scholarly journals att, a target for regulation by tra2 in the testes of Drosophila melanogaster, encodes alternative RNAs and alternative proteins.

1996 ◽  
Vol 16 (8) ◽  
pp. 4222-4230 ◽  
Author(s):  
S J Madigan ◽  
P Edeen ◽  
J Esnayra ◽  
M McKeown
Keyword(s):  
Rna Processing ◽  
Transmembrane Domain ◽  
Somatic Tissue ◽  
Open Reading Frame ◽  
Graves Disease ◽  
Carrier Protein ◽  
Reading Frame ◽  
Protein Levels ◽  
Somatic Tissues ◽  
Promoter Usage

We have identified a gene, alternative testis transcripts (att), which is alternatively expressed, at both the RNA and protein levels, in testes and somatic tissues. The testis-specific RNA differs from somatic RNAs in both promoter usage and RNA processing and is dependent on the function of the transformer 2 gene. The differences between the somatic and testis RNAs have substantial consequences at the protein level. The somatic RNAs encode a protein with homology to the mammalian Graves' disease carrier proteins. The testis RNA lacks the initiation codons used in somatic tissue and encodes two different proteins. One of these begins in a testis-specific exon, uses a reading frame different from that for the somatic protein, and is completely novel. The other protein initiates translation in the frame of the somatic RNA at a Len CUG codon which is within the open reading frame for the somatic protein. This produces a novel truncated version of the Graves' disease carrier protein-like protein that lacks all sequences N terminal to the first transmembrane domain.

The Drosophila suppressor of sable gene encodes a polypeptide with regions similar to those of RNA-binding proteins

1991 ◽  
Vol 11 (2) ◽  
pp. 894-905
Author(s):  
R A Voelker ◽  
W Gibson ◽  
J P Graves ◽  
J F Sterling ◽  
M T Eisenberg
Keyword(s):  
Rna Processing ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Open Reading Frame ◽  
In Vitro Translation ◽  
Rna Recognition Motif ◽  
Reading Frame ◽  
Cdna Sequences ◽  
Suppressor Of Sable

The nucleotide sequence of the Drosophila melanogaster suppressor of sable [su(s)] gene has been determined. Comparison of genomic and cDNA sequences indicates that an approximately 7,860-nucleotide primary transcript is processed into an approximately 5-kb message, expressed during all stages of the life cycle, that contains an open reading frame capable of encoding a 1,322-amino-acid protein of approximately 150 kDa. The putative protein contains an RNA recognition motif-like region and a highly charged arginine-, lysine-, serine-, aspartic or glutamic acid-rich region that is similar to a region contained in several RNA-processing proteins. In vitro translation of in vitro-transcribed RNA from a complete cDNA yields a product whose size agrees with the size predicted by the open reading frame. Antisera against su(s) fusion proteins recognize the in vitro-translated protein and detect a protein of identical size in the nuclear fractions from tissue culture cells and embryos. The protein is also present in smaller amounts in cytoplasmic fractions of embryos. That the su(s) protein has regions similar in structure to RNA-processing protein is consistent with its known role in affecting the transcript levels of those alleles that it suppresses.

scholarly journals Nrf1D is the first candidate secretory transcription factor in the blood plasma, with its precursor existing as a unique redox-sensitive transmembrane CNC-bZIP protein in somatic tissues

2018 ◽  
Author(s):  
Jianxin Yuan ◽  
Hongxia Wang ◽  
Shaojun Li ◽  
Yuancai Xiang ◽  
Shaofan Hu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Blood Plasma ◽  
Leucine Zipper ◽  
Transmembrane Domain ◽  
Stop Codon ◽  
Salient Feature ◽  
Bzip Protein ◽  
Protein Levels ◽  
Somatic Tissues ◽  
Alternatively Spliced

ABSTRACTAmongst multiple distinct isoforms, Nrf1D is synthesized from translation of an alternatively-spliced transcript of Nrf1 mRNA, with a naturally-occurring deletion of its stop codon-flanking 1466 nucleotides. This molecular event leads to the reading frameshift mutation, which results in a constitutive substitution of the intact Nrf1’s C-terminal 72 amino acids (aa, covering the second half of the leucine zipper motif to C-terminal Neh3L domain) by an additional extended 80-aa stretch to generate a unique variant Nrf1D. The C-terminal extra 80-aa region of Nrf1D was identified to fold into a redox-sensitive transmembrane domain that enables it to be tightly integrated within the endoplasmic reticulum (ER) membranes. Notably, the salient feature of Nrf1D confers it to be distinguishable from prototypic Nrf1, such that Nrf1D is endowed with only a less ability than wild-type Nrf1 at mediating target gene expression. Further evidence has been presented revealing that both mRNA and protein levels of Nrf1D were detected to varying extents in somatic tissues. Surprisingly, we also found the existence of Nrf1D-derived isoforms in the blood plasma, implying that it is a candidate secretory transcription factor, although its precursor acts as an integral transmembrane-bound CNC-bZIP protein that entails dynamic topologies, before being unleashed from the ER to enter the blood plasma.

scholarly journals Isolation, characterization, and expression of cDNAs encoding murine alpha-mannosidase II, a Golgi enzyme that controls conversion of high mannose to complex N-glycans.

1991 ◽  
Vol 115 (6) ◽  
pp. 1521-1534 ◽  
Author(s):  
K W Moremen ◽  
P W Robbins
Keyword(s):  
Amino Acids ◽  
Catalytic Domain ◽  
Transmembrane Domain ◽  
Full Length ◽  
Open Reading Frame ◽  
Cdna Clones ◽  
Northern Blots ◽  
Reactive Material ◽  
Reading Frame ◽  
High Mannose

Golgi alpha-mannosidase II (GlcNAc transferase I-dependent alpha 1,3[alpha 1,6] mannosidase, EC 3.2.1.114) catalyzes the final hydrolytic step in the N-glycan maturation pathway acting as the committed step in the conversion of high mannose to complex type structures. We have isolated overlapping clones from a murine cDNA library encoding the full length alpha-mannosidase II open reading frame and most of the 5' and 3' untranslated region. The coding sequence predicts a type II transmembrane protein with a short cytoplasmic tail (five amino acids), a single transmembrane domain (21 amino acids), and a large COOH-terminal catalytic domain (1,124 amino acids). This domain organization which is shared with the Golgi glycosyl-transferases suggests that the common structural motifs may have a functional role in Golgi enzyme function or localization. Three sets of polyadenylated clones were isolated extending 3' beyond the open reading frame by as much as 2,543 bp. Northern blots suggest that these polyadenylated clones totaling 6.1 kb in length correspond to minor message species smaller than the full length message. The largest and predominant message on Northern blots (7.5 kb) presumably extends another approximately 1.4-kb downstream beyond the longest of the isolated clones. Transient expression of the alpha-mannosidase II cDNA in COS cells resulted in 8-12-fold overexpression of enzyme activity, and the appearance of cross-reactive material in a perinuclear membrane array consistent with a Golgi localization. A region within the catalytic domain of the alpha-mannosidase II open reading frame bears a strong similarity to a corresponding sequence in the rat liver endoplasmic reticulum alpha-mannosidase and the vacuolar alpha-mannosidase of Saccharomyces cerevisiae. Partial human alpha-mannosidase II cDNA clones were also isolated and the gene was localized to human chromosome 5.

scholarly journals Open reading frame correction using antisense oligonucleotides for the treatment of cystic fibrosis caused by CFTR-W1282X

2021 ◽  
Author(s):  
Wren E. Michaels ◽  
Cecilia Pena-Rasgado ◽  
Rusudan Kotaria ◽  
Robert J. Bridges ◽  
Michelle L. Hastings
Keyword(s):  
Cystic Fibrosis ◽  
Protein Function ◽  
Antisense Oligonucleotides ◽  
Gene Mutations ◽  
Severe Form ◽  
Open Reading Frame ◽  
Common Mutation ◽  
Reading Frame ◽  
Protein Levels ◽  
Cftr Protein

CFTR gene mutations that result in the introduction of premature termination codons (PTCs) are common in cystic fibrosis (CF). This mutation type causes a severe form of the disease, likely because of low CFTR mRNA expression as a result of nonsense mediated mRNA decay (NMD), as well as production of a non-functional, truncated CFTR protein. Current therapeutics for CF, which target residual protein function, are less effective in patients with these types of mutations, due in part to low CFTR protein levels. Splice-switching antisense oligonucleotides (ASOs) designed to induce skipping of exons in order to restore the mRNA open reading frame have shown therapeutic promise pre-clinically and clinically for a number of diseases. We hypothesized that ASO-mediated skipping of CFTR exon 23 would recover CFTR activity associated with terminating mutations in the exon, including CFTR p.W1282X, the 5th most common mutation in CF. Here, we show that CFTR lacking the amino acids encoding exon 23 is partially functional and responsive to corrector and modulator drugs currently in clinical use. ASO-induced exon 23 skipping rescued CFTR expression and chloride current in primary human bronchial epithelial cells isolated from homozygote CFTR-W1282X patients. These results support the use of ASOs in treating CF patients with CFTR class I mutations in exon 23 that result in unstable CFTR mRNA and truncations of the CFTR protein.

scholarly journals Regulation of Melanocortin-5 Receptor Pharmacology by Two Isoforms of MRAP2 in Ricefield Eel (Monopterus albus)

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. A508-A508
Author(s):  
Ting Liu ◽  
Ti-Lin Yi ◽  
Dai-Qin Yang ◽  
Ya-Xiong Tao
Keyword(s):  
Amino Acids ◽  
Binding Affinity ◽  
Transmembrane Domain ◽  
Open Reading Frame ◽  
Acid Oxidation ◽  
Intracellular Camp ◽  
Acth Stimulation ◽  
Monopterus Albus ◽  
Reading Frame ◽  
Significant Difference

Abstract The melanocortin-5 receptor (MC5R) has been implicated in the regulation of exocrine gland secretion, immune regulation, and muscle fatty acid oxidation. However, its function in fish is not well established. Melanocortin-2 receptor accessory protein 2 (MRAP2) can modulate trafficking, ligand binding, and signaling of melanocortin receptors. Ricefield eel (Monopterus albus) is an economically and evolutionarily important fish widely distributed in tropics and subtropics. To explore potential interaction between eel MC5R and MRAP2, herein we cloned ricefield eel mc5r, mrap2X1 and mrap2X2. Eel mc5r consisted of a 1056 bp open reading frame encoding a protein of 351 amino acids. Eel mrap2X1 consisted of a 708 bp open reading frame encoding a protein of 235 amino acids, while eel mrap2X2consisted of a 567 bp open reading frame encoding a protein of 188 amino acids. Multiple sequence alignment showed that maMRAP2X1 and maMRAP2X2 shared 90.43% identity. Interestingly, maMRAP2X2 lost the transmembrane domain. Phylogenetic analysis showed that maMC5R and maMRAP2s were closely related to piscine MC5Rs and MRAP2s, respectively. The maMC5R was further demonstrated to be a functional receptor and could be modulated by maMRAP2s in pharmacological studies. Three agonists, [Nle4, D-Phe7]-alpha-melanocyte stimulating hormone (NDP-MSH), alpha-MSH, and adrenocorticotropin (ACTH), could bind to maMC5R and induce intracellular cAMP production dose-dependently. Compared to human MC5R (hMC5R), maMC5R displayed a significantly decreased Bmax but higher binding affinity to alpha-MSH or ACTH. No significant difference in constitutive activity was observed between hMC5R and maMC5R. When stimulated with α-MSH and ACTH, maMC5R showed significantly lower EC50 and Rmax than that of hMC5R. Eel MRAP2s had no effect on cell surface and total expression of maMC5R, whereas they significantly increased Bmax. Only maMRAP2X2 significantly decreased the binding affinity of ACTH. Both maMRAP2X1 and maMRAP2X2 significantly reduced Rmax but did not affect EC50 in response to alpha-MSH or ACTH stimulation. The availability of maMC5R pharmacological characteristics and the modulation by maMRAP2s will facilitate the investigation of its function in regulating diverse physiological processes in ricefield eel.

scholarly journals Quantitating Translational Control: mRNA Abundance-Dependent and Independent Contributions and the mRNA Sequences That Specify Them

2017 ◽  
Author(s):  
Jingyi Jessica Li ◽  
Guo-Liang Chew ◽  
Mark D. Biggin
Keyword(s):  
Translational Control ◽  
Mrna Level ◽  
Open Reading Frame ◽  
Mrna Abundance ◽  
Mrna Levels ◽  
Mrna Sequence ◽  
Translation Rate ◽  
Reading Frame ◽  
Protein Levels ◽  
Selective Pressures

AbstractTranslation rate per mRNA molecule correlates positively with mRNA abundance. As a result, protein levels do not scale linearly with mRNA levels, but instead scale with the abundance of mRNA raised to the power of an “amplification exponent”. Here we show that to quantitate translational control, the translation rate must be decomposed into two components. One, TRmD, depends on the mRNA level and defines the amplification exponent. The other, TRmIND, is independent of mRNA amount and impacts the correlation coefficient between protein and mRNA levels. We show that in S. cerevisiae TRmD represents ∼20% of the variance in translation and directs an amplification exponent of 1.20 with a 95% confidence interval [1.14, 1.26]. TRmIND constitutes the remaining ∼80% of the variance in translation and explains ∼5% of the variance in protein expression. We also find that TRmD and TRmIND are preferentially determined by different mRNA sequence features: TRmIND by the length of the open reading frame and TRmD both by a ∼60 nucleotide element that spans the initiating AUG and by codon and amino acid frequency. Our work provides more appropriate estimates of translational control and implies that TRmIND is under different evolutionary selective pressures than TRmD.

Complete sequence of rabbit kidney aminopeptidase N and mRNA localization in rabbit kidney by in situ hybridization

1993 ◽  
Vol 71 (5-6) ◽  
pp. 278-287 ◽  
Author(s):  
Xiao-Feng Yang ◽  
Pierre Emmanuel Milhiet ◽  
Florence Gaudoux ◽  
Philippe Crine ◽  
Guy Boileau
Keyword(s):  
In Situ Hybridization ◽  
Transmembrane Domain ◽  
Complete Sequence ◽  
Aminopeptidase N ◽  
Full Length ◽  
Open Reading Frame ◽  
Rabbit Kidney ◽  
Mrna Levels ◽  
Reading Frame

We have isolated and sequenced a full-length cDNA for rabbit kidney aminopeptidase N (APN). The 3-kilobase cDNA contains 12 nucleotides of the 5′ noncoding region, a 2898 nucleotide long open reading frame, and 113 nucleotides of the 3′ untranslated region. The open reading frame encodes a type II membrane protein of 966 amino acid residues composed of a 10 residue NH2-terminal cytosolic domain, a 23 residue transmembrane domain, and a large 933 residue ectodomain that contains the active site. Rabbit APN has eight potential N-glycosylation sites and seven cysteine residues, one of which is located in the transmembrane domain. Computer analysis showed that the enzymes from human, rat, and rabbit were highly conserved, except for the stalk region immediately downstream from the transmembrane domain. Using in situ hybridization techniques we showed that in rabbit kidney, APN mRNA is present in proximal tubules but not in glomeruli, which corresponds to the localization of the protein observed by immunohistochemistry. Taken together, our results strongly suggest that the expression of APN in kidney is modulated at mRNA levels and not at translational and (or) posttranslational levels.Key words: aminopeptidase N, rabbit kidney, full-length sequence, in situ hybridization.

scholarly journals The Drosophila suppressor of sable gene encodes a polypeptide with regions similar to those of RNA-binding proteins.

1991 ◽  
Vol 11 (2) ◽  
pp. 894-905 ◽  
Author(s):  
R A Voelker ◽  
W Gibson ◽  
J P Graves ◽  
J F Sterling ◽  
M T Eisenberg
Keyword(s):  
Rna Processing ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Open Reading Frame ◽  
In Vitro Translation ◽  
Rna Recognition Motif ◽  
Reading Frame ◽  
Cdna Sequences ◽  
Suppressor Of Sable

The nucleotide sequence of the Drosophila melanogaster suppressor of sable [su(s)] gene has been determined. Comparison of genomic and cDNA sequences indicates that an approximately 7,860-nucleotide primary transcript is processed into an approximately 5-kb message, expressed during all stages of the life cycle, that contains an open reading frame capable of encoding a 1,322-amino-acid protein of approximately 150 kDa. The putative protein contains an RNA recognition motif-like region and a highly charged arginine-, lysine-, serine-, aspartic or glutamic acid-rich region that is similar to a region contained in several RNA-processing proteins. In vitro translation of in vitro-transcribed RNA from a complete cDNA yields a product whose size agrees with the size predicted by the open reading frame. Antisera against su(s) fusion proteins recognize the in vitro-translated protein and detect a protein of identical size in the nuclear fractions from tissue culture cells and embryos. The protein is also present in smaller amounts in cytoplasmic fractions of embryos. That the su(s) protein has regions similar in structure to RNA-processing protein is consistent with its known role in affecting the transcript levels of those alleles that it suppresses.

scholarly journals Nrf1D Is the First Candidate Secretory Transcription Factor in the Blood Plasma, Its Precursor Existing as a Unique Redox-Sensitive Transmembrane CNC-bZIP Protein in Hemopoietic and Somatic Tissues

2018 ◽  
Vol 19 (10) ◽  
pp. 2940 ◽  
Author(s):  
Jianxin Yuan ◽  
Hongxia Wang ◽  
Yuancai Xiang ◽  
Shaofan Hu ◽  
Shaojun Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Blood Plasma ◽  
Leucine Zipper ◽  
Transmembrane Domain ◽  
De Novo ◽  
Stop Codon ◽  
Salient Feature ◽  
Bzip Protein ◽  
Protein Levels ◽  
Somatic Tissues

Among multiple distinct isoforms, Nrf1D is synthesized from a de novo translation of an alternatively-spliced transcript of Nrf1 mRNA, as accompanied by a naturally-occurring deletion of its stop codon-flanking 1466 nucleotides. This molecular event leads to the generation of a reading frameshift mutation, which results in a constitutive substitution of the intact Nrf1’s C-terminal 72 amino acids (aa, covering the second half of the leucine zipper motif to C-terminal Neh3L domain) by an additional extended 80-aa stretch to generate a unique variant Nrf1D. The C-terminal extra 80-aa region of Nrf1D was herein identified to be folded into a redox-sensitive transmembrane domain, enabling it to be tightly integrated within the endoplasmic reticulum (ER) membranes. Notably, the salient feature of Nrf1D enables it to be distinguishable from prototypic Nrf1, such that Nrf1D is endowed with a lesser ability than wild-type Nrf1 to mediate target gene expression. Further evidence has also been presented revealing that both mRNA and protein levels of Nrf1D, together with other isoforms similar to those of Nrf1, were detected to varying extents in hemopoietic and somatic tissues. Surprisingly, we found the existence of Nrf1D-derived isoforms in blood plasma, implying that it is a candidate secretory transcription factor, albeit its precursor acts as an integral transmembrane-bound CNC-bZIP protein that entails dynamic topologies across membranes, before being unleashed from the ER to enter the blood.

scholarly journals Leader Proteinase of the Beet Yellows Closterovirus: Mutation Analysis of the Function in Genome Amplification

2000 ◽  
Vol 74 (20) ◽  
pp. 9766-9770 ◽  
Author(s):  
Chih-Wen Peng ◽  
Valerian V. Dolja
Keyword(s):  
Mutation Analysis ◽  
Open Reading Frame ◽  
Structural Flexibility ◽  
Rna Amplification ◽  
Reading Frame ◽  
Protein Levels ◽  
Terminal Domain ◽  
Fold Reduction ◽  
Rna Accumulation ◽  
Terminal Element

ABSTRACT The beet yellows closterovirus leader proteinase (L-Pro) possesses a C-terminal proteinase domain and a nonproteolytic N-terminal domain. It was found that although L-Pro is not essential for basal-level replication, deletion of its N-terminal domain resulted in a 1,000-fold reduction in RNA accumulation. Mutagenic analysis of the N-terminal domain revealed its structural flexibility except for the 54-codon-long, 5′-terminal element in the corresponding open reading frame that is critical for efficient RNA amplification at both RNA and protein levels.

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