scholarly journals A Highly Conserved Sequence in the 3′-Untranslated Region of the Drosophila Adh Gene Plays a Functional Role in Adh Expression

Genetics ◽  
1999 ◽  
Vol 151 (2) ◽  
pp. 667-674 ◽  
Author(s):  
John Parsch ◽  
Wolfgang Stephan ◽  
Soichi Tanda
Keyword(s):  
Amino Acid ◽  
Untranslated Region ◽  
Functional Role ◽  
P Element ◽  
Evolutionary Significance ◽  
Base Sequence ◽  
Twofold Increase ◽  
Conserved Sequence ◽  
Adh Gene ◽  
Adh Activity

Abstract Phylogenetic analysis identified a highly conserved eight-base sequence (AAGGCTGA) within the 3′-untranslated region (UTR) of the Drosophila alcohol dehydrogenase gene, Adh. To examine the functional significance of this conserved motif, we performed in vitro deletion mutagenesis on the D. melanogaster Adh gene followed by P-element-mediated germline transformation. Deletion of all or part of the eight-base sequence leads to a twofold increase in in vivo ADH enzymatic activity. The increase in activity is temporally and spatially general and is the result of an underlying increase in Adh transcript. These results indicate that the conserved 3′-UTR motif plays a functional role in the negative regulation of Adh gene expression. The evolutionary significance of our results may be understood in the context of the amino acid change that produces the ADH-F allele and also leads to a twofold increase in ADH activity. While there is compelling evidence that the amino acid replacement has been a target of positive selection, the conservation of the 3′-UTR sequence suggests that it is under strong purifying selection. The selective difference between these two sequence changes, which have similar effects on ADH activity, may be explained by different metabolic costs associated with the increase in activity.

scholarly journals Use of P-Element-Mediated Transformation to Identify the Molecular Basis of Naturally Occurring Variants Affecting Adh Expression in Drosophila melanogaster

Genetics ◽  
1987 ◽  
Vol 115 (1) ◽  
pp. 129-140
Author(s):  
Cathy C Laurie-Ahlberg ◽  
Lynn F Stam
Keyword(s):  
Drosophila Melanogaster ◽  
Amino Acid ◽  
Molecular Basis ◽  
Amino Acid Replacement ◽  
Activity Level ◽  
P Element ◽  
Flanking Sequence ◽  
Replacement Substitution ◽  
The Difference ◽  
Adh Activity

ABSTRACT The purpose of the work reported here is to identify the molecular basis of the difference in level of expression between the polymorphic Slow and Fast alcohol dehydrogenase (Adh) alleles in Drosophila melanogaster . Previous studies have shown that Fast lines typically have a two- to threefold higher activity level than Slow lines and they also have a substantially higher level of ADH-protein (estimated immunologically). The results of a restriction fragment length polymorphism study in relation to ADH activity variation had previously suggested that the difference in Adh expression between allozymes might not be due entirely to the amino acid replacement substitution, but could be due in part to linkage disequilibrium with a regulatory site polymorphism. Here we describe an approach that makes use of P-element-mediated transformation in order to identify the nucleotide substitution(s) responsible for this difference in ADH level. This approach consists of generating recombinants in vitro between Adh region clones derived from a typical Slow/Fast pair of alleles and then testing for the effects of particular restriction fragments on expression in vivo by transformation. Using this approach, the effect on both ADH activity and ADH-protein level clearly maps to a 2.3-kb restriction fragment that includes all of the Adh coding sequence and some intron and 3' flanking sequence, but excludes all of the 5' flanking sequence of the distal (adult) transcriptional unit. Comparison of Kreitman's DNA sequences for this fragment from several Slow and Fast alleles showing the typical difference in activity level shows that only three nucleotide substitutions distinguish all Fast from all Slow alleles. Thus, it is likely that one or more of these substitutions causes the major difference in Adh expression between allozymic classes. One of these substitutions is, of course, the Slow/Fast amino acid replacement substitution (at 1490) while the other two are nearby third position silent substitutions (at 1443 and 1527). A quantiative analysis of variation among transformant stocks shows that the P-element transformation approach can be used to localize even relatively small effects on gene expression (on the order of 20%).

scholarly journals Antimutator mutations in the alpha subunit of Escherichia coli DNA polymerase III: identification of the responsible mutations and alignment with other DNA polymerases.

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1039-1044 ◽  
Author(s):  
I J Fijalkowska ◽  
R M Schaaper
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Alpha Subunit ◽  
Sequence Motifs ◽  
Dna Polymerase Iii ◽  
Conserved Sequence ◽  
Polymerase Iii ◽  
Dna Replication Errors

Abstract The dnaE gene of Escherichia coli encodes the DNA polymerase (alpha subunit) of the main replicative enzyme, DNA polymerase III holoenzyme. We have previously identified this gene as the site of a series of seven antimutator mutations that specifically decrease the level of DNA replication errors. Here we report the nucleotide sequence changes in each of the different antimutator dnaE alleles. For each a single, but different, amino acid substitution was found among the 1,160 amino acids of the protein. The observed substitutions are generally nonconservative. All affected residues are located in the central one-third of the protein. Some insight into the function of the regions of polymerase III containing the affected residues was obtained by amino acid alignment with other DNA polymerases. We followed the principles developed in 1990 by M. Delarue et al. who have identified in DNA polymerases from a large number of prokaryotic and eukaryotic sources three highly conserved sequence motifs, which are suggested to contain components of the polymerase active site. We succeeded in finding these three conserved motifs in polymerase III as well. However, none of the amino acid substitutions responsible for the antimutator phenotype occurred at these sites. This and other observations suggest that the effect of these mutations may be exerted indirectly through effects on polymerase conformation and/or DNA/polymerase interactions.

scholarly journals Identification and Analysis of Novel Amino-Acid Sequence Repeats inBacillus anthracisstr.AmesProteome Using Computational Tools

2007 ◽  
Vol 2007 ◽  
pp. 1-23 ◽  
Author(s):  
G. R. Hemalatha ◽  
D. Satyanarayana Rao ◽  
L. Guruprasad
Keyword(s):  
Amino Acid ◽  
Amino Acid Residue ◽  
Protein Sequence ◽  
Amino Acid Residues ◽  
Sequence Motifs ◽  
Computational Tools ◽  
Conserved Sequence ◽  
Conserved Sequence Motifs ◽  
Multiple Copies ◽  
Domain 3

We have identified four repeats and ten domains that are novel in proteins encoded by theBacillus anthracisstr.Amesproteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 57-amino-acid-residue PxV domain, (2) 122-amino-acid-residue FxF domain, (3) 111-amino-acid-residue YEFF domain, (4) 109-amino-acid-residue IMxxH domain, (5) 103-amino-acid-residue VxxT domain, (6) 84-amino-acid-residue ExW domain, (7) 104-amino-acid-residue NTGFIG domain, (8) 36-amino-acid-residue NxGK repeat, (9) 95-amino-acid-residue VYV domain, (10) 75-amino-acid-residue KEWE domain, (11) 59-amino-acid-residue AFL domain, (12) 53-amino-acid-residue RIDVK repeat, (13) (a) 41-amino-acid-residue AGQF repeat and (b) 42-amino-acid-residue GSAL repeat. A repeat or domain type is characterized by specific conserved sequence motifs. We discuss the presence of these repeats and domains in proteins from other genomes and their probable secondary structure.

scholarly journals Satellites in the prokaryote world

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Juan A. Subirana ◽  
Xavier Messeguer
Keyword(s):  
Amino Acid ◽  
Tandem Repeats ◽  
Reference Group ◽  
Evolutionary Relationship ◽  
Short Length ◽  
Evolutionary Significance ◽  
Leptospira Interrogans ◽  
Amino Acid Repeats ◽  
Representative Species ◽  
Eukaryotic Genomes

Abstract Background Satellites or tandem repeats are very abundant in many eukaryotic genomes. Occasionally they have been reported to be present in some prokaryotes, but to our knowledge there is no general comparative study on their occurrence. For this reason we present here an overview of the distribution and properties of satellites in a set of representative species. Our results provide novel insights into the evolutionary relationship between eukaryotes, Archaea and Bacteria. Results We have searched all possible satellites present in the NCBI reference group of genomes in Archaea (142 species) and in Bacteria (119 species), detecting 2735 satellites in Archaea and 1067 in Bacteria. We have found that the distribution of satellites is very variable in different organisms. The archaeal Methanosarcina class stands out for the large amount of satellites in their genomes. Satellites from a few species have similar characteristics to those in eukaryotes, but most species have very few satellites: only 21 species in Archaea and 18 in Bacteria have more than 4 satellites/Mb. The distribution of satellites in these species is reminiscent of what is found in eukaryotes, but we find two significant differences: most satellites have a short length and many of them correspond to segments of genes coding for amino acid repeats. Transposition of non-coding satellites throughout the genome occurs rarely: only in the bacteria Leptospira interrogans and the archaea Methanocella conradii we have detected satellite families of transposed satellites with long repeats. Conclusions Our results demonstrate that the presence of satellites in the genome is not an exclusive feature of eukaryotes. We have described a few prokaryotes which do contain satellites. We present a discussion on their eventual evolutionary significance.

scholarly journals A Novel Distinct Genetic Variant of Tomato Torrado Virus with Substantially Shorter RNA1-Specific 3’untranslated Region (3’UTR)

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2454
Author(s):  
Marta Budziszewska ◽  
Przemysław Wieczorek
Keyword(s):  
Amino Acid ◽  
Genetic Variability ◽  
Untranslated Region ◽  
Genetic Variant ◽  
Sequencing Data ◽  
Sequence Analyses ◽  
Nucleotide Substitutions ◽  
Systemic Necrosis ◽  
Single Nucleotide

Tomato torrado virus (ToTV) induces severe systemic necrosis in Solanum lycopersicum. This work aimed at describing the genetic variability of necrosis-inducing ToTV-Wal’17 collected in 2017, derived from the ToTV-Wal’03 after long-term passages in plants. Sequence analyses of the ToTV-Wal’17 indicated twenty-eight single nucleotide substitutions in coding sequence of both RNAs, twelve of which resulted in amino acid changes in viral polyproteins. Moreover the sequencing data revealed that the 3’UTR of ToTV-Wal’17 RNA1 was 394 nts shorter in comparison to Wal’03. The performed sequence analyses revealed that 3’UTR of RNA1 of ToTV-Wal’17 is the most divergent across all previously described European isolates.

Expression of a duplicate Na,K-ATPase β1-isoform in the European eel (Anguilla anguilla)

2000 ◽  
Vol 279 (1) ◽  
pp. R222-R229 ◽  
Author(s):  
Christopher P. Cutler ◽  
Stephane Brezillon ◽  
Songul Bekir ◽  
Ian L. Sanders ◽  
Neil Hazon ◽  
...  
Keyword(s):  
Amino Acid ◽  
Functional Role ◽  
Intestinal Epithelial Cells ◽  
Anguilla Anguilla ◽  
European Eel ◽  
Mrna Levels ◽  
Intestinal Epithelial ◽  
Developmentally Regulated ◽  
Regulated Expression ◽  
Seawater Acclimation

Recent studies on teleost fish have suggested that their genomes have undergone ancient polyploidization events resulting in the duplication of the genome. A duplicate copy of the Na,K-ATPase β1-isoform (called β233) has been identified in the European eel ( Anguilla anguilla). The β233-isoform shares high levels of nucleotide (74.8%) and amino acid (69.9%) homology with the eel β1-subunit as well as other vertebrate β1-sequences. Compared with the widely expressed β1-isoform, expression of β233-mRNA is mainly restricted to epithelial tissues. Seawater acclimation induced increases in β233-mRNA levels in kidney, gill, and intestine of migratory “silver” but not the nonmigratory “yellow” adult eels, suggesting that the factors responsible for this upregulation are themselves developmentally regulated. Expression of a variably glycosylated 40- to 52-kDa β233-protein in both gill “chloride” and intestinal epithelial cells suggests that the β233-isoform of Na,K-ATPase may play an important functional role in the major osmoregulatory tissues of euryhaline fish such as the eel.

scholarly journals Regulated expression of nuclear protein(s) in myogenic cells that binds to a conserved 3' untranslated region in pro alpha 1 (I) collagen cDNA.

1989 ◽  
Vol 9 (7) ◽  
pp. 2828-2836 ◽  
Author(s):  
T Herget ◽  
M Burba ◽  
M Schmoll ◽  
K Zimmermann ◽  
A Starzinski-Powitz
Keyword(s):  
Untranslated Region ◽  
Nuclear Protein ◽  
Protein S ◽  
Target Sequence ◽  
Conserved Sequence ◽  
L6 Myotubes ◽  
Double Stranded Dna ◽  
Nuclear Extracts ◽  
Collagen Genes

We describe the identification and DNA-binding properties of nuclear proteins from rat L6 myoblasts which recognize an interspecies conserved 3' untranslated segment of pro alpha 1 (I) collagen cDNA. Levels of the two pro alpha 1 (I) collagen RNAs, present in L6 myoblasts, decreased drastically between 54 and 75 h after induction of myotube formation in serum-free medium. Both mRNAs contained a conserved sequence segment of 135 nucleotides (termed tame sequence) in the 3' untranslated region that had 96% homology to the human and murine pro alpha 1 (I) collagen genes. The cDNA of this tame sequence was specifically recognized by nuclear protein(s) from L6 myoblasts, as judged by gel retardation assays and DNase I footprints. The tame-binding protein(s) was able to recognize its target sequence on double-stranded DNA but bound also to the appropriate single-stranded oligonucleotide. Protein that bound to the tame sequence was undetectable in nuclear extracts of L6 myotubes that did not accumulate the two collagen mRNAs. Therefore, the activity of this nuclear protein seems to be linked to accumulation of the sequences that it recognizes in vitro. The collagen RNAs and the nuclear tame-binding proteins reappeared after a change of medium, which further suggests that the RNAs and the protein(s) are coordinately regulated.

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