1
|
Mitra A, Dasgupta A, Mitra D. Cellular HSF1 expression is induced during HIV-1 infection by activation of its promoter mediated through the cooperative interaction of HSF1 and viral Nef protein. Arch Biochem Biophys 2024; 754:109947. [PMID: 38417690 DOI: 10.1016/j.abb.2024.109947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
The Human Immunodeficiency Virus-1 (HIV-1) tends to activate cellular promoters driving expression of pro-viral genes by complex host-virus interactions for productive infection. We have previously demonstrated that expression of such a positive host factor HSF1 (heat shock factor 1) is elevated during HIV-1 infection; however, the mechanism remains to be elucidated. In the present study, we therefore examined whether HSF1 promoter is induced during HIV-1 infection leading to up-regulation of hsf1 gene expression. We mapped the putative transcription start site (TSS) predicted by Eukaryotic promoter database and deletion constructs of the predicted promoter region were tested through luciferase assay to identify the active promoter. The 347 bp upstream to 153 bp downstream region around the putative TSS displayed the highest activity and both Sp1 (stimulating protein 1) and HSF1 itself were identified to be important for its basal activation. Activity of HSF1 promoter was further stimulated during HIV-1 infection in CD4+ T cells, where interestingly the HSF1-site itself seems to play a major role. In addition, HIV-1 protein Nef (negative factor) was also observed to be responsible for the virus-mediated induction of hsf1 gene expression. Chromatin-immunoprecipitation assays further demonstrate that Nef and HSF1 are co-recruited to the HSF1-binding site and cooperatively act on this promoter. The interplay between host HSF1 and viral Nef on HSF1 promoter eventually leads to increase in HSF1 expression during HIV-1 infection. Understanding the mechanism of HSF1 up-regulation during HIV-1 infection might contribute to future antiviral strategies as HSF1 is a positive regulator of virus replication.
Collapse
Affiliation(s)
- Alapani Mitra
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune - 411007, Maharashtra, India.
| | - Anindita Dasgupta
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune - 411007, Maharashtra, India.
| | - Debashis Mitra
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune - 411007, Maharashtra, India.
| |
Collapse
|
2
|
Albacar M, Zekhnini A, Pérez-Valle J, Martínez JL, Casamayor A, Ariño J. Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization. Microb Cell Fact 2023; 22:63. [PMID: 37013612 PMCID: PMC10071690 DOI: 10.1186/s12934-023-02074-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Adaptation to alkalinization of the medium in fungi involves an extensive remodeling of gene expression. Komagataella phaffii is an ascomycetous yeast that has become an organism widely used for heterologous protein expression. We explore here the transcriptional impact of moderate alkalinization in this yeast, in search of suitable novel promoters able to drive transcription in response to the pH signal. RESULTS In spite of a minor effect on growth, shifting the cultures from pH 5.5 to 8.0 or 8.2 provokes significant changes in the mRNA levels of over 700 genes. Functional categories such as arginine and methionine biosynthesis, non-reductive iron uptake and phosphate metabolism are enriched in induced genes, whereas many genes encoding iron-sulfur proteins or members of the respirasome were repressed. We also show that alkalinization is accompanied by oxidative stress and we propose this circumstance as a common trigger of a subset of the observed changes. PHO89, encoding a Na+/Pi cotransporter, appears among the most potently induced genes by high pH. We demonstrate that this response is mainly based on two calcineurin-dependent response elements located in its promoter, thus indicating that alkalinization triggers a calcium-mediated signal in K. phaffii. CONCLUSIONS This work defines in K. phaffii a subset of genes and diverse cellular pathways that are altered in response to moderate alkalinization of the medium, thus setting the basis for developing novel pH-controlled systems for heterologous protein expression in this fungus.
Collapse
Affiliation(s)
- Marcel Albacar
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Abdelghani Zekhnini
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Jorge Pérez-Valle
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - José L Martínez
- Department of Biotechnology and Biomedicine, Section for Synthetic Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Antonio Casamayor
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain.
| |
Collapse
|
3
|
Iyer K, Mitra A, Mitra D. Identification of 5' upstream sequence involved in HSPBP1 gene transcription and its downregulation during HIV-1 infection. Virus Res 2023; 324:199034. [PMID: 36581045 DOI: 10.1016/j.virusres.2022.199034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 12/14/2022] [Accepted: 12/25/2022] [Indexed: 12/27/2022]
Abstract
The Human Immunodeficiency Virus-1 (HIV-1) is known to modulate the host environment for successful replication and propagation like other viruses. The virus utilises its proteins to interact with or modulate host factors and host signalling pathways that may otherwise restrict the virus. A previous study from our lab has shown that the host heat shock protein 70 (HSP70) binding protein (HSPBP1) is a co-chaperone that inhibits viral replication. We have also shown that the virus downregulates HSPBP1 during infection. However, the mechanism of downregulation remains to be elucidated. In the present study, we hypothesized that the HSPBP1 promoter may be repressed during infection leading to its downmodulation at the RNA and protein levels. The 5' upstream region of the HSPBP1 gene was first mapped and it was identified that a fragment comprising of a ∼600 bp upstream region of the transcription start site show the highest promoter-like activity. Further, the Sp1 transcription factor was shown to be essential for normal promoter activation. Our results further demonstrate that HIV-1 downregulates the activity of the identified promoter. It was seen that the viral transactivator protein, Tat, was responsible for the downmodulation of the HSPBP1 promoter. HIV-1 Tat is known to bind and regulate several cellular promoters during infection, thereby making the environment conducive for establishment of the virus. Our results further show that Tat is recruited to the HSPBP1 promoter and in the presence of Tat, recruitment of Sp1 on HSPBP1 promoter was decreased, which explains the suppression of HSPBP1 during HIV-1 infection. Therefore, this study further adds to the list of cellular promoters that are modulated by Tat during HIV-1 infection either directly or indirectly.
Collapse
Affiliation(s)
- Kruthika Iyer
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Alapani Mitra
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Debashis Mitra
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India.
| |
Collapse
|
4
|
de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R. Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biol 2022; 23:163. [PMID: 35883107 PMCID: PMC9316731 DOI: 10.1186/s13059-022-02728-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/06/2022] [Indexed: 12/22/2022] Open
Abstract
Background Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA methylation on endogenous promoters; however, the downstream effects have not yet been comprehensively assessed. Results Here, we simultaneously induce methylation at thousands of promoters in human cells using an engineered zinc finger-DNMT3A fusion protein, enabling us to test the effect of forced DNA methylation upon transcription, chromatin accessibility, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that transcriptional responses to DNA methylation are highly context-specific, including lack of repression, as well as cases of increased gene expression, which appears to be driven by the eviction of methyl-sensitive transcriptional repressors. Furthermore, we find that some regulatory networks can override DNA methylation and that promoter methylation can cause alternative promoter usage. DNA methylation deposited at promoter and distal regulatory regions is rapidly erased after removal of the zinc finger-DNMT3A fusion protein, in a process combining passive and TET-mediated demethylation. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. Conclusions These findings have important implications for epigenome engineering and demonstrate that the response of promoters to DNA methylation is more complex than previously appreciated. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02728-5.
Collapse
Affiliation(s)
- Alex de Mendoza
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia. .,School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Trung Viet Nguyen
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Daniel Poppe
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Sam Buckberry
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Matthew R Grimmer
- Department of Biochemistry and Molecular Medicine, University of Southern California, 1450 Biggy St, Los Angeles, CA, 90089, USA.,Integrated Genetics and Genomics, University of California, Davis, 451 Health Sciences Dr, Davis, CA, 95616, USA.,Department of Neurological Surgery, University of California, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Sabine Stolzenburg
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Ozren Bogdanovic
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia.,School of BioScience, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, University of Southern California, 1450 Biggy St, Los Angeles, CA, 90089, USA
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.,School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
| |
Collapse
|
5
|
Yan J, Zhao Y, Du J, Wang Y, Wang S, Wang Q, Zhao X, Xu W, Zhao K. RNA sensor MDA5 suppresses LINE-1 retrotransposition by regulating the promoter activity of LINE-1 5'-UTR. Mob DNA 2022; 13:10. [PMID: 35414110 PMCID: PMC9003951 DOI: 10.1186/s13100-022-00268-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/29/2022] [Indexed: 01/10/2023] Open
Abstract
Background Type 1 long interspersed elements, or LINE-1, are the only retroelements that replicate autonomously in human cells. The retrotransposition process of LINE-1 can trigger the activation of the innate immune system and has been proposed to play a role in the development of several autoimmune diseases, including Aicardi-Goutières syndrome (AGS). In contrast, all known AGS-associated proteins, except MDA5, have been reported to affect LINE-1 activity. Thus, MDA5 is likely to also function as a LINE-1 suppressor. Results MDA5 was found to potently suppress LINE-1 activity in a reporter-based LINE-1 retrotransposition assay. Although MDA5 is an endogenous RNA sensor able to activate the innate immune system, increased interferon (IFN) expression only contributed in part to MDA5-mediated LINE-1 suppression. Instead, MDA5 potently regulated the promoter activity of LINE-1 5′-UTR, as confirmed by transiently expressed myc-tagged MDA5 or knockdown of endogenous MDA5 expression. Consequently, MDA5 effectively reduced the generation of LINE-1 RNA and the subsequent expression of LINE-1 ORF1p and ORF2p. Interestingly, despite MDA5 being a multi-domain protein, the N-terminal 2CARD domain alone is sufficient to interact with LINE-1 5′-UTR and inhibit LINE-1 promoter activity. Conclusion Our data reveal that MDA5 functions as a promoter regulator; it directly binds to the LINE-1 5′-UTR and suppresses its promoter activity. Consequently, MDA5 reduces LINE-1 RNA and protein levels, and ultimately inhibits LINE-1 retrotransposition. In contrast, MDA5-induced IFN expression only plays a mild role in MDA5-mediated LINE-1 suppression. In addition, the N-terminal 2CARD domain was found to be a functional region for MDA5 upon inhibition of LINE-1 replication. Thus, our data suggest that besides being an initiator of the innate immune system, MDA5 is also an effector against LINE-1 activity, potentially forming a feedback loop by suppressing LINE-1-induced innate immune activation. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00268-0.
Collapse
Affiliation(s)
- Jiaxiu Yan
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Neonatology, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Clinical Laboratory, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yifei Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Juan Du
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China.,Center for Pathogen Biology and Infectious Diseases, First Hospital of Jilin University, Changchun, Jilin, China.,Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yu Wang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Shaohua Wang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Qing Wang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Respiratory Medicine, First Hospital of Jilin University, Changchun, Jilin, China
| | - Xu Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Xu
- Department of Clinical Laboratory, First Hospital of Jilin University, Changchun, Jilin, China.
| | - Ke Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China. .,Center for Pathogen Biology and Infectious Diseases, First Hospital of Jilin University, Changchun, Jilin, China. .,Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, First Hospital of Jilin University, Changchun, Jilin, China.
| |
Collapse
|
6
|
Garrigós-Martínez J, Vuoristo K, Nieto-Taype MA, Tähtiharju J, Uusitalo J, Tukiainen P, Schmid C, Tolstorukov I, Madden K, Penttilä M, Montesinos-Seguí JL, Valero F, Glieder A, Garcia-Ortega X. Bioprocess performance analysis of novel methanol-independent promoters for recombinant protein production with Pichia pastoris. Microb Cell Fact 2021; 20:74. [PMID: 33757505 DOI: 10.1186/s12934-021-01564-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/12/2021] [Indexed: 11/30/2022] Open
Abstract
Background Pichia pastoris is a powerful and broadly used host for recombinant protein production (RPP), where past bioprocess performance has often been directed with the methanol regulated AOX1 promoter (PAOX1), and the constitutive GAP promoter (PGAP). Since promoters play a crucial role in an expression system and the bioprocess efficiency, innovative alternatives are constantly developed and implemented. Here, a thorough comparative kinetic characterization of two expression systems based on the commercial PDF and UPP promoters (PPDF, PUPP) was first conducted in chemostat cultures. Most promising conditions were subsequently tested in fed-batch cultivations. These new alternatives were compared with the classical strong promoter PGAP, using the Candida antarctica lipase B (CalB) as model protein for expression system performance. Results Both the PPDF and PUPP-based expression systems outperformed similar PGAP-based expression in chemostat cultivations, reaching ninefold higher specific production rates (qp). CALB transcription levels were drastically higher when employing the novel expression systems. This higher expression was also correlated with a marked upregulation of unfolded protein response (UPR) related genes, likely from an increased protein burden in the endoplasmic reticulum (ER). Based on the chemostat results obtained, best culture strategies for both PPDF and PUPP expression systems were also successfully implemented in 15 L fed-batch cultivations where qp and product to biomass yield (YP/X*) values were similar than those obtained in chemostat cultivations. Conclusions As an outcome of the macrokinetic characterization presented, the novel PPDF and PUPP were observed to offer much higher efficiency for CalB production than the widely used PGAP-based methanol-free alternative. Thus, both systems arise as highly productive alternatives for P. pastoris-based RPP bioprocesses. Furthermore, the different expression regulation patterns observed indicate the level of gene expression can be adjusted, or tuned, which is interesting when using Pichia pastoris as a cell factory for different products of interest. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01564-9.
Collapse
|
7
|
Chetverina D, Erokhin M, Schedl P. GAGA factor: a multifunctional pioneering chromatin protein. Cell Mol Life Sci 2021; 78:4125-4141. [PMID: 33528710 DOI: 10.1007/s00018-021-03776-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/08/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022]
Abstract
The Drosophila GAGA factor (GAF) is a multifunctional protein implicated in nucleosome organization and remodeling, activation and repression of gene expression, long distance enhancer-promoter communication, higher order chromosome structure, and mitosis. This broad range of activities poses questions about how a single protein can perform so many seemingly different and unrelated functions. Current studies argue that GAF acts as a "pioneer" factor, generating nucleosome-free regions of chromatin for different classes of regulatory elements. The removal of nucleosomes from regulatory elements in turn enables other factors to bind to these elements and carry out their specialized functions. Consistent with this view, GAF associates with a collection of chromatin remodelers and also interacts with proteins implicated in different regulatory functions. In this review, we summarize the known activities of GAF and the functions of its protein partners.
Collapse
Affiliation(s)
- Darya Chetverina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia.
| | - Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| |
Collapse
|
8
|
Meiri H, Osol G, Cetin I, Gizurarson S, Huppertz B. Personalized Therapy Against Preeclampsia by Replenishing Placental Protein 13 (PP13) Targeted to Patients With Impaired PP13 Molecule or Function. Comput Struct Biotechnol J 2017; 15:433-446. [PMID: 29034064 PMCID: PMC5633742 DOI: 10.1016/j.csbj.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/27/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022] Open
Abstract
Hypertensive disorders affect about one third of all people aged 20 and above, and are treated with anti-hypertensive drugs. Preeclampsia (PE) is one form of such disorders that only develops during pregnancy. It affects ten million pregnant women globally and additionally causes fetal loss and major newborn disabilities. The syndrome's origin is multifactorial, and anti-hypertensive drugs are ineffective in treating it. Biomarkers are helpful for predict its development. Generic drugs, such as low dose aspirin, were proven effective in preventing preterm PE. However, it does not cure the majority of cases and many studies are underway for fighting PE with extended use of additional generic drugs, or through new drug development programs. This review focuses on placental protein 13 (PP13). This protein is only expressed in the placenta. Impaired PP13 DNA structure and/or its reduced mRNA expression leads to lower blood PP13 level that predict a higher risk of developing PE. Two polymorphic PP13 variants have been identified: (1) The promoter PP13 variant with an "A/A" genotype in the -98 position (versus "A/C" or "C/C"). Having the "A/A" genotype is coupled to lower PP13 expression, mainly during placental syncytiotrophoblast differentiation and, if associated with obesity and history of previous preeclampsia, it accurately predicts higher risk for developing the disorder. (2) A thymidine deletion at position 221 causes a frame shift in the open reading frame, and the formation of an early stop codon resulting in the formation of DelT221, a truncated variant of PP13. In pregnant rodents, both short- and long- term replenishment of PP13 causes reversible hypotension and vasodilation of uterine vessels. Long-term exposure is also accompanied by the development of larger placentas and newborns. Also, only w/t PP13 is capable of inducing leukocyte apoptosis, providing maternal immune tolerance to pregnancy. Based on published data, we propose a targeted PP13 therapy to fight PE, and consider the design and conduct of animal studies to explore this hypothesis. Accordingly, a new targeted therapy can be implemented in humans combining prediction and prevention.
Collapse
Affiliation(s)
- Hamutal Meiri
- Hy Laboratories, Rehovot, and TeleMarpe, Tel Aviv, Israel
| | - George Osol
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Vermont, Burlington, VT, USA
| | - Irene Cetin
- Department of Obstetrics and Gynecology, University of Milano, Italy
- Department of Mother and Child, Hospital Luigi Sacco, and Center for Fetal Research “Giorgio Pardi”, Milano, Italy
| | - Sveinbjörn Gizurarson
- Faculty of Pharmaceutical Sciences, School of Health Science, University of Iceland, Reykjavik, Iceland
| | - Berthold Huppertz
- Institute of Cell Biology, Histology and Embryology & Biobank Graz, Medical University of Graz, Graz, Austria
| |
Collapse
|
9
|
Boyce AKJ, Epp AL, Nagarajan A, Swayne LA. Transcriptional and post-translational regulation of pannexins. Biochim Biophys Acta Biomembr 2017; 1860:72-82. [PMID: 28279657 DOI: 10.1016/j.bbamem.2017.03.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 12/21/2022]
Abstract
Pannexins are a 3-membered family of proteins that form large pore ion and metabolite channels in vertebrates. The impact of pannexins on vertebrate biology is intricately tied to where and when they are expressed, and how they are modified, once produced. The purpose of this review is therefore to outline our current understanding of transcriptional and post-translational regulation of pannexins. First, we briefly summarize their discovery and characteristics. Next, we describe several aspects of transcriptional regulation, including cell and tissue-specific expression, dynamic expression over development and disease, as well as new insights into the underlying molecular machinery involved. Following this, we delve into the role of post-translational modifications in the regulation of trafficking and channel properties, highlighting important work on glycosylation, phosphorylation, S-nitrosylation and proteolytic cleavage. Embedded throughout, we also highlight important knowledge gaps and avenues of future research. This article is part of a Special Issue entitled: Gap Junction Proteins edited by Jean Claude Herve.
Collapse
Affiliation(s)
- Andrew K J Boyce
- Division of Medical Sciences and Island Medical Program, University of Victoria, Victoria V8P 5C2, Canada
| | - Anna L Epp
- Division of Medical Sciences and Island Medical Program, University of Victoria, Victoria V8P 5C2, Canada
| | - Archana Nagarajan
- Division of Medical Sciences and Island Medical Program, University of Victoria, Victoria V8P 5C2, Canada
| | - Leigh Anne Swayne
- Division of Medical Sciences and Island Medical Program, University of Victoria, Victoria V8P 5C2, Canada; Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver V6T 1Z3, Canada.
| |
Collapse
|
10
|
Abstract
Pyruvate plays an essential role in the central carbon metabolism of multiple organisms and is used as a raw material in the chemical, biochemical and pharmaceutical industries. To meet demand, large amounts of pyruvate are produced through fermentation processes. Here we describe a simple and efficient method for producing pyruvate in Escherichia coli. To stop carbon flux from pyruvate to fatty acids, the accBC genes, which encode the enzyme that catalyzes the first step of fatty acid biosynthesis and is essential for vegetative growth, were manipulated within the genome; its native promoter was replaced with the tetracycline (or doxycycline)-regulated promoter and the corresponding transcriptional regulator genes. The resulting strain grew normally in the presence of doxycycline, but showed poor growth upon withdrawal of doxycycline. Using this strain, we developed a high pyruvate producing strain (strain LAFCPCPt-accBC-aceE), in which the tetracycline-regulated promoter was also introduced upstream of aceE, and the ackA-pta, adhE, cra, ldhA, pflB and poxB genes were deleted. After determining the optimal culture conditions for this strain, the final pyruvate concentration reached 26.1 g L-1 after 72 h with a theoretical yield of 55.6 %. These levels are high enough to indicate that the developed strain has the potential for application to industrial production of pyruvate.
Collapse
|
11
|
Sassi H, Delvigne F, Kar T, Nicaud JM, Coq AMCL, Steels S, Fickers P. Deciphering how LIP2 and POX2 promoters can optimally regulate recombinant protein production in the yeast Yarrowia lipolytica. Microb Cell Fact 2016; 15:159. [PMID: 27651221 PMCID: PMC5028966 DOI: 10.1186/s12934-016-0558-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 11/13/2022] Open
Abstract
Background In recent years, the non-conventional model yeast species Yarrowia lipolytica has received much attention because it is a useful cell factory for producing recombinant proteins. In this species, expression vectors involving LIP2 and POX2 promoters have been developed and used successfully for protein production at yields similar to or even higher than those of other cell factories, such as Pichia pastoris. However, production processes involving these promoters can be difficult to manage, especially if carried out at large scales in fed-batch bioreactors, because they require hydrophobic inducers, such as oleic acid or methyl oleate. Thus, the challenge has become to reduce loads of hydrophobic substrates while simultaneously promoting recombinant protein production. One possible solution is to replace a portion of the inducer with a co-substrate that can serve as an alternative energy source. However, implementing such an approach would require detailed knowledge of how carbon sources impact promoter regulation, which is surprisingly still lacking for the LIP2 and POX2 promoters. This study’s aim was thus to better characterize promoter regulation and cell metabolism in Y. lipolytica cultures grown in media supplemented with different carbon sources. Results pPOX2 induction could be detected when glucose or glycerol was used as sole carbon source, which meant these carbon source could not prevent promoter induction. In addition, when a mixture of glucose and oleic acid was used in complex medium, pPOX2 induction level was lower that that of pLIP2. In contrast, pLIP2 induction was absent when glucose was present in the culture medium, which meant that cell growth could occur without any recombinant gene expression. When a 40/60 mixture of glucose and oleic acid (w/w) was used, a tenfold increase in promoter induction, as compared to when an oleic-acid-only medium was observed. It was also clear that individual cells were adapting metabolically to use both glucose and oleic acid. Indeed, no distinct subpopulations that specialized on glucose versus oleic acid were observed; such an outcome would have led to producer and non-producer phenotypes. In medium containing both glucose and oleic acid, cells tended to directly metabolize oleic acid instead of storing it in lipid bodies. Conclusions This study found that pLIP2 is a promoter of choice as compared to pPOX2 to drive gene expression for recombinant protein production by Y. lipolytica used as cell factory. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0558-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hosni Sassi
- Biotechnology and Bioprocesses, Université libre de Bruxelles, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium
| | - Frank Delvigne
- Microbial Processes and Interactions, University of Liège-Gembloux AgroBio Tech, Passage des Déportés, 2, B-5030, Gembloux, Belgium
| | - Tambi Kar
- Microbial Processes and Interactions, University of Liège-Gembloux AgroBio Tech, Passage des Déportés, 2, B-5030, Gembloux, Belgium
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en Josas, France
| | - Sebastien Steels
- Microbial Processes and Interactions, University of Liège-Gembloux AgroBio Tech, Passage des Déportés, 2, B-5030, Gembloux, Belgium
| | - Patrick Fickers
- Biotechnology and Bioprocesses, Université libre de Bruxelles, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium. .,Microbial Processes and Interactions, University of Liège-Gembloux AgroBio Tech, Passage des Déportés, 2, B-5030, Gembloux, Belgium.
| |
Collapse
|
12
|
Lee EJ, Kang YC, Park WH, Jeong JH, Pak YK. Negative transcriptional regulation of mitochondrial transcription factor A (TFAM) by nuclear TFAM. Biochem Biophys Res Commun 2014; 450:166-71. [PMID: 24875355 DOI: 10.1016/j.bbrc.2014.05.082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 05/19/2014] [Indexed: 11/23/2022]
Abstract
The nuclear DNA-encoded mitochondrial transcription factor A (TFAM) is synthesized in cytoplasm and transported into mitochondria. TFAM enhances both transcription and replication of mitochondrial DNA. It is unclear, however, whether TFAM plays a role in regulating nuclear gene expression. Here, we demonstrated that TFAM was localized to the nucleus and mitochondria by immunostaining, subcellular fractionation, and TFAM-green fluorescent protein hybrid protein studies. In HT22 hippocampal neuronal cells, human TFAM (hTFAM) overexpression suppressed human Tfam promoter-mediated luciferase activity in a dose-dependent manner. The mitochondria targeting sequence-deficient hTFAM also repressed Tfam promoter activity to the same degree as hTFAM. It indicated that nuclear hTFAM suppressed Tfam expression without modulating mitochondrial activity. The repression required for nuclear respiratory factor-1 (NRF-1), but hTFAM did not bind to the NRF-1 binding site of its promoter. TFAM was co-immunoprecipitated with NRF-1. Taken together, we suggest that nuclear TFAM down-regulate its own gene expression as a NRF-1 repressor, showing that TFAM may play different roles depending on its subcellular localizations.
Collapse
|
13
|
Brown AJ, Mainwaring DO, Sweeney B, James DC. Block decoys: transcription-factor decoys designed for in vitro gene regulation studies. Anal Biochem 2013; 443:205-10. [PMID: 24036039 DOI: 10.1016/j.ab.2013.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 08/21/2013] [Accepted: 09/03/2013] [Indexed: 11/22/2022]
Abstract
Transcription-factor decoys are short synthetic oligodeoxynucleotides that sequester cognate transcription factors and prevent their binding at target promoters. Current methods of decoy formation have primarily been optimized for potential therapeutic applications. However, they are not ideally suited to in vitro investigations into multi-transcription factor-mediated processes that may require multiple regulatory elements to be inhibited in varying combinations. In this study we describe a novel method for chimeric decoy formation in which blocks containing discrete transcription factor binding sites are combined into circular molecules. Unlike currently available methods, block decoys allow rapid construction of chimeric decoys targeting multiple regulatory elements. Further, they enable fine-tuning of binding-site copy ratios within chimeras, allowing sophisticated control of the cellular transcriptional landscape. We show that block decoys are exonuclease-resistant and specifically inhibit expression from target binding sites. The potential of block decoys to inhibit multiple elements simultaneously was demonstrated using a chimeric decoy containing molar optimized ratios of three regulatory elements, NF-κB-RE, CRE, and E-box. The chimeric decoy inhibited expression from all three elements simultaneously at equivalent levels. The primary intended use of block decoys is in vitro gene regulation studies in which bespoke chimeras can be rapidly constructed and utilized to determine a promoter's functional regulation.
Collapse
|