1
|
Xiao J, Zhang Y, Zhang J, Liu B, Wang H, Yang R, Yin Y, Zhang X. Identification of cis-acting elements upstream of regR gene in streptococcus pneumoniae. Microb Pathog 2023; 182:106263. [PMID: 37481005 DOI: 10.1016/j.micpath.2023.106263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
The identification and characterization of functional cis-acting elements is of fundamental importance for comprehending the regulatory mechanisms of gene transcription and bacterial pathogenesis. The transcription factor RegR has been demonstrated to control both competence and virulence in Streptococcus pneumoniae. Despite the clear contribution of RegR to these pathways, the mechanisms underlying its transcriptional regulation remain poorly understood. In this study, we conducted mutational analysis, gene dissection and luciferase activity assays to characterize the cis-elements situated upstream of the regR gene. Our findings revealed that a 311 bp 3'-terminal DNA sequence of the spd0300 gene represents a central region of the upstream cis-acting element of regR. Further investigations identified two structurally similar enhancer-like sequences within this region which feature prominently in the regulation of regR transcription. Furthermore, employing DNA pull-down assays allowed us to enrich the trans-acting factors with the potential to interact with these cis-acting elements. Notably, we found that the competence regulator ComE was implicated in the regulation of regR transcription, a finding which was corroborated by electrophoretic mobility shift assays (EMSA) and quantitative real-time PCR analyses (qRT-PCR). Taken together, our data thus provide fresh insight into the transcriptional regulation of regR.
Collapse
Affiliation(s)
- Jiangming Xiao
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, 400016, China
| | - Yapeng Zhang
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, 400016, China
| | | | - Bichen Liu
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, 400016, China
| | - Hanyi Wang
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, 400016, China
| | - Rui Yang
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, 400016, China
| | - Yibing Yin
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, 400016, China
| | - Xuemei Zhang
- Department of Laboratory Medicine, Key Laboratory of Diagnostic Medicine (Ministry of Education), Chongqing Medical University, Chongqing, 400016, China.
| |
Collapse
|
2
|
Irigoyen S, Ramasamy M, Misra A, McKnight TD, Mandadi KK. A BTB-TAZ protein is required for gene activation by Cauliflower mosaic virus 35S multimerized enhancers. PLANT PHYSIOLOGY 2022; 188:397-410. [PMID: 34597402 PMCID: PMC8774732 DOI: 10.1093/plphys/kiab450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) BTB-TAZ DOMAIN PROTEIN 2 (BT2) contains an N-terminal BTB domain, a central TAZ zinc-finger protein-protein interaction domain, and a C-terminal calmodulin-binding domain. We previously demonstrated that BT2 regulates telomerase activity and mediates multiple responses to nutrients, hormones, and abiotic stresses in Arabidopsis. Here, we describe the essential role of BT2 in activation of genes by multimerized Cauliflower mosaic virus 35S (35S) enhancers. Loss of BT2 function in several well-characterized 35S enhancer activation-tagged lines resulted in suppression of the activation phenotypes. Suppression of the phenotypes was associated with decreased transcript abundance of the tagged genes. Nuclear run-on assays, mRNA decay studies, and bisulfite sequencing revealed that BT2 is required to maintain the transcriptionally active state of the multimerized 35S enhancers, and lack of BT2 leads to hypermethylation of the 35S enhancers. The TAZ domain and the Ca++/calmodulin-binding domain of BT2 are critical for its function and 35S enhancer activity. We further demonstrate that BT2 requires CULLIN3 and two bromodomain-containing Global Transcription factor group E proteins (GTE9 and GTE11), to regulate 35S enhancer activity. We propose that the BT2-CULLIN3 ubiquitin ligase, through interactions with GTE9 and GTE11, regulates 35S enhancer activity in Arabidopsis.
Collapse
Affiliation(s)
- Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 79596, USA
| | | | - Anjali Misra
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Thomas D McKnight
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 79596, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
| |
Collapse
|
3
|
Gao L, Tober J, Gao P, Chen C, Tan K, Speck NA. RUNX1 and the endothelial origin of blood. Exp Hematol 2018; 68:2-9. [PMID: 30391350 PMCID: PMC6494457 DOI: 10.1016/j.exphem.2018.10.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 10/28/2022]
Abstract
The transcription factor RUNX1 is required in the embryo for formation of the adult hematopoietic system. Here, we describe the seminal findings that led to the discovery of RUNX1 and of its critical role in blood cell formation in the embryo from hemogenic endothelium (HE). We also present RNA-sequencing data demonstrating that HE cells in different anatomic sites, which produce hematopoietic progenitors with dissimilar differentiation potentials, are molecularly distinct. Hemogenic and non-HE cells in the yolk sac are more closely related to each other than either is to hemogenic or non-HE cells in the major arteries. Therefore, a major driver of the different lineage potentials of the committed erythro-myeloid progenitors that emerge in the yolk sac versus hematopoietic stem cells that originate in the major arteries is likely to be the distinct molecular properties of the HE cells from which they are derived. We used bioinformatics analyses to predict signaling pathways active in arterial HE, which include the functionally validated pathways Notch, Wnt, and Hedgehog. We also used a novel bioinformatics approach to assemble transcriptional regulatory networks and predict transcription factors that may be specifically involved in hematopoietic cell formation from arterial HE, which is the origin of the adult hematopoietic system.
Collapse
Affiliation(s)
- Long Gao
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joanna Tober
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Gao
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Changya Chen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kai Tan
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Nancy A Speck
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
4
|
Najafi M, Rahimi Mianji G, Ansari Pirsaraie Z. Cloning and comparative analysis of gene structure in promoter site of alpha-s1 casein gene in Naeinian goat and sheep. Meta Gene 2014; 2:854-61. [PMID: 25606467 PMCID: PMC4287881 DOI: 10.1016/j.mgene.2014.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 07/14/2014] [Accepted: 11/02/2014] [Indexed: 11/30/2022] Open
Abstract
The 5' end or alpha-S1 casein promoter has a significant role in milk protein gene expression. The understanding of the translation process of alpha-S1 casein mutants will provide us an opportunity to make the best selection in livestock providing more proteins in milk. Blood samples were taken from three hundred of Naeinian goats and sheep, and DNA extraction was done using modified salting out method. Polymerase chain reactions (PCR) were carried out using a specific primer pairs for amplification a fragment of 1133 bp from part of 5'-UTR and exon 1 of alpha s1 casein gene. The AluI and HinfI restriction enzyme treatment of all samples provided the same homozygous AA genotype in both species. Subsequently, one sample of each species was selected and cloned, and the final sequences were analyzed by BioEdit, CLC genomic, Mega4 and DNASIS MAX software. Several polymorphisms are recognized between Naeinian goat and sheep that are presented on motif sites. In this research, the interested location, including exon I and a part of 5', was analyzed, and genetic element comparisons were done between Naeinian goat and sheep. The number and location of probable binding sites can have a crucial role as a result of antagonistic and synergistic effects on gene regulation activities.
Collapse
Affiliation(s)
- Mojtaba Najafi
- Department of Animal Science, Sari Agriculture sciences and Natural Resources University, Iran
| | | | | |
Collapse
|
5
|
Morange M. What history tells us XXXV. Enhancers: their existence and characteristics have raised puzzling issues since their discovery. J Biosci 2014; 39:741-5. [PMID: 25431403 DOI: 10.1007/s12038-014-9482-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michel Morange
- Centre Cavailles, Republique des Savoirs USR 3608, Ecole Normale Superieure, 29 rue d'Ulm, 75230 Paris Cedex 05, France,
| |
Collapse
|
6
|
Koia J, Moyle R, Hendry C, Lim L, Botella JR. Pineapple translation factor SUI1 and ribosomal protein L36 promoters drive constitutive transgene expression patterns in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2013; 81:327-36. [PMID: 23263857 DOI: 10.1007/s11103-012-0002-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 12/12/2012] [Indexed: 05/10/2023]
Abstract
The availability of a variety of promoter sequences is necessary for the genetic engineering of plants, in basic research studies and for the development of transgenic crops. In this study, the promoter and 5' untranslated regions of the evolutionally conserved protein translation factor SUI1 gene and ribosomal protein L36 gene were isolated from pineapple and sequenced. Each promoter was translationally fused to the GUS reporter gene and transformed into the heterologous plant system Arabidopsis thaliana. Both the pineapple SUI1 and L36 promoters drove GUS expression in all tissues of Arabidopsis at levels comparable to the CaMV35S promoter. Transient assays determined that the pineapple SUI1 promoter also drove GUS expression in a variety of climacteric and non-climacteric fruit species. Thus the pineapple SUI1 and L36 promoters demonstrate the potential for using translation factor and ribosomal protein genes as a source of promoter sequences that can drive constitutive transgene expression patterns.
Collapse
Affiliation(s)
- Jonni Koia
- University of Queensland, Brisbane, 4072, Australia
| | | | | | | | | |
Collapse
|
7
|
|
8
|
Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA. Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci U S A 2012; 109:19498-503. [PMID: 23129659 PMCID: PMC3511131 DOI: 10.1073/pnas.1210678109] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cis-regulatory elements (CREs) control gene expression by recruiting transcription factors (TFs) and other DNA binding proteins. We aim to understand how individual nucleotides contribute to the function of CREs. Here we introduce CRE analysis by sequencing (CRE-seq), a high-throughput method for producing and testing large numbers of reporter genes in mammalian cells. We used CRE-seq to assay >1,000 single and double nucleotide mutations in a 52-bp CRE in the Rhodopsin promoter that drives strong and specific expression in mammalian photoreceptors. We find that this particular CRE is remarkably complex. The majority (86%) of single nucleotide substitutions in this sequence exert significant effects on regulatory activity. Although changes in the affinity of known TF binding sites explain some of these expression changes, we present evidence for complex phenomena, including binding site turnover and TF competition. Analysis of double mutants revealed complex, nucleotide-specific interactions between residues in different TF binding sites. We conclude that some mammalian CREs are finely tuned by evolution and function through complex, nonadditive interactions between bound TFs. CRE-seq will be an important tool to uncover the rules that govern these interactions.
Collapse
Affiliation(s)
- Jamie C. Kwasnieski
- Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and
| | - Ilaria Mogno
- Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and
| | - Connie A. Myers
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Barak A. Cohen
- Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and
| |
Collapse
|
9
|
Scheele GA, Kern HF. Selective Regulation of Gene Expression in the Exocrine Pancreas. Compr Physiol 2011. [DOI: 10.1002/cphy.cp060325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
10
|
The nucleotides on the stem-loop RNA structure in the junction region of the hepatitis E virus genome are critical for virus replication. J Virol 2010; 84:13040-4. [PMID: 20943962 DOI: 10.1128/jvi.01475-10] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The roles of conserved nucleotides on the stem-loop (SL) structure in the intergenic region of the hepatitis E virus (HEV) genome in virus replication were determined by using Huh7 cells transfected with HEV SL mutant replicons containing reporter genes. One or two nucleotide mutations of the AGA motif on the loop significantly reduced HEV replication, and three or more nucleotide mutations on the loop abolished HEV replication. Mutations on the stem and of the subgenome start sequence also significantly inhibited HEV replication. The results indicated that both the sequence and the SL structure in the junction region play important roles in HEV replication.
Collapse
|
11
|
Fluhr R, Kuhlemeier C, Nagy F, Chua NH. Organ-specific and light-induced expression of plant genes. Science 2010; 232:1106-12. [PMID: 17754498 DOI: 10.1126/science.232.4754.1106] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Light plays a pivotal role in the development of plants. The photoregulation of plant genes involves recognition of light quality and quantity by phytochrome and other light receptors. Two gene families, rbcS and Cab, which code for abundant proteins active in photosynthesis, the small subunit of ribulose bisphosphate carboxylase and the chlorophyll a/b binding protein, show a 20-to 50-fold increase in transcript abundance in the light. Analyses in calli and transgenic plants of deletions of the rbcS gene and of chimeric constructions has allowed localization of two regions involved in light-induced transcription. One element is confined to a 33-base pair region surrounding the TATA box. In addition, an enhancer-like element contained within a 240-base pair fragment can confer phytochrome-induced transcription and organ specificity on nonregulated promoters.
Collapse
|
12
|
Ow DW, Jacobs JD, Howell SH. Functional regions of the cauliflower mosaic virus 35S RNA promoter determined by use of the firefly luciferase gene as a reporter of promoter activity. Proc Natl Acad Sci U S A 2010; 84:4870-4. [PMID: 16578811 PMCID: PMC305207 DOI: 10.1073/pnas.84.14.4870] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cauliflower mosaic virus (CaMV) 35S RNA promoter has been dissected and examined in a transient expression system using the firefly luciferase gene as a reporter of promoter activity. Deletion analysis has shown that the 35S RNA promoter is composed of at least three regions-distal, medial, and proximal-which are essential for activity. The distal region contains three smaller elements homologous to the simian virus 40 "core" enhancer element, the medial region possesses a CCAAT-like box, and the proximal region contains a TATA box. A DNA segment encompassing the distal region is capable of activating the CaMV 35S core promoter in an orientation-independent, but not position-independent, fashion. The distal region can also activate a heterologous weak promoter, the CaMV 19S RNA promoter, albeit not to the high levels of the 35S RNA promoter. Multimers of the distal region are able to activate the 35S RNA promoter core to even greater levels of expression than the native 35S promoter. These experiments demonstrate that elements outside the boundaries of the core promoter (composed of proximal and medial elements) are recognized in a plant cell transient expression system.
Collapse
Affiliation(s)
- D W Ow
- Department of Biology, C016, University of California San Diego, LaJolla, CA 92093
| | | | | |
Collapse
|
13
|
Guarino LA, Gonzalez MA, Summers MD. Complete Sequence and Enhancer Function of the Homologous DNA Regions of Autographa californica Nuclear Polyhedrosis Virus. J Virol 2010; 60:224-9. [PMID: 16789259 PMCID: PMC253920 DOI: 10.1128/jvi.60.1.224-229.1986] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleotide sequence of the five regions of homologous DNA in the genome of Autographa californica nuclear polyhedrosis virus DNA was determined. The homology of repeated sequences within a region was 65 to 87%, and the consensus sequences for each region were 88% homologous to each other. Sequences proximal to the EcoRI sites were most conserved, while the distal sequences were least conserved. The EcoRI sites formed the core of a 28-base-pair imperfect inverted repeat. All homologous regions functioned as enhancers in a transient expression assay. A single EcoRI minifragment located between EcoRI-Q and -L enhanced the expression of 39CAT as efficiently as the regions containing numerous EcoRI repeats did.
Collapse
Affiliation(s)
- L A Guarino
- Department of Entomology, Texas A&M University, and Texas Agricultural Experiment Station, College Station, Texas 77843-2475
| | | | | |
Collapse
|
14
|
Yoshinobu K, Baudino L, Santiago-Raber ML, Morito N, Dunand-Sauthier I, Morley BJ, Evans LH, Izui S. Selective up-regulation of intact, but not defective env RNAs of endogenous modified polytropic retrovirus by the Sgp3 locus of lupus-prone mice. THE JOURNAL OF IMMUNOLOGY 2009; 182:8094-103. [PMID: 19494335 DOI: 10.4049/jimmunol.0900263] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Endogenous retroviruses are implicated in the pathogenesis of systemic lupus erythematosus (SLE). Because four different classes of endogenous retroviruses, i.e., ecotropic, xenotropic, polytropic, or modified polytropic (mPT), are expressed in mice, we investigated the possibility that a particular class of endogenous retroviruses is associated with the development of murine SLE. We observed >15-fold increased expression of mPT env (envelope) RNA in livers of all four lupus-prone mice, as compared with those of nine nonautoimmune strains of mice. This was not the case for the three other classes of retroviruses. Furthermore, we found that in addition to intact mPT transcripts, many strains of mice expressed two defective mPT env transcripts which carry a deletion in the env sequence of the 3' portion of the gp70 surface protein and the 5' portion of the p15E transmembrane protein, respectively. Remarkably, in contrast to nonautoimmune strains of mice, all four lupus-prone mice expressed abundant levels of intact mPT env transcripts, but only low or nondetectable levels of the mutant env transcripts. The Sgp3 (serum gp70 production 3) locus derived from lupus-prone mice was responsible for the selective up-regulation of the intact mPT env RNA. Finally, we observed that single-stranded RNA-specific TLR7 played a critical role in the production of anti-gp70 autoantibodies. These data suggest that lupus-prone mice may possess a unique genetic mechanism responsible for the expression of mPT retroviruses, which could act as a triggering factor through activating TLR7 for the development of autoimmune responses in mice predisposed to SLE.
Collapse
Affiliation(s)
- Kumiko Yoshinobu
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Ito Y. RUNX genes in development and cancer: regulation of viral gene expression and the discovery of RUNX family genes. Adv Cancer Res 2008; 99:33-76. [PMID: 18037406 DOI: 10.1016/s0065-230x(07)99002-8] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mouse embryonal carcinoma (EC) cells, also called teratocarcinoma stem cells, are nonpermissive for polyomavirus growth, whereas differentiated derivatives of the cells are permissive. Mutant viruses capable of growing in EC cells can be isolated. They have genomic alterations within the viral enhancer, which is required for viral gene expression and DNA replication. This viral regulatory region was considered as a potential probe for mouse cell differentiation. The 24-bp-long A element within the enhancer was identified as a minimum element, which also shows a lower activity in EC cells compared with the differentiated cells. Transcription factors PEA1/AP1, PEA2/PEBP2, and PEA3/ETS were identified as A element-binding proteins. All of them are absent in EC cells and induced to be expressed when the cells are differentiated. Although PEBP2 has a weaker transactivation activity compared with other two, it is essential for the enhancer function of the A element. Purification and cDNA cloning revealed that PEBP2 has two subunits, DNA-binding alpha (PEBP2alpha) and non-DNA-binding beta (PEBP2beta). PEBP2alpha was found to be highly homologous to a Drosophila segmentation gene, runt, and a human gene AML1 that was identified as a part of the fusion gene, AML1/ETO (MTG8) generated by t(8;21) chromosome translocation associated with acute myelogenous leukemia (AML). Core-binding factor (CBF), which interacts with a murine retrovirus enhancer, was found to be identical to PEBP2. runt, PEBP2alpha and AML1 are now termed RUNX family, which are involved in cell specification during development. There are three mammalian RUNX genes, RUNX1, RUNX2, and RUNX3. RUNX1 is essential for generation of hematopoietic stem cells and is involved in human leukemia. RUNX2 is essential for skeletal development and has an oncogenic potential. RUNX3 is expressed in wider ranges of tissues and has multiple roles. Among others, RUNX3 is a major tumor suppressor of gastric and many other solid tumors.
Collapse
Affiliation(s)
- Yoshiaki Ito
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| |
Collapse
|
16
|
Sivamani E, Qu R. Expression enhancement of a rice polyubiquitin gene promoter. PLANT MOLECULAR BIOLOGY 2006; 60:225-39. [PMID: 16429261 DOI: 10.1007/s11103-005-3853-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Accepted: 10/06/2005] [Indexed: 05/06/2023]
Abstract
An 808 bp promoter from a rice polyubiquitin gene, rubi3, has been isolated. The rubi3 gene contained an open reading frame of 1,140 bp encoding a pentameric polyubiquitin arranged as five tandem, head-to-tail repeats of 76 aa. The 1,140 bp 5' UTR intron of the gene enhanced its promoter activity in transient expression assays by 20-fold. Translational fusion of the GUS reporter gene to the coding sequence of the ubiquitin monomer enhanced GUS enzyme activity in transient expression assays by 4.3-fold over the construct containing the original rubi3 promoter (including the 5' UTR intron) construct. The enhancing effect residing in the ubiquitin monomer coding sequence has been narrowed down to the first 9 nt coding for the first three amino acid residues of the ubiquitin protein. Mutagenesis at the third nucleotide of this 9 nt sequence still maintains the enhancing effect, but leads to translation of the native GUS protein rather than a fusion protein. The resultant 5' regulatory sequence, consisting of the rubi3 promoter, 5' UTR exon and intron, and the mutated first 9 nt coding sequence, has an activity nearly 90-fold greater than the rubi3 promoter only (without the 5' UTR intron), and 2.2-fold greater than the maize Ubi1 gene promoter (including its 5' UTR intron). The newly created expression vector is expected to enhance transgene expression in monocot plants. Considering the high conservation of the polyubiquitin gene structure in higher plants, the observed enhancement in gene expression may apply to 5' regulatory sequences of other plant polyubiquitin genes.
Collapse
Affiliation(s)
- Elumalai Sivamani
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695-7620, USA
| | | |
Collapse
|
17
|
Shirasawa-Seo N, Sano Y, Nakamura S, Murakami T, Gotoh Y, Naito Y, Hsia CN, Seo S, Mitsuhara I, Kosugi S, Ohashi Y. The promoter of Milk vetch dwarf virus component 8 confers effective gene expression in both dicot and monocot plants. PLANT CELL REPORTS 2005; 24:155-63. [PMID: 15812660 DOI: 10.1007/s00299-005-0917-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Revised: 12/28/2004] [Accepted: 01/04/2005] [Indexed: 05/24/2023]
Abstract
The activity of a predicted promoter, PMC8, from Milk vetch dwarf virus was evaluated by comparing it with the cauliflower mosaic virus 35S RNA promoter (P35S) and PNCR, a promoter from Soybean chlorotic mottle virus. When the GUS fusion gene was introduced into tobacco, PMC8 showed a similar expression profile to P35S but with a more intense expression in proliferating tissues. The usefulness of PMC8 was confirmed by driving NPTII for selection of kanamycin-resistant tobacco plants with improved transformation efficiency. PMC8 was also effective in transgenic rice plants. Thus, PMC8 is useful as an alternative to P35S in both dicotyledonous and monocotyledonous plants, especially for gene expression in proliferating tissues.
Collapse
Affiliation(s)
- Naomi Shirasawa-Seo
- Miyagi Prefectural Agriculture and Horticulture Research Center, Takadate-kawakami, Natori, Miyagi, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Ramunno L, Cosenza G, Rando A, Illario R, Gallo D, Di Berardino D, Masina P. The goat alphas1-casein gene: gene structure and promoter analysis. Gene 2004; 334:105-11. [PMID: 15256260 DOI: 10.1016/j.gene.2004.03.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Revised: 02/24/2004] [Accepted: 03/05/2004] [Indexed: 11/28/2022]
Abstract
The level of alphas1-casein in goat milk shows strong variations determined by at least 15 alleles associated with four different efficiencies of protein synthesis. The nucleotide sequence of the whole goat alphas1-casein-encoding gene (CSN1S1) plus 1973 nucleotides at the 5' flanking region and 610 nucleotides at the 3' flanking region was determined and aligned with its bovine counterpart. The gene is spread over 16.7 kb and consists of 19 exons varying in length from 24 bp (exons 5, 6, 7, 8, 10, 13 and 16) to 385 bp (exon 19) and 18 introns from 90 bp of intron 10 to 1685 bp of intron 2. Furthermore, highly conserved sequences, mainly located in the 5' flanking region, were found between this gene and other casein-encoding genes. Finally, seven interspersed repeated elements (10 in the bovine CSN1S1 gene) were also identified at four different locations of the sequenced region: 5' untranscribed region and introns 2, 8 and 11.
Collapse
Affiliation(s)
- Luigi Ramunno
- Dipartimento di Scienze Zootecniche e Ispezione degli Alimenti, Università degli Studi di Napoli Federico II, Via Università 133, 80055 Portici (Na), Italy.
| | | | | | | | | | | | | |
Collapse
|
19
|
Iwamoto M, Higo H, Higo K. Strong expression of the rice catalase gene CatB promoter in protoplasts and roots of both a monocot and dicots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2004; 42:241-9. [PMID: 15051048 DOI: 10.1016/j.plaphy.2004.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2003] [Accepted: 01/30/2004] [Indexed: 05/24/2023]
Abstract
The rice (Oryza sativa L.) catalase (EC 1.11.1.6) gene CatB is expressed in roots and cultured cells. We examined the promoter activity of its 5'-flanking region in a monocot and in two dicots. Transient expression assays in rice Oc and tobacco BY-2 suspension cell protoplasts showed that CatB's 5'-flanking DNA fragments (nucleotides -1066 to +298) had about 20 and 3-4 times as much promoter activity, respectively, as the CaMV 35S promoter. Serial deletion analyses of the CatB promoter region revealed that the shortest fragment (-56 to +298) still had about 10 times as much promoter activity as the CaMV 35S promoter in rice protoplasts. In tobacco protoplasts, the activity of the fragment (-56 to +298) was about half of the CaMV 35S promoter. Transgenic rice and Arabidopsis plants carrying GUS genes driven by the 5'-truncated CatB promoters were generated and their GUS activity was examined. The region ranging from -329 to +298 showed preferential expression in the roots of rice and Arabidopsis, and in the shoot apical meristems of Arabidopsis. In situ hybridization revealed that CatB was highly expressed in branch root primordia and root apices of rice. Fusion of the GUS gene to the region (-329 to +298) conferred strong expression in these same areas, indicating that the presence of this region was sufficient to express CatB specifically in the roots. There may be new regulatory element(s) in this region, because it contained no previously known cis-regulatory elements specific for gene expression in roots.
Collapse
Affiliation(s)
- Masao Iwamoto
- Genome and Biodiversity Research Center, National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
| | | | | |
Collapse
|
20
|
Wu JH, Lee IN. Studies of apolipoprotein (a) promoter from subjects with different plasma lipoprotein (a) concentrations. Clin Biochem 2003; 36:241-6. [PMID: 12810151 DOI: 10.1016/s0009-9120(03)00002-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
OBJECTIVE High plasma lipoprotein (a) [Lp(a)] level is closely related to coronary heart disease and cerebral thrombosis. The Lp(a) concentration is determined primarily by apolipoprotein (a) [apo(a)] gene and APO(a) mRNA abundance has been found to vary with apo(a) isoform. Our objective is to investigate whether APO(a) promoter activity is related to plasma Lp(a) level. DESIGN AND METHODS The 5' 1.4 kilobases (kb) promoter region of APO(a) was cloned into plasmid pGL-2 basic that carries luciferase reporter system. The promoter activity was assayed in HepG2 cells. DNA sequence of the promoter was also determined. RESULTS Few nucleotide changes besides the variations at the five polymorphic sites: -1270 (TTTTA repeat), -868 (T repeat), -772 (A/G variation), +93 (C/T variation) and +121 (A/G variation) were observed in these promoters. APO(a) promoter activity differed in subjects with different plasma Lp(a) levels. CONCLUSION The sequence variation of APO(a) promoter region may contribute to the variation of its transcription activity.
Collapse
Affiliation(s)
- June H Wu
- Department of microbiology and Immunology, College of Medicine, Chang Gung University, Kwei San, Tao Yuan, Taiwan.
| | | |
Collapse
|
21
|
Wasylyk B, Wasylyk C, Matthes H, Wintzerith M, Chambon P. Transcription from the SV40 early-early and late-early overlapping promoters in the absence of DNA replication. EMBO J 2002; 2:1605-11. [PMID: 11892819 PMCID: PMC555330 DOI: 10.1002/j.1460-2075.1983.tb01631.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Transcription for a hybrid SV40 promoter-beta globin coding sequence recombinant initiates from both early-early (EE) and late-early (LE) SV40 start sites (EES and LES) in the absence of DNA replication. The 72-bp repeat is essential to potentiate the elements of the two overlapping EE and LE promoters (EEP and LEP). Two current models, which can account for the EE to LE shift in RNA chain initiation during the SV40 replication cycle, are that LE transcription is linked to replication and occurs on newly replicated DNA molecules or that there are two promoter elements, a stronger EEP and a weaker LEP, T antigen repressing the EEP late in infection. Our results support the second model. A 5'-TATTTAT-3' to 5'-TATCGAT-3' mutation in the putative SV40 TATA box decreases transcription from EES, increases transcription from LES, and inhibits DNA replication. Therefore, this element acts as a classical TATA box for transcription, and yet is also important for DNA replication.
Collapse
Affiliation(s)
- B Wasylyk
- Laboratoire de Génétique Moléculaire des Eucaryotes du CNRS, Unité 184 de Biologie Moléculaire et de Génie Génétique de l'INSERM, Faculté de Médicine, Strasbourg, France
| | | | | | | | | |
Collapse
|
22
|
Lymar ES, Clark AM, Reeves R, Griswold MD. Clusterin gene in rat sertoli cells is regulated by a core-enhancer element. Biol Reprod 2000; 63:1341-51. [PMID: 11058537 DOI: 10.1095/biolreprod63.5.1341] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Clusterin is a ubiquitous glycoprotein that is promiscuously expressed at a low basal level but can be highly induced by a variety of stress conditions. In contrast, in some secretory cells associated with tissue-fluid interfaces such as the Sertoli cells in the testis, clusterin demonstrates high constitutive expression. In this study, we address the mechanisms that regulate the constitutive expression of the clusterin gene by using primary cultures of immature rat Sertoli cells. We have identified a region of the rat clusterin gene promoter that activated transcription only in Sertoli cells and that mapped between positions -426 and -311. Sequence analysis of this region revealed a high concentration of potential regulatory elements. Using gel-shift assays combined with hydroxyl radical footprinting, we identified the elements recognized by the Sertoli cell nuclear factors. Comparison of the interactions with this region of the nuclear factors from different cell types demonstrated that recognition of the core-enhancer element is specific for the Sertoli cells, and in vitro, the core region was recognized by the transcription factor CBF. Transient transfections showed that a core enhancer is responsible for more than a half of the total promoter activity and is an essential element for the cell-specific activity of the Sertoli-specific region. In addition to the core enhancer, tandem Sp1 sites are also required for maximal activity of this region.
Collapse
Affiliation(s)
- E S Lymar
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
| | | | | | | |
Collapse
|
23
|
Cai Z, de Bruijn M, Ma X, Dortland B, Luteijn T, Downing RJ, Dzierzak E. Haploinsufficiency of AML1 affects the temporal and spatial generation of hematopoietic stem cells in the mouse embryo. Immunity 2000; 13:423-31. [PMID: 11070161 DOI: 10.1016/s1074-7613(00)00042-x] [Citation(s) in RCA: 200] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The AML1:CBFbeta transcription factor complex is essential for definitive hematopoiesis. Null mutations in mouse AML1 result in midgestational lethality with a complete lack of fetal liver hematopoiesis. While the cell autonomous nature and expression pattern of AML1 suggest an intrinsic role for this transcription factor in the developing hematopoietic system, no direct link to a functional cell type has been made. Here, we examine the consequences of AML1 loss in hematopoietic stem cells (HSC) of the mouse embryo. We demonstrate an absolute requirement for AML1 in functional HSCs. Moreover, haploinsufficiency results in a dramatic change in the temporal and spatial distribution of HSCs, leading to their early appearance in the normal position in the aorta-gonad-mesonephros region and also in the yolk sac.
Collapse
Affiliation(s)
- Z Cai
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | | | | | | | | | | | | |
Collapse
|
24
|
Wang J, Jiang J, Oard JH. Structure, expression and promoter activity of two polyubiquitin genes from rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2000; 156:201-211. [PMID: 10936527 DOI: 10.1016/s0168-9452(00)00255-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We have isolated two rice polyubiquitin genes designated as RUBQ1 and RUBQ2 by screening a Bacterial Artificial Chromosome (BAC) genomic library with a 32P-labeled ubiquitin cDNA probe. DNA sequence data revealed that both genes contained an open reading frame encoding a hexameric precursor ubiquitin and an intron immediate upstream of the initiation codon. The deduced amino acid sequences of both genes were identical to each other and to other plant ubiquitin sequences. Several putative regulatory elements such as enhancer core and heat shock consensus sequences were found in the 5'-upstream regions of both genes. Northern blot analyses using the 3'-untranslated region as gene specific probes showed that both genes were actively expressed in all rice plant tissues tested. Differential expression was observed in roots where RUBQ2 appeared to be predominantly expressed. Chimeric genes containing the 5'-upstream region including the intron of RUBQ1 or RUBQ2 and the beta-glucuronidase (GUS) coding region were constructed and transferred into rice suspension cells via particle bombardment. GUS activity from constructs containing RUBQ1 and RUBQ2 promoters in rice suspension cells was ten to 15-fold greater than those using the Cauliflower Mosaic Virus 35S (CaMV 35S) promoter, and two to threefold greater than constructs with the maize polyubiquitin Ubi1 promoter. The results demonstrate the potential usefulness of the two rice polyubiquitin promoters in rice or other monocot transformation systems.
Collapse
Affiliation(s)
- J Wang
- Department of Agronomy, Louisiana Agricultural Experiment Station, Louisiana State University Agricultural Center, 70803, Baton Rouge, LA, USA
| | | | | |
Collapse
|
25
|
Shiels B, Fox M, McKellar S, Kinnaird J, Swan D. An upstream element of the TamS1 gene is a site of DNA-protein interactions during differentiation to the merozoite in Theileria annulata. J Cell Sci 2000; 113 ( Pt 12):2243-52. [PMID: 10825296 DOI: 10.1242/jcs.113.12.2243] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Apicomplexan parasites are major pathogens of humans and domesticated animals. A fundamental aspect of apicomplexan biology, which may provide novel molecular targets for parasite control, is the regulation of stage differentiation. Studies carried out on Theileria annulata, a bovine apicomplexan parasite, have provided evidence that a stochastic process controls differentiation from the macroschizont to the merozoite stage. It was postulated that this process involves the presence of regulators of merozoite gene expression in the preceding stage of the life cycle, and that during differentiation a quantitative increase of these factors occurs. This study was carried out to test these postulations. Nuclear run-on analysis showed that TamS1 expression is controlled, at least in part, at the transcriptional level. The transcription start site showed homology with the consensus eukaryotic initiator motif, and study of the 5′ upstream region by the electrophoretic mobility-shift assay demonstrated that a 23 bp motif specifically bound factors from parasite-enriched nuclear extracts. Three complexes were shown to bind to a 9 bp core binding site (5′-TTTGTAGGG-3′). Two of these complexes were present in macroschizont extracts but were found at elevated levels during differentiation. Both complexes contain a polypeptide of the same molecular mass and may be related via the formation of homodimer or heterodimer complexes. The third complex appears to be distinct and was detected at time points associated with the transition to high level merozoite gene expression.
Collapse
Affiliation(s)
- B Shiels
- Department of Veterinary Parasitology, University of Glasgow, Glasgow, G61 1QH, UK.
| | | | | | | | | |
Collapse
|
26
|
Miller CM, Smith NC, Johnson AM. Cytokines, nitric oxide, heat shock proteins and virulence in Toxoplasma. PARASITOLOGY TODAY (PERSONAL ED.) 1999; 15:418-22. [PMID: 10481156 DOI: 10.1016/s0169-4758(99)01515-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Elucidating the factors that play important roles in the expression of virulence by parasites is crucial to understanding disease pathogenesis and to developing control strategies rationally. Here, Kate Miller, Nick Smith and Alan Johnson, using Toxoplasma gondii as a model, argue that the interactions between the immune system and 70 kDa heat shock proteins of apicomplexan parasites profoundly influence parasite virulence.
Collapse
Affiliation(s)
- C M Miller
- Molecular Parasitology Unit, Department of Cell and Molecular Biology, University of Technology, Sydney, Westbourne Street, Gore Hill, New South Wales, Australia 2065.
| | | | | |
Collapse
|
27
|
Tanaka K, Fisher SE, Craig IW. Characterization of novel promoter and enhancer elements of the mouse homologue of the Dent disease gene, CLCN5, implicated in X-linked hereditary nephrolithiasis. Genomics 1999; 58:281-92. [PMID: 10373326 DOI: 10.1006/geno.1999.5839] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The murine homologue of the human chloride channel gene, CLCN5, defects in which are responsible for Dent disease, has been cloned and characterized. We isolated the entire coding region of mouse Clcn5 cDNA and approximately 45 kb of genomic sequence embracing the gene. To study its transcriptional control, the 5' upstream sequences of the mouse Clcn5 gene were cloned into a luciferase reporter vector. Deletion analysis of 1.5 kb of the 5' flanking sequence defined an active promoter region within 128 bp of the putative transcription start site, which is associated with a TATA motif but lacks a CAAT consensus. Within this sequence, there is a motif with homology to a purine-rich sequence responsible for the kidney-specific promoter activity of the rat CLC-K1 gene, another member of the chloride-channel gene family expressed in kidney. An enhancer element that confers a 10- to 20-fold increase in the promoter activity of the mouse Clcn5 gene was found within the first intron. The organization of the human CLCN5 and mouse Clcn5 gene structures is highly conserved, and the sequence of the murine protein is 98% similar to that of human, with its highest expression seen in the kidney. This study thus provides the first identification of the transcriptional control region of, and the basis for an understanding of the regulatory mechanism that controls, this kidney-specific, chloride-channel gene.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- COS Cells
- Chloride Channels/genetics
- DNA/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Enhancer Elements, Genetic
- Exons
- Fanconi Syndrome/genetics
- Female
- Gene Expression
- Genes/genetics
- Genetic Linkage
- Humans
- Introns
- Luciferases/genetics
- Luciferases/metabolism
- Male
- Mice
- Mice, Inbred Strains
- Molecular Sequence Data
- Open Reading Frames
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Deletion
- Sequence Homology, Amino Acid
- Tissue Distribution
- Transcription, Genetic
- Urinary Calculi/genetics
- X Chromosome/genetics
Collapse
Affiliation(s)
- K Tanaka
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | | | | |
Collapse
|
28
|
Yan Y, Smant G, Stokkermans J, Qin L, Helder J, Baum T, Schots A, Davis E. Genomic organization of four beta-1,4-endoglucanase genes in plant-parasitic cyst nematodes and its evolutionary implications. Gene 1998; 220:61-70. [PMID: 9767113 DOI: 10.1016/s0378-1119(98)00413-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The genomic organization of genes encoding beta-1,4-endoglucanases (cellulases) from the plant-parasitic cyst nematodes Heterodera glycines and Globodera rostochiensis (HG-eng1, Hg-eng2, GR-eng1, and GR-eng2) was investigated. HG-eng1 and GR-eng1 both contained eight introns and structural domains of 2151 and 2492bp, respectively. HG-eng2 and GR-eng2 both contained seven introns and structural domains of 2324 and 2388bp, respectively. No significant similarity in intron sequence or size was observed between HG-eng1 and HG-eng2, whereas the opposite was true between GR-eng1 and GR-eng2. Intron positions among all four cyst nematode cellulase genes were conserved identically in relation to the predicted amino acid sequence. HG-eng1, GR-eng1, and GR-eng2 had several introns demarcated by 5'-GCellipsisAG-3' in the splice sites, and all four nematode cellulase genes had the polyadenylation and cleavage signal sequence 5'-GAUAAA-3'-both rare occurences in eukaryotic genes. The 5'- flanking regions of each nematode cellulase gene, however, had signature sequences typical of eukaryotic promoter regions, including a TATA box, bHLH-type binding sites, and putative silencer, repressor, and enhancer elements. Database searches and subsequent phylogenetic comparison of the catalytic domain of the nematode cellulases placed the nematode genes in one group, with Family 5, subfamily 2, glycosyl hydrolases from Scotobacteria and Bacilliaceae as the most homologous groups. The overall amino acid sequence identity among the four nematode cellulases was from 71 to 83%, and the amino acid sequence identity to bacterial Family 5 cellulases ranged from 33 to 44%. The eukaryotic organization of the four cyst nematode cellulases suggests that they share a common ancestor, and their strong homology to prokaryotic glycosyl hydrolases may be indicative of an ancient horizontal gene transfer.
Collapse
Affiliation(s)
- Y Yan
- Plant Pathology Department, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Lee IY, Westaway D, Smit AF, Wang K, Seto J, Chen L, Acharya C, Ankener M, Baskin D, Cooper C, Yao H, Prusiner SB, Hood LE. Complete genomic sequence and analysis of the prion protein gene region from three mammalian species. Genome Res 1998; 8:1022-37. [PMID: 9799790 DOI: 10.1101/gr.8.10.1022] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we sequenced 10(5) bp of DNA from clones containing human, sheep, and mouse PrP genes isolated in cosmids or lambda phage. Our findings are as follows: (1) Although the human PrP transcript does not include the untranslated exon 2 found in its mouse and sheep counterparts, the large intron of the human PrP gene contains an exon 2-like sequence flanked by consensus splice acceptor and donor sites. (2) The mouse Prnpa but not the Prnpb allele found in 44 inbred lines contains a 6593 nucleotide retroviral genome inserted into the anticoding strand of intron 2. This intracisternal A-particle element is flanked by duplications of an AAGGCT nucleotide motif. (3) We found that the PrP gene regions contain from 40% to 57% genome-wide repetitive elements that independently increased the size of the locus in all three species by numerous mutations. The unusually long sheep PrP 3'-untranslated region contains a "fossil" 1.2-kb mariner transposable element. (4) We identified sequences in noncoding DNA that are conserved between the three species and may represent biologically functional sites.
Collapse
Affiliation(s)
- I Y Lee
- Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195-7730 USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Yao F, Svensjö T, Winkler T, Lu M, Eriksson C, Eriksson E. Tetracycline repressor, tetR, rather than the tetR-mammalian cell transcription factor fusion derivatives, regulates inducible gene expression in mammalian cells. Hum Gene Ther 1998; 9:1939-50. [PMID: 9741432 DOI: 10.1089/hum.1998.9.13-1939] [Citation(s) in RCA: 200] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This article describes the first (to our knowledge) tetracycline-inducible regulatory system that demonstrates that the tetracycline repressor (tetR) alone, rather than tetR-mammalian cell transcription factor fusion derivatives, can function as a potent trans-modulator to regulate gene expression in mammalian cells. With proper positioning of tetracycline operators downstream of the TATA element and of human epidermal growth factor (hEGF) as a reporter, we show that gene expression from the tetracycline operator-bearing hCMV major immediate-early enhancer-promoter (pcmvtetO) can be regulated by tetR over three orders of magnitude in response to tetracycline when (1) the reporter was cotransfected with tetR-expressing plasmid in transient expression assays, and (2) the reporter unit was stably integrated into the chromosome of a tetR-expressing cell line. This level of tetR-mediated inducible gene regulation is significantly higher than that of other repression-based mammalian cell transcription switch systems. In an in vivo porcine wound model, close to 60-fold tetR-mediated regulatory effects were detected and it was reversed when tetracycline was administered. Collectively, this study provides a direct implementation of this tetracycline-inducible regulatory switch for controlling gene expression in vitro, in vivo, and in gene therapy.
Collapse
Affiliation(s)
- F Yao
- Division of Plastic Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | | | | | | | | |
Collapse
|
31
|
Kienker LJ, Ghosh MR, Tucker PW. Regulatory Elements in the Promoter of a Murine TCRD V Gene Segment. THE JOURNAL OF IMMUNOLOGY 1998. [DOI: 10.4049/jimmunol.161.2.791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
TCRD V segments rearrange in an ordered fashion during human and murine thymic development. Recombination requires the accessibility of substrate gene segments, and transcriptional enhancers and promoters have been shown to regulate the accessible chromatin configuration. We therefore investigated the regulation of TCRD V rearrangements by characterizing the promoter of the first TCRD V segment to be rearranged, DV101S1, under the influence of its own enhancer. Sequences required for full promoter activity were identified by transient transfections of normal and mutated promoters into a human γδ lymphoma, and necessary elements fall between −86 and +66 nt, relative to the major transcription start site. They include a cAMP responsive element (CRE) at −62, an Ets site at −39, a TATA box at −26, the major transcriptional start site sequence (−8 to −5 and −2 to +11), and a downstream sequence (+12 to +33). Gel shift analyses and in vitro DNase I footprinting showed that nuclear proteins bind to the functionally relevant CRE, Ets, +1 to +10 sequence, and the +17 to +21 sequence. Nuclear proteins also bind to an E box at −52, and GATA-3 binds to a GATA motif at −5, as shown by Ab ablation-supershift experiments, but mutations that abrogated protein binding to these sites failed to affect DV101S1 promoter activity. We conclude that not all protein-binding sites within the DV101S1 minimal promoter are important for enhancer driven TCRD gene transcription. Further, the possibility remains that the GATA and E box sites function in enhancer independent DV101S1 germline transcription.
Collapse
Affiliation(s)
- Laura J. Kienker
- *Harold C. Simmons Arthritis Research Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75235; and
| | - Maya R. Ghosh
- †Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712
| | - Philip W. Tucker
- †Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712
| |
Collapse
|
32
|
Barat C, Rassart E. Members of the GATA family of transcription factors bind to the U3 region of Cas-Br-E and graffi retroviruses and transactivate their expression. J Virol 1998; 72:5579-88. [PMID: 9621016 PMCID: PMC110213 DOI: 10.1128/jvi.72.7.5579-5588.1998] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cas-Br-E and Graffi are two murine viruses that induce myeloid leukemia in mice: while Cas-Br-E induces mostly non-T, non-B leukemia composed of very immature cells, Graffi causes exclusively a granulocytic leukemia (E. Rassart, J. Houde, C. Denicourt, M. Ru, C. Barat, E. Edouard, L. Poliquin, and D. Bergeron, Curr. Top. Microbiol. Immunol. 211:201-210, 1995). In an attempt to understand the basis of the myeloid specificity of these two retroviruses, we used DNase I footprinting analysis and gel mobility shift assays to identify a number of protein binding sites within the Cas-Br-E and Graffi U3 regions. Two protected regions include potential GATA binding sites. Methylation interference analysis with different hematopoietic nuclear extracts showed the importance of the G residues in these GATA sites, and supershift assays clearly identified the binding factors as GATA-1, GATA-2, and GATA-3. Transient assays with long terminal repeat (LTR)-chloramphenicol acetyltransferase constructs showed that these three GATA family members are indeed able to transactivate Cas-Br-E and Graffi LTRs. Thus, the availability and relative abundance of the various members of the GATA family of transcription factors in a given cell type could influence the transcriptional tissue specificity of murine leukemia viruses and hence their disease specificity.
Collapse
Affiliation(s)
- C Barat
- Laboratoire de Biologie Moléculaire, Département de Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada H3C 3P8
| | | |
Collapse
|
33
|
Zaiman AL, Nieves A, Lenz J. CBF, Myb, and Ets binding sites are important for activity of the core I element of the murine retrovirus SL3-3 in T lymphocytes. J Virol 1998; 72:3129-37. [PMID: 9525638 PMCID: PMC109765 DOI: 10.1128/jvi.72.4.3129-3137.1998] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Transcriptional enhancers within the long terminal repeats of murine leukemia viruses are major determinants of the pathogenic properties of these viruses. Mutations were introduced into the adjacent binding sites for three transcription factors within the enhancer of the T-cell-lymphomagenic virus SL3-3. The sites that were tested were, in 5'-to-3' order, a binding site for core binding factor (CBF) called core II, a binding site for c-Myb, a site that binds members of the Ets family of factors, and a second CBF binding site called core I. Mutation of each site individually reduced transcriptional activity in T lymphocytes. However, mutation of the Myb and core I binding sites had larger effects than mutation of the Ets or core II site. The relative effects on transcription in T cells paralleled the effects of the same mutations on viral lymphomagenicity, consistent with the idea that the role of these sequences in viral lymphomagenicity is indeed to regulate transcription in T cells. Mutations were also introduced simultaneously into multiple sites in the SL3-3 enhancer. The inhibitory effects of these mutations indicated that the transcription factor in T cells that recognizes the core I element of SL3-3, presumably CBF, needed to synergize with one or more factors bound at the upstream sites to function. This was tested further by generating a multimer construct that contained five tandem core I elements linked to a basal long terminal repeat promoter. This construct was inactive in T cells. However, transcriptional activity was detected with a multimer construct in which the transcription factor binding sites upstream of the core were also present. These results are consistent with the hypothesis that CBF requires heterologous transcription factors bound at nearby sites to function in T cells.
Collapse
Affiliation(s)
- A L Zaiman
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | |
Collapse
|
34
|
Abstract
To identify promoter regions that impart differential temporal regulation of channel catfish virus (CCV) genes, the transcriptional kinetics of an immediate-early gene and prospective early and late genes were characterized. A cDNA clone, designated IE3C, representing a third immediate-early transcript was identified. The 5' end of the IE3C transcript was mapped to nucleotides 15,368 and 131,043 in the terminal repeat regions of the CCV genome. The full length of the transcript represented by the IE3C clone is 1,412 bp, and it most likely codes for the protein specified by open reading frame (ORF) 12. The putative product of ORF12 contains a consensus RING finger metal binding motif (C3HC4 structure). Temporal expression studies, in conjunction with protein synthesis and DNA replication inhibition, demonstrated that the IE3C transcript belongs to an immediate-early kinetic class, the ORF5 transcript is a member of the early kinetic class, and ORF39 and ORF46 are true late-kinetic-class genes. Additionally, we demonstrated that ORF38 transcription overlaps ORF39 and the products presumably share the same poly(A) signal. The 5' ends of the transcripts encoding ORF38, ORF39, and ORF46 were mapped to nucleotides 44,862, 45,254, and 59,644, respectively, and potential transcriptional control elements were located.
Collapse
Affiliation(s)
- S Huang
- College of Veterinary Medicine, Mississippi State University, Mississippi 39762, USA
| | | |
Collapse
|
35
|
Abstract
Antizyme is a polyamine-inducible protein involved in feedback regulation of cellular polyamine levels. Recently, we isolated genomic clones for the human antizyme gene and determined its chromosomal location (Matsufuji et al., Genomics 38 (1996) 112-114). In the present study, we report complete nucleotide sequence and organization of the human antizyme gene. The organizations of human and rat genes are very similar, but their introns show divergency in terms of the length and nucleotide sequence. Luciferase reporter assay revealed that the 5'-flanking region of the human gene had a strong transcriptional activity in NIH-3T3 with and without addition of spermidine. The promoter was also effective in transfected COS7 and HeLa cells. A 223-bp region at the proximity of the transcriptional start points carries several regulatory sequence motifs including a TATA box, CAAT boxes and GC boxes, and was shown to be important for the strong transcriptional activity.
Collapse
Affiliation(s)
- T Hayashi
- Department of Biochemistry II, The Jikei University School of Medicine, Tokyo, Japan
| | | | | |
Collapse
|
36
|
Baum C, Itoh K, Meyer J, Laker C, Ito Y, Ostertag W. The potent enhancer activity of the polycythemic strain of spleen focus-forming virus in hematopoietic cells is governed by a binding site for Sp1 in the upstream control region and by a unique enhancer core motif, creating an exclusive target for PEBP/CBF. J Virol 1997; 71:6323-31. [PMID: 9261349 PMCID: PMC191905 DOI: 10.1128/jvi.71.9.6323-6331.1997] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The polycythemic strain of the spleen focus-forming virus (SFFVp) contains the most potent murine retroviral enhancer configuration known so far for gene expression in myeloerythroid hematopoietic cells. In the present study, we mapped two crucial elements responsible for the high activity of the SFFVp enhancer to an altered upstream control region (UCR) containing a GC-rich motif (5'-GGGCGGG-3') and to a unique enhancer core (5'-TGCGGTC-3'). Acquisition of these motifs accounts for half of the activity of the complete retroviral enhancer in hematopoietic cells, irrespective of the developmental stage or lineage. Furthermore, the UCR motif contains the major determinant for the enhancer activity of SFFVp in embryonic stem (ES) cells. Using electrophoretic mobility shift assays, we show that the UCR of SFFVp, but not of Friend murine leukemia virus, is targeted by the ubiquitous transcriptional activator, Sp1. The core motif of SFFVp creates a specific and high-affinity target for polyomavirus enhancer binding protein/core binding factor (PEBP/CBF) and excludes access of CAAT/enhancer binding protein. Cotransfection experiments with ES cells imply that PEBP/CBF cooperates with the neighboring element, LVb (the only conserved Ets consensus in the SFFVp enhancer), and that the Sp1 motif in the UCR stimulates transactivation through the Ets-PEBP interaction. Putative secondary structures of the retroviral enhancers are proposed based on these data.
Collapse
Affiliation(s)
- C Baum
- Heinrich-Pette-Institute for Experimental Virology and Immunology, Department of Cell & Virus Genetics, Hamburg, Germany
| | | | | | | | | | | |
Collapse
|
37
|
Lyons PD, Blalock JE. Pro-opiomelanocortin gene expression and protein processing in rat mononuclear leukocytes. J Neuroimmunol 1997; 78:47-56. [PMID: 9307227 DOI: 10.1016/s0165-5728(97)00081-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Although production of pro-opiomelanocortin (POMC) mRNA and POMC-derived peptides in extrapituitary tissues, including immune tissues, has been demonstrated, questions remain concerning the nature of POMC transcripts and peptide products. With regard to POMC gene expression in lymphocytes, the expression of full-length mRNA and POMC has been questioned. In the present report, we have tested for the existence of these molecules. Western blot analysis with an antibody against POMC-derived adrenocorticotropic hormone (ACTH) specifically identified identical immunoreactive (ir) species in both rat anterior pituitary (AP) and splenocyte cell extracts. The relative molecular weights were those expected for nonglycosylated ACTH, as well as its biosynthetic intermediate, and POMC. Mitogen stimulation of splenic mononuclear cells (MNC) enhanced the levels of these three molecular species. Primer extension analysis identified a band which migrated with a size equivalent to a full-length POMC transcript (approximately 816 nt) in both mitogen-stimulated MNC and AP mRNA. Macrophages produced POMC protein and mRNA among unstimulated splenocytes, while lymphocytes could be induced to produce POMC mRNA upon stimulation. 5' RACE-tailed PCR products were cloned and sequenced. A mRNA encoding all three POMC exons was identified in Concanavalin A (ConA)-stimulated MNC and was identical to that from the anterior pituitary. These results unequivocally demonstrate that mononuclear cells produce full-length POMC transcripts. Its regulation in lymphocytes is distinct from that in macrophages which constitutively produce POMC-derived peptides and mRNA. Also, the biosynthetic pathway of ACTH from POMC in splenic MNC stimulated with ConA appears to be identical to that in rat corticotrophs.
Collapse
Affiliation(s)
- P D Lyons
- Department of Physiology and Biophysics, University of Alabama at Birmingham, 35294-0005, USA
| | | |
Collapse
|
38
|
Gum JR, Hicks JW, Kim YS. Identification and characterization of the MUC2 (human intestinal mucin) gene 5'-flanking region: promoter activity in cultured cells. Biochem J 1997; 325 ( Pt 1):259-67. [PMID: 9224654 PMCID: PMC1218553 DOI: 10.1042/bj3250259] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The initiation point for MUC2 gene transcription is located within a 7000-base GC-rich region of the mucin gene cluster found on chromosome 11p15.5. The promoter activity of the 5'-flanking region of the MUC2 gene was examined following its cloning into the luciferase-producing pGL2-Basic reporter vector. A short segment comprising bases -91 to -73 relative to the start of transcription was found to be important for basal promoter activity in all cell lines tested. Electrophoretic mobility shift assays demonstrated nuclear protein binding to this region, which contains the consensus CACCC motif (5'-GCCACACCC). This element has been shown to be functionally important in several promoters that are active in diverse cell types. Competition experiments using an Sp1 oligonucleotide and antibody supershift experiments indicated that both Sp1 and other Sp1 family members bind to this element. Inclusion of the region between bases -228 and -171 in pGL2-Basic constructs increased normalized luciferase reporter activity by almost 3-fold in C1a cells, which produce relatively high levels of MUC2 mRNA. Significantly lower levels of normalized luciferase activity resulted when the same construct was transfected into cultured cell lines that express low or undetectable levels of MUC2, suggesting a possible role for this region in conferring cell-type specificity of expression. We also demonstrate, using actinomycin D, that the MUC2 mRNA is long-lived, at least in cultured cells. Moreover, no evidence was found that the MUC2 mRNA turned over more rapidly in LS174T cells, which produce relatively low levels of MUC2 mRNA, as compared with C1a cells, which produce high levels of mRNA. Thus a long mRNA half-life appears to be an important mechanism involved in achieving elevated levels of MUC2 mRNA.
Collapse
Affiliation(s)
- J R Gum
- Gastrointestinal Research Laboratory (151M2), Department of Veterans' Affairs Medical Center and Departments of Anatomy, Medicine and Pathology, University of California, San Francisco, CA 94121, USA
| | | | | |
Collapse
|
39
|
Clausse N, Jackers P, Jarès P, Joris B, Sobel ME, Castronovo V. Identification of the active gene coding for the metastasis-associated 37LRP/p40 multifunctional protein. DNA Cell Biol 1996; 15:1009-23. [PMID: 8985115 DOI: 10.1089/dna.1996.15.1009] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A 37LRP/p40 polypeptide is of major interest because it is consistently up-regulated in cancer cells in correlation with their invasive and metastatic phenotype. Furthermore, this polypeptide presents intriguing multifunctional properties because it has been characterized as the precursor of the metastasis-associated 67-kD laminin receptor (67LR) and as a cytoplasmic ribosomal-associated protein. The isolation of the 37LRP/p40 gene is a prerequisite for identifying the molecular mechanisms responsible for the constant up-regulation of the 67LR expression in cancer cells. To date, the active 37LRP/p40 gene has never been identified in any species due to the existence of multiple pseudogenes in most vertebrates genomes. In this study, we report for the first time the gene structure and potential regulatory sequences of the 37 LRP/p40 gene. The chicken genome was selected to undergo this characterization because it is the only known vertebrate that bears a single 37 LRP/p40 gene copy. The 37 LRP/p40 active gene is composed of 7 exons and 6 introns and bears features characteristic of a ribosomal protein gene. It does not bear a classical TATA box and it exhibits several transcription initiation sites as demonstrated by RNase protection assay and primer extension. Analysis of potential regulatory regions suggests that gene expression is driven not only by the 5' genomic region but also by the 5' untranslated and intron 1 sequences. On the basis of gene structure and extensive protein evolutionary study, we found that the carboxyterminal domain of the protein is a conserved lock-and-key structure/function domain that could be involved in the biosynthesis of the higher-molecular-weight 67-kD laminin receptor in vertebrates, whereas the central core of the protein would be responsible for the ribosome associated function. The first identification of the active 37LRP/p40 gene presented in this study is a critical step toward the isolation of the corresponding human gene and the understanding of the molecular mechanisms involved in the up-regulation of its expression during tumor invasion and metastasis.
Collapse
Affiliation(s)
- N Clausse
- Metastasis Research Laboratory, University of Liège, Belgium
| | | | | | | | | | | |
Collapse
|
40
|
Vrati S, Brookes DE, Boyle DB, Both GW. Nucleotide sequence of ovine adenovirus tripartite leader sequence and homologues of the IVa2, DNA polymerase and terminal proteins. Gene 1996; 177:35-41. [PMID: 8921842 DOI: 10.1016/0378-1119(96)00266-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Ovine adenovirus OAV287 was previously isolated from sheep in Western Australia. Here we describe a portion of its genome between map units 10.3 and 31.7 which includes major ORFs for homologues of the IVa2 polypeptide and the DNA replication proteins, Terminal protein and DNA polymerase, as well as the N-terminal portion of the 52/55-kDa polypeptide. In addition, as a prelude to possible adaptation of this virus as a vector we have mapped the elements which make up the tripartite leader sequence of late mRNAs, thereby defining the probable location of the OAV major late promoter. In other human and animal adenovirus genomes, one or two VA RNA genes are encoded between the ORFs for Terminal protein and 52/55-kDa polypeptides. In OAV, these ORFs overlap, suggesting that if VA RNA genes are present, they may lie elsewhere in the OAV genome.
Collapse
Affiliation(s)
- S Vrati
- CSIRO Division of Biomolecular Engineering, North Ryde, N.S.W., Australia
| | | | | | | |
Collapse
|
41
|
Zaiman AL, Lenz J. Transcriptional activation of a retrovirus enhancer by CBF (AML1) requires a second factor: evidence for cooperativity with c-Myb. J Virol 1996; 70:5618-29. [PMID: 8764076 PMCID: PMC190522 DOI: 10.1128/jvi.70.8.5618-5629.1996] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Transcriptional enhancer sequences within the long terminal repeats (LTRs) of murine leukemia viruses are the primary genetic determinants of the tissue specificity and potency of the oncogenic potential of these retroviruses. SL3-3 (SL3) is a murine leukemia virus that induces T-cell lymphomas. The LTR enhancer of this virus contains two binding sites for the transcription factor CBF (also called AML1 and PEBP2) that flank binding sites for c-Myb and the Ets family of factors. Using cotransfection assays in P19 cells, we report here that CBF and c-Myb cooperatively stimulate transcription from the SL3 LTR. By itself, c-Myb had no stimulatory effect on transcription. However, when cotransfected with a cDNA encoding one form of the alpha subunit of CBF called CBFalpha2-451, a level of transactivation higher than that seen with CBFalpha2-451 alone was detected. The negative regulatory domain near the carboxyl terminus of c-Myb did not affect this activity. Electrophoretic mobility shift assays indicated that CBF and c-Myb bind to DNA independently. Therefore, it appears that the cooperative stimulation of transcription by these factors occurs at a step in the process of transcription after the two factors are bound to the enhancer. Sequences near the carboxyl terminus of CBFalpha2-451 were important for cooperativity with c-Myb, consistent with previous reports that this region contains an activation domain. However, CBFalpha2-451 failed to activate transcription from a version of the SL3 LTR in which the enhancer was replaced with five tandem CBF-binding sites. Thus, it appears that transcriptional activation of the SL3 enhancer by CBF requires that an appropriate heterologous transcription factor be bound to a neighboring site in the regulatory sequences.
Collapse
Affiliation(s)
- A L Zaiman
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | |
Collapse
|
42
|
Ito Y. Structural alterations in the transcription factor PEBP2/CBF linked to four different types of leukemia. J Cancer Res Clin Oncol 1996; 122:266-74. [PMID: 8609149 DOI: 10.1007/bf01261402] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Polyomavirus enhancer binding protein 2 (PEBP2), also called core binding factor (CBF), is a heterodimer composed of the alpha and the beta subunits. Structural alterations of each of the two subunits generated by recurrent chromosome translocations/inversion are associated with acute myeloid leukemia or acute lymphoblastic leukemia. Chimeric proteins containing a part of either the alpha or beta subunits have a potential to affect the transcriptional regulation through the PEBP2/CBF site. Structure and function of PEBP2/CBF and possible mechanisms of leukemogenesis caused by the chimeric proteins are summarized.
Collapse
Affiliation(s)
- Y Ito
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Japan
| |
Collapse
|
43
|
Jiang SW, Eberhardt NL. TEF-1 transrepression in BeWo cells is mediated through interactions with the TATA-binding protein, TBP. J Biol Chem 1996; 271:9510-8. [PMID: 8621623 DOI: 10.1074/jbc.271.16.9510] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Transcription enhancer factor-1 (TEF-1) has been implicated in transactivating a placental enhancer (CSEn) that regulates human chorionic somatomammotropin (hCS) gene activity. We demonstrated that TEF-1 represses hCS promoter activity in choriocarcinoma (BeWo) cells (Jiang, S.W., and Eberhardt, N.L. (1995) J. Biol. Chem. 270, 13609-13915), suggesting that TEF-1 interacts with basal transcription factors. Here we demonstrate that hTEF-1 overexpression inhibits minimal hCS promoters containing TATA and/or initiator elements, Rous sarcoma virus and thymidine kinase promoters in BeWo cells. Cotransfection of TEF-1 antisense oligonucleotides alleviated exogenous TEF-1-mediated repression and increased basal hCS promoter activity, indicating that endogenous TEF-1 exerts repressor activity. GST-TEF-1 fusion peptides fixed to glutathione-Sepharose beads retained in vitro-generated human TATA-binding protein, hTBP. The TEF-1 proline-rich domain was essential for TBP binding, but polypeptides also containing the zinc finger domain bound TBP with higher apparent affinity. TBP supershifted hTEF-GT-IIC DNA complexes, but TEF-1 inhibited in vitro binding of TBP to the TATA motif. Coexpression of TBP and TEF-1 in BeWo cells alleviated TEF-1-mediated transrepression, indicating that the TBP-TEF-1 interaction is functional in vivo. The data indicate that TEF-1 transrepression is mediated by direct interactions with TBP, possibly by inhibiting preinitiation complex formation.
Collapse
Affiliation(s)
- S W Jiang
- Endocrine Research Unit, Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | | |
Collapse
|
44
|
Braks JA, Broers CA, Danger JM, Martens GJ. Structural organization of the gene encoding the neuroendocrine chaperone 7B2. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 236:60-7. [PMID: 8617287 DOI: 10.1111/j.1432-1033.1996.00060.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The neuroendocrine-specific polypeptide 7B2 is a constituent of the regulated secretary pathway. Recently, 7B2 was found to function as a molecular chaperone for prohormone convertase PC2. This report describes the genomic organization of the 7B2 gene which consists of six exons. Exon I corresponds to the 5'-untranslated mRNA region, while exons 2 and 3 encode the signal peptide and the amino-terminal half of the 7B2 protein that is distantly related to a subclass of molecular chaperones. The carboxy-terminal half of 7B2, responsible for its inhibitory action on PC2, is encoded by exons 4-6. Primer-extension analysis showed that the human 7B2 gene is transcribed from multiple transcription-initiation sites. The human 7B2 gene promoter contains a cAMP-responsive element, an AP-1 site, and several Pit-1/GHF-1-binding domains and heat-shock-element-like sequences but no obvious TATA or CAAT boxes. Of further interest is the finding of two DNA elements which are common to the promoter regions of the 7B2 gene and other genes selectively expressed in neuroendocrine tissues.
Collapse
Affiliation(s)
- J A Braks
- Department of Animal Physiology, University of Nijmegen, The Netherlands
| | | | | | | |
Collapse
|
45
|
Odagiri H, Wang J, German MS. Function of the human insulin promoter in primary cultured islet cells. J Biol Chem 1996; 271:1909-15. [PMID: 8567638 DOI: 10.1074/jbc.271.4.1909] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Pancreatic islet beta cells regulate the rate of insulin gene transcription in response to a number of nutrients, the most potent of which is glucose. To test for its regulation by glucose, the promoter sequence was isolated from the human insulin gene. When linked to chloramphenicol acetyltransferase and transfected into primary islet cultures, the human insulin promoter is activated by glucose. In parallel islet transfections, glucose also activates the L-pyruvate kinase and islet amyloid chain ketoacid dehydrogenase E1a promoter, but it does not affect the beta cell glucose kinase promoter. Using deletion and substitution mutations of the proximal human insulin promoter, we mapped a metabolic response element to the E box, E1, at -100 base pairs relative to the transcription start site. Although the isolated E1 element responds to glucose, inclusion of either of two AT-rich sequences, A1 or A2/C1 on either side of E1, results in dramatic synergistic activation. Inclusion of A2/C1 also increases the response to glucose. The A2-E1-A1 region alone, however, does not explain all of the activity of the human insulin promoter in cultured islets, and other transcriptionally important elements likely to contribute to the glucose response as well.
Collapse
Affiliation(s)
- H Odagiri
- Hormone Research Institute, University of California at San Francisco 94143-0534, USA
| | | | | |
Collapse
|
46
|
Okuda T, van Deursen J, Hiebert SW, Grosveld G, Downing JR. AML1, the target of multiple chromosomal translocations in human leukemia, is essential for normal fetal liver hematopoiesis. Cell 1996; 84:321-30. [PMID: 8565077 DOI: 10.1016/s0092-8674(00)80986-1] [Citation(s) in RCA: 1477] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The AML1-CBF beta transcription factor is the most frequent target of chromosomal rearrangements in human leukemia. To investigate its normal function, we generated mice lacking AML1. Embryos with homozygous mutations in AML1 showed normal morphogenesis and yolk sac-derived erythropoiesis, but lacked fetal liver hematopoiesis and died around E12.5. Sequentially targeted AML1-/-es cell retained their capacity to differentiate into primitive erythroid cells in vitro; however, no myeloid or erythroid progenitors of definitive hematopoietic origin were detected in either the yolk sac or fetal livers of mutant embryos. Moreover, this hematopoietic defect was intrinsic to the stem cells in that AML1-/-ES cells failed to contribute to hematopoiesis in chimeric animals. These results suggest that AML1-regulated target genes are essential for definitive hematopoiesis of all lineages.
Collapse
Affiliation(s)
- T Okuda
- Department of Pathology and Laboratory Medicine, St. Jude Children's Research Hospital Memphis, Tennessee 38105, USA
| | | | | | | | | |
Collapse
|
47
|
Gray WM, Fassler JS. Isolation and analysis of the yeast TEA1 gene, which encodes a zinc cluster Ty enhancer-binding protein. Mol Cell Biol 1996; 16:347-58. [PMID: 8524314 PMCID: PMC231009 DOI: 10.1128/mcb.16.1.347] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A genetic screen for mutants that affect the activity of internal regulatory sequences of Ty retrotransposons led to the identification of a new gene encoding a DNA-binding protein that interacts with the downstream enhancer-like region of Ty1 elements. The TEA1 (Ty enhancer activator) gene sequence predicts a protein of 86.9 kDa whose N terminus contains a zinc cluster and dimerization motif typical of the Gal4-type family of DNA-binding proteins. The C terminus encodes an acidic domain with a net negative charge of -10 and the ability to mediate transcriptional activation. Like other zinc cluster proteins, purified Tea1 was found to bind to a partially palindromic CGGNxCCG repeat motif located in the Ty1 enhancer region. The Ty1 Tea1 binding site has a spacing of 10 and is located near binding sites for the DNA-binding proteins Rap1 and Mcm1. Analysis of the phenotype of tea1 deletion mutants confirmed that the TEA1 gene is required for activation from the internal Ty1 enhancer characterized in this study and makes a modest contribution to normal Ty1 levels in the cell. Hence, Tea1, like Rap1, is a member of a small family of downstream activators in Saccharomyces cerevisiae. Further analysis of the Tea1 protein and its interactions may provide insight into the mechanism of downstream activation in yeast cells.
Collapse
Affiliation(s)
- W M Gray
- Department of Biological Sciences, University of Iowa, Iowa City 52242, USA
| | | |
Collapse
|
48
|
Griffiths SA, Good VM, Gordon LA, Hudson EA, Barrett MC, Munks RJ, Manson MM. Characterization of a promoter for gamma-glutamyl transpeptidase activated in rat liver in response to aflatoxin B1 and ethoxyquin. Mol Carcinog 1995; 14:251-62. [PMID: 8519414 DOI: 10.1002/mc.2940140405] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
gamma-Glutamyl transpeptidase (GGT) is normally absent from adult rat hepatocytes but is induced by a range of xenobiotics, including carcinogens and chemoprotective agents. As many as six mRNA species for this enzyme have been described in both rat and mouse, with various degrees of tissue specificity. These originate from one gene and have separate promoters within alternative 5' untranslated sequences. By using a cDNA-derived sequence specific for GGT mRNA III to screen a rat genomic library, a clone that contains the promoter region for this mRNA was isolated and characterized. The transcriptional start site lay some 3.5 kb upstream from that already characterized for mRNA II in rat kidney. Luciferase activity was obtained after transfection of rat hepatoma-derived cell lines with constructs containing the putative promoter III fused to a luc reporter. Although this promoter lacks a TATA box, a sequence close to the start site that binds the transcription factor TFIID in vitro was identified. By using PCR techniques, mRNA III (homologous to both mouse III and IV) and an mRNA (IV) with homology to VI in mouse were found in ethoxyquin- and aflatoxin B1-treated rat liver and kidney as well as in a hepatoma-derived cell line. No evidence was found for a product homologous to mRNA from promoter V described in the mouse.
Collapse
Affiliation(s)
- S A Griffiths
- MRC Toxicology Unit, University of Leicester, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
49
|
Moens U, Johansen T, Johnsen JI, Seternes OM, Traavik T. Noncoding control region of naturally occurring BK virus variants: sequence comparison and functional analysis. Virus Genes 1995; 10:261-75. [PMID: 8560788 DOI: 10.1007/bf01701816] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The human polyomavirus BK (BKV) has a proven oncogenic potential, but its contribution to tumorigenesis under natural conditions remains undetermined. As for other primate polyomaviruses, the approximately 5.2 kbp double-stranded circular genome of BKV has three functional regions: the coding regions for the two early (T, t antigens) and four late (agno, capsid proteins; VP1-3) genes separated by a noncoding control region (NCCR). The NCCR contains the origin of replication as well as a promoter/enhancer with a mosaic of cis-acting elements involved in the regulation of both early and late transcription. Since the original isolation of BKV in 1971, a number of other strains have been identified. Most strains reveal a strong sequence conservation in the protein coding regions of the genome, while the NCCR exhibits considerable variation between different BKV isolates. This variation is due to deletions, duplications, and rearrangements of a basic set of sequence blocks. Comparative studies have proven that the anatomy of the NCCR may determine the transcriptional activities governed by the promoter/enhancer, the host cell tropism and permissivity, as well as the oncogenic potential of a given BKV strain. In most cases, however, the NCCR sequence of new isolates was determined after the virus had been passaged several times in more or less arbitrarily chosen cell cultures, a process known to predispose for NCCR rearrangements. Following the development of the polymerase chain reaction (PCR), it has become feasible to obtain naturally occurring BKV NCCRs, and their sequences, in samples taken directly from infected human individuals. Hence, the biological significance of BKV NCCR variation may be studied without prior propagation of the virus in cell culture. Such variation has general interest, because the BKV NCCRs represent typical mammalian promoter/enhancers, with a large number of binding motifs for cellular transacting factors, which can be conveniently handled for experimental purposes. This communication reviews the naturally occurring BKV NCCR variants, isolated and sequenced directly from human samples, that have been reported so far. The sequences of the different NCCRs are compared and analyzed for the presence of proven and putative cellular transcription factor binding sites. Differences in biological properties between BKV variants are discussed in light of their aberrant NCCR anatomies and the potentially modifying influence of transacting factors.
Collapse
Affiliation(s)
- U Moens
- Department of Virology, University of Tromsø, Norway
| | | | | | | | | |
Collapse
|
50
|
Lee S, Greenspan DS. Transcriptional promoter of the human alpha 1(V) collagen gene (COL5A1). Biochem J 1995; 310 ( Pt 1):15-22. [PMID: 7646438 PMCID: PMC1135848 DOI: 10.1042/bj3100015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have characterized the 5' region of the human alpha 1(V) collagen gene (COL5A1). The transcriptional promoter is shown to have a number of features characteristic of the promoters of 'housekeeping' and growth-control-related genes. It lacks obvious TATA and CAAT boxes, has multiple transcription start sites, has a high GC content, lies within a well-defined CpG island and has a number of consensus sites for the potential binding of transcription factor Sp1. This type of promoter structure, while unusual for a collagen gene, is consistent with the broad distribution of expression of COL5A1 and is reminiscent of the promoter structures of the genes encoding type VI collagen, which has a similarly broad distribution of expression. Stepwise deletion of COL5A1 5' sequences, placed upstream of a heterologous reporter gene, yielded a gradual decrease in promoter activity, indicating that the COL5A1 promoter is composed of an array of cis-acting elements. A minimal promoter region contained within the 212 bp immediately upstream of the major transcription start site contained no consensus sequences for the binding of known transcription factors, but gel mobility shift assays showed this region to bind nuclear factors, including Sp1, at a number of sites. The major transcription start site is flanked by an upstream 34-bp oligopurine/oligopyrimidine stretch, or 'GAGA' box, and a downstream 56-bp GAGA box which contains a 10-bp mirror repeat and is sensitive to cleavage with S1 nuclease.
Collapse
Affiliation(s)
- S Lee
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison 53706, USA
| | | |
Collapse
|