleotide polymorphism (SNP) analysis identified 265 genes containing conserved non-synonymous SNPs in CV strains. Ten genes in the pathogenicity category were identified in this group. Comparisons of type 3 secretion system, type 6 secretion system (T6SS) clusters, and associated effectors did not indicate a correlation with the CV phenotype except for one T6SS VGR effector potentially associated with the CV phenotype. This is the first R. solanacearum genomic comparative analysis of multiple strains with different temperature related virulence. The candidate genes identified by this comparison are potential factors involved in virulence at low temperatures that need to be investigated. The high percentage of transcriptional regulators among the genes present only in CV strains supports the hypothesis that temperature dependent regulation of virulence genes explains the differential virulence phenotype at low temperatures. This comparison contributes to find new possible connections of temperature dependent virulence to the previously described complex regulatory system involving quorum-sensing, phenotype conversion (phcA), acyl-HSL production and responses to SA. It also added novel candidate T6SS effectors and useful detailed information about the T6SS in R. solanacearum.
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Affiliation(s)
- Ana M. Bocsanczy
- Mid-Florida Research and Education Center, Department of Plant Pathology, University of Florida, ApopkaFL, United States
| | - Jose C. Huguet-Tapia
- Department of Plant Pathology, University of Florida, GainesvilleFL, United States
| | - David J. Norman
- Mid-Florida Research and Education Center, Department of Plant Pathology, University of Florida, ApopkaFL, United States
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Olorunleke FE, Kieu NP, De Waele E, Timmerman M, Ongena M, Höfte M. Coregulation of the cyclic lipopeptides orfamide and sessilin in the biocontrol strain Pseudomonas sp. CMR12a. Microbiologyopen 2017. [PMID: 28621084 PMCID: PMC5635164 DOI: 10.1002/mbo3.499] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cyclic lipopeptides (CLPs) are synthesized by nonribosomal peptide synthetases (NRPS), which are often flanked by LuxR‐type transcriptional regulators. Pseudomonas sp. CMR12a, an effective biocontrol strain, produces two different classes of CLPs namely sessilins and orfamides. The orfamide biosynthesis gene cluster is flanked up‐ and downstream by LuxR‐type regulatory genes designated ofaR1 and ofaR2, respectively, whereas the sessilin biosynthesis gene cluster has one LuxR‐type regulatory gene which is situated upstream of the cluster and is designated sesR. Our study investigated the role of these three regulators in the biosynthesis of orfamides and sessilins. Phylogenetic analyses positioned OfaR1 and OfaR2 with LuxR regulatory proteins of similar orfamide‐producing Pseudomonas strains and the SesR with that of the tolaasin producer, Pseudomonas tolaasii. LC‐ESI‐MS analyses revealed that sessilins and orfamides are coproduced and that production starts in the late exponential phase. However, sessilins are secreted earlier and in large amounts, while orfamides are predominantly retained in the cell. Deletion mutants in ofaR1 and ofaR2 lost the capacity to produce both orfamides and sessilins, whereas the sesR mutant showed no clear phenotype. Additionally, RT‐PCR analysis showed that in the sessilin cluster, a mutation in either ofaR1 or ofaR2 led to weaker transcripts of the biosynthesis genes, sesABC, and putative transporter genes, macA1B1. In the orfamide cluster, mainly the biosynthesis genes ofaBC were affected, while the first biosynthesis gene ofaA and putative macA2B2 transport genes were still transcribed. A mutation in either ofaR1, ofaR2, or sesR genes did not abolish the transcription of any of the other two.
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Affiliation(s)
- Feyisara E Olorunleke
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nam P Kieu
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Evelien De Waele
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Marc Timmerman
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Marc Ongena
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Abstract
During the development of a multicellular organism from a zygote, a large number of epigenetic interactions take place on every level of suborganismal organization. This raises the possibility that the system of epigenetic interactions may compensate or "buffer" some of the changes that occur as mutations on its lowest levels, and thus stabilize the phenotype with respect to mutations. This hypothetical phenomenon will be called "epigenetic stability." Its potential importance stems from the fact that phenotypic variation with a genetic basis is an essential prerequisite for evolution. Thus, variation in epigenetic stability might profoundly affect attainable rates of evolution. While representing a systemic property of a developmental system, epigenetic stability might itself be genetically determined and thus be subject to evolutionary change. Whether or not this is the case should ideally be answered directly, that is, by experimentation. The time scale involved and our insufficient quantitative understanding of developmental pathways will probably preclude such an approach in the foreseeable future. Preliminary answers are sought here by using a biochemically motivated model of a small but central part of a developmental pathway. Modeled are sets of transcriptional regulators that mutually regulate each other's expression and thereby form stable gene expression patterns. Such gene-expression patterns, crucially involved in determining developmental pattern formation events, are most likely subject to strong stabilizing natural selection. After long periods of stabilizing selection, the fraction of mutations causing changes in gene-expression patterns is substantially reduced in the model. Epigenetic stability has increased. This phenomenon is found for widely varying regulatory scenarios among transcription factor genes. It is discussed that only epistatic (nonlinear) gene interactions can cause such change in epigenetic stability. Evidence from paleontology, molecular evolution, development, and genetics, consistent with the existence of variation in epigenetic stability, is discussed. The relation of epigenetic stability to developmental canalization is outlined. Experimental scenarios are suggested that may provide further evidence.
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Affiliation(s)
- Andreas Wagner
- Yale University, Department of Biology, Center for Computational Ecology, OML327, P.O. Box 208104, New Haven, Connecticut, 06520-8104
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Vaschetto LM. Understanding the role of protein interaction motifs in transcriptional regulators: implications for crop improvement. Brief Funct Genomics 2017; 16:152-155. [PMID: 27288433 DOI: 10.1093/bfgp/elw022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently, the conjunction of disciplines such as developmental biology and proteomics enabled the dissection of diverse cellular processes, by analysis of their transcriptional regulatory pathways. In particular, it has been shown that transcription factor interactions play critical roles in the development of many complex traits and control cellular phenotypic plasticity, whereas protein phosphorylation modifications regulate protein activity at the posttranslational level. The present work posits that protein-protein interactions by functional motifs, as well as the phosphorylation state in these sites, are fundamental plant biological phenotype determinants, whose elucidation and understanding will allow manipulation of complex traits, thereby contributing to the design of novel methodologies for molecular breeders and plant physiologists.
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Sadiq FA, Flint S, Li Y, Liu T, Lei Y, Sakandar HA, He G. New mechanistic insights into the motile-to-sessile switch in various bacteria with particular emphasis on Bacillus subtilis and Pseudomonas aeruginosa: a review. Biofouling 2017; 33:306-326. [PMID: 28347177 DOI: 10.1080/08927014.2017.1304541] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/04/2017] [Indexed: 06/06/2023]
Abstract
A biofilm is a complex assemblage of microbial communities adhered to a biotic or an abiotic surface which is embedded within a self-produced matrix of extracellular polymeric substances. Many transcriptional regulators play a role in triggering a motile-sessile switch and in consequently producing the biofilm matrix. This review is aimed at highlighting the role of two nucleotide signaling molecules (c-di-GMP and c-di-AMP), toxin antitoxin modules and a novel transcriptional regulator BolA in biofilm formation in various bacteria. In addition, it highlights the common themes that have appeared in recent research regarding the key regulatory components and signal transduction pathways that help Bacillus subtilis and Pseudomonas aeruginosa to acquire the biofilm mode of life.
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Affiliation(s)
- Faizan A Sadiq
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | - Steve Flint
- b School of Food and Nutrition , Massey University , Palmerston North , New Zealand
| | - Yun Li
- c School of Life Sciences and Food Technology , Hanshan Normal University , Chaozhou , PR China
| | - TongJie Liu
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | - Yuan Lei
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | | | - GuoQing He
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
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