scholarly journals Genomic organization of human lactate dehydrogenase-A gene

1985 ◽  
Vol 231 (3) ◽  
pp. 537-541 ◽  
Author(s):  
F Z Chung ◽  
H Tsujibo ◽  
U Bhattacharyya ◽  
F S Sharief ◽  
S S-L Li
Keyword(s):  
Lactate Dehydrogenase ◽  
Translation Initiation ◽  
Human Placenta ◽  
Genomic Organization ◽  
Genomic Clone ◽  
Random Coil ◽  
Protein Coding ◽  
Untranslated Sequence ◽  
Translation Initiation Codon ◽  
Human Genomic

A human genomic clone containing the lactate dehydrogenase-A (LDH-A) gene of approx. 12 kilobases in length was isolated and characterized. The protein-coding sequence is interrupted by six introns, and the positions of these introns are at the random coil regions or near the ends of secondary structures located on the surface of the LDH-A molecule. An additional intron is present at 24 nucleotides 5′ to the translation initiation codon ATG, while the 3′ untranslated sequence of 565 nucleotides is not interrupted. The genomic blot analysis of human placenta DNA indicates the presence of multiple LDH-A gene-related sequences.

scholarly journals Structure of the human lactate dehydrogenase B gene

1989 ◽  
Vol 257 (3) ◽  
pp. 921-924 ◽  
Author(s):  
T Takeno ◽  
S S L Li
Keyword(s):  
Lactate Dehydrogenase ◽  
Translation Initiation ◽  
Initiation Site ◽  
Initiation Codon ◽  
Translation Initiation Site ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Sequence ◽  
Human Genomic ◽  
Human And Mouse

Human genomic clones containing parts of the lactate dehydrogenase B (LDH-B) gene (approx. 25 kb in length) were isolated and characterized. The protein-coding sequence of human LDH-B gene is interrupted by six introns at codons nos. 42-43, 82, 140, 198, 237 and 278-279, and the positions of these introns are homologous to those of LDH-A genes from man and mouse. The 5' non-coding region of human LDH-B gene is interrupted by an intron six nucleotide residues upstream of the ATG translation-initiation site, whereas those of human and mouse LDH-A genes are interrupted at 24 nucleotide residues 5' to the ATG initiation codon. As is the case of LDH-A genes from man and mouse, there is no intron in the 3' non-coding region of human LDH-B gene.

scholarly journals Nucleotide sequence of the putative regulatory region of mouse lactate dehydrogenase-A gene

1986 ◽  
Vol 235 (2) ◽  
pp. 435-439 ◽  
Author(s):  
K M Fukasawa ◽  
S S L Li
Keyword(s):  
Lactate Dehydrogenase ◽  
Nucleotide Sequence ◽  
Cyclic Amp ◽  
Regulatory Region ◽  
Base Pairs ◽  
Protein Coding ◽  
Untranslated Sequence ◽  
Eukaryotic Genes ◽  
Putative Regulatory Region ◽  
Processed Pseudogene

The nucleotide sequence of approx. 3 kilobases including the regulatory region, a non-coding exon and the first protein-coding exon from mouse lactate dehydrogenase-A (LDH-A) gene has been determined. The putative initiation sites of transcription and translation were deduced by comparing the nucleotide sequence of mouse LDH-A gene with those of a mouse LDH-A processed pseudogene and the LDH-A full-length cDNAs from rat and human. The tentative TATA and CAAT boxes, and the hexanucleotides CCGCCC have been identified. The sequence of AAATCTTGCTCAA of mouse LDH-A gene has also been found to show striking homology to the cyclic AMP-responsive sequences of eukaryotic genes regulated by cyclic AMP. It has been reported previously that the protein-coding sequence of mouse LDH-A gene is interrupted by six introns and the 3′ untranslated sequence of 485 nucleotides is not interrupted [Li, Tiano, Fukasawa, Yagi, Shimiza, Sharief, Nakashima & Pan (1985) Eur. J. Biochem. 149, 215-225]. An additional intron of 1653 base-pairs was found in the 5′ untranslated sequence of 101 nucleotides at 24 nucleotides upstream to the translation start site. Thus, mouse LDH-A gene containing seven introns spans approx. 11 kilobases and its length of mature mRNA is 1582 nucleotides, excluding the poly(A) tail.

scholarly journals The Role of eIF1 in Translation Initiation Codon Selection in Caenorhabditiselegans

Genetics ◽  
2010 ◽  
Vol 186 (4) ◽  
pp. 1187-1196 ◽  
Author(s):  
Lisa L. Maduzia ◽  
Anais Moreau ◽  
Nausicaa Poullet ◽  
Sebastien Chaffre ◽  
Yinhua Zhang
Keyword(s):  
Translation Initiation ◽  
Initiation Codon ◽  
Translation Initiation Codon ◽  
Codon Selection

Physiological Dysfunctions Associated with Mutations of the Imprinted Gnas Locus

Physiology ◽  
2008 ◽  
Vol 23 (4) ◽  
pp. 221-229 ◽  
Author(s):  
Stefan Krechowec ◽  
Antonius Plagge
Keyword(s):  
Signal Transduction ◽  
Mouse Models ◽  
Genomic Organization ◽  
Receptor Activation ◽  
Deficient Mouse ◽  
Protein Coding ◽  
Alternative Protein ◽  
Stimulatory G Protein ◽  
Protein Variants ◽  
Complex Arrangement

The ubiquitous Gαs-subunit of the trimeric, stimulatory G-protein plays a central role in receptor-mediated signal transduction, coupling receptor activation with the production of cAMP. The Gαs-encoding locus Gnas is now known to consist of a complex arrangement of several protein-coding and noncoding transcripts. We provide an overview of its genomic organization, its regulation by genomic imprinting, and a summary of the physiological roles of the alternative protein variants Gαs and XLαs as determined from deficient mouse models.

scholarly journals Molecular Characterization of Two Lactate Dehydrogenase Genes with a Novel Structural Organization on the Genome of Lactobacillus sp. Strain MONT4

2004 ◽  
Vol 70 (10) ◽  
pp. 6290-6295 ◽  
Author(s):  
Jennifer Weekes ◽  
Gülhan Ü. Yüksel
Keyword(s):  
Escherichia Coli ◽  
Lactate Dehydrogenase ◽  
Sequence Analysis ◽  
Molecular Characterization ◽  
Northern Blot ◽  
Structural Organization ◽  
Genomic Organization ◽  
The Individual

ABSTRACT Two lactate dehydrogenase (ldh) genes from Lactobacillus sp. strain MONT4 were cloned by complementation in Escherichia coli DC1368 (ldh pfl) and were sequenced. The sequence analysis revealed a novel genomic organization of the ldh genes. Subcloning of the individual ldh genes and their Northern blot analyses indicated that the genes are monocistronic.

scholarly journals Link Between Short tandem Repeats and Translation Initiation Site Selection

2018 ◽  
Author(s):  
M Arabfard ◽  
K Kavousi ◽  
A Delbari ◽  
M Ohadi
Keyword(s):  
Amino Acids ◽  
Translation Initiation ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Initiation Site ◽  
Translation Initiation Site ◽  
Vertebrate Species ◽  
Protein Coding ◽  
Human Specific ◽  
Short Tandem

AbstractRecent work in yeast and humans suggest that evolutionary divergence in cis-regulatory sequences impact translation initiation sites (TISs). Cis-elements can also affect the efficacy and amount of protein synthesis. Despite their vast biological implication, the landscape and relevance of short tandem repeats (STRs)/microsatellites to the human protein-coding gene TISs remain largely unknown. Here we characterized the STR distribution at the 120 bp cDNA sequence upstream of all annotated human protein-coding gene TISs based on the Ensembl database. Furthermore, we performed a comparative genomics study of all annotated orthologous TIS-flanking sequences across 47 vertebrate species (755,956 transcripts), aimed at identifying human-specific STRs in this interval. We also hypothesized that STRs may be used as genetic codes for the initiation of translation. The initial five amino acid sequences (excluding the initial methionine) that were flanked by STRs in human were BLASTed against the initial orthologous five amino acids in other vertebrate species (2,025,817 pair-wise TIS comparisons) in order to compare the number of events in which human-specific and non-specific STRs occurred with homologous and non-homologous TISs (i.e. ≥50% and <50% similarity of the five amino acids). We characterized human-specific STRs and a bias of this compartment in comparison to the overall (human-specific and non-specific) distribution of STRs (Mann Whitney p=1.4 × 10−11). We also found significant enrichment of non-homologous TISs flanked by human-specific STRs (p<0.00001). In conclusion, our data indicate a link between STRs and TIS selection, which is supported by differential evolution of the human-specific STRs in the TIS upstream flanking sequence.AbbreviationscDNAComplementary DNACDSCoding DNA sequenceSTRShort Tandem RepeatTISTranslation Initiation SiteTSSTranscription Start Site

scholarly journals RUFY4 exists as two translationally regulated isoforms, that localize to the mitochondrion in activated macrophages

2021 ◽  
Vol 8 (7) ◽  
pp. 202333
Author(s):  
Jan Valečka ◽  
Voahirana Camosseto ◽  
David G. McEwan ◽  
Seigo Terawaki ◽  
Zhuangzhuang Liu ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Translation Initiation ◽  
Messenger Rna ◽  
Activated Macrophages ◽  
Truncated Form ◽  
Fyve Domain ◽  
Alternative Translation ◽  
Translation Initiation Codon ◽  
Molecular Patterns

We report here that RUFY4, a newly characterized member of the ‘RUN and FYVE domain-containing’ family of proteins previously associated with autophagy enhancement, is highly expressed in alveolar macrophages (AM). We show that RUFY4 interacts with mitochondria upon stimulation by microbial-associated molecular patterns of AM and dendritic cells. RUFY4 interaction with mitochondria and other organelles is dependent on a previously uncharacterized OmpH domain located immediately upstream of its C-terminal FYVE domain. Further, we demonstrate that rufy4 messenger RNA can be translated from an alternative translation initiation codon, giving rise to a N-terminally truncated form of the molecule lacking most of its RUN domain and with enhanced potential for its interaction with mitochondria. Our observations point towards a role of RUFY4 in selective mitochondria clearance in activated phagocytes.

scholarly journals Comparative Analyses of Chloroplast Genomes of Cucurbitaceae Species: Lights into Selective Pressures and Phylogenetic Relationships

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2165 ◽  
Author(s):  
Xiao Zhang ◽  
Tao Zhou ◽  
Jia Yang ◽  
Jingjing Sun ◽  
Miaomiao Ju ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Sequence Divergence ◽  
Economic Plant ◽  
Genome Sequences ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Representative Species ◽  
Translation Initiation Codon

Cucurbitaceae is the fourth most important economic plant family with creeping herbaceous species mainly distributed in tropical and subtropical regions. Here, we described and compared the complete chloroplast genome sequences of ten representative species from Cucurbitaceae. The lengths of the ten complete chloroplast genomes ranged from 155,293 bp (C. sativus) to 158,844 bp (M. charantia), and they shared the most common genomic features. 618 repeats of three categories and 813 microsatellites were found. Sequence divergence analysis showed that the coding and IR regions were highly conserved. Three protein-coding genes (accD, clpP, and matK) were under selection and their coding proteins often have functions in chloroplast protein synthesis, gene transcription, energy transformation, and plant development. An unconventional translation initiation codon of psbL gene was found and provided evidence for RNA editing. Applying BI and ML methods, phylogenetic analysis strongly supported the position of Gomphogyne, Hemsleya, and Gynostemma as the relatively original lineage in Cucurbitaceae. This study suggested that the complete chloroplast genome sequences were useful for phylogenetic studies. It would also determine potential molecular markers and candidate DNA barcodes for coming studies and enrich the valuable complete chloroplast genome resources of Cucurbitaceae.

Novel Mutation of the Translation Initiation Codon of the α1-Globin Gene (ATG>AAG orHBA1:c.2T>A)

Hemoglobin ◽  
2016 ◽  
Vol 40 (5) ◽  
pp. 369-370 ◽  
Author(s):  
John S. Waye ◽  
Barry Eng ◽  
Meredith Hanna ◽  
Betty-Ann Hohenadel ◽  
Lisa Nakamura ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Novel Mutation ◽  
Globin Gene ◽  
Initiation Codon ◽  
Translation Initiation Codon

scholarly journals A heterodimer of evolved designer-recombinases precisely excises a human genomic DNA locus

2019 ◽  
Vol 48 (1) ◽  
pp. 472-485 ◽  
Author(s):  
Felix Lansing ◽  
Maciej Paszkowski-Rogacz ◽  
Lukas Theo Schmitt ◽  
Paul Martin Schneider ◽  
Teresa Rojo Romanos ◽  
...  
Keyword(s):  
Human Genome ◽  
Genome Editing ◽  
Large Scale ◽  
Genome Engineering ◽  
Genomic Sequence ◽  
Safe Alternative ◽  
Protein Coding ◽  
Dna Binding Specificity ◽  
Human Genomic ◽  
Human Genomic Sequence

Abstract Site-specific recombinases (SSRs) such as the Cre/loxP system are useful genome engineering tools that can be repurposed by altering their DNA-binding specificity. However, SSRs that delete a natural sequence from the human genome have not been reported thus far. Here, we describe the generation of an SSR system that precisely excises a 1.4 kb fragment from the human genome. Through a streamlined process of substrate-linked directed evolution we generated two separate recombinases that, when expressed together, act as a heterodimer to delete a human genomic sequence from chromosome 7. Our data indicates that designer-recombinases can be generated in a manageable timeframe for precision genome editing. A large-scale bioinformatics analysis suggests that around 13% of all human protein-coding genes could be targetable by dual designer-recombinase induced genomic deletion (dDRiGD). We propose that heterospecific designer-recombinases, which work independently of the host DNA repair machinery, represent an efficient and safe alternative to nuclease-based genome editing technologies.

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