Analysis of the human ornithine aminotransferase gene family

The CREB Transcription Factor Controls Transcriptional Activity of the Human RIC8B Gene

Proper regulation of gene expression is essential for normal development, cellular growth, and differentiation. Differential expression profiles of mRNA coding for vertebrate Ric-8B during embryo and adult stages have been observed. In addition, Ric-8B is expressed in few cerebral nuclei subareas. These facts point to a dynamic control of RIC8B gene expression. In order to understand the transcriptional regulation of this gene, we searched for cis-elements in the sequence of the human RIC8B promoter region, identifying binding sites for the basic/leucine zipper (bZip) CREB transcription factor family (CRE sites) and C/EBP transcription factor family (C/EBP sites). CRE sites were found clustered near the transcription start site, while the C/EBP sites were found clustered at around 300 bp upstream the CRE sites. Here, we demonstrate the ability of CREB1 and C/EBPβ to bind their respective elements identified in the RIC8B promoter. Comparative protein-DNA interaction analyses revealed only the proximal elements as high affinity sites for CREB1 and only the distal elements as high affinity sites for C/EBPβ. Chromatin immunoprecipitation analyses, carried out using a human neuroblastoma cell line, confirmed the preferential association of CREB to the proximal region of the RIC8B promoter. By performing luciferase reporter assays, we found the CRE sites as the most relevant elements for its transcriptional activity. Taken together, these data show the existence of functional CREB and C/EBP binding sites in the human RIC8B gene promoter, a particular distribution of these sites and demonstrate a relevant role of CREB in stimulating transcriptional activity of this gene. J. Cell. Biochem. 117: 1797-1805, 2016. © 2016 Wiley Periodicals, Inc.

Disruption of arginase II alters prostate tumor formation in TRAMP mice

BACKGROUND

Arginase II (AII) is involved in the polyamine synthetic pathway, and elevated levels of expression have been found in a high proportion of prostate cancer samples and patients. However, the biological function of arginase II in prostate cancer still remains to be elucidated. In this study, we utilized the TRAMP mouse prostate cancer model to better understand the contribution of AII on tumor development.

METHODS

AII expression was determined in prostates from TRAMP mice at 23 weeks of age by real-time RT-PCR and Western blot analysis. Additionally, AII expression was disrupted in the TRAMP model by crossbreeding arginase II knockout (AII KO) mice with TRAMP mice in order to generate the TRAMP/AII KO line. In each group, genito-urinary (GU) tract weights were determined and a pathological evaluation of the tumors was completed.

RESULTS

AII expression was only detectable in those mice without the presence of macroscopic tumors; it was also absent in the TRAMP-C2 cell line, which is characteristic of an advanced prostate tumor. Assessment of the GU weights revealed larger average GU weights in the TRAMP/AII KO mice compared to TRAMP mice. Additionally, a greater percentage of more advanced pathology was found in the TRAMP/AII KO group compared to the TRAMP cohort.

CONCLUSIONS

Based on these results, AII deficiency in the TRAMP model seems to accelerate prostate tumor progression, leading to an overall more advanced cancer stage in these mice. These findings support the possibility that prostatic arginase II could be a potentially useful marker of disease progression.

The simian virus 40 core C enhancer-like element is a positive regulator in the rat alpha1B adrenergic receptor gene proximal promoter

Transcription of the rat alpha1B adrenergic receptor (alpha1B AR) gene is controlled by three promoters (P1, P2, and P3), which generate 2.3-, 2.7-, and 3.3-kb transcripts, respectively. The expression of the 2.3-kb mRNA species is tissue-specific. To explore the underlying mechanism, the P1 promoter was analyzed. DNase I footprinting of the P1 promoter yielded three protected regions: Plfl(-49 to -62); P1f2 (-73 to -90), and P1f3 (-95 to -115). Sequence analysis of P1f3 revealed the presence of an SV40 core C enhancer-like element. In gel mobility shift assays, P1f3 was found to bind a sequence specific protein, which was competed away by a SV40 core C enhancer consensus oligonucleotide. Mutations of this enhancer-like core sequence within P1f3 significantly reduced specific protein binding to P1f3 and inhibited P1 promoter activity. The distribution of the protein which binds to P1f3 is restricted. These findings suggest that the P1 promoter is controlled by a cell-type-specific transcription factor, which may account for the tissue-specific expression of 2.3-kb rat alpha1B AR mRNA species.

Transcriptional regulation of genes for ornithine cycle enzymes

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Sequence of the promoter region of the mouse gene encoding ornithine aminotransferase

We have isolated and sequenced the promoter region of the mouse gene (mOAT) encoding ornithine aminotransferase. A comparison of these mOAT sequences with previously reported sequences for the rat and human genes encoding OAT, rOAT and hOAT, respectively, revealed a 256-bp region flanking the transcription start point that is highly conserved between the three genes. This region contains sequence motifs resembling binding sites for general transcription factors, as well as other trans-acting regulatory proteins.

Promoter region of the rat gene encoding ornithine aminotransferase: transcriptional activity, sequence, and DNase-I-hypersensitive sites

In the rat, the gene (rOAT) encoding ornithine aminotransferase (OAT) is expressed in all cell types examined; however, regulation of rOAT expression is complex and cell-type specific. Various regions of the rOAT 5' flanking domain were cloned upstream from the cat reporter gene, and the expression of these OAT::cat fusions was examined following transfection into rat kidney epithelial cells (NRK-52E), human embryonic kidney cells (293), and rat hepatoma cells (H-4-II-E). Although these experiments suggested the presence of one or more positive regulatory elements between nucleotides -661 and -158, and one or more negative elements upstream from nt -897, none of these putative elements appeared to function in a cell-type-specific manner. The nt sequence of 2531 bp of the rOAT domain flanking the promoter revealed several putative promoter/enhancer elements in positions analogous to the human OAT gene, numerous AGGTCA-like motifs related to the binding sites for the estrogen and thyroid hormone receptors, and multiple motifs resembling a putative regulatory element associated with genes encoding enzymes of the urea cycle. Finally, sensitivity of the 5' end of rOAT to cleavage by DNase I was examined, as DNase-I-hypersensitive sites (DHS) are often found in association with cis-acting regulatory elements. Two DHS were identified; one DHS approximately 140 bp upstream, and the second DHS approximately 300 bp downstream, of the transcription start point (tsp). These data provide the foundation upon which to base future studies aimed at elucidating the molecular mechanisms through which rOAT expression is regulated in a cell-type specific manner.

Isolation and characterization of the rat gene encoding ornithine aminotransferase

Herein we describe the isolation and characterization of the rat gene encoding ornithine aminotransferase (rOAT). Six unique genomic clones were characterized and assigned to two nonoverlapping contigs representing approx. 33 kb of the rat genome. The 5' contig contains the rOAT promoter, exons 1 and 3, and a portion of exon 4; an exon corresponding to exon 2 of the human OAT gene (hOAT) was not identified. The rOAT promoter contains several putative regulatory elements in positions similar to hOAT. The 3' contig contains exons 7 through 11 in their entirety. Data presented and discussed herein suggest that approx. 3.0 kb of uncloned genomic DNA, containing the remainder of exon 4 and all of exons 5 and 6, separate the two contigs. Together, these data suggest that rOAT extends over approx. 20 kb and is organized into at least 10 exons, thereby closely resembling hOAT in size and exon/intron organization. Isolation of rOAT provides an important tool for examining the molecular mechanisms through which estrogen and thyroid hormone regulate transcription of this gene in a cell-type specific manner.

A 15-bp deletion in exon 5 of the ornithine aminotransferase (OAT) locus associated with gyrate atrophy

Gyrate atrophy of the choroid and retina (GA) is an autosomal recessive disorder in which a deficiency of the mitochondrial matrix enzyme ornithine aminotransferase (OAT) leads to progressive blindness. Previously, we and others have reported a number of missense mutations and splice defects in the OAT gene associated with GA. In the present case, through sequencing of the PCR amplified cDNA products, we have detected a novel 15-bp deletion within exon 5 of the OAT gene which retains the original reading frame. The deleted PCR product is the only one produced from the patient's mRNA, while mRNA from the patient's mother yields both deleted and normal length PCR products. The alternate, apparently nonexpressing OAT allele in this patient was inherited from the father, who displays only the normal length PCR product. The codon at the deletion joint remains unaltered, predicting the loss of the pentapeptide Tyr-Thr-Val-Lys-Gly without any other amino acid change. The breakpoints are adjacent to or within two copies of a 4-bp direct repeat, which may have implications for the mechanism of deletion.

The ornithine aminotransferase-encoding gene family of rat: cloning, characterization, and evolutionary relationships between a single expressed gene and three pseudogenes

As a first step towards understanding the molecular mechanisms through which the expression of the gene (OAT) encoding ornithine aminotransferase (OAT) is regulated in a tissue-specific manner, we have used a near full length OAT cDNA to isolate related sequences from a rat genomic DNA library. Twenty-one unique clones representing five contigs and spanning approximately 140 kb of genomic DNA were isolated and characterized. From these clones we have identified a single expressed OAT gene and three processed pseudogenes. The comparison of the EcoRI, BamHI, and HindIII fragments contained within these genomic clones with those detected in total genomic DNA by the cDNA probe suggests that essentially all of the OAT-related sequences in the rat genome have been isolated. Thus, the tissue-specific regulation of OAT gene expression appears to be effected through a single expressed gene. Data are presented which suggest that the OAT-1, OAT-2, and OAT-3 pseudogenes arose approximately 28.5, 7.3, and 25.1 Myr ago, respectively. Mutation rates are presented for each codon position of the expressed rat and human OAT genes. The region of the rat genome flanking the boundary of the OAT-3 pseudogene is of additional interest as it shares considerable identity to sequences contained within expressed genes and flanking other processed pseudogenes.