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Rezaei S, Timani KA, He JJ. Metformin Treatment Leads to Increased HIV Transcription and Gene Expression through Increased CREB Phosphorylation and Recruitment to the HIV LTR Promoter. Aging Dis 2024; 15:831-850. [PMID: 37450926 PMCID: PMC10917544 DOI: 10.14336/ad.2023.0705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
Antiretroviral therapy has effectively suppressed HIV infection and replication and prolonged the lifespan of HIV-infected individuals. In the meantime, various complications including type 2 diabetes associated with the long-term antiviral therapy have shown steady increases. Metformin has been the front-line anti-hyperglycemic drug of choice and the most widely prescribed medication for the treatment of type 2 diabetes. However, little is known about the effects of Metformin on HIV infection and replication. In this study, we showed that Metformin treatment enhanced HIV gene expression and transcription in HIV-transfected 293T and HIV-infected Jurkat and human PBMC. Moreover, we demonstrated that Metformin treatment resulted in increased CREB expression and phosphorylation, and TBP expression. Furthermore, we showed that Metformin treatment increased the recruitment of phosphorylated CREB and TBP to the HIV LTR promoter. Lastly, we showed that inhibition of CREB phosphorylation/activation significantly abrogated Metformin-enhanced HIV gene expression. Taken together, these results demonstrated that Metformin treatment increased HIV transcription, gene expression, and production through increased CREB phosphorylation and recruitment to the HIV LTR promoter. These findings may help design the clinical management plan and HIV cure strategy of using Metformin to treat type 2 diabetes, a comorbidity with an increasing prevalence, in people living with HIV.
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Affiliation(s)
- Sahar Rezaei
- Department of Microbiology and Immunology, Rosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA.
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA.
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA.
| | - Khalid A Timani
- Department of Microbiology and Immunology, Rosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA.
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA.
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA.
| | - Johnny J He
- Department of Microbiology and Immunology, Rosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA.
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA.
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA.
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2
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Hayes E, Winston N, Stocco C. Molecular crosstalk between insulin-like growth factors and follicle-stimulating hormone in the regulation of granulosa cell function. Reprod Med Biol 2024; 23:e12575. [PMID: 38571513 PMCID: PMC10988955 DOI: 10.1002/rmb2.12575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/11/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024] Open
Abstract
Background The last phase of folliculogenesis is driven by follicle-stimulating hormone (FSH) and locally produced insulin-like growth factors (IGFs), both essential for forming preovulatory follicles. Methods This review discusses the molecular crosstalk of the FSH and IGF signaling pathways in regulating follicular granulosa cells (GCs) during the antral-to-preovulatory phase. Main findings IGFs were considered co-gonadotropins since they amplify FSH actions in GCs. However, this view is not compatible with data showing that FSH requires IGFs to stimulate GCs, that FSH renders GCs sensitive to IGFs, and that FSH signaling interacts with factors downstream of AKT to stimulate GCs. New evidence suggests that FSH and IGF signaling pathways intersect at several levels to regulate gene expression and GC function. Conclusion FSH and locally produced IGFs form a positive feedback loop essential for preovulatory follicle formation in all species. Understanding the mechanisms by which FSH and IGFs interact to control GC function will help design new interventions to optimize follicle maturation, perfect treatment of ovulatory defects, improve in vitro fertilization, and develop new contraceptive approaches.
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Affiliation(s)
- Emily Hayes
- Department of Physiology and BiophysicsUniversity of Illinois Chicago College of MedicineChicagoIllinoisUSA
| | - Nicola Winston
- Department of Obstetrics and GynecologyUniversity of Illinois Chicago College of MedicineChicagoIllinoisUSA
| | - Carlos Stocco
- Department of Physiology and BiophysicsUniversity of Illinois Chicago College of MedicineChicagoIllinoisUSA
- Department of Obstetrics and GynecologyUniversity of Illinois Chicago College of MedicineChicagoIllinoisUSA
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3
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Martinez-Yamout MA, Nasir I, Shnitkind S, Ellis JP, Berlow RB, Kroon G, Deniz AA, Dyson HJ, Wright PE. Glutamine-rich regions of the disordered CREB transactivation domain mediate dynamic intra- and intermolecular interactions. Proc Natl Acad Sci U S A 2023; 120:e2313835120. [PMID: 37971402 PMCID: PMC10666024 DOI: 10.1073/pnas.2313835120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
The cyclic AMP response element (CRE) binding protein (CREB) is a transcription factor that contains a 280-residue N-terminal transactivation domain and a basic leucine zipper that mediates interaction with DNA. The transactivation domain comprises three subdomains, the glutamine-rich domains Q1 and Q2 and the kinase inducible activation domain (KID). NMR chemical shifts show that the isolated subdomains are intrinsically disordered but have a propensity to populate local elements of secondary structure. The Q1 and Q2 domains exhibit a propensity for formation of short β-hairpin motifs that function as binding sites for glutamine-rich sequences. These motifs mediate intramolecular interactions between the CREB Q1 and Q2 domains as well as intermolecular interactions with the glutamine-rich Q1 domain of the TATA-box binding protein associated factor 4 (TAF4) subunit of transcription factor IID (TFIID). Using small-angle X-ray scattering, NMR, and single-molecule Förster resonance energy transfer, we show that the Q1, Q2, and KID regions remain dynamically disordered in a full-length CREB transactivation domain (CREBTAD) construct. The CREBTAD polypeptide chain is largely extended although some compaction is evident in the KID and Q2 domains. Paramagnetic relaxation enhancement reveals transient long-range contacts both within and between the Q1 and Q2 domains while the intervening KID domain is largely devoid of intramolecular interactions. Phosphorylation results in expansion of the KID domain, presumably making it more accessible for binding the CBP/p300 transcriptional coactivators. Our study reveals the complex nature of the interactions within the intrinsically disordered transactivation domain of CREB and provides molecular-level insights into dynamic and transient interactions mediated by the glutamine-rich domains.
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Affiliation(s)
- Maria A. Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Irem Nasir
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Sergey Shnitkind
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Jamie P. Ellis
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Rebecca B. Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Gerard Kroon
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
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4
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Park GT, Moon JK, Park S, Park SK, Baek J, Seo MS. Genome-wide analysis of KIX gene family for organ size regulation in soybean ( Glycine max L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1252016. [PMID: 37828927 PMCID: PMC10565003 DOI: 10.3389/fpls.2023.1252016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
The KIX domain, conserved among various nuclear and co-activator factors, acts as a binding site that interacts with other transcriptional activators and co-activators, playing a crucial role in gene expression regulation. In plants, the KIX domain is involved in plant hormone signaling, stress response regulation, cell cycle control, and differentiation, indicating its potential relevance to crop productivity. This study aims to identify and characterize KIX domains within the soybean (Glycine max L.) genome to predict their potential role in improving crop productivity. The conservation and evolutionary history of the KIX domains were explored in 59 plant species, confirming the presence of the KIX domains in diverse plants. Specifically, 13 KIX domains were identified within the soybean genome and classified into four main groups, namely GmKIX8/9, GmMED15, GmHAC, and GmRECQL, through sequence alignment, structural analysis, and phylogenetic tree construction. Association analysis was performed between KIX domain haplotypes and soybean seed-related agronomic traits using re-sequencing data from a core collection of 422 accessions. The results revealed correlations between SNP variations observed in GmKIX8-3 and GmMED15-4 and soybean seed phenotypic traits. Additionally, transcriptome analysis confirmed significant expression of the KIX domains during the early stages of soybean seed development. This study provides the first characterization of the structural, expression, genomic haplotype, and molecular features of the KIX domain in soybean, offering a foundation for functional analysis of the KIX domain in soybean and other plants.
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Affiliation(s)
- Gyu Tae Park
- Crop Foundation Research Division, National Institute of Crop Sciences, Rural Development Administration (RDA), Wanju-gun, Republic of Korea
| | - Jung-Kyung Moon
- Crop Foundation Research Division, National Institute of Crop Sciences, Rural Development Administration (RDA), Wanju-gun, Republic of Korea
| | - Sewon Park
- Crop Foundation Research Division, National Institute of Crop Sciences, Rural Development Administration (RDA), Wanju-gun, Republic of Korea
| | - Soo-Kwon Park
- Crop Foundation Research Division, National Institute of Crop Sciences, Rural Development Administration (RDA), Wanju-gun, Republic of Korea
| | - JeongHo Baek
- Gene Engineering Division, National Institute of Agricultural Science, Rural Development Administration (RDA), Jeonju, Republic of Korea
| | - Mi-Suk Seo
- Crop Foundation Research Division, National Institute of Crop Sciences, Rural Development Administration (RDA), Wanju-gun, Republic of Korea
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5
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Compton SE, Kitchen-Goosen SM, DeCamp LM, Lau KH, Mabvakure B, Vos M, Williams KS, Wong KK, Shi X, Rothbart SB, Krawczyk CM, Jones RG. LKB1 controls inflammatory potential through CRTC2-dependent histone acetylation. Mol Cell 2023:S1097-2765(23)00288-5. [PMID: 37172591 DOI: 10.1016/j.molcel.2023.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/17/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023]
Abstract
Deregulated inflammation is a critical feature driving the progression of tumors harboring mutations in the liver kinase B1 (LKB1), yet the mechanisms linking LKB1 mutations to deregulated inflammation remain undefined. Here, we identify deregulated signaling by CREB-regulated transcription coactivator 2 (CRTC2) as an epigenetic driver of inflammatory potential downstream of LKB1 loss. We demonstrate that LKB1 mutations sensitize both transformed and non-transformed cells to diverse inflammatory stimuli, promoting heightened cytokine and chemokine production. LKB1 loss triggers elevated CRTC2-CREB signaling downstream of the salt-inducible kinases (SIKs), increasing inflammatory gene expression in LKB1-deficient cells. Mechanistically, CRTC2 cooperates with the histone acetyltransferases CBP/p300 to deposit histone acetylation marks associated with active transcription (i.e., H3K27ac) at inflammatory gene loci, promoting cytokine expression. Together, our data reveal a previously undefined anti-inflammatory program, regulated by LKB1 and reinforced through CRTC2-dependent histone modification signaling, that links metabolic and epigenetic states to cell-intrinsic inflammatory potential.
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Affiliation(s)
- Shelby E Compton
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Susan M Kitchen-Goosen
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA; Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Lisa M DeCamp
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA; Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Kin H Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Batsirai Mabvakure
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Matthew Vos
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA; Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Kelsey S Williams
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA; Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Xiaobing Shi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Connie M Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA; Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Russell G Jones
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA; Metabolism and Nutrition (MeNu) Program, Van Andel Institute, Grand Rapids, MI, USA.
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6
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Bentley EP, Scholl D, Wright PE, Deniz AA. Coupling of binding and differential subdomain folding of the intrinsically disordered transcription factor CREB. FEBS Lett 2023; 597:917-932. [PMID: 36480418 PMCID: PMC10089947 DOI: 10.1002/1873-3468.14554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
The cyclic AMP response element binding protein (CREB) contains a basic leucine zipper motif (bZIP) that forms a coiled coil structure upon dimerization and specific DNA binding. Although this state is well characterized, key features of CREB bZIP binding and folding are not well understood. We used single-molecule Förster resonance energy transfer (smFRET) to probe conformations of CREB bZIP subdomains. We found differential folding of the basic region and leucine zipper in response to different binding partners; a strong and previously unreported DNA-independent dimerization affinity; folding upon binding to nonspecific DNA; and evidence of long-range interdomain interactions in full-length CREB that modulate DNA binding. These studies provide new insights into DNA binding and dimerization and have implications for CREB function.
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Affiliation(s)
- Emily P. Bentley
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Daniel Scholl
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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7
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Liang ZX, Liu HS, Xiong L, Zeng ZW, Zheng XB, Kang L, Lan P, Wu XR. GAS6 From CD200+ Adipose-Derived Stem Cells Mitigates Colonic Inflammation in a Macrophage-Dependent Manner. J Crohns Colitis 2023; 17:289-301. [PMID: 36006655 DOI: 10.1093/ecco-jcc/jjac123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS Stem cell therapy is a promising cell-based treatment modality for inflammatory bowel diseases [IBD], but its application is limited by the nature of cell heterogeneity. METHODS Single-cell RNA-sequencing was performed on the adipose-derived stem cells [ADSCs]. The in vitro immunomodulatory effect of ADSCs was evaluated by co-culturing with human CD4+ T cells or macrophages. The in vivo therapeutic value of ADSCs was assessed using a murine colitis model induced by dextran sulphate sodium [DSS] or 2,4,6-trinitrobenzene sulphonic acid [TNBS]. RESULTS CD200+ ADSCs were identified as a novel subpopulation of ADSCs, based on gene ontology analysis of immunoregulatory functions. The immunoregulatory functions of these cells were further confirmed by co-culturing with CD4+ T cells or macrophages. Administration of CD200+ ADSCs effectively reduced intestinal inflammation in IBD mice models. Furthermore, we found CD200+ ADSCs-derived GAS6 exerted protective effects on experimental colitis by promoting macrophage M2 polarization via the Mer/PI3K/Akt/GSK3β signalling pathway. CONCLUSIONS This study uncovered the heterogeneity in ADSCs, in which CD200+ ADSCs presents as an alternative to conventional treatment of IBD.
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Affiliation(s)
- Zhen-Xing Liang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Hua-Shan Liu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li Xiong
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zi-Wei Zeng
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Bin Zheng
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liang Kang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ping Lan
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Xian-Rui Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
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8
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Mutation in Smek2 regulating hepatic glucose metabolism causes hypersarcosinemia and hyperhomocysteinemia in rats. Sci Rep 2023; 13:3053. [PMID: 36810603 PMCID: PMC9944932 DOI: 10.1038/s41598-022-26115-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/09/2022] [Indexed: 02/24/2023] Open
Abstract
Suppressor of mek1 (Dictyostelium) homolog 2 (Smek2), was identified as one of the responsible genes for diet-induced hypercholesterolemia (DIHC) of exogenously hypercholesterolemic (ExHC) rats. A deletion mutation in Smek2 leads to DIHC via impaired glycolysis in the livers of ExHC rats. The intracellular role of Smek2 remains obscure. We used microarrays to investigate Smek2 functions with ExHC and ExHC.BN-Dihc2BN congenic rats that harbor a non-pathological Smek2 allele from Brown-Norway rats on an ExHC background. Microarray analysis revealed that Smek2 dysfunction leads to extremely low sarcosine dehydrogenase (Sardh) expression in the liver of ExHC rats. Sarcosine dehydrogenase demethylates sarcosine, a byproduct of homocysteine metabolism. The ExHC rats with dysfunctional Sardh developed hypersarcosinemia and homocysteinemia, a risk factor for atherosclerosis, with or without dietary cholesterol. The mRNA expression of Bhmt, a homocysteine metabolic enzyme and the hepatic content of betaine (trimethylglycine), a methyl donor for homocysteine methylation were low in ExHC rats. Results suggest that homocysteine metabolism rendered fragile by a shortage of betaine results in homocysteinemia, and that Smek2 dysfunction causes abnormalities in sarcosine and homocysteine metabolism.
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9
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Sheikh A, Fleckenstein JM. Interactions of pathogenic Escherichia coli with CEACAMs. Front Immunol 2023; 14:1120331. [PMID: 36865539 PMCID: PMC9971599 DOI: 10.3389/fimmu.2023.1120331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
The pathogenic Escherichia coli can be parsed into specific variants (pathovars) depending on their phenotypic behavior and/or expression of specific virulence factors. These pathogens are built around chromosomally-encoded core attributes and through acquisition of specific virulence genes that direct their interaction with the host. Engagement of E. coli pathovars with CEACAMs is determined both by core elements common to all E. coli as well as extrachromosomally-encoded pathovar-specific virulence traits, which target amino terminal immunoglobulin variable-like (IgV) regions of CEACAMs. Emerging data suggests that engagement of CEACAMs does not unilaterally benefit the pathogen and that these interactions may also provide an avenue for pathogen elimination.
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Affiliation(s)
- Alaullah Sheikh
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - James M. Fleckenstein
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Infectious Diseases, Medicine Service, Veterans Affairs Saint Louis Health Care System, Saint Louis, MO, United States
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10
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Kim J, Kaang BK. Cyclic AMP response element-binding protein (CREB) transcription factor in astrocytic synaptic communication. Front Synaptic Neurosci 2023; 14:1059918. [PMID: 36685081 PMCID: PMC9845270 DOI: 10.3389/fnsyn.2022.1059918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/24/2022] [Indexed: 01/05/2023] Open
Abstract
Astrocytes are known to actively participate in synaptic communication by forming structures called tripartite synapses. These synapses consist of presynaptic axon terminals, postsynaptic dendritic spines, and astrocytic processes where astrocytes release and receive transmitters. Although the transcription factor cyclic AMP response element (CRE)-binding protein (CREB) has been actively studied as an important factor for mediating synaptic activity-induced responses in neurons, its role in astrocytes is relatively unknown. Synaptic signals are known to activate various downstream pathways in astrocytes, which can activate the CREB transcription factor. Therefore, there is a need to summarize studies on astrocytic intracellular pathways that are induced by synaptic communication resulting in activation of the CREB pathway. In this review, we discuss the various neurotransmitter receptors and intracellular pathways that can induce CREB activation and CREB-induced gene regulation in astrocytes.
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11
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Differential Regulation of the BDNF Gene in Cortical and Hippocampal Neurons. J Neurosci 2022; 42:9110-9128. [PMID: 36316156 PMCID: PMC9761680 DOI: 10.1523/jneurosci.2535-21.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 09/18/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is a widely expressed neurotrophin that supports the survival, differentiation, and signaling of various neuronal populations. Although it has been well described that expression of BDNF is strongly regulated by neuronal activity, little is known whether regulation of BDNF expression is similar in different brain regions. Here, we focused on this fundamental question using neuronal populations obtained from rat cerebral cortices and hippocampi of both sexes. First, we thoroughly characterized the role of the best-described regulators of BDNF gene - cAMP response element binding protein (CREB) family transcription factors, and show that activity-dependent BDNF expression depends more on CREB and the coactivators CREB binding protein (CBP) and CREB-regulated transcriptional coactivator 1 (CRTC1) in cortical than in hippocampal neurons. Our data also reveal an important role of CREB in the early induction of BDNF mRNA expression after neuronal activity and only modest contribution after prolonged neuronal activity. We further corroborated our findings at BDNF protein level. To determine the transcription factors regulating BDNF expression in these rat brain regions in addition to CREB family, we used in vitro DNA pulldown assay coupled with mass spectrometry, chromatin immunoprecipitation (ChIP), and bioinformatics, and propose a number of neurodevelopmentally important transcription factors, such as FOXP1, SATB2, RAI1, BCL11A, and TCF4 as brain region-specific regulators of BDNF expression. Together, our data reveal complicated brain region-specific fine-tuning of BDNF expression.SIGNIFICANCE STATEMENT To date, majority of the research has focused on the regulation of brain-derived neurotrophic factor (BDNF) in the brain but much less is known whether the regulation of BDNF expression is universal in different brain regions and neuronal populations. Here, we report that the best described regulators of BDNF gene from the cAMP-response element binding protein (CREB) transcription factor family have a more profound role in the activity-dependent regulation of BDNF in cortex than in hippocampus. Our results indicate a brain region-specific fine tuning of BDNF expression. Moreover, we have used unbiased determination of novel regulators of the BDNF gene and report a number of neurodevelopmentally important transcription factors as novel potential regulators of the BDNF expression.
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12
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Circ-CREBBP inhibits sperm apoptosis via the PI3K-Akt signaling pathway by sponging miR-10384 and miR-143-3p. Commun Biol 2022; 5:1339. [PMID: 36476986 PMCID: PMC9729231 DOI: 10.1038/s42003-022-04263-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Male reproductive diseases are becoming increasingly prominent, and sperm quality is an important indicator to reflect these diseases. Seminal plasma extracellular vesicles (SPEVs) are involved in sperm motility. However, their effects on sperm remain unclear. Here, we identified 222 differentially expressed circRNAs in SPEVs between boars with high or low sperm motility. We found that circ-CREBBP promoted sperm motility and inhibited sperm apoptosis by sponging miR-10384 and miR-143-3p. In addition, miR-10384 and miR-143-3p can regulate the expression of MCL1, CREB1 and CREBBP. Furthermore, we demonstrated that MCL1 interacted directly with BAX and that CREBBP interacted with CREB1 in sperm. We showed that inhibition of circ-CREBBP can reduce the expression of MCL1, CREB1 and CREBBP and increase the expression of BAX and CASP3, thus promoting sperm apoptosis. Our results suggest that circ-CREBBP may be a promising biomarker and therapeutic target for male reproductive diseases.
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Cho JH, Kim K, Cho HC, Lee J, Kim EK. Silencing of hypothalamic FGF11 prevents diet-induced obesity. Mol Brain 2022; 15:75. [PMID: 36064426 PMCID: PMC9447329 DOI: 10.1186/s13041-022-00962-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/21/2022] [Indexed: 11/18/2022] Open
Abstract
Fibroblast growth factor 11 (FGF11) is a member of the intracellular fibroblast growth factor family. Here, we report the central role of FGF11 in the regulation of metabolism. Lentiviral injection of Fgf11 shRNA into the arcuate nucleus of the mouse hypothalamus decreased weight gain and fat mass, increased brown adipose tissue thermogenesis, and improved glucose and insulin intolerances under high-fat diet conditions. Fgf11 was expressed in the NPY–expressing neurons, and Fgf11 knockdown considerably decreased Npy expression and projection, leading to increased expression of tyrosine hydroxylase in the paraventricular nucleus. Mechanistically, FGF11 regulated Npy gene expression through the glycogen synthase kinase 3–cAMP response element-binding protein pathway. Our study defines the physiological significance of hypothalamic FGF11 in the regulation of metabolism in response to overnutrition such as high-fat diet.
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Affiliation(s)
- Jae Hyun Cho
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, 333, Techno Jungang-Daero, Hyeonpung-Myeon, Daegu, Dalseonggun, 42988, South Korea
| | - Kyungchan Kim
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, 333, Techno Jungang-Daero, Hyeonpung-Myeon, Daegu, Dalseonggun, 42988, South Korea
| | - Han Chae Cho
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, 333, Techno Jungang-Daero, Hyeonpung-Myeon, Daegu, Dalseonggun, 42988, South Korea
| | - Jaemeun Lee
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, 333, Techno Jungang-Daero, Hyeonpung-Myeon, Daegu, Dalseonggun, 42988, South Korea
| | - Eun-Kyoung Kim
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, 333, Techno Jungang-Daero, Hyeonpung-Myeon, Daegu, Dalseonggun, 42988, South Korea. .,Neurometabolomics Research Center, Daegu Gyeongbuk Institute of Science and Technology, 333, Techno Jungang-Daero, Hyeonpung-Myeon, Daegu, Dalseonggun, 42988, South Korea.
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Król M, Kupnicka P, Bosiacki M, Chlubek D. Mechanisms Underlying Anti-Inflammatory and Anti-Cancer Properties of Stretching-A Review. Int J Mol Sci 2022; 23:ijms231710127. [PMID: 36077525 PMCID: PMC9456560 DOI: 10.3390/ijms231710127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 02/07/2023] Open
Abstract
Stretching is one of the popular elements in physiotherapy and rehabilitation. When correctly guided, it can help minimize or slow down the disabling effects of chronic health conditions. Most likely, the benefits are associated with reducing inflammation; recent studies demonstrate that this effect from stretching is not just systemic but also local. In this review, we present the current body of knowledge on the anti-inflammatory properties of stretching at a molecular level. A total of 22 papers, focusing on anti-inflammatory and anti-cancer properties of stretching, have been selected and reviewed. We show the regulation of oxidative stress, the expression of pro- and anti-inflammatory genes and mediators, and remodeling of the extracellular matrix, expressed by changes in collagen and matrix metalloproteinases levels, in tissues subjected to stretching. We point out that a better understanding of the anti-inflammatory properties of stretching may result in increasing its importance in treatment and recovery from diseases such as osteoarthritis, systemic sclerosis, and cancer.
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Affiliation(s)
- Małgorzata Król
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Patrycja Kupnicka
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
- Correspondence:
| | - Mateusz Bosiacki
- Chair and Department of Functional Diagnostics and Physical Medicine, Pomeranian Medical University, Żołnierska 54, 71-210 Szczecin, Poland
| | - Dariusz Chlubek
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
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Activation of cAMP Signaling in Response to α-Phellandrene Promotes Vascular Endothelial Growth Factor Levels and Proliferation in Human Dermal Papilla Cells. Int J Mol Sci 2022; 23:ijms23168959. [PMID: 36012223 PMCID: PMC9409021 DOI: 10.3390/ijms23168959] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Dermal papilla cells (DPCs) are growth factor reservoirs that are specialized for hair morphogenesis and regeneration. Due to their essential role in hair growth, DPCs are commonly used as an in vitro model to investigate the effects of hair growth-regulating compounds and their molecular mechanisms of action. Cyclic adenosine monophosphate (cAMP), an intracellular second messenger, is currently employed as a growth-promoting target molecule. In a pilot test, we found that α-phellandrene, a naturally occurring phytochemical, increased cAMP levels in DPCs. Therefore, we sought to determine whether α-phellandrene increases growth factors and proliferation in human DPCs and to identify the underlying mechanisms. We demonstrated that α-phellandrene promotes cell proliferation concentration-dependently. In addition, it increases the cAMP downstream effectors, such as protein kinase A catalytic subunit (PKA Cα) and phosphorylated cAMP-responsive element-binding protein (CREB). Also, among the CREB-dependent growth factor candidates, we identified that α-phellandrene selectively upregulated vascular endothelial growth factor (VEGF) mRNA expression in DPCs. Notably, the beneficial effects of α-phellandrene were nullified by a cAMP inhibitor. This study demonstrated the cAMP-mediated growth effects in DPCs and the therapeutic potential of α-phellandrene for preventing hair loss.
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Icariin promotes mouse Leydig cell testosterone synthesis via the Esr1/Src/Akt/Creb/Sf-1 pathway. Toxicol Appl Pharmacol 2022; 441:115969. [DOI: 10.1016/j.taap.2022.115969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 11/21/2022]
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A propolis-derived small molecule ameliorates metabolic syndrome in obese mice by targeting the CREB/CRTC2 transcriptional complex. Nat Commun 2022; 13:246. [PMID: 35017472 PMCID: PMC8752738 DOI: 10.1038/s41467-021-27533-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 11/16/2021] [Indexed: 12/28/2022] Open
Abstract
The molecular targets and mechanisms of propolis ameliorating metabolic syndrome are not fully understood. Here, we report that Brazilian green propolis reduces fasting blood glucose levels in obese mice by disrupting the formation of CREB/CRTC2 transcriptional complex, a key regulator of hepatic gluconeogenesis. Using a mammalian two-hybrid system based on CREB-CRTC2, we identify artepillin C (APC) from propolis as an inhibitor of CREB-CRTC2 interaction. Without apparent toxicity, APC protects mice from high fat diet-induced obesity, decreases fasting glucose levels, enhances insulin sensitivity and reduces lipid levels in the serum and liver by suppressing CREB/CRTC2-mediated both gluconeogenic and SREBP transcriptions. To develop more potential drugs from APC, we designed and found a novel compound, A57 that exhibits higher inhibitory activity on CREB-CRTC2 association and better capability of improving insulin sensitivity in obese animals, as compared with APC. In this work, our results indicate that CREB/CRTC2 is a suitable target for developing anti-metabolic syndrome drugs.
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Wu L, Zhang Y, Ren J. Epigenetic modification in alcohol use disorder and alcoholic cardiomyopathy: From pathophysiology to therapeutic opportunities. Metabolism 2021; 125:154909. [PMID: 34627873 DOI: 10.1016/j.metabol.2021.154909] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 02/07/2023]
Abstract
Alcohol consumption prompts detrimental psychological, pathophysiological and health issues, representing one of the major causes of death worldwide. Alcohol use disorder (AUD), which is characterized by compulsive alcohol intake and loss of control over alcohol usage, arises from a complex interplay between genetic and environmental factors. More importantly, long-term abuse of alcohol is often tied with unfavorable cardiac remodeling and contractile alterations, a cadre of cardiac responses collectively known as alcoholic cardiomyopathy (ACM). Recent evidence has denoted a pivotal role for ethanol-triggered epigenetic modifications, the interface between genome and environmental cues, in the organismal and cellular responses to ethanol exposure. To-date, three major epigenetic mechanisms (DNA methylation, histone modifications, and RNA-based mechanisms) have been identified for the onset and development of AUD and ACM. Importantly, these epigenetic changes induced by alcohol may be detectable in the blood, thus offering diagnostic, therapeutic, and prognostic promises of epigenetic markers for AUD and alcoholic complications. In addition, several epigenetic drugs have shown efficacies in the management of alcohol abuse, loss of control for alcohol usage, relapse, drinking-related anxiety and behavior in withdrawal. In this context, medications targeting epigenetic modifications may hold promises for pharmaceutical management of AUD and ACM.
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Affiliation(s)
- Lin Wu
- Department of Cardiology and Shanghai Institute of Cardiovascular Diseases, Fudan University Zhongshan Hospital, Shanghai 200032, China
| | - Yingmei Zhang
- Department of Cardiology and Shanghai Institute of Cardiovascular Diseases, Fudan University Zhongshan Hospital, Shanghai 200032, China
| | - Jun Ren
- Department of Cardiology and Shanghai Institute of Cardiovascular Diseases, Fudan University Zhongshan Hospital, Shanghai 200032, China; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
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Fatafta H, Kav B, Bundschuh BF, Loschwitz J, Strodel B. Disorder-to-order transition of the amyloid-β peptide upon lipid binding. Biophys Chem 2021; 280:106700. [PMID: 34784548 DOI: 10.1016/j.bpc.2021.106700] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 12/18/2022]
Abstract
There is mounting evidence that Alzheimer's disease progression and severity are linked to neuronal membrane damage caused by aggregates of the amyloid-β (Aβ) peptide. However, the detailed mechanism behind the membrane damage is not well understood yet. Recently, the lipid-chaperone hypothesis has been put forward, based on which the formation of complexes between Aβ and free lipids enables an easy insertion of Aβ into membranes. In order to test this hypothesis, we performed numerous all-atom molecular dynamics simulations. We studied the complex formation between individual lipids, considering both POPC and DPPC, and Aβ and examined whether the resulting complexes would be able to insert into lipid membranes. Complex formation at a one-to-one ratio was readily observed, yet with minimal effects on Aβ's characteristics. Most importantly, the peptide remains largely disordered in 1:1 complexes, and the complex does not insert into the membrane; instead, it is adsorbed to the membrane surface. The results change considerably once Aβ forms a complex with a POPC cluster composed of three lipid molecules. The hydrophobic interactions between Aβ and the lipid tails cause the peptide to fold into either a helical or a β-sheet structure. These observations provide atomic insight into the disorder-to-order transition that is needed for membrane insertion or amyloid aggregation to proceed.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Bastian F Bundschuh
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany
| | - Jennifer Loschwitz
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitütstrasse 1, 40225 Düsseldorf, Germany.
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20
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Cooper DG, Jiang Y, Skuodas S, Wang L, Fassler JS. Possible Role for Allelic Variation in Yeast MED15 in Ecological Adaptation. Front Microbiol 2021; 12:741572. [PMID: 34733258 PMCID: PMC8558680 DOI: 10.3389/fmicb.2021.741572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
The propensity for Saccharomyces cerevisiae yeast to ferment sugars into ethanol and CO2 has long been useful in the production of a wide range of food and drink. In the production of alcoholic beverages, the yeast strain selected for fermentation is crucial because not all strains are equally proficient in tolerating fermentation stresses. One potential mechanism by which domesticated yeast may have adapted to fermentation stresses is through changes in the expression of stress response genes. MED15 is a general transcriptional regulator and RNA Pol II Mediator complex subunit which modulates the expression of many metabolic and stress response genes. In this study, we explore the role of MED15 in alcoholic fermentation. In addition, we ask whether MED15 alleles from wine, sake or palm wine yeast improve fermentation activity and grape juice fermentation stress responses. And last, we investigate to what extent any differences in activity are due to allelic differences in the lengths of three polyglutamine tracts in MED15. We find that strains lacking MED15 are deficient in fermentation and fermentation stress responses and that MED15 alleles from alcoholic beverage yeast strains can improve both the fermentation capacity and the response to ethanol stresses when transplanted into a standard laboratory strain. Finally, we find that polyglutamine tract length in the Med15 protein is one determinant in the efficiency of the alcoholic fermentation process. These data lead to a working model in which polyglutamine tract length and other types of variability within transcriptional hubs like the Mediator subunit, Med15, may contribute to a reservoir of transcriptional profiles that may provide a fitness benefit in the face of environmental fluctuations.
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Affiliation(s)
- David G Cooper
- Biology Department, University of Iowa, Iowa City, IA, United States
| | - Yishuo Jiang
- Biology Department, University of Iowa, Iowa City, IA, United States
| | - Sydney Skuodas
- Biology Department, University of Iowa, Iowa City, IA, United States
| | - Luying Wang
- Biology Department, University of Iowa, Iowa City, IA, United States
| | - Jan S Fassler
- Biology Department, University of Iowa, Iowa City, IA, United States
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21
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Wang L, Ruan C, Bao A, Li H. Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn. BMC PLANT BIOLOGY 2021; 21:464. [PMID: 34641783 PMCID: PMC8513341 DOI: 10.1186/s12870-021-03239-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 09/29/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Yellowhorn (Xanthoceras sorbifolium), an endemic woody oil-bearing tree, has become economically important and is widely cultivated in northern China for bioactive oil production. However, the regulatory mechanisms of seed development and lipid biosynthesis affecting oil production in yellowhorn are still elusive. MicroRNAs (miRNAs) play crucial roles in diverse aspects of biological and metabolic processes in seeds, especially in seed development and lipid metabolism. It is still unknown how the miRNAs regulate the seed development and lipid biosynthesis in yellowhorn. RESULTS Here, based on investigations of differences in the seed growth tendency and embryo oil content between high-oil-content and low-oil-content lines, we constructed small RNA libraries from yellowhorn embryos at four seed development stages of the two lines and then profiled small RNA expression using high-throughput sequencing. A total of 249 known miRNAs from 46 families and 88 novel miRNAs were identified. Furthermore, by pairwise comparisons among the four seed development stages in each line, we found that 64 miRNAs (53 known and 11 novel miRNAs) were differentially expressed in the two lines. Across the two lines, 15, 11, 10, and 7 differentially expressed miRNAs were detected at 40, 54, 68, and 81 days after anthesis, respectively. Bioinformatic analysis was used to predict a total of 2654 target genes for 141 differentially expressed miRNAs (120 known and 21 novel miRNAs). Most of these genes were involved in the fatty acid biosynthetic process, regulation of transcription, nucleus, and response to auxin. Using quantitative real-time PCR and an integrated analysis of miRNA and mRNA expression, miRNA-target regulatory modules that may be involved in yellowhorn seed size, weight, and lipid biosynthesis were identified, such as miR172b-ARF2 (auxin response factor 2), miR7760-p3_1-AGL61 (AGAMOUS-LIKE 61), miR319p_1-FAD2-2 (omega-6 fatty acid desaturase 2-2), miR5647-p3_1-DGAT1 (diacylglycerol acyltransferase 1), and miR7760-p5_1-MED15A (Mediator subunit 15a). CONCLUSIONS This study provides new insights into the important regulatory roles of miRNAs in the seed development and lipid biosynthesis in yellowhorn. Our results will be valuable for dissecting the post-transcriptional and transcriptional regulation of seed development and lipid biosynthesis, as well as improving yellowhorn in northern China.
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Affiliation(s)
- Li Wang
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao, 266100, China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China.
| | - Aomin Bao
- Institute of Economic Forest, Tongliao Academy of Forestry Science and Technology, Tongliao, 028000, China
| | - He Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
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22
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Ramms DJ, Raimondi F, Arang N, Herberg FW, Taylor SS, Gutkind JS. G αs-Protein Kinase A (PKA) Pathway Signalopathies: The Emerging Genetic Landscape and Therapeutic Potential of Human Diseases Driven by Aberrant G αs-PKA Signaling. Pharmacol Rev 2021; 73:155-197. [PMID: 34663687 PMCID: PMC11060502 DOI: 10.1124/pharmrev.120.000269] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many of the fundamental concepts of signal transduction and kinase activity are attributed to the discovery and crystallization of cAMP-dependent protein kinase, or protein kinase A. PKA is one of the best-studied kinases in human biology, with emphasis in biochemistry and biophysics, all the way to metabolism, hormone action, and gene expression regulation. It is surprising, however, that our understanding of PKA's role in disease is largely underappreciated. Although genetic mutations in the PKA holoenzyme are known to cause diseases such as Carney complex, Cushing syndrome, and acrodysostosis, the story largely stops there. With the recent explosion of genomic medicine, we can finally appreciate the broader role of the Gαs-PKA pathway in disease, with contributions from aberrant functioning G proteins and G protein-coupled receptors, as well as multiple alterations in other pathway components and negative regulators. Together, these represent a broad family of diseases we term the Gαs-PKA pathway signalopathies. The Gαs-PKA pathway signalopathies encompass diseases caused by germline, postzygotic, and somatic mutations in the Gαs-PKA pathway, with largely endocrine and neoplastic phenotypes. Here, we present a signaling-centric review of Gαs-PKA-driven pathophysiology and integrate computational and structural analysis to identify mutational themes commonly exploited by the Gαs-PKA pathway signalopathies. Major mutational themes include hotspot activating mutations in Gαs, encoded by GNAS, and mutations that destabilize the PKA holoenzyme. With this review, we hope to incite further study and ultimately the development of new therapeutic strategies in the treatment of a wide range of human diseases. SIGNIFICANCE STATEMENT: Little recognition is given to the causative role of Gαs-PKA pathway dysregulation in disease, with effects ranging from infectious disease, endocrine syndromes, and many cancers, yet these disparate diseases can all be understood by common genetic themes and biochemical signaling connections. By highlighting these common pathogenic mechanisms and bridging multiple disciplines, important progress can be made toward therapeutic advances in treating Gαs-PKA pathway-driven disease.
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Affiliation(s)
- Dana J Ramms
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Francesco Raimondi
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Nadia Arang
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Friedrich W Herberg
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Susan S Taylor
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - J Silvio Gutkind
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
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23
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Strodel B. Energy landscapes of protein aggregation and conformation switching in intrinsically disordered proteins. J Mol Biol 2021; 433:167182. [PMID: 34358545 DOI: 10.1016/j.jmb.2021.167182] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 11/24/2022]
Abstract
The protein folding problem was apparently solved recently by the advent of a deep learning method for protein structure prediction called AlphaFold. However, this program is not able to make predictions about the protein folding pathways. Moreover, it only treats about half of the human proteome, as the remaining proteins are intrinsically disordered or contain disordered regions. By definition these proteins differ from natively folded proteins and do not adopt a properly folded structure in solution. However these intrinsically disordered proteins (IDPs) also systematically differ in amino acid composition and uniquely often become folded upon binding to an interaction partner. These factors preclude solving IDP structures by current machine-learning methods like AlphaFold, which also cannot solve the protein aggregation problem, since this meta-folding process can give rise to different aggregate sizes and structures. An alternative computational method is provided by molecular dynamics simulations that already successfully explored the energy landscapes of IDP conformational switching and protein aggregation in multiple cases. These energy landscapes are very different from those of 'simple' protein folding, where one energy funnel leads to a unique protein structure. Instead, the energy landscapes of IDP conformational switching and protein aggregation feature a number of minima for different competing low-energy structures. In this review, I discuss the characteristics of these multifunneled energy landscapes in detail, illustrated by molecular dynamics simulations that elucidated the underlying conformational transitions and aggregation processes.
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Affiliation(s)
- Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstrasse 1, 40225Düsseldorf, Germany
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24
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Taurochenodeoxycholic acid mediates cAMP-PKA-CREB signaling pathway. Chin J Nat Med 2021; 18:898-906. [PMID: 33357720 DOI: 10.1016/s1875-5364(20)60033-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 12/12/2022]
Abstract
Taurochenodeoxycholic acid (TCDCA) is one of the main effective components of bile acid, playing critical roles in apoptosis and immune responses through the TGR5 receptor. In this study, we reveal the interaction between TCDCA and TGR5 receptor in TGR5-knockdown H1299 cells and the regulation of inflammation via the cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA)-cAMP response element binding (CREB) signal pathway in NR8383 macrophages. In TGR5-knockdown H1299 cells, TCDCA significantly activated cAMP level via TGR5 receptor, indicating TCDCA can bind to TGR5; in NR8383 macrophages TCDCA increased cAMP content compared to treatment with the adenylate cyclase (AC) inhibitor SQ22536. Moreover, activated cAMP can significantly enhance gene expression and protein levels of its downstream proteins PKA and CREB compared with groups of inhibitors. Additionally, TCDCA decreased tumour necrosis factor-α (TNF-α), interleukin-1β (IL-1β), IL-6, IL-8 and IL-12 through nuclear factor kappa light chain enhancer of activated B cells (NF-κB) activity. PKA and CREB are primary regulators of anti-inflammatory and immune response. Our results thus demonstrate TCDCA plays an essential anti-inflammatory role via the signaling pathway of cAMP-PKA-CREB induced by TGR5 receptor.
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Pan L, Zhang XF, Wei WS, Zhang J, Li ZZ. The cardiovascular protective effect and mechanism of calycosin and its derivatives. Chin J Nat Med 2021; 18:907-915. [PMID: 33357721 DOI: 10.1016/s1875-5364(20)60034-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Indexed: 12/12/2022]
Abstract
Cardiovascular disease is the main cause of mortality and morbidity in the world, especially in developing countries. Drug therapy is one of the main ways to treat cardiovascular diseases. Among them, great progress has been made in the treatment of cardiovascular diseases with traditional Chinese medicine. In terms of experimental research, the mechanism of traditional Chinese medicine in the treatment of cardiovascular diseases has been thoroughly discussed in vitro and in vivo. In terms of clinical treatment, traditional Chinese medicine with flavonoids, saponins and alkaloids as the main effective components has a definite effect on the treatment of cardiovascular diseases such as arrhythmia, myocardial ischemia, angina pectoris and myocardial infarction, with high safety and good application prospects. With the further research on the effective ingredients, mechanism and adverse reactions of traditional Chinese medicine, it will be beneficial to the effectiveness of traditional Chinese medicine, reduce side effects and promote the modernization of traditional Chinese medicine. Calycosin and its derivatives, the main bioactive flavonoids in Astragalus membranaceus have multiple biological effects, such as antioxidant, pro-angiogenesis, anti-tumour, and anti-inflammatory effects. Based on the above biological effects, calycosin has been shown to have good potential for cardiovascular protection. The potent antioxidant effect of calycosin may play an important role in the cardiovascular protective potential. For injured cardiac myocytes, calycosin and its derivatives can alleviate the cell damage mainly marked by the release of myocardial enzymes and reduce the death level of cardiac myocytes mainly characterized by apoptosis through various mechanisms. For vascular endothelial cells, calycosin also has multiple effects and multiple mechanisms, such as promoting vascular endothelial cell proliferation, exerting vasodilating effect and directly affecting the synthesis function of endothelial cells. The present review will address the bioactivity of calycosin in cardiovascular diseases such as protective effects on cardiac myocytes and vascular endothelial cells and elucidate main mechanism of calycosin and its derivatives to exert the above biological effects.
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Affiliation(s)
- Li Pan
- Department of Cardiopulmonary Bypass, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Xuan-Fen Zhang
- Department of Orthopaedic Surgery, Lanzhou University Second Hospital, Lanzhou 730000, China.
| | - Wan-Sheng Wei
- Department of Cardiopulmonary Bypass, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Jing Zhang
- Department of Cardiopulmonary Bypass, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Zhen-Zhen Li
- Department of Cardiopulmonary Bypass, Lanzhou University Second Hospital, Lanzhou 730000, China
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26
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Chen B, Wang P, Liang X, Jiang C, Ge Y, Dworkin LD, Gong R. Permissive effect of GSK3β on profibrogenic plasticity of renal tubular cells in progressive chronic kidney disease. Cell Death Dis 2021; 12:432. [PMID: 33931588 PMCID: PMC8087712 DOI: 10.1038/s41419-021-03709-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 02/06/2023]
Abstract
Renal tubular epithelial cells (TECs) play a key role in renal fibrogenesis. After persistent injuries that are beyond self-healing capacity, TECs will dedifferentiate, undergo growth arrest, convert to profibrogenic phenotypes, and resort to maladaptive plasticity that ultimately results in renal fibrosis. Evidence suggests that glycogen synthase kinase (GSK) 3β is centrally implicated in kidney injury. However, its role in renal fibrogenesis is obscure. Analysis of publicly available kidney transcriptome database demonstrated that patients with progressive chronic kidney disease (CKD) exhibited GSK3β overexpression in renal tubulointerstitium, in which the predefined hallmark gene sets implicated in fibrogenesis were remarkably enriched. In vitro, TGF-β1 treatment augmented GSK3β expression in TECs, concomitant with dedifferentiation, cell cycle arrest at G2/M phase, excessive accumulation of extracellular matrix, and overproduction of profibrotic cytokines like PAI-1 and CTGF. All these profibrogenic phenotypes were largely abrogated by GSK3β inhibitors or by ectopic expression of a dominant-negative mutant of GSK3β but reinforced in cells expressing the constitutively active mutant of GSK3β. Mechanistically, GSK3β suppressed, whereas inhibiting GSK3β facilitated, the activity of cAMP response element-binding protein (CREB), which competes for CREB-binding protein, a transcriptional coactivator essential for TGF-β1/Smad signaling pathway to drive TECs profibrogenic plasticity. In vivo, in mice with folic acid-induced progressive CKD, targeting of GSK3β in renal tubules via genetic ablation or by microdose lithium mitigated the profibrogenic plasticity of TEC, concomitant with attenuated interstitial fibrosis and tubular atrophy. Collectively, GSK3β is likely a pragmatic therapeutic target for averting profibrogenic plasticity of TECs and improving renal fibrosis.
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Affiliation(s)
- Bohan Chen
- Division of Kidney Disease and Hypertension, Department of Medicine, Rhode Island Hospital, Brown University School of Medicine, Providence, RI, 02903, USA
- Division of Nephrology, Department of Medicine, University of Toledo College of Medicine, Toledo, OH, 43614, USA
| | - Pei Wang
- Division of Kidney Disease and Hypertension, Department of Medicine, Rhode Island Hospital, Brown University School of Medicine, Providence, RI, 02903, USA
| | - Xianhui Liang
- Division of Kidney Disease and Hypertension, Department of Medicine, Rhode Island Hospital, Brown University School of Medicine, Providence, RI, 02903, USA
| | - Chunming Jiang
- Division of Kidney Disease and Hypertension, Department of Medicine, Rhode Island Hospital, Brown University School of Medicine, Providence, RI, 02903, USA
| | - Yan Ge
- Division of Kidney Disease and Hypertension, Department of Medicine, Rhode Island Hospital, Brown University School of Medicine, Providence, RI, 02903, USA
- Division of Nephrology, Department of Medicine, University of Toledo College of Medicine, Toledo, OH, 43614, USA
| | - Lance D Dworkin
- Division of Kidney Disease and Hypertension, Department of Medicine, Rhode Island Hospital, Brown University School of Medicine, Providence, RI, 02903, USA
- Division of Nephrology, Department of Medicine, University of Toledo College of Medicine, Toledo, OH, 43614, USA
| | - Rujun Gong
- Division of Kidney Disease and Hypertension, Department of Medicine, Rhode Island Hospital, Brown University School of Medicine, Providence, RI, 02903, USA.
- Division of Nephrology, Department of Medicine, University of Toledo College of Medicine, Toledo, OH, 43614, USA.
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27
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Creb5 establishes the competence for Prg4 expression in articular cartilage. Commun Biol 2021; 4:332. [PMID: 33712729 PMCID: PMC7955038 DOI: 10.1038/s42003-021-01857-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 02/12/2021] [Indexed: 12/13/2022] Open
Abstract
A hallmark of cells comprising the superficial zone of articular cartilage is their expression of lubricin, encoded by the Prg4 gene, that lubricates the joint and protects against the development of arthritis. Here, we identify Creb5 as a transcription factor that is specifically expressed in superficial zone articular chondrocytes and is required for TGF-β and EGFR signaling to induce Prg4 expression. Notably, forced expression of Creb5 in chondrocytes derived from the deep zone of the articular cartilage confers the competence for TGF-β and EGFR signals to induce Prg4 expression. Chromatin-IP and ATAC-Seq analyses have revealed that Creb5 directly binds to two Prg4 promoter-proximal regulatory elements, that display an open chromatin conformation specifically in superficial zone articular chondrocytes; and which work in combination with a more distal regulatory element to drive induction of Prg4 by TGF-β. Our results indicate that Creb5 is a critical regulator of Prg4/lubricin expression in the articular cartilage.
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28
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Ariza A, Funahashi Y, Kozawa S, Omar Faruk M, Nagai T, Amano M, Kaibuchi K. Dynamic subcellular localization and transcription activity of the SRF cofactor MKL2 in the striatum are regulated by MAPK. J Neurochem 2021; 157:1774-1788. [PMID: 33449379 DOI: 10.1111/jnc.15303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 01/16/2023]
Abstract
Dopamine type 1 receptor (D1R) signaling activates protein kinase A (PKA), which then activates mitogen-activated protein kinase (MAPK) through Rap1, in striatal medium spiny neurons (MSNs). MAPK plays a pivotal role in reward-related behavior through the activation of certain transcription factors. How D1R signaling regulates behavior through transcription factors remains largely unknown. CREB-binding protein (CBP) promotes transcription through hundreds of different transcription factors and is also important for reward-related behavior. To identify transcription factors regulated by dopamine signaling in MSNs, we performed a phosphoproteomic analysis using affinity beads coated with CBP. We obtained approximately 40 novel candidate proteins in the striatum of the C57BL/6 mouse brain after cocaine administration. Among them, the megakaryoblastic leukemia-2 (MKL2) protein, a transcriptional coactivator of serum response factor (SRF), was our focus. We found that the interaction between CBP and MKL2 was increased by cocaine administration. Additionally, MKL2, CBP and SRF formed a ternary complex in vivo. The C-terminal domain of MKL2 interacted with CBP-KIX and was phosphorylated by MAPK in COS7 cells. The activation of PKA-MAPK signaling induced the nuclear localization of MKL2 and increased SRF-dependent transcriptional activity in neurons. These results demonstrate that dopamine signaling regulates the interaction of MKL2 with CBP in a phosphorylation-dependent manner and thereby controls SRF-dependent gene expression. Cover Image for this issue: https://doi.org/10.1111/jnc.15067.
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Affiliation(s)
- Anthony Ariza
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yasuhiro Funahashi
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.,Research Project for Neural and Tumor Signaling, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Sachi Kozawa
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Md Omar Faruk
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Taku Nagai
- Division of Behavioral Neuropharmacology, Project Office for Neuropsychological Research Center, Fujita Health University, Toyoake, Aichi, Japan
| | - Mutsuki Amano
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.,Research Project for Neural and Tumor Signaling, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
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29
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Akinsiku OE, Soremekun OS, Soliman MES. Update and Potential Opportunities in CBP [Cyclic Adenosine Monophosphate (cAMP) Response Element-Binding Protein (CREB)-Binding Protein] Research Using Computational Techniques. Protein J 2021; 40:19-27. [PMID: 33394237 PMCID: PMC7868315 DOI: 10.1007/s10930-020-09951-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2020] [Indexed: 11/29/2022]
Abstract
CBP [cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB)-binding protein] is one of the most researched proteins for its therapeutic function. Several studies have identified its vast functions and interactions with other transcription factors to initiate cellular signals of survival. In cancer and other diseases such as Alzheimer's, Rubinstein-taybi syndrome, and inflammatory diseases, CBP has been implicated and hence an attractive target in drug design and development. In this review, we explore the various computational techniques that have been used in CBP research, furthermore we identified computational gaps that could be explored to facilitate the development of highly therapeutic CBP inhibitors.
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Affiliation(s)
- Oluwayimika E Akinsiku
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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30
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Fatafta H, Samantray S, Sayyed-Ahmad A, Coskuner-Weber O, Strodel B. Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:135-185. [PMID: 34656328 DOI: 10.1016/bs.pmbts.2021.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure but do exhibit some dynamical and structural ordering. The structural plasticity of IDPs indicates that entropy-driven motions are crucial for their function. Many IDPs undergo function-related disorder-to-order transitions upon by their interaction with specific binding partners. Approaches that are based on both experimental and theoretical tools enable the biophysical characterization of IDPs. Molecular simulations provide insights into IDP structural ensembles and disorder-to-order transition mechanisms. However, such studies depend strongly on the chosen force field parameters and simulation techniques. In this chapter, we provide an overview of IDP characteristics, review all-atom force fields recently developed for IDPs, and present molecular dynamics-based simulation methods that allow IDP ensemble generation as well as the characterization of disorder-to-order transitions. In particular, we introduce metadynamics, replica exchange molecular dynamics simulations, and also kinetic models resulting from Markov State modeling, and provide various examples for the successful application of these simulation methods to IDPs.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Suman Samantray
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; AICES Graduate School, RWTH Aachen University, Aachen, Germany
| | | | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, Istanbul, Turkey
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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31
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Liu WL, Chiang FT, Kao JTW, Chiou SH, Lin HL. GSK3 modulation in acute lung injury, myocarditis and polycystic kidney disease-related aneurysm. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118798. [PMID: 32693109 PMCID: PMC7368652 DOI: 10.1016/j.bbamcr.2020.118798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/10/2020] [Accepted: 07/11/2020] [Indexed: 12/17/2022]
Abstract
GSK3 are involved in different physical and pathological conditions and inflammatory regulated by macrophages contribute to significant mechanism. Infection stimuli may modulate GSK3 activity and influence host cell adaption, immune cells infiltration or cytokine expressions. To further address the role of GSK3 modulation in macrophages, the signal transduction of three major organs challenged by endotoxin, virus and genetic inherited factors are briefly introduced (lung injury, myocarditis and autosomal dominant polycystic kidney disease). As a result of pro-inflammatory and anti-inflammatory functions of GSK3 in different microenvironments and stages of macrophages (M1/M2), the rational resolution should be considered by adequately GSK3.
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Affiliation(s)
- Wei-Lun Liu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan,Division of Critical Care Medicine, Department of Emergency and Critical Care Medicine, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan,Center For Innovation, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Fu-Tien Chiang
- Department of Internal Medicine, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan,Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, Taipei, Taiwan
| | - Juliana Tze-Wah Kao
- Division of Nephrology, Department of Internal Medicine, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei, Taiwan,Division of Nephrology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan,Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Heng-Liang Lin
- Center For Innovation, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan; Division of Fund Managing, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan.
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32
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Chatterjee S, Angelakos CC, Bahl E, Hawk JD, Gaine ME, Poplawski SG, Schneider-Anthony A, Yadav M, Porcari GS, Cassel JC, Giese KP, Michaelson JJ, Lyons LC, Boutillier AL, Abel T. The CBP KIX domain regulates long-term memory and circadian activity. BMC Biol 2020; 18:155. [PMID: 33121486 PMCID: PMC7597000 DOI: 10.1186/s12915-020-00886-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
Background CREB-dependent transcription necessary for long-term memory is driven by interactions with CREB-binding protein (CBP), a multi-domain protein that binds numerous transcription factors potentially affecting expression of thousands of genes. Identifying specific domain functions for multi-domain proteins is essential to understand processes such as cognitive function and circadian clocks. We investigated the function of the CBP KIX domain in hippocampal memory and gene expression using CBPKIX/KIX mice with mutations that prevent phospho-CREB (Ser133) binding. Results We found that CBPKIX/KIX mice were impaired in long-term memory, but not learning acquisition or short-term memory for the Morris water maze. Using an unbiased analysis of gene expression in the dorsal hippocampus after training in the Morris water maze or contextual fear conditioning, we discovered dysregulation of CREB, CLOCK, and BMAL1 target genes and downregulation of circadian genes in CBPKIX/KIX mice. Given our finding that the CBP KIX domain was important for transcription of circadian genes, we profiled circadian activity and phase resetting in CBPKIX/KIX mice. CBPKIX/KIX mice exhibited delayed activity peaks after light offset and longer free-running periods in constant dark. Interestingly, CBPKIX/KIX mice displayed phase delays and advances in response to photic stimulation comparable to wildtype littermates. Thus, this work delineates site-specific regulation of the circadian clock by a multi-domain protein. Conclusions These studies provide insight into the significance of the CBP KIX domain by defining targets of CBP transcriptional co-activation in memory and the role of the CBP KIX domain in vivo on circadian rhythms. Graphical abstract ![]()
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Affiliation(s)
- Snehajyoti Chatterjee
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France.,LNCA, CNRS UMR 7364, Strasbourg, France.,Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Christopher C Angelakos
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ethan Bahl
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Joshua D Hawk
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Marie E Gaine
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Shane G Poplawski
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Pharmacology Graduate Group, University of Pennsylvania, Philadelphia, USA
| | - Anne Schneider-Anthony
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France.,LNCA, CNRS UMR 7364, Strasbourg, France
| | - Manish Yadav
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Giulia S Porcari
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jean-Christophe Cassel
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
| | - K Peter Giese
- Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Jacob J Michaelson
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, Iowa, USA.,Department of Communication Sciences and Disorders, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa, USA.,Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Lisa C Lyons
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Anne-Laurence Boutillier
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France. .,LNCA, CNRS UMR 7364, Strasbourg, France.
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.
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Cross E, Duncan-Flavell PJ, Howarth RJ, Hobbs JI, Thomas NS, Bunyan DJ. Screening of a large Rubinstein-Taybi cohort identified many novel variants and emphasizes the importance of the CREBBP histone acetyltransferase domain. Am J Med Genet A 2020; 182:2508-2520. [PMID: 32827181 DOI: 10.1002/ajmg.a.61813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 01/20/2023]
Abstract
Pathogenic variants within the CREBBP and EP300 genes account for the majority of individuals with Rubinstein-Taybi syndrome (RSTS). Data are presented from a large cohort of 395 individuals referred for diagnostic testing of CREBBP, and of the 19 CREBBP missense variants classified as likely pathogenic in this study, 17 were within the histone acetyltransferase (HAT) domain, providing evidence that this domain is critical to the normal function of the CREBBP protein (CBP). The data presented here, combined with other published results, suggest that the presence of a missense variant within the CBP HAT domain can be considered as moderate evidence of pathogenicity in the context of official variant interpretation guidelines. Within our study cohort, 129 had a pathogenic or likely pathogenic CREBBP variant and 5 had a variant of uncertain significance (VUS) which warranted familial studies. 147 of the remaining probands were also screened for EP300 and a further 16 pathogenic or likely pathogenic variants were identified, plus one VUS. Therefore, this analysis has provided a molecular diagnosis in at least 145 individuals with RSTS (37%) and identified a wide range of variants (n = 133) of which 103 were novel.
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Affiliation(s)
- Esther Cross
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | | | - Rachel J Howarth
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | - James I Hobbs
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | - Nicholas Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.,Faculty of Medicine, University of Southampton, Southampton, UK
| | - David J Bunyan
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.,Faculty of Medicine, University of Southampton, Southampton, UK
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34
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Poon CH, Heng BC, Lim LW. New insights on brain-derived neurotrophic factor epigenetics: from depression to memory extinction. Ann N Y Acad Sci 2020; 1484:9-31. [PMID: 32808327 DOI: 10.1111/nyas.14458] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/21/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022]
Abstract
Advances in characterizing molecular profiles provide valuable insights and opportunities for deciphering the neuropathology of depression. Although abnormal brain-derived neurotrophic factor (BDNF) expression in depression has gained much support from preclinical and clinical research, how it mediates behavioral alterations in the depressed state remains largely obscure. Environmental factors contribute significantly to the onset of depression and produce robust epigenetic changes. Epigenetic regulation of BDNF, as one of the most characterized gene loci in epigenetics, has recently emerged as a target in research on memory and psychiatric disorders. Specifically, epigenetic alterations of BDNF exons are heavily involved in mediating memory functions and antidepressant effects. In this review, we discuss key research on stress-induced depression from both preclinical and clinical studies, which revealed that differential epigenetic regulation of specific BDNF exons is associated with depression pathophysiology. Considering that BDNF has a central role in depression, we argue that memory extinction, an adaptive response to fear exposure, is dependent on BDNF modulation and holds promise as a prospective target for alleviating or treating depression and anxiety disorders.
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Affiliation(s)
- Chi Him Poon
- Neuromodulation Laboratory, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Boon Chin Heng
- Peking University School of Stomatology, Beijing, China.,Department of Biological Sciences, Sunway University, Selangor, Malaysia
| | - Lee Wei Lim
- Neuromodulation Laboratory, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Biological Sciences, Sunway University, Selangor, Malaysia
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35
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Ashok C, Selvam M, Ponne S, Parcha PK, Raja KMP, Baluchamy S. CREB acts as a common transcription factor for major epigenetic repressors; DNMT3B, EZH2, CUL4B and E2F6. Med Oncol 2020; 37:68. [PMID: 32710193 DOI: 10.1007/s12032-020-01395-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/16/2020] [Indexed: 12/28/2022]
Abstract
CREB signaling is known for several decades, but how it regulates both positive and negative regulators of cell proliferation is not well understood. On the other hand functions of major epigenetic repressors such as DNMT3B, EZH2 and CUL4B for their repressive epigenetic modifications on chromatin have also been well studied. However, there is very limited information available on how these repressors are regulated at their transcriptional level. Here, using computational tools and molecular techniques including site directed mutagenesis, promoter reporter assay, chromatin immunoprecipitation (ChIP), we identified that CREB acts as a common transcription factor for DNMT3B, EZH2, CUL4B and E2F6. ChIP assay revealed that pCREB binds to promoters of these repressors at CREs and induce their transcription. As expected, the expression of these repressors and their associated repressive marks particularly H3K27me3 and H2AK119ub are increased and decreased upon CREB overexpression and knock-down conditions respectively in the cancer cells indicating that CREB regulates the functions of these repressors by activating their transcription. Since CREB and these epigenetic repressors are overexpressed in various cancer types, our findings showed the molecular relationship between them and indicate that CREB is an important therapeutic target for cancer therapy.
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Affiliation(s)
- Cheemala Ashok
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India
| | - Murugan Selvam
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India
| | - Saravanaraman Ponne
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India
| | - Phani K Parcha
- Department of Biochemistry and Molecular Biology, Pondicherry Central University, Pondicherry, 605014, India
| | | | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, R. V. Nagar, Kalapet, Pondicherry, 605014, India.
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36
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Hiebert CW, Moscou MJ, Hewitt T, Steuernagel B, Hernández-Pinzón I, Green P, Pujol V, Zhang P, Rouse MN, Jin Y, McIntosh RA, Upadhyaya N, Zhang J, Bhavani S, Vrána J, Karafiátová M, Huang L, Fetch T, Doležel J, Wulff BBH, Lagudah E, Spielmeyer W. Stem rust resistance in wheat is suppressed by a subunit of the mediator complex. Nat Commun 2020; 11:1123. [PMID: 32111840 PMCID: PMC7048732 DOI: 10.1038/s41467-020-14937-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/11/2020] [Indexed: 11/18/2022] Open
Abstract
Stem rust is an important disease of wheat that can be controlled using resistance genes. The gene SuSr-D1 identified in cultivar ‘Canthatch’ suppresses stem rust resistance. SuSr-D1 mutants are resistant to several races of stem rust that are virulent on wild-type plants. Here we identify SuSr-D1 by sequencing flow-sorted chromosomes, mutagenesis, and map-based cloning. The gene encodes Med15, a subunit of the Mediator Complex, a conserved protein complex in eukaryotes that regulates expression of protein-coding genes. Nonsense mutations in Med15b.D result in expression of stem rust resistance. Time-course RNAseq analysis show a significant reduction or complete loss of differential gene expression at 24 h post inoculation in med15b.D mutants, suggesting that transcriptional reprogramming at this time point is not required for immunity to stem rust. Suppression is a common phenomenon and this study provides novel insight into suppression of rust resistance in wheat. Stem rust is an important disease of wheat and resistance present in some cultivars can be suppressed by the SuSr-D1 locus. Here the authors show that SuSr-D1 encodes a subunit of the Mediator Complex and that nonsense mutations are sufficient to abolish suppression and confer stem rust resistance.
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Affiliation(s)
- Colin W Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada.
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK.
| | - Tim Hewitt
- Plant Breeding Institute Cobbitty, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia.,CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Inma Hernández-Pinzón
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK
| | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK
| | - Vincent Pujol
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Peng Zhang
- Plant Breeding Institute Cobbitty, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Matthew N Rouse
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA
| | - Yue Jin
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA
| | - Robert A McIntosh
- Plant Breeding Institute Cobbitty, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
| | | | - Jianping Zhang
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Sridhar Bhavani
- CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market, Nairobi, 00621, Kenya
| | - Jan Vrána
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Li Huang
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Tom Fetch
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | | | - Evans Lagudah
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT, 2601, Australia.
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Perez DR, Sklar LA, Chigaev A, Matlawska-Wasowska K. Drug repurposing for targeting cyclic nucleotide transporters in acute leukemias - A missed opportunity. Semin Cancer Biol 2020; 68:199-208. [PMID: 32044470 DOI: 10.1016/j.semcancer.2020.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/01/2019] [Accepted: 02/03/2020] [Indexed: 02/08/2023]
Abstract
While current treatment regimens for acute leukemia can dramatically improve patient survival, there remains room for improvement. Due to its roles in cell differentiation, cell survival, and apoptotic signaling, modulation of the cyclic AMP (cAMP) pathway has provided a meaningful target in hematological malignancies. Several studies have demonstrated that gene expression profiles associated with increased pro-survival cAMP activity or downregulation of various pro-apoptotic factors associated with the cAMP pathway are apparent in acute leukemia patients. Previous work to increase leukemia cell intracellular cAMP focused on the use of cAMP analogs, stimulating cAMP production via transmembrane-associated adenylyl cyclases, or decreasing cAMP degradation by inhibiting phosphodiesterase activity. However, targeting cyclic nucleotide efflux by ATP-binding cassette (ABC) transporters represents an unexplored approach for modulation of intracellular cyclic nucleotide levels. Preliminary studies have shown that inhibition of cAMP efflux can stimulate leukemia cell differentiation, cell growth arrest, and apoptosis, indicating that targeting cAMP efflux may show promise for future therapeutic development. Furthermore, inhibition of cyclic nucleotide transporter activity may also contribute multiple anticancer benefits by reducing extracellular pro-survival signaling in malignant cells. Hence, several opportunities for drug repurposing may exist for targeting cyclic nucleotide transporters.
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Affiliation(s)
- Dominique R Perez
- Department of Pathology, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA; Center for Molecular Discovery, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Larry A Sklar
- Department of Pathology, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA; Center for Molecular Discovery, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Alexandre Chigaev
- Department of Pathology, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA; Center for Molecular Discovery, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA.
| | - Ksenia Matlawska-Wasowska
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA; Department of Pediatrics, Division of Hematology-Oncology, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA.
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38
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In Vivo Imaging of the Coupling between Neuronal and CREB Activity in the Mouse Brain. Neuron 2019; 105:799-812.e5. [PMID: 31883788 DOI: 10.1016/j.neuron.2019.11.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/16/2019] [Accepted: 11/25/2019] [Indexed: 01/15/2023]
Abstract
Sensory experiences cause long-term modifications of neuronal circuits by modulating activity-dependent transcription programs that are vital for regulation of long-term synaptic plasticity and memory. However, it has not been possible to precisely determine the interaction between neuronal activity patterns and transcription factor activity. Here we present a technique using two-photon fluorescence lifetime imaging (2pFLIM) with new FRET biosensors to chronically image in vivo signaling of CREB, an activity-dependent transcription factor important for synaptic plasticity, at single-cell resolution. Simultaneous imaging of the red-shifted CREB sensor and GCaMP permitted exploration of how experience shapes the interplay between CREB and neuronal activity in the neocortex of awake mice. Dark rearing increased the sensitivity of CREB activity to Ca2+ elevations and prolonged the duration of CREB activation to more than 24 h in the visual cortex. This technique will allow researchers to unravel the transcriptional dynamics underlying experience-dependent plasticity in the brain.
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39
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Phosphorylation of Npas4 by MAPK Regulates Reward-Related Gene Expression and Behaviors. Cell Rep 2019; 29:3235-3252.e9. [DOI: 10.1016/j.celrep.2019.10.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/02/2019] [Accepted: 10/28/2019] [Indexed: 02/06/2023] Open
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40
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Noda N, Ishimoto T, Mori H, Ozawa T. Enhanced bioluminescent sensor for longitudinal detection of CREB activation in living cells. Photochem Photobiol Sci 2019; 18:2740-2747. [PMID: 31573014 DOI: 10.1039/c9pp00249a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB) is associated with memory formation and controls cell survival and proliferation via regulation of downstream gene expression in tumorigenesis. As a transcription factor, CREB binds to cAMP response elements. Phosphorylation of CREB triggers transcriptional activation of CREB downstream genes following the interaction of the kinase-inducible domain (KID) of CREB with the KID interaction domain (KIX) of CREB-binding protein. Nevertheless, because of the lack of single-cell analytical techniques, little is known about spatiotemporal regulation of CREB phosphorylation. To analyze CREB activation in single living cells, we developed genetically encoded bioluminescent sensors using luciferase-fragment complementation: the sensors are designed based on KID-KIX interaction with a single-molecule format. The luminescence intensity of the sensor, designated as CREX (a sensor of CREB activation based on KID(CREB)-KIX interaction), increased by phosphorylation of CREB. Moreover, the luminescence intensity of CREX was sufficient to detect CREB activation in live-cell bioluminescence imaging for single-cell analysis because of the higher sensitivity. CREX sensor is expected to contribute to elucidation of the spatiotemporal regulation of CREB phosphorylation by applying single-cell analysis.
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Affiliation(s)
- Natsumi Noda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Tetsuya Ishimoto
- Department of Molecular Neuroscience, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hisashi Mori
- Department of Molecular Neuroscience, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Takeaki Ozawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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41
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Dwivedi N, Maji S, Waseem M, Thakur P, Kumar V, Parida SK, Thakur JK. The Mediator subunit OsMED15a is a transcriptional co-regulator of seed size/weight-modulating genes in rice. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194432. [PMID: 31525461 DOI: 10.1016/j.bbagrm.2019.194432] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 11/17/2022]
Abstract
Although several transcription factors (TFs) that regulate seed size/weight in plants are known, the molecular landscape regulating this important trait is unclear. Here, we report that a Mediator subunit, OsMED15a, links rice grain size/weight-regulating TFs to their target genes. Expression analysis and high-resolution quantitative trait loci (QTL) mapping suggested that OsMED15a is involved in rice seed development. OsMED15a has an N-terminal, three-helical KIX domain. Two of these helices, α1 and α3, and three amino acids, 76LRC78, within OsMED15a helix α3 were important for its interaction with several proteins, including interactions with the transactivation domains of two NAC-type TFs, OsNAC024 and OsNAC025. Moreover, OsMED15a, OsNAC024, and OsNAC025 all exhibited increased expression during seed development, and we identified several grain size/weight-associated SNPs in these genes in 509 low- and high-grain-weight rice genotypes. RNAi-mediated repression of OsMED15a expression down-regulated the expression of the grain size/weight regulating genes GW2, GW5 and DR11 and reduced grain length, weight, and yield. Of note, both OsNAC024 and OsNAC025 bound to the promoters of these three genes. We conclude that the transactivation domains of OsNAC024 and OsNAC025 target the KIX domain of OsMED15a in the regulation of grain size/weight-associated genes such as GW2, GW5, and D11. We propose that the integrated molecular-genetics approach used here could help identify networks of functional alleles of other regulator and co-regulator genes and thereby inform efforts for marker-assisted introgression of useful alleles in rice crop improvement.
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Affiliation(s)
- Nidhi Dwivedi
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sourobh Maji
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mohd Waseem
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pallabi Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vinay Kumar
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K Parida
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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42
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Hou L, Li B, Ding D, Kang L, Wang X. CREB-B acts as a key mediator of NPF/NO pathway involved in phase-related locomotor plasticity in locusts. PLoS Genet 2019; 15:e1008176. [PMID: 31150381 PMCID: PMC6561586 DOI: 10.1371/journal.pgen.1008176] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/12/2019] [Accepted: 05/07/2019] [Indexed: 12/14/2022] Open
Abstract
Gene expression changes in neural systems are essential for environment-induced behavioral plasticity in animals; however, neuronal signaling pathways mediating the effect of external stimuli on transcriptional changes are largely unknown. Recently, we have demonstrated that the neuropeptide F (NPF)/nitric oxide (NO) signaling pathway plays a regulatory role in phase-related locomotor plasticity in the migratory locust, Locusta migratoria. Here, we report that a conserved transcription factor, cAMP response element-binding protein B (CREB-B), is a key mediator involved in the signaling pathway from NPF2 to NOS in the migratory locust, triggering locomotor activity shift between solitarious and gregarious phases. We find that CREB-B directly activates brain NOS expression by interacting with NOS promoter region. The phosphorylation at serine 110 site of CREB-B dynamically changes in response to population density variation and is negatively controlled by NPF2. The involvement of CREB-B in NPF2-regulated locomotor plasticity is further validated by RNAi experiment and behavioral assay. Furthermore, we reveal that protein kinase A mediates the regulatory effects of NPF2 on CREB-B phosphorylation and NOS transcription. These findings highlight a precise signal cascade underlying environment-induced behavioral plasticity.
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Affiliation(s)
- Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Beibei Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ding Ding
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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43
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Cooper DG, Fassler JS. Med15: Glutamine-Rich Mediator Subunit with Potential for Plasticity. Trends Biochem Sci 2019; 44:737-751. [PMID: 31036407 DOI: 10.1016/j.tibs.2019.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/16/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023]
Abstract
The Mediator complex is required for basal activity of the RNA polymerase (Pol) II transcriptional apparatus and for responsiveness to some activator proteins. Med15, situated in the Mediator tail, plays a role in transmitting regulatory information from distant DNA-bound transcription factors to the transcriptional apparatus poised at promoters. Yeast Med15 and its orthologs share an unusual, glutamine-rich amino acid composition. Here, we discuss this sequence feature and the tendency of polyglutamine tracts to vary in length among strains of Saccharomyces cerevisiae, and we propose that different polyglutamine tract lengths may be adaptive within certain domestication habitats.
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Affiliation(s)
- David G Cooper
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Jan S Fassler
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
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44
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Glotfelty EJ, Delgado TE, Tovar-y-Romo LB, Luo Y, Hoffer BJ, Olson L, Karlsson TE, Mattson MP, Harvey BK, Tweedie D, Li Y, Greig NH. Incretin Mimetics as Rational Candidates for the Treatment of Traumatic Brain Injury. ACS Pharmacol Transl Sci 2019; 2:66-91. [PMID: 31396586 PMCID: PMC6687335 DOI: 10.1021/acsptsci.9b00003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Indexed: 12/17/2022]
Abstract
Traumatic brain injury (TBI) is becoming an increasing public health issue. With an annually estimated 1.7 million TBIs in the United States (U.S) and nearly 70 million worldwide, the injury, isolated or compounded with others, is a major cause of short- and long-term disability and mortality. This, along with no specific treatment, has made exploration of TBI therapies a priority of the health system. Age and sex differences create a spectrum of vulnerability to TBI, with highest prevalence among younger and older populations. Increased public interest in the long-term effects and prevention of TBI have recently reached peaks, with media attention bringing heightened awareness to sport and war related head injuries. Along with short-term issues, TBI can increase the likelihood for development of long-term neurodegenerative disorders. A growing body of literature supports the use of glucagon-like peptide-1 (GLP-1), glucose-dependent insulinotropic peptide (GIP), and glucagon (Gcg) receptor (R) agonists, along with unimolecular combinations of these therapies, for their potent neurotrophic/neuroprotective activities across a variety of cellular and animal models of chronic neurodegenerative diseases (Alzheimer's and Parkinson's diseases) and acute cerebrovascular disorders (stroke). Mild or moderate TBI shares many of the hallmarks of these conditions; recent work provides evidence that use of these compounds is an effective strategy for its treatment. Safety and efficacy of many incretin-based therapies (GLP-1 and GIP) have been demonstrated in humans for the treatment of type 2 diabetes mellitus (T2DM), making these compounds ideal for rapid evaluation in clinical trials of mild and moderate TBI.
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Affiliation(s)
- Elliot J. Glotfelty
- Translational
Gerontology Branch, and Laboratory of Neurosciences, Intramural
Research Program, National Institute on
Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
- Department
of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Thomas E. Delgado
- Translational
Gerontology Branch, and Laboratory of Neurosciences, Intramural
Research Program, National Institute on
Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Luis B. Tovar-y-Romo
- Division
of Neuroscience, Institute of Cellular Physiology, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Yu Luo
- Department
of Molecular Genetics, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Barry J. Hoffer
- Department
of Neurosurgery, Case Western Reserve University
School of Medicine, Cleveland, Ohio 44106, United States
| | - Lars Olson
- Department
of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Mark P. Mattson
- Translational
Gerontology Branch, and Laboratory of Neurosciences, Intramural
Research Program, National Institute on
Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Brandon K. Harvey
- Molecular
Mechanisms of Cellular Stress and Inflammation Unit, Integrative Neuroscience
Department, National Institute on Drug Abuse,
National Institutes of Health, Baltimore, Maryland 21224, United States
| | - David Tweedie
- Translational
Gerontology Branch, and Laboratory of Neurosciences, Intramural
Research Program, National Institute on
Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Yazhou Li
- Translational
Gerontology Branch, and Laboratory of Neurosciences, Intramural
Research Program, National Institute on
Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Nigel H. Greig
- Translational
Gerontology Branch, and Laboratory of Neurosciences, Intramural
Research Program, National Institute on
Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
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45
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Vincent M, Uversky VN, Schnell S. On the Need to Develop Guidelines for Characterizing and Reporting Intrinsic Disorder in Proteins. Proteomics 2019; 19:e1800415. [PMID: 30793871 PMCID: PMC6571172 DOI: 10.1002/pmic.201800415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/05/2019] [Indexed: 01/02/2023]
Abstract
Since the early 2000s, numerous computational tools have been created and used to predict intrinsic disorder in proteins. At present, the output from these algorithms is difficult to interpret in the absence of standards or references for comparison. There are many reasons to establish a set of standard-based guidelines to evaluate computational protein disorder predictions. This viewpoint explores a handful of these reasons, including standardizing nomenclature to improve communication, rigor and reproducibility, and making it easier for newcomers to enter the field. An approach for reporting predicted disorder in single proteins with respect to whole proteomes is discussed. The suggestions are not intended to be formulaic; they should be viewed as a starting point to establish guidelines for interpreting and reporting computational protein disorder predictions.
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Affiliation(s)
- Michael Vincent
- Interdisciplinary Biological Sciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Moscow region, Russia
| | - Santiago Schnell
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Michigan 48109, USA
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46
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Sharma P, Srivastava P, Seth A, Tripathi PN, Banerjee AG, Shrivastava SK. Comprehensive review of mechanisms of pathogenesis involved in Alzheimer's disease and potential therapeutic strategies. Prog Neurobiol 2018; 174:53-89. [PMID: 30599179 DOI: 10.1016/j.pneurobio.2018.12.006] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/04/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022]
Abstract
AD is a progressive neurodegenerative disorder and a leading cause of dementia in an aging population worldwide. The enormous challenge which AD possesses to global healthcare makes it as urgent as ever for the researchers to develop innovative treatment strategies to fight this disease. An in-depth analysis of the extensive available data associated with the AD is needed for a more comprehensive understanding of underlying molecular mechanisms and pathophysiological pathways associated with the onset and progression of the AD. The currently understood pathological and biochemical manifestations include cholinergic, Aβ, tau, excitotoxicity, oxidative stress, ApoE, CREB signaling pathways, insulin resistance, etc. However, these hypotheses have been criticized with several conflicting reports for their involvement in the disease progression. Several issues need to be addressed such as benefits to cost ratio with cholinesterase therapy, the dilemma of AChE selectivity over BChE, BBB permeability of peptidic BACE-1 inhibitors, hurdles related to the implementation of vaccination and immunization therapy, and clinical failure of candidates related to newly available targets. The present review provides an insight to the different molecular mechanisms involved in the development and progression of the AD and potential therapeutic strategies, enlightening perceptions into structural information of conventional and novel targets along with the successful applications of computational approaches for the design of target-specific inhibitors.
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Affiliation(s)
- Piyoosh Sharma
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Pavan Srivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Ankit Seth
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Prabhash Nath Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Anupam G Banerjee
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Sushant K Shrivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India.
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47
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Shnitkind S, Martinez-Yamout MA, Dyson HJ, Wright PE. Structural Basis for Graded Inhibition of CREB:DNA Interactions by Multisite Phosphorylation. Biochemistry 2018; 57:6964-6972. [PMID: 30507144 PMCID: PMC6474821 DOI: 10.1021/acs.biochem.8b01092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphorylation of the kinase inducible domain (KID) of the cyclic AMP response element binding transcription factor (CREB) regulates its function through several mechanisms. Transcriptional activation occurs following phosphorylation at serine 133, but multisite phosphorylation in a neighboring region termed the CK cassette, residues 108-117, results in inhibition of CREB-mediated transcription. A molecular-level understanding of the mechanism of these opposing reactions has been lacking, in part because of the difficulty of preparing multiply phosphorylated CREB in vitro. By substituting a single residue, we have generated an engineered mammalian CREB in which the CK cassette can be phosphorylated in vitro by casein kinases and have characterized its interactions with cyclic AMP response element DNA. Phosphorylation of the CK cassette promotes an intramolecular interaction between the KID domain and the site of DNA binding, the basic region of the C-terminal basic leucine zipper (bZip) domain. Competition between the phosphorylated KID domain and DNA for bZip binding results in a decreased affinity of CREB for DNA. The binding free energy calculated from the dissociation constant is directly proportional to the number of phosphate groups in the CK cassette, indicating that the DNA binding is regulated by a rheostat-like mechanism. The rheostat is modulated by variation of the concentration of cations such as Mg2+ and by alternative isoforms such as the natural CREB isoform that lacks residues 162-272. Multisite phosphorylation of CREB represents a versatile mechanism by which transcription can be tuned to meet the variable needs of the cell.
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Affiliation(s)
- Sergey Shnitkind
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla California 92037
| | - Maria A. Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla California 92037
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla California 92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla California 92037
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Sonntag T, Ostojić J, Vaughan JM, Moresco JJ, Yoon YS, Yates JR, Montminy M. Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment. iScience 2018; 11:134-145. [PMID: 30611118 PMCID: PMC6317279 DOI: 10.1016/j.isci.2018.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/12/2018] [Accepted: 12/13/2018] [Indexed: 11/18/2022] Open
Abstract
The second messenger 3',5'-cyclic adenosine monophosphate (cAMP) stimulates gene expression via the cAMP-regulated transcriptional coactivator (CRTC) family of cAMP response element-binding protein coactivators. In the basal state, CRTCs are phosphorylated by salt-inducible kinases (SIKs) and sequestered in the cytoplasm by 14-3-3 proteins. cAMP signaling inhibits the SIKs, leading to CRTC dephosphorylation and nuclear translocation. Here we show that although all CRTCs are regulated by SIKs, their interactions with Ser/Thr-specific protein phosphatases are distinct. CRTC1 and CRTC2 associate selectively with the calcium-dependent phosphatase calcineurin, whereas CRTC3 interacts with B55 PP2A holoenzymes via a conserved PP2A-binding region (amino acids 380-401). CRTC3-PP2A complex formation was induced by phosphorylation of CRTC3 at S391, facilitating the subsequent activation of CRTC3 by dephosphorylation at 14-3-3 binding sites. As stimulation of mitogenic pathways promoted S391 phosphorylation via the activation of ERKs and CDKs, our results demonstrate how a ubiquitous phosphatase enables cross talk between growth factor and cAMP signaling pathways at the level of a transcriptional coactivator.
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Affiliation(s)
- Tim Sonntag
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jelena Ostojić
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joan M Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Young-Sil Yoon
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marc Montminy
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Golec E, Lind L, Qayyum M, Blom AM, King BC. The Noncoding RNA nc886 Regulates PKR Signaling and Cytokine Production in Human Cells. THE JOURNAL OF IMMUNOLOGY 2018; 202:131-141. [PMID: 30518569 DOI: 10.4049/jimmunol.1701234] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/29/2018] [Indexed: 12/17/2022]
Abstract
Protein kinase RNA-activated (PKR) is a cytoplasmic receptor for dsRNA, and as such is involved in detection of viral infection. On binding dsRNA, PKR dimerizes, autophosphorylates, and then phosphorylates its substrate, eukaryotic translation initiation factor 2 subunit α (eIF2α), causing inhibition of mRNA translation and shutdown of viral protein production. However, active PKR has also been found to be involved in the NF-κB signaling pathway by inducing phosphorylation of IκBα. PKR is regulated by the noncoding RNA nc886, which has altered expression in cancer. We have found that expression of nc886 is highly upregulated during activation of human CD4+ T cells. As has been described in other cell types, nc886 bound to PKR in human T cell lysates, preventing PKR phosphorylation by polyinosinic:polycytidylic acid or HIV trans-activation response element RNA in lysates of T cell lines or primary human CD4+ T cells. Using clonal human T cell lines, we found that nc886 expression was strictly required for IFN-γ and IL-2 expression and secretion after T cell activation but did not affect proliferation or activation-induced cell death. In stimulated human PBMCs, nc886 expression strongly correlated with IFN-γ expression. Although nc886 inhibited PKR activation by dsRNA, it was required for PKR phosphorylation during T cell stimulation, with subsequent NF-κB signaling and CREB phosphorylation. nc886 also regulated PKR phosphorylation during human monocyte-derived macrophage activation. We have therefore identified nc886 as a noncoding RNA marker of T cell activation and regulator of PKR-dependent signaling.
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Affiliation(s)
- Ewelina Golec
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, 21428 Malmö, Sweden
| | - Liza Lind
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, 21428 Malmö, Sweden
| | - Munazza Qayyum
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, 21428 Malmö, Sweden
| | - Anna M Blom
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, 21428 Malmö, Sweden
| | - Ben C King
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, 21428 Malmö, Sweden
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Ciafrè S, Carito V, Ferraguti G, Greco A, Chaldakov GN, Fiore M, Ceccanti M. How alcohol drinking affects our genes: an epigenetic point of view. Biochem Cell Biol 2018; 97:345-356. [PMID: 30412425 DOI: 10.1139/bcb-2018-0248] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This work highlights recent studies in epigenetic mechanisms that play a role in alcoholism, which is a complex multifactorial disorder. There is a large body of evidence showing that alcohol can modify gene expression through epigenetic processes, namely DNA methylation and nucleosomal remodeling via histone modifications. In that regard, chronic exposure to ethanol modifies DNA and histone methylation, histone acetylation, and microRNA expression. The alcohol-mediated chromatin remodeling in the brain promotes the transition from use to abuse and addiction. Unravelling the multiplex pattern of molecular modifications induced by ethanol could support the development of new therapies for alcoholism and drug addiction targeting epigenetic processes.
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Affiliation(s)
- Stefania Ciafrè
- a Institute of Translational Pharmacology, IFT-CNR, 100 via del Fosso del Cavaliere, Rome 00133, Italy
| | - Valentina Carito
- b Institute of Cell Biology and Neurobiology, IBCN-CNR, c/o Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - Giampiero Ferraguti
- c Department of Experimental Medicine, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - Antonio Greco
- d Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - George N Chaldakov
- e Laboratory of Cell Biology, Department of Anatomy and Histology, Medical University, BG-9002 Varna, Bulgaria
| | - Marco Fiore
- b Institute of Cell Biology and Neurobiology, IBCN-CNR, c/o Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - Mauro Ceccanti
- f Centro Riferimento Alcologico Regione Lazio, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
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