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Jian Jun Gao, Diesl V, Wittmann T, Morrison DC, Ryan JL, Vogel SN, Follettie MT. Bacterial LPS and CpG DNA differentially induce gene expression profiles in mouse macrophages. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/09680519030090040401] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bacterial DNA containing unmethylated CpG dinucleotides (CpG DNA) is a potent immune stimulating agent that holds strong promise in the treatment of many disorders. Studies have established that CpG DNA triggers an immune response through activated expression of genes in immune cells including macrophages. To dissect further the molecular mechanism(s) by which CpG DNA activates the immune system, we studied macrophage gene expression profiles in response to CpG DNA using microarray technology. Since CpG DNA is reported to use the TLR9 receptor that shares homology with the TLR4 receptor used by bacterial lipopolysaccharide (LPS), we also evaluated gene expression profiles in macrophages stimulated by LPS versus CpG DNA. Both CpG DNA and LPS modulate expression of a large array of genes. However, LPS modulated the expression of a much greater number of genes than did CpG DNA and all genes induced or repressed by CpG DNA were also induced or repressed by LPS. These data indicate that the CpG DNA signaling pathway through TLR9 activates only a subset of genes induced by the LPS TLR4 signaling pathway.
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Affiliation(s)
- Jian Jun Gao
- Department of Basic Medical Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA,
| | | | - Tatiana Wittmann
- Department of Basic Medical Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - David C. Morrison
- Department of Basic Medical Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - John L. Ryan
- Genetics Institute, Cambridge, Massachusetts, USA
| | - Stefanie N. Vogel
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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2
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Dann SG, Ryskin M, Barsotti AM, Golas J, Shi C, Miranda M, Hosselet C, Lemon L, Lucas J, Karnoub M, Wang F, Myers JS, Garza SJ, Follettie MT, Geles KG, Klippel A, Rollins RA, Fantin VR. Reciprocal regulation of amino acid import and epigenetic state through Lat1 and EZH2. EMBO J 2015; 34:1773-85. [PMID: 25979827 DOI: 10.15252/embj.201488166] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/14/2015] [Indexed: 12/26/2022] Open
Abstract
Lat1 (SLC7A5) is an amino acid transporter often required for tumor cell import of essential amino acids (AA) including Methionine (Met). Met is the obligate precursor of S-adenosylmethionine (SAM), the methyl donor utilized by all methyltransferases including the polycomb repressor complex (PRC2)-specific EZH2. Cell populations sorted for surface Lat1 exhibit activated EZH2, enrichment for Met-cycle intermediates, and aggressive tumor growth in mice. In agreement, EZH2 and Lat1 expression are co-regulated in models of cancer cell differentiation and co-expression is observed at the invasive front of human lung tumors. EZH2 knockdown or small-molecule inhibition leads to de-repression of RXRα resulting in reduced Lat1 expression. Our results describe a Lat1-EZH2 positive feedback loop illustrated by AA depletion or Lat1 knockdown resulting in SAM reduction and concomitant reduction in EZH2 activity. shRNA-mediated knockdown of Lat1 results in tumor growth inhibition and points to Lat1 as a potential therapeutic target.
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Affiliation(s)
| | | | | | | | - Celine Shi
- Pfizer Oncology Research Unit, Pearl River, NY, USA
| | | | | | - Luanna Lemon
- Pfizer Oncology Research Unit, Pearl River, NY, USA
| | - Judy Lucas
- Pfizer Oncology Research Unit, Pearl River, NY, USA
| | | | - Fang Wang
- Pfizer Oncology Research Unit, Pearl River, NY, USA
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3
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Loganzo F, Tan X, Sung M, Jin G, Myers JS, Melamud E, Wang F, Diesl V, Follettie MT, Musto S, Lam MH, Hu W, Charati MB, Khandke K, Kim KSK, Cinque M, Lucas J, Graziani E, Maderna A, O'Donnell CJ, Arndt KT, Gerber HP. Tumor cells chronically treated with a trastuzumab-maytansinoid antibody-drug conjugate develop varied resistance mechanisms but respond to alternate treatments. Mol Cancer Ther 2015; 14:952-63. [PMID: 25646013 DOI: 10.1158/1535-7163.mct-14-0862] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/22/2015] [Indexed: 11/16/2022]
Abstract
Antibody-drug conjugates (ADC) are emerging as clinically effective therapy. We hypothesized that cancers treated with ADCs would acquire resistance mechanisms unique to immunoconjugate therapy and that changing ADC components may overcome resistance. Breast cancer cell lines were exposed to multiple cycles of anti-Her2 trastuzumab-maytansinoid ADC (TM-ADC) at IC80 concentrations followed by recovery. The resistant cells, 361-TM and JIMT1-TM, were characterized by cytotoxicity, proteomic, transcriptional, and other profiling. Approximately 250-fold resistance to TM-ADC developed in 361-TM cells, and cross-resistance was observed to other non-cleavable-linked ADCs. Strikingly, these 361-TM cells retained sensitivity to ADCs containing cleavable mcValCitPABC-linked auristatins. In JIMT1-TM cells, 16-fold resistance to TM-ADC developed, with cross-resistance to other trastuzumab-ADCs. Both 361-TM and JIMT1-TM cells showed minimal resistance to unconjugated mertansine (DM1) and other chemotherapeutics. Proteomics and immunoblots detected increased ABCC1 (MRP1) drug efflux protein in 361-TM cells, and decreased Her2 (ErbB2) in JIMT1-TM cells. Proteomics also showed alterations in various pathways upon chronic exposure to the drug in both cell models. Tumors derived from 361-TM cells grew in mice and were refractory to TM-ADC compared with parental cells. Hence, acquired resistance to trastuzumab-maytansinoid ADC was generated in cultured cancer cells by chronic drug treatment, and either increased ABCC1 protein or reduced Her2 antigen were primary mediators of resistance. These ADC-resistant cell models retain sensitivity to other ADCs or standard-of-care chemotherapeutics, suggesting that alternate therapies may overcome acquired ADC resistance. Mol Cancer Ther; 14(4); 952-63. ©2015 AACR.
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Affiliation(s)
| | | | | | | | | | | | - Fang Wang
- Pfizer Oncology, Pearl River, New York
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4
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Rollins RA, Barsotti AM, Ryskin M, Zhong W, Zhang WG, Giannakou A, Loreth C, Diesl V, Follettie MT, Golas J, Lee M, Nichols T, Fan C, Li G, Dann S, Rejto PA, Arndt KT, Verhelle D. Abstract 5144: Epigenetic reprogramming by tumor-derived EZH2 gain of function mutants leads to aggressive 3D-cell morphologies in both epithelial and melanoma cells. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-5144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In addition to numerous genetic changes underlying cellular transformation, cancer cells are also characterized by epigenetic changes that are likely to play important roles in disease progression. EZH2 is an epigenetic repressor that plays well-established roles in development. In addition to widespread overexpression in a variety of tumors, the discovery of gain of function (GOF) mutations of EZH2 in diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, and melanoma strongly suggests an important function for this histone methyltransferase in cancer. To ascertain the function of elevated EZH2 catalytic activity, we expressed either wild-type EZH2 (WT) or EZH2 GOF mutants in both non-tumorigenic (immortalized epithelial cells) and tumorigenic (melanoma cells) settings. In both systems, EZH2 GOF mutants greatly increased global levels of H3K27me3 and decreased H3K27me2 levels, similar to the epigenetic pattern seen in DLBCL cell lines with endogenous EZH2 GOF mutations.
In epithelial cells, expression of an EZH2 GOF mutant caused striking changes in 3D-morphology and gene changes that are indicative of cells that have undergone an epithelial to mesenchymal transition. In the disease relevant melanoma cells, several distinct EZH2 GOF mutants (but not EZH2 WT) caused prominent branching morphology in 3D-culture. Interestingly, these GOF mutants did not affect 2D-cell morphology or proliferation of melanoma cells. Furthermore, catalytic inhibition of EZH2 GOF mutants with a commercially available tool compound attenuated the 3D-phenotype. Importantly, EZH2 inhibition in melanoma cells expressing an endogenous GOF mutation also caused similar changes in 3D-morphology. RNA-seq analysis revealed genes involved in processes such as cell adhesion and axonal guidance that were down-regulated by EZH2 GOF mutants. Finally, melanoma cells expressing ectopic EZH2 GOF mutants formed larger tumors than control cells in mouse xenograft studies. Collectively, these results suggest that EZH2 GOF mutants may alter the interaction of tumor cells with their microenvironment and in this way provide a selective advantage to such tumors.
Citation Format: Robert A. Rollins, Anthony M. Barsotti, Michael Ryskin, Wenyan Zhong, Wei-Guo Zhang, Andreas Giannakou, Christine Loreth, Veronica Diesl, Maximillian T. Follettie, Jonathon Golas, Michelle Lee, Timothy Nichols, Conglin Fan, Gary Li, Stephen Dann, Paul A. Rejto, Kim T. Arndt, Dominique Verhelle. Epigenetic reprogramming by tumor-derived EZH2 gain of function mutants leads to aggressive 3D-cell morphologies in both epithelial and melanoma cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5144. doi:10.1158/1538-7445.AM2014-5144
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5
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Damelin M, Geles KG, Follettie MT, Yuan P, Baxter M, Golas J, DiJoseph JF, Karnoub M, Huang S, Diesl V, Behrens C, Choe SE, Rios C, Gruzas J, Sridharan L, Dougher M, Kunz A, Hamann PR, Evans D, Armellino D, Khandke K, Marquette K, Tchistiakova L, Boghaert ER, Abraham RT, Wistuba II, Zhou BBS. Delineation of a cellular hierarchy in lung cancer reveals an oncofetal antigen expressed on tumor-initiating cells. Cancer Res 2011; 71:4236-46. [PMID: 21540235 DOI: 10.1158/0008-5472.can-10-3919] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Poorly differentiated tumors in non-small cell lung cancer (NSCLC) have been associated with shorter patient survival and shorter time to recurrence following treatment. Here, we integrate multiple experimental models with clinicopathologic analysis of patient tumors to delineate a cellular hierarchy in NSCLC. We show that the oncofetal protein 5T4 is expressed on tumor-initiating cells and associated with worse clinical outcome in NSCLC. Coexpression of 5T4 and factors involved in the epithelial-to-mesenchymal transition were observed in undifferentiated but not in differentiated tumor cells. Despite heterogeneous expression of 5T4 in NSCLC patient-derived xenografts, treatment with an anti-5T4 antibody-drug conjugate resulted in complete and sustained tumor regression. Thus, the aggressive growth of heterogeneous solid tumors can be blocked by therapeutic agents that target a subpopulation of cells near the top of the cellular hierarchy.
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Affiliation(s)
- Marc Damelin
- Oncology Research Unit, Pfizer Inc., Pearl River, New York, USA.
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6
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Damelin MI, Geles KG, Follettie MT, Yuan P, Baxter M, Golas J, Huang S, DiJoseph J, Diesl V, Behrens C, Choe SE, Rios C, Gruzas J, Sridharan L, Dougher M, Kunz A, Hamann PR, Evans D, Armellino D, Khandke K, Marquette K, Tchistiakova L, Boghaert E, Abraham RT, Wistuba II, Zhou BBS. Abstract 475: Delineation of a cellular hierarchy in lung cancer reveals an oncofetal antigen expressed on tumor-initiating cells. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Poorly differentiated tumors in non-small cell lung cancer (NSCLC) are refractory to chemotherapy and associated with short survival time. Here we integrate multiple experimental models with clinicopathological analysis of patient tumors to delineate a cellular hierarchy in NSCLC. We demonstrate that the oncofetal protein 5T4 is expressed on tumor-initiating cells and associated with worse clinical outcome in NSCLC. Coexpression of 5T4 and factors involved in the epithelial-to-mesenchymal transition was observed in undifferentiated but not in differentiated tumor cells. Despite heterogeneous expression of 5T4 in NSCLC patient-derived xenografts, treatment with an anti-5T4 antibody-drug conjugate resulted in complete and sustained tumor regression. Thus, the aggressive growth of heterogeneous solid tumors can be blocked by therapeutic agents that target a subpopulation of cells near the top of the cellular hierarchy.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 475. doi:10.1158/1538-7445.AM2011-475
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Affiliation(s)
| | | | | | - Ping Yuan
- 2MD Anderson Cancer Center, Houston, TX
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Byrne MC, Whitley MZ, Follettie MT. Preparation of mRNA for expression monitoring. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.26. [PMID: 18428486 DOI: 10.1002/0471142301.ns0426s16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The ability to construct comprehensive gene expression profiles comprising hundreds to thousands of genes whose RNA levels are monitored simultaneously represents an exciting new capability in molecular biology. This is accomplished by hybridizing mRNA, which has been quantitatively amplified and labeled with biotin, to DNA chips that display thousands of nucleotides complementary to the mRNAs of interest. In this unit, rationale for starting with poly(A(+)) versus total RNA is discussed, and strategies for choosing oligonucleotides for chip design is presented. Protocols on RNA amplification and labeling, and purifying and quantifying the cDNA and in vitro transcription products are included.
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Affiliation(s)
- M C Byrne
- Genetics Institute/Wyeth Research, Cambridge, Massachusetts, USA
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8
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Abstract
This unit provides protocols for the amplification and labeling of mRNA (and the necessary controls) for hybridization to oligonucleotide arrays. It also describes methods for processing and normalizing the raw gene expression data in preparation for clustering and further analysis.
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Affiliation(s)
- M C Byrne
- Genetics Institute, Cambridge, Massachusetts, USA
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9
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Abstract
The ability to construct comprehensive gene expression profiles comprising hundreds to thousands of genes whose RNA levels are monitored simultaneously represents an exciting new capability in molecular biology. This is accomplished by hybridizing mRNA, which has been quantitatively amplified and labeled with biotin, to DNA chips that display thousands of nucleotides complementary to the mRNAs of interest. In this unit, rationale for starting with poly(A(+)) vs. total RNA is discussed, and strategies for choosing oligonucleotides for chip design is presented. Protocols on RNA amplification and labeling, and purifying and quantifying the cDNA and in vitro transcription products are included.
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Affiliation(s)
- M C Byrne
- Genetics Institute, Cambridge, Massachusetts, USA
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10
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Affiliation(s)
- Jiang Wu
- Biological Technologies, Wyeth Research, Cambridge, Massachusetts 02140
| | - Quazi Shakey
- Biological Technologies, Wyeth Research, Cambridge, Massachusetts 02140
| | - Wei Liu
- Biological Technologies, Wyeth Research, Cambridge, Massachusetts 02140
| | - Alwin Schuller
- Biological Technologies, Wyeth Research, Cambridge, Massachusetts 02140
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11
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Mellott TJ, Follettie MT, Diesl V, Hill AA, Lopez-Coviella I, Blusztajn JK. Prenatal choline availability modulates hippocampal and cerebral cortical gene expression. FASEB J 2007; 21:1311-23. [PMID: 17264169 DOI: 10.1096/fj.06-6597com] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An increased supply of the essential nutrient choline during fetal development [embryonic day (E) 11-17] in rats causes life-long improvements in memory performance, whereas choline deficiency during this time impairs certain aspects of memory. We analyzed mRNA expression in brains of prenatally choline-deficient, choline-supplemented, or control rats of various ages [postnatal days (P) 1 to 34 for hippocampus and E16 to P34 for cortex] using oligonucleotide microarrays and found alterations in gene expression levels evoked by prenatal choline intake that were, in most cases, transient occurring during the P15-P34 period. We selected a subset of genes, encoding signaling proteins, and verified the microarray data by reverse transcriptase-polymerase chain reaction analyses. Prenatally choline-supplemented rats had the highest expression of calcium/calmodulin (CaM)-dependent protein kinase (CaMK) I and insulin-like growth factor (IGF) II (Igf2) in the cortex and of the transcription factor Zif268/EGR1 in the cortex and hippocampus. Prenatally choline deficient rats had the highest expression of CaMKIIbeta, protein kinase Cbeta2, and GABA(B) receptor 1 isoforms c and d in the hippocampus. Similar changes in the expression of the proteins encoded by these genes were observed using immunoblot analyses. These data show that the prenatal supply of choline causes multiple modifications in the developmental patterns of expression of genes known to influence learning and memory and provide molecular correlates for the cognitive changes evoked by altered availability of choline in utero.
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Affiliation(s)
- Tiffany J Mellott
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, 715 Albany St., Boston, MA 02118, USA
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12
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Follettie MT, Ellis DK, Donaldson DD, Hill AA, Diesl V, DeClercq C, Sypek JP, Dorner AJ, Wills-Karp M. Gene expression analysis in a murine model of allergic asthma reveals overlapping disease and therapy dependent pathways in the lung. Pharmacogenomics J 2006; 6:141-52. [PMID: 16402082 DOI: 10.1038/sj.tpj.6500357] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Accumulating evidence in animal models and human asthma support a central role for IL-13 signaling in disease pathogenesis. In order to identify asthma and therapy associated genes, global transcriptional changes were monitored in mouse lung following antigen challenge (ovalbumin (OVA)), either alone or in the presence of a soluble IL-13 antagonist. Changes in whole lung gene expression after instillation of mIL-13 were also measured both in wild type and STAT6 deficient mice. A striking overlap in the gene expression profiles induced by either OVA challenge or mIL-13 was observed, further strengthening the relationship of IL-13 signaling to asthma. Consistent with results from functional studies, a subset of the OVA-induced gene expression was significantly inhibited by a soluble IL-13 antagonist while IL-13-modulated gene expression was completely attenuated in the absence of STAT6-mediated signaling. Results from these experiments greatly expand our understanding of asthma and provide novel molecular targets for therapy and potential biomarkers of IL-13 antagonism.
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Affiliation(s)
- M T Follettie
- Department of Molecular Profiling and Biomarker Discovery, Cambridge, MA 02140, USA.
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13
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Follettie MT, Pinard M, Keith JC, Wang L, Chelsky D, Hayward C, Kearney P, Thibault P, Paramithiotis E, Dorner AJ, Harris HA. Organ messenger ribonucleic acid and plasma proteome changes in the adjuvant-induced arthritis model: responses to disease induction and therapy with the estrogen receptor-beta selective agonist ERB-041. Endocrinology 2006; 147:714-23. [PMID: 16269464 DOI: 10.1210/en.2005-0600] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Two receptors [estrogen receptor (ER)alpha and ERbeta] mediate the manifold effects of estrogens throughout the body. Although a clear role has been established for ERalpha in the classical effects of estrogen activity, the physiological role of ERbeta is less well understood. A small-molecule ERbeta selective agonist, ERB-041, has potent antiinflammatory activity in the Lewis rat model of adjuvant-induced arthritis. To characterize the response of target organs and pathways responsible for this antiinflammatory effect, mRNA expression profiling of the spleen, lymph node, and liver was performed, in conjunction with a global analysis of the plasma proteome. We find that the expression of a large number of genes and proteins are altered in the disease model and the majority of these are partially or fully reversed by ERB-041 treatment. Regulated pathways include the acute-phase response, eicosanoid synthesis, fatty acid metabolism, and iron metabolism. In addition, many of the regulated genes and proteins are known to be dysregulated in human rheumatoid arthritis, providing further evidence that the manifestations of the Lewis rat adjuvant-induced arthritis model bear similarity to the human disease.
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Abstract
Expression of the forkhead transcription factor FoxM1 correlates with proliferative status in a variety of normal and transformed cell types. Elevated expression of FoxM1 has been noted in both hepatocellular carcinoma and basal cell carcinoma. However, whether FoxM1 expression is essential for the viability of transformed cells is unknown. We report here that the expression of FoxM1 is significantly elevated in primary breast cancer. Microarray analysis shows that FoxM1 regulates genes that are essential for faithful chromosome segregation and mitosis, including Nek2, KIF20A, and CENP-A. Loss of FoxM1 expression generates mitotic spindle defects, delays cells in mitosis, and induces mitotic catastrophe. Time-lapse microscopy indicates that depletion of FoxM1 generates cells that enter mitosis but are unable to complete cell division, resulting in either mitotic catastrophe or endoreduplication. These findings indicate that FoxM1 depletion causes cell death due to mitotic catastrophe and that inhibiting FoxM1 represents a therapeutic strategy to target breast cancer.
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Affiliation(s)
- Diane R Wonsey
- Department of Discovery Medicine, Wyeth Research, Cambridge, Massachusetts, USA.
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15
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Lopez-Coviella I, Follettie MT, Mellott TJ, Kovacheva VP, Slack BE, Diesl V, Berse B, Thies RS, Blusztajn JK. Bone morphogenetic protein 9 induces the transcriptome of basal forebrain cholinergic neurons. Proc Natl Acad Sci U S A 2005; 102:6984-9. [PMID: 15870197 PMCID: PMC1088172 DOI: 10.1073/pnas.0502097102] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [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: 12/14/2004] [Indexed: 01/19/2023] Open
Abstract
Basal forebrain cholinergic neurons (BFCN) participate in processes of learning, memory, and attention. Little is known about the genes expressed by BFCN and the extracellular signals that control their expression. Previous studies showed that bone morphogenetic protein (BMP) 9 induces and maintains the cholinergic phenotype of embryonic BFCN. We measured gene expression patterns in septal cultures of embryonic day 14 mice and rats grown in the presence or absence of BMP9 by using species-specific microarrays and validated the RNA expression data of selected genes by immunoblot and immunocytochemistry analysis of their protein products. BMP9 enhanced the expression of multiple genes in a time-dependent and, in most cases, reversible manner. The set of BMP9-responsive genes was concordant between mouse and rat and included genes encoding cell-cycle/growth control proteins, transcription factors, signal transduction molecules, extracellular matrix, and adhesion molecules, enzymes, transporters, and chaperonins. BMP9 induced the p75 neurotrophin receptor (NGFR), a marker of BFCN, and Cntf and Serpinf1, two trophic factors for cholinergic neurons, suggesting that BMP9 creates a trophic environment for BFCN. To determine whether the genes induced by BMP9 in culture were constituents of the BFCN transcriptome, we purified BFCN from embryonic day 18 mouse septum by using fluorescence-activated cell sorting of NGFR(+) cells and profiled mRNA expression of these and NGFR(-) cells. Approximately 30% of genes induced by BMP9 in vitro were overexpressed in purified BFCN, indicating that they belong to the BFCN transcriptome in situ and suggesting that BMP signaling contributes to maturation of BFCN in vivo.
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Affiliation(s)
- Ignacio Lopez-Coviella
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
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16
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Gao JJ, Diesl V, Wittmann T, Morrison DC, Ryan JL, Vogel SN, Follettie MT. Bacterial LPS and CpG DNA differentially induce gene expression profiles in mouse macrophages. J Endotoxin Res 2004; 9:237-43. [PMID: 12935354 DOI: 10.1179/096805103225001431] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Bacterial DNA containing unmethylated CpG dinucleotides (CpG DNA) is a potent immune stimulating agent that holds strong promise in the treatment of many disorders. Studies have established that CpG DNA triggers an immune response through activated expression of genes in immune cells including macrophages. To dissect further the molecular mechanism(s) by which CpG DNA activates the immune system, we studied macrophage gene expression profiles in response to CpG DNA using microarray technology. Since CpG DNA is reported to use the TLR9 receptor that shares homology with the TLR4 receptor used by bacterial lipopolysaccharide (LPS), we also evaluated gene expression profiles in macrophages stimulated by LPS versus CpG DNA. Both CpG DNA and LPS modulate expression of a large array of genes. However, LPS modulated the expression of a much greater number of genes than did CpG DNA and all genes induced or repressed by CpG DNA were also induced or repressed by LPS. These data indicate that the CpG DNA signaling pathway through TLR9 activates only a subset of genes induced by the LPS TLR4 signaling pathway.
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Affiliation(s)
- Jian Jun Gao
- Department of Basic Medical Sciences, University of Missouri-Kansas City, Kansas City, MO 64108, USA.
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17
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Gao JJ, Diesl V, Wittmann T, Morrison DC, Ryan JL, Vogel SN, Follettie MT. Regulation of gene expression in mouse macrophages stimulated with bacterial CpG‐DNA and lipopolysaccharide. J Leukoc Biol 2002. [DOI: 10.1189/jlb.72.6.1234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Jian Jun Gao
- Department of Basic Medical Sciences, University of Missouri‐Kansas City
| | | | - Tatiana Wittmann
- Department of Basic Medical Sciences, University of Missouri‐Kansas City
| | - David C. Morrison
- Department of Basic Medical Sciences, University of Missouri‐Kansas City
| | - John L. Ryan
- Genetics Institute, Cambridge, Massachusetts; and
| | - Stefanie N. Vogel
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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18
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Gao JJ, Diesl V, Wittmann T, Morrison DC, Ryan JL, Vogel SN, Follettie MT. Regulation of gene expression in mouse macrophages stimulated with bacterial CpG-DNA and lipopolysaccharide. J Leukoc Biol 2002; 72:1234-45. [PMID: 12488506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Abstract
CpG-DNA is known as a potent immunostimulating agent and may contribute in therapeutic treatment of many immune disorders. CpG-DNA triggers innate and acquired immune responses through activated expression of various genes in immune cells, including macrophages. To define the molecular mechanism(s) by which CpG-DNA activates immune cells, we studied macrophage gene expression following CpG-DNA exposure using high-density oligonucleotide microarrays. As CpG-DNA receptor Toll-like receptor 9 (TLR9) shares homology with the lipopolysaccharide (LPS)-TLR4 receptor, we compared gene expression profiles in macrophages stimulated by LPS versus CpG-DNA. CpG-DNA and LPS modulate expression of many genes encoding cytokines, cell surface receptors, transcription factors, and proteins related to cell proliferation/differentiation. However, LPS modulated expression of significantly more genes than did CpG-DNA, and all genes induced or repressed by CpG-DNA were induced or repressed by LPS. We conclude that CpG-DNA signaling through TLR9 activates a subset of genes induced by LPS-TLR4 signaling.
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Affiliation(s)
- Jian Jun Gao
- Department of Basic Medical Sciences, University of Missouri-Kansas City, 64108, USA.
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Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996; 14:1675-80. [PMID: 9634850 DOI: 10.1038/nbt1296-1675] [Citation(s) in RCA: 2517] [Impact Index Per Article: 89.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The human genome encodes approximately 100,000 different genes, and at least partial sequence information for nearly all will be available soon. Sequence information alone, however, is insufficient for a full understanding of gene function, expression, regulation, and splice-site variation. Because cellular processes are governed by the repertoire of expressed genes, and the levels and timing of expression, it is important to have experimental tools for the direct monitoring of large numbers of mRNAs in parallel. We have developed an approach that is based on hybridization to small, high-density arrays containing tens of thousands of synthetic oligonucleotides. The arrays are designed based on sequence information alone and are synthesized in situ using a combination of photolithography and oligonucleotide chemistry. RNAs present at a frequency of 1:300,000 are unambiguously detected, and detection is quantitative over more than three orders of magnitude. This approach provides a way to use directly the growing body of sequence information for highly parallel experimental investigations. Because of the combinatorial nature of the chemistry and the ability to synthesize small arrays containing hundreds of thousands of specifically chosen oligonucleotides, the method is readily scalable to the simultaneous monitoring of tens of thousands of genes.
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Lu Z, DiBlasio-Smith EA, Grant KL, Warne NW, LaVallie ER, Collins-Racie LA, Follettie MT, Williamson MJ, McCoy JM. Histidine Patch Thioredoxins. J Biol Chem 1996. [DOI: 10.1074/jbc.271.9.5059] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Lu Z, DiBlasio-Smith EA, Grant KL, Warne NW, LaVallie ER, Collins-Racie LA, Follettie MT, Williamson MJ, McCoy JM. Histidine patch thioredoxins. Mutant forms of thioredoxin with metal chelating affinity that provide for convenient purifications of thioredoxin fusion proteins. J Biol Chem 1996; 271:5059-65. [PMID: 8617783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A cluster of surface amino acid residues on Escherichia coli thioredoxin were systematically mutated in order to provide the molecule with an ability to chelate metal ions. The combined effect of two histidine mutants, E30H and Q62H, gave thioredoxin the capacity to bind to nickel ions immobilized on iminodiacetic acid- and nitrilotriacetic acid-Sepharose resins. Even though these two histidines were more than 30 residues apart in thioredoxin's primary sequence, they were found to satisfy the geometric constraints for metal ion coordination as a result of the thioredoxin tertiary fold. A third histidine mutation, S1H, provided additional metal ion chelation affinity, but the native histidine at position 6 of thioredoxin was found not to participate in binding. All of the histidine mutants exhibited decreased thermal stability as compared with wild-type thioredoxin; however, the introduction of an additional mutation, D26A, increased their melting temperatures beyond that of wild-type thioredoxin. The metal chelating abilities of these histidine mutants of thioredoxin were successfully utilized for convenient purifications of human interleukin-8 and -11 expressed in E. coli as soluble thioredoxin fusion proteins.
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Affiliation(s)
- Z Lu
- Genetics Institute, Inc., Cambridge, Massachusetts 02140, USA
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22
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Jetten MS, Follettie MT, Sinskey AJ. Effect of different levels of aspartokinase on the lysine production by Corynebacterium lactofermentum. Appl Microbiol Biotechnol 1995; 43:76-82. [PMID: 7766138 DOI: 10.1007/bf00170626] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A 2.9-kb SacI fragment containing the ask-asd operon, encoding aspartokinase and aspartatesemialdehyde dehydrogenase, was cloned from an aminoethylcysteine-resistant, lysine-producing Corynebacterium lactofermentum strain. Enzymatic analysis showed that the aspartokinase (ASK) activity was completely resistant to inhibition by mixtures of lysine and threonine. Comparison of the deduced amino acid sequence of the beta submit of the ask gene showed three amino acid residue changes with ask gene encoding wild-type, feedback-sensitive enzymes. Three C. lactofermentum strains, one being aspartokinase-negative, one carrying two ask genes on the chromosome and one having a sixfold higher specific ASK activity than the parental strain, were constructed by transconjugation and electroporation, and used to analyse the role of ASK in the lysine production by C. lactofermentum. The results indicate that, in this study, feed-back-resistant ASK is necessary for high-level lysine production, but dispensable for lysine and diaminopimelate synthesis required for cell growth.
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Affiliation(s)
- M S Jetten
- Department of Micrbiology and Enzymology, Kluyver Laboratory for Biotechnology, Delft University of Technology, The Netherlands
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Colón GE, Jetten MS, Nguyen TT, Gubler ME, Follettie MT, Sinskey AJ, Stephanopoulos G. Effect of inducible thrB expression on amino acid production in Corynebacterium lactofermentum ATCC 21799. Appl Environ Microbiol 1995; 61:74-8. [PMID: 7887627 PMCID: PMC167261 DOI: 10.1128/aem.61.1.74-78.1995] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Amplification of the operon homdr-thrB encoding a feedback-insensitive homoserine dehydrogenase and a wild-type homoserine kinase in a Corynebacterium lactofermentum lysine-producing strain resulted in both homoserine and threonine accumulation, with some residual lysine production. A plasmid enabling separate transcriptional control of each gene was constructed to determine the effect of various enzyme activity ratios on metabolite accumulation. By increasing the activity of homoserine kinase relative to homoserine dehydrogenase activity, homoserine accumulation in the medium was essentially eliminated and the final threonine titer was increased by about 120%. Furthermore, a fortuitous result of the cloning strategy was an unexplained increase in homoserine dehydrogenase activity. This resulted in a further decrease in lysine production along with a concomitant increase in threonine accumulation.
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Affiliation(s)
- G E Colón
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge 02139
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Affiliation(s)
- M S Jetten
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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Jetten MSM, Pitoc GA, Follettie MT, Sinskey AJ. Regulation of phospho(enol)-pyruvate-and oxaloacetate-converting enzymes in Corynebacterium glutamicum. Appl Microbiol Biotechnol 1994. [DOI: 10.1007/bf00166080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Jetten MSM, Pitoc GA, Follettie MT, Sinskey AJ. Regulation of phospho(enol)-pyruvate- and oxaloacetate-converting enzymes in Corynebacterium glutamicum. Appl Microbiol Biotechnol 1994. [DOI: 10.1007/s002530050105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Abstract
Two promoters required for expression of the ask-asd genes, encoding aspartokinase (AK) and aspartate-semialdehyde dehydrogenase (ASD), in Corynebacterium flavum N13, askP1 and askP2, have been identified by deletion analysis and S1 nuclease mapping. Transcription from askP1 initiates 35 and 38 bp upstream of the ask structural gene. A second promoter, askP2, lies within the ask coding region, upstream of the translation start site of the AK beta subunit and can direct the expression of AK beta and ASD. Western immunoblot analysis and heterologous expression in Escherichia coli demonstrate that two separate polypeptides, a 44.8-kDa alpha subunit and an 18.5-kDa beta subunit, are expressed from the C. flavum N13 ask gene from distinct, in-frame translation initiation sites. A second AK mutation, G345D, which reduces the sensitivity of AK to concerted feedback inhibition by threonine plus lysine, was identified.
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Affiliation(s)
- M T Follettie
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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Eikmanns BJ, Follettie MT, Griot MU, Sinskey AJ. The phosphoenolpyruvate carboxylase gene of Corynebacterium glutamicum: molecular cloning, nucleotide sequence, and expression. Mol Gen Genet 1989; 218:330-9. [PMID: 2779518 DOI: 10.1007/bf00331286] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The ppc gene of Corynebacterium glutamicum encoding phosphoenolpyruvate (PEP) carboxylase was isolated by complementation of a ppc mutant of Escherichia coli using a cosmid gene bank of chromosomal C. glutamicum DNA. By subsequent subcloning into the plasmid pUC8 and deletion analysis, the ppc gene could be located on a 3.3 kb SalI fragment. This fragment was able to complement the E. coli ppc mutant and conferred PEP carboxylase activity to the mutant. The complete nucleotide sequence of the ppc gene including 5' and 3' flanking regions has been determined and the primary structure of PEP carboxylase was deduced. The sequence predicts a 919 residue protein product (molecular weight of 103 154) which shows 34% similarity with the respective E. coli enzyme.
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Affiliation(s)
- B J Eikmanns
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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Abstract
The genes encoding the three terminal enzymes in the threonine biosynthetic pathway, homoserine dehydrogenase (hom), homoserine kinase (thrB) and threonine synthase (thrC) have been isolated from Corynebacterium glutamicum. The C. glutamicum hom and thrB genes were subcloned on a 3.6 kb SalI-generated chromosomal fragment. The C. glutamicum thrC gene was shown not to be linked to the hom-thrB locus. L-methionine represses the cloned homoserine dehydrogenase and homoserine kinase similar to that of the chromosomally encoded hom and thrB gene products. Northern hybridization analysis demonstrates that this repression is mediated at the level of transcription and that hom-thrB represents an operon in C. glutamicum.
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Affiliation(s)
- M T Follettie
- Department of Applied Biological Sciences, Massachusetts Institute of Technology, Cambridge 02139
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30
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Peoples OP, Liebl W, Bodis M, Maeng PJ, Follettie MT, Archer JA, Sinskey AJ. Nucleotide sequence and fine structural analysis of the Corynebacterium glutamicum hom-thrB operon. Mol Microbiol 1988; 2:63-72. [PMID: 2835591 DOI: 10.1111/j.1365-2958.1988.tb00007.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The complete nucleotide sequence of the Corynebacterium glutamicum hom-thrB operon has been determined and the structural genes and promoter region mapped. A polypeptide of Mr 46,136 is encoded by hom and a polypeptide of Mr 32,618 is encoded by thrB. Both predicted protein sequences show amino acid sequence homology to their counterparts in Escherichia coli and Bacillus subtilis. The promoter region has been mapped by S1-nuclease and deletion analysis. Located between -88, RNA start site and -219 (smallest deletion clone with complete activity) are sequence elements similar to those found in E. coli and B. subtilis promoters. Although there are no obvious attenuator-like structures in the 5'-untranslated region, there is a dyad-symmetry element, which may act as an operator.
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Affiliation(s)
- O P Peoples
- Department of Applied Biological Sciences, Massachusetts Institute of Technology, Cambridge 02139
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Abstract
The pheA gene of Corynebacterium glutamicum encoding prephenate dehydratase was isolated from a gene bank constructed in C. glutamicum. The specific activity of prephenate dehydratase was increased six-fold in strains harboring the cloned gene. Genetic and structural evidence is presented which indicates that prephenate dehydratase and chorismate mutase were catalyzed by separate enzymes in this species. The C. glutamicum pheA gene, subcloned in both orientations with respect to the Escherichia coli vector pUC8, was able to complement an E. coli pheA auxotroph. The nucleotide sequence of the C. glutamicum pheA gene predicts a 315-residue protein product with a molecular weight of 33,740. The deduced protein product demonstrated sequence homology to the C-terminal two-thirds of the bifunctional E. coli enzyme chorismate mutase-P-prephenate dehydratase.
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32
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Yoshihama M, Higashiro K, Rao EA, Akedo M, Shanabruch WG, Follettie MT, Walker GC, Sinskey AJ. Cloning vector system for Corynebacterium glutamicum. J Bacteriol 1985; 162:591-7. [PMID: 3921526 PMCID: PMC218889 DOI: 10.1128/jb.162.2.591-597.1985] [Citation(s) in RCA: 123] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A protoplast transformation system has been developed for Corynebacterium glutamicum by using a C. glutamicum-Bacillus subtilis chimeric vector. The chimera was constructed by joining a 3.0-kilobase cryptic C. glutamicum plasmid and the B. subtilis plasmid pBD10. The neomycin resistance gene on the chimera, pHY416, was expressed in C. glutamicum, although the chloramphenicol resistance gene was not. The various parameters in the transformation protocol were analyzed separately and optimized. The resulting transformation system is simple and routinely yields 10(4) transformants per microgram of plasmid DNA.
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