scholarly journals Translated anti-sense product of the Na/phosphate co-transporter (NaPi-II)

1998 ◽  
Vol 332 (2) ◽  
pp. 483-489 ◽  
Author(s):  
Birgit HUELSEWEH ◽  
Beate KOHL ◽  
Hartmut HENTSCHEL ◽  
Rolf K. H. KINNE ◽  
Andreas WERNER
Keyword(s):  
Genomic Sequence ◽  
Biological Significance ◽  
Rnase H ◽  
Open Reading Frame ◽  
Regulatory Function ◽  
Female Gonad ◽  
Putative Open Reading Frame ◽  
Reading Frame ◽  
Sense Transcript ◽  
Protein Protein Interaction

The homeostasis of Pi in marine teleosts is maintained by renal Pi secretion as well as by Pi reabsorption. A Na/Pi co-transport system belonging to the NaPi-II protein family is instrumental in tightly controlled renal Pi handling in mammals and fish. We have isolated an NaPi-II related cDNA from winter flounder. It was cloned from a female gonad cDNA library and is 624 bp long. The transcript is expressed in female and male flounder gonads as well as in kidney and intestine, although at very low levels. RNase H digestion experiments revealed an opposite orientation of the transcript with regard to NaPi-II-related mRNA. The anti-sense orientation was confirmed by genomic sequence analysis and Southern blotting. Alluding to the sense transcript, the anti-sense transcript was denoted IPAN. The open reading frame of IPAN encodes a basic protein of 68 amino acid residues. Immunohistochemistry confined the anti-sense related protein, Ipan, to a submembranous compartment of immature oocytes, suggesting a role in oocyte development. In kidney and intestine Ipan is partly co-localized with the Na/Pi co-transporter, implying a regulatory function for the anti-sense protein. However, direct protein–protein interaction could not be established. The existence of a putative open reading frame in other species extends the biological significance of the novel protein.

scholarly journals Identification of an Active Reverse Transcriptase Enzyme Encoded by a Human Endogenous HERV-K Retrovirus

1999 ◽  
Vol 73 (3) ◽  
pp. 2365-2375 ◽  
Author(s):  
Ben Berkhout ◽  
Maarten Jebbink ◽  
Jozsef Zsíros
Keyword(s):  
Reverse Transcriptase ◽  
Human Genome ◽  
Genetic Recombination ◽  
Biochemical Properties ◽  
Rnase H ◽  
Open Reading Frame ◽  
Biologically Active ◽  
Virus Family ◽  
Reading Frame ◽  
Reverse Transcriptase Enzyme

ABSTRACT Of the numerous endogenous retroviral elements that are present in the human genome, the abundant HERV-K family is distinct because several members are transcriptionally active and coding for biologically active proteins. A detailed phylogeny of the HERV-K family based on the partial sequence of the reverse transcriptase (RT) gene revealed a high incidence of an intact RT open reading frame within the HML-2 subgroup of HERV-K elements. In this study, we report the cloning of six full-length HML-2 RT genes, of which five contain an uninterrupted open reading frame. The RT enzymes were expressed as glutathione S-transferase fusion proteins inEscherichia coli, and several HERV-K RT enzymes demonstrated polymerase as well as RNase H activity. Several biochemical properties of the RT polymerase were analyzed, including the template requirements and optimal reaction conditions (temperature, type of divalent cation). Inspection of the nucleotide sequence of the HERV-K RT genes demonstrated a mosaic structure, suggesting that a high level of genetic recombination has occurred in this virus family, which is a hallmark of replication by means of reverse transcription. The selective pressure to maintain the RT coding potential is illustrated by the sequence of a particular HERV-K isolate that contains three 1-nucleotide deletions within a small RT segment, thus maintaining the open reading frame. These combined results may suggest that these endogenous RT enzymes still have a biological function. It is possible that the RT activity was involved in the spread of this major class of retroelements by retrotransposition, and in fact it cannot be excluded that this retrovirus group is still mobile. The endogenous RT activity may also have been involved in the shaping of the human genome, e.g., by formation of pseudogenes.

scholarly journals Unveiling a Ghost Proteome in the Glioblastoma Non-Coding RNAs

2021 ◽  
Vol 9 ◽  
Author(s):  
Tristan Cardon ◽  
Isabelle Fournier ◽  
Michel Salzet
Keyword(s):  
Signaling Pathways ◽  
Protein Interaction ◽  
Brain Cancer ◽  
Transfer Rna ◽  
Open Reading Frame ◽  
Total Resection ◽  
Rna Regulation ◽  
Reading Frame ◽  
Protein Protein Interaction ◽  
Non Coding Rnas

Glioblastoma is the most common brain cancer in adults. Nevertheless, the median survival time is 15 months, if treated with at least a near total resection and followed by radiotherapy in association with temozolomide. In glioblastoma (GBM), variations of non-coding ribonucleic acid (ncRNA) expression have been demonstrated in tumor processes, especially in the regulation of major signaling pathways. Moreover, many ncRNAs present in their sequences an Open Reading Frame (ORF) allowing their translations into proteins, so-called alternative proteins (AltProt) and constituting the “ghost proteome.” This neglected world in GBM has been shown to be implicated in protein–protein interaction (PPI) with reference proteins (RefProt) reflecting involvement in signaling pathways linked to cellular mobility and transfer RNA regulation. More recently, clinical studies have revealed that AltProt is also involved in the patient’s survival and bad prognosis. We thus propose to review the ncRNAs involved in GBM and highlight their function in the disease.

scholarly journals Regulation of an Osmoticum-Responsive Gene in Anabaena sp. Strain PCC 7120

1998 ◽  
Vol 180 (23) ◽  
pp. 6332-6337 ◽  
Author(s):  
Steven H. Schwartz ◽  
Todd A. Black ◽  
Karin Jäger ◽  
Jean-Michel Panoff ◽  
C. Peter Wolk
Keyword(s):  
Genomic Sequence ◽  
Response Regulator ◽  
Sequence Similarity ◽  
Open Reading Frame ◽  
Response Regulators ◽  
Reading Frame ◽  
Regulatory Systems ◽  
Entire Open Reading Frame ◽  
Anabaena Sp ◽  
Pcc 7120

ABSTRACT Salt-induced genes in the cyanobacterium Anabaena sp. strain PCC 7120 were identified by use of a Tn5-based transposon bearing luxAB as a reporter. The genomic sequence adjacent to one site of insertion of the transposon was identical in part to the sequence of thelti2 gene, which was previously identified in a differential screen for cold-induced transcripts in Anabaena variabilis. The lti2-like gene was induced by sucrose and other osmotica and by low temperature, in addition to salt. Regulatory components necessary for the induction of this gene by osmotica were sought by a further round of transposon mutagenesis. One mutant that displayed reduced transcriptional activity of thelti2-like gene in response to exposure to osmotica had an insertion in an open reading frame, which was denoted orrA, whose predicted product showed sequence similarity to response regulators from two-component regulatory systems. The corresponding mutation was reconstructed and was shown, like the second-site transposon mutation, to result in reduced response to osmotic stress. Induction of the lux reporter gene by osmotica was restored by complementation with a genomic fragment containing the entire open reading frame for the presumptive response regulator, whereas a fragment containing a truncated copy of the open reading frame for the response regulator did not complement the mutation.

scholarly journals An Exported Rhodanese-Like Protein Is Induced during Growth of Acidithiobacillus ferrooxidans in Metal Sulfides and Different Sulfur Compounds

2002 ◽  
Vol 68 (4) ◽  
pp. 1837-1845 ◽  
Author(s):  
Pablo Ramírez ◽  
Héctor Toledo ◽  
Nicolas Guiliani ◽  
Carlos A. Jerez
Keyword(s):  
Signal Peptide ◽  
Acidithiobacillus Ferrooxidans ◽  
Deinococcus Radiodurans ◽  
Genomic Sequence ◽  
Sulfur Metabolism ◽  
Putative Open Reading Frame ◽  
Genomic Context ◽  
Structural Domains ◽  
Reading Frame ◽  
Putative Signal Peptide

ABSTRACT By proteomic analysis we found a 21-kDa protein (P21) from Acidithiobacillus ferrooxidans ATCC 19859 whose synthesis was greatly increased by growth of the bacteria in pyrite, thiosulfate, elemental sulfur, CuS, and ZnS and was almost completely repressed by growth in ferrous iron. After we determined the N-terminal amino acid sequence of P21, we used the available preliminary genomic sequence of A. ferrooxidans ATCC 23270 to isolate the DNA region containing the p21 gene. The nucleotide sequence of this DNA fragment contained a putative open reading frame (ORF) coding for a 23-kDa protein. This difference in size was due to the presence of a putative signal peptide in the ORF coding for P21. When p21 was cloned and overexpressed in Escherichia coli, the signal peptide was removed, resulting in a mature protein with a molecular mass of 21 kDa and a calculated isoelectric point of 9.18. P21 exhibited 27% identity and 42% similarity to the Deinococcus radiodurans thiosulfate-sulfur transferase (rhodanese; EC 2.8.1.1) and similar values in relation to other rhodaneses, conserving structural domains and an active site with a cysteine, both characteristic of this family of proteins. However, the purified recombinant P21 protein did not show rhodanese activity. Unlike cytoplasmic rhodaneses, P21 was located in the periphery of A. ferrooxidans cells, as determined by immunocytochemical analysis, and was regulated depending on the oxidizable substrate. The genomic context around gene p21 contained other ORFs corresponding to proteins such as thioredoxins and sulfate-thiosulfate binding proteins, clearly suggesting the involvement of P21 in inorganic sulfur metabolism in A. ferrooxidans.

The Drosophila gene asteroid encodes a novel protein and displays dosage-sensitive interactions with Star and Egfr

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 295-302 ◽  
Author(s):  
Michael A Kotarski ◽  
Deborah A Leonard ◽  
Sean A Bennett ◽  
Clifton P Bishop ◽  
Stephen D Wahn ◽  
...  
Keyword(s):  
Amino Acids ◽  
Egf Receptor ◽  
Open Reading Frame ◽  
Cdna Clones ◽  
Putative Open Reading Frame ◽  
Morphogenetic Furrow ◽  
Calculated Molecular Mass ◽  
Reading Frame ◽  
Ribonuclease Protection ◽  
Novel Protein

The asteroid gene of Drosophila was found to lie within 189 bp of Star. Asteroid cDNA clones were isolated and sequenced and a single putative open reading frame was identified that encodes a novel protein of 815 amino acids with a calculated molecular mass of 93 kilodaltons. Using cDNA probes, asteroid transcripts were localized to the proliferative tissues of embryos and to the mitotically active tissue anterior to the morphogenetic furrow in eye imaginal discs. Ribonuclease protection assays identified a mutation of asteroid that acts as a dominant enhancer of Star mutations and also enhances the Ellipse mutation, EgfrE1. Based on these data, a model for asteroid gene function in EGF receptor signaling is presented.Key words: Drosophila, asteroid, Star, EGF receptor, eye development.

scholarly journals Functional Expression and Characterization of the Two Cyclic Amidohydrolase Enzymes, Allantoinase and a Novel Phenylhydantoinase, from Escherichia coli

2000 ◽  
Vol 182 (24) ◽  
pp. 7021-7028 ◽  
Author(s):  
Geun Joong Kim ◽  
Dong Eun Lee ◽  
Hak-Sung Kim
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Physical Map ◽  
Open Reading Frame ◽  
Putative Open Reading Frame ◽  
Protein Fusion ◽  
Aromatic Side Chain ◽  
Native Form ◽  
Reading Frame ◽  
E Coli

ABSTRACT A superfamily of cyclic amidohydrolases, including dihydropyrimidinase, allantoinase, hydantoinase, and dihydroorotase, all of which are involved in the metabolism of purine and pyrimidine rings, was recently proposed based on the rigidly conserved structural domains in identical positions of the related enzymes. With these conserved domains, two putative cyclic amidohydrolase genes fromEscherichia coli, flanked by related genes, were identified and characterized. From the genome sequence of E. coli, theallB gene and a putative open reading frame, tentatively designated as a hyuA (for hydantoin-utilizing enzyme) gene, were predicted to express hydrolases. In contrast to allB, high-level expression of hyuA in E. coli of a single protein was unsuccessful even under various induction conditions. We expressed HyuA as a maltose binding protein fusion protein and AllB in its native form and then purified each of them by conventional procedures. allB was found to encode a tetrameric allantoinase (453 amino acids) which specifically hydrolyzes the purine metabolite allantoin to allantoic acid. Another open reading frame, hyuA, located near 64.4 min on the physical map and known as a UUG start, coded for d-stereospecific phenylhydantoinase (465 amino acids) which is a homotetramer. As a novel enzyme belonging to a cyclic amidohydrolase superfamily, E. coli phenylhydantoinase exhibited a distinct activity toward the hydantoin derivative with an aromatic side chain at the 5′ position but did not readily hydrolyze the simple cyclic ureides. The deduced amino acid sequence of the novel phenylhydantoinase shared a significant homology (>45%) with those of allantoinase and dihydropyrimidinase, but its functional role still remains to be elucidated. Despite the unclear physiological function of HyuA, its presence, along with the allantoin-utilizing AllB, strongly suggested that the cyclic ureides might be utilized as nutrient sources in E. coli.

scholarly journals Extralarge XLαs (XXLαs), a Variant of Stimulatory G Protein α-Subunit (Gsα), Is a Distinct, Membrane-Anchored GNAS Product that Can Mimic Gsα

Endocrinology ◽  
2009 ◽  
Vol 150 (8) ◽  
pp. 3567-3575 ◽  
Author(s):  
Cumhur Aydin ◽  
Nurgul Aytan ◽  
Mathew J. Mahon ◽  
Hesham A. W. Tawfeek ◽  
Neil W. Kowall ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
G Protein ◽  
Biological Significance ◽  
Open Reading Frame ◽  
Mouse Heart ◽  
Rt Pcr ◽  
Α Subunit ◽  
Reading Frame ◽  
Stimulatory G Protein ◽  
Constitutively Active

GNAS gives rise to multiple imprinted gene products, including the α-subunit of the stimulatory G protein (Gsα) and its variant XLαs. Based on genomic sequence, the translation of XLαs begins from the middle of a long open reading frame, suggesting the existence of an N-terminally extended variant termed extralarge XLαs (XXLαs). Although XXLαs, like Gsα and XLαs, would be affected by most disease-causing GNAS mutations, its authenticity and biological significance remained unknown. Here we identified a mouse cDNA clone that comprises the entire open reading frame encoding XXLαs. Whereas XXLαs mRNA was readily detected in mouse heart by RT-PCR, it appeared virtually absent in insulinoma-derived INS-1 cells. By Northern blots and RT-PCR, XXLαs mRNA was detected primarily in the mouse brain, cerebellum, and spleen. Immunohistochemistry using a specific anti-XXLαs antibody demonstrated XXLαs protein in multiple brain areas, including dorsal hippocampus and cortex. In transfected cells, full-length human XXLαs was localized to the plasma membrane and mediated isoproterenol- and cholera toxin-stimulated cAMP accumulation. XXLαs-R844H, which bears a mutation analogous to that in the constitutively active Gsα mutant Gsα-R201H (gsp oncogene), displayed elevated basal signaling. However, unlike Gsα-R201H, which mostly remains in the cytoplasm, both XXLαs-R844H and a constitutively active XLαs mutant localized to the plasma membrane. Hence, XXLαs is a distinct GNAS product and can mimic Gsα, but the constitutively active XXLαs and Gsα mutants differ from each other regarding subcellular targeting. Our findings suggest that XXLαs deficiency or hyperactivity may contribute to the pathogenesis of diseases caused by GNAS mutations.

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