scholarly journals Structural defects of a Pax8 mutant that give rise to congenital hypothyroidism

1999 ◽  
Vol 341 (1) ◽  
pp. 89-93 ◽  
Author(s):  
Gianluca TELL ◽  
Lucia PELLIZZARI ◽  
Gennaro ESPOSITO ◽  
Carlo PUCILLO ◽  
Paolo Emidio MACCHIA ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Congenital Hypothyroidism ◽  
Dna Sequences ◽  
Dna Interaction ◽  
Structural Defects ◽  
Molecular Defect ◽  
Wild Type ◽  
Coding Region ◽  
Induced Fit ◽  
Helical Content

Pax proteins are transcriptional regulators that play important roles during embryogenesis. These proteins recognize specific DNA sequences via a conserved element: the paired domain (Prd domain). The low level of organized secondary structure, in the free state, is a general feature of Prd domains; however, these proteins undergo a dramatic gain in α-helical content upon interaction with DNA (‘induced fit’). Pax8 is expressed in the developing thyroid, kidney and several areas of the central nervous system. In humans, mutations of the Pax8 gene, which are mapped to the coding region of the Prd domain, give rise to congenital hypothyroidism. Here, we have investigated the molecular defects caused by a mutation in which leucine at position 62 is substituted for an arginine. Leu62 is conserved among Prd domains, and contributes towards the packing together of helices 1 and 3. The binding affinity of the Leu62Arg mutant for a specific DNA sequence (the C sequence of thyroglobulin promoter) is decreased 60-fold with respect to the wild-type Pax8 Prd domain. However, the affinities with which the wild-type and the mutant proteins bind to a non-specific DNA sequence are very similar. CD spectra demonstrate that, in the absence of DNA, both wild-type Pax8 and the Leu62Arg mutant possess a low α-helical content; however, in the Leu62Arg mutant, the gain in α-helical content upon interaction with DNA is greatly reduced with respect to the wild-type protein. Thus the molecular defect of the Leu62Arg mutant causes a reduced capability for induced fit upon DNA interaction.

scholarly journals Macronuclear transformation with specific DNA fragments controls the content of the new macronuclear genome in Paramecium tetraurelia.

1991 ◽  
Vol 11 (2) ◽  
pp. 1133-1137 ◽  
Author(s):  
Y You ◽  
K Aufderheide ◽  
J Morand ◽  
K Rodkey ◽  
J Forney
Keyword(s):  
Cell Line ◽  
Dna Sequences ◽  
Mutant Cell ◽  
Restriction Pattern ◽  
Paramecium Tetraurelia ◽  
Wild Type ◽  
Coding Region ◽  
Cytoplasmic Factor ◽  
In The Wild ◽  
Dna Restriction

A previously isolated mutant cell line called d48 contains a complete copy of the A surface antigen gene in the micronuclear genome, but the gene is not incorporated into the macronucleus. Previous experiments have shown that a cytoplasmic factor made in the wild-type macronucleus can rescue the mutant. Recently, S. Koizumi and S. Kobayashi (Mol. Cell. Biol. 9:4398-4401, 1989) observed that injection of a plasmid containing the A gene into the d48 macronucleus rescued the cell line after autogamy. It is shown here that an 8.8-kb EcoRI fragment containing only a portion of the A gene coding region is sufficient for the rescue of d48. The inability of other A gene fragments to rescue the mutant shows that this effect is dependent upon specific Paramecium DNA sequences. Rescue results in restoration of the wild-type DNA restriction pattern in the macronucleus. These results are consistent with a model in which the macronuclear A locus normally makes an additional gene product that is required for correct processing of the micronuclear copy of the A gene.

scholarly journals Macronuclear transformation with specific DNA fragments controls the content of the new macronuclear genome in Paramecium tetraurelia

1991 ◽  
Vol 11 (2) ◽  
pp. 1133-1137
Author(s):  
Y You ◽  
K Aufderheide ◽  
J Morand ◽  
K Rodkey ◽  
J Forney
Keyword(s):  
Cell Line ◽  
Dna Sequences ◽  
Mutant Cell ◽  
Restriction Pattern ◽  
Paramecium Tetraurelia ◽  
Wild Type ◽  
Coding Region ◽  
Cytoplasmic Factor ◽  
In The Wild ◽  
Dna Restriction

A previously isolated mutant cell line called d48 contains a complete copy of the A surface antigen gene in the micronuclear genome, but the gene is not incorporated into the macronucleus. Previous experiments have shown that a cytoplasmic factor made in the wild-type macronucleus can rescue the mutant. Recently, S. Koizumi and S. Kobayashi (Mol. Cell. Biol. 9:4398-4401, 1989) observed that injection of a plasmid containing the A gene into the d48 macronucleus rescued the cell line after autogamy. It is shown here that an 8.8-kb EcoRI fragment containing only a portion of the A gene coding region is sufficient for the rescue of d48. The inability of other A gene fragments to rescue the mutant shows that this effect is dependent upon specific Paramecium DNA sequences. Rescue results in restoration of the wild-type DNA restriction pattern in the macronucleus. These results are consistent with a model in which the macronuclear A locus normally makes an additional gene product that is required for correct processing of the micronuclear copy of the A gene.

scholarly journals DNA Sequence Analyses Support the Role of Interrupted Gap Repair in the Origin of Internal Deletions of the Maize Transposon, MuDR

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 603-618 ◽  
Author(s):  
An-Ping Hsia ◽  
Patrick S Schnable
Keyword(s):  
Dna Sequence ◽  
Physical Mapping ◽  
Dna Sequences ◽  
Coding Region ◽  
Sequence Analyses ◽  
Break Points ◽  
The Relationship ◽  
Derivatives Of

Abstract Previous research has demonstrated that the autonomous Cy transposon can activate the excision of Mu transposons. To determine the relationship between Cy and the more recently described autonomous Mu transposon, MuDR, a Cy transposon inserted at the mutable a1 allele, a1-m5216, was isolated and cloned. DNA sequence analyses established that this Cy insertion is identical to MuDR (Mu9, GenBank accession No.: m76978.gb_pl). Therefore, Cy will henceforth be termed MuDR:Cy. Defective derivatives of MuDR:Cy were isolated that had lost their capacity to activate their own excision or the excision of a Mu7 transposon. Most of these derivatives are nonautonomous transposons because they can excise, but only in the presence of unlinked MuDR:Cy transposons. Physical mapping and DNA sequence analyses have established that six of these defective derivatives carry internal deletions. It has been proposed previously that such deletions arise via interrupted gap repair. The DNA sequences of the break points associated with all four sequenced deletions are consistent with this model. The finding that three of the excision-defective derivatives carry deletions that disrupt the coding region of the mudrA (but not the mudrB) transcript supports the view that mudrA plays a role in the excision of Mu transposons.

Multi-Fractal Analysis for Feature Extraction from DNA Sequences

2012 ◽  
pp. 100-118
Author(s):  
Witold Kinsner ◽  
Hong Zhang
Keyword(s):  
Feature Extraction ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Window Size ◽  
Signal Spectrum ◽  
Coding Region ◽  
Lévy Walk ◽  
Fractal Measures ◽  
Levy Walk ◽  
Biological Functionality

This paper presents estimations of multi-scale (multi-fractal) measures for feature extraction from deoxyribonucleic acid (DNA) sequences, and demonstrates the intriguing possibility of identifying biological functionality using information contained within the DNA sequence. We have developed a technique that seeks patterns or correlations in the DNA sequence at a higher level than the local base-pair structure. The technique has three main steps: (i) transforms the DNA sequence symbols into a modified Lévy walk, (ii) transforms the Lévy walk into a signal spectrum, and (iii) breaks the spectrum into sub-spectra and treats each of these as an attractor from which the multi-fractal dimension spectrum is estimated. An optimal minimum window size and volume element size are found for estimation of the multi-fractal measures. Experimental results show that DNA is multi-fractal, and that the multi-fractality changes depending upon the location (coding or non-coding region) in the sequence.

Isolation and sequence analysis of the floral homeotic gene BAP2 in Brassica rapa

2006 ◽  
Vol 3 (2) ◽  
pp. 141-146
Author(s):  
Lu Guang-Yuan ◽  
Wu Xiao-Ming ◽  
Chen Bi-Yun ◽  
Gao Gui-Zhen ◽  
Xu Kun
Keyword(s):  
Brassica Rapa ◽  
Dna Sequences ◽  
Nuclear Localization Signal ◽  
Sequence Comparison ◽  
Homeotic Gene ◽  
Wild Type ◽  
Coding Region ◽  
Meristem Development ◽  
Localization Signal ◽  
Ap2 Domain

AbstractThe Arabidopsis homeotic gene AP2 is essential for floral meristem development and organ specification. In this study, we report the isolation and sequence comparison of the AP2 homologue of Brassica rapa (BAP2). The results showed that the BAP2 DNA sequence was 2138 bp in length and contained nine introns. It shared 90% identity with AP2 in the coding region. The putative BAP2 polypeptide contained a nuclear localization signal (NLS) sequence and two copies of highly conserved AP2 domain, suggesting that BAP2 may function similarly to AP2. Two nucleotide variations were detected in DNA sequences from wild-type and apetalous B. rapa plants at the BAP2 locus, while the putative polypeptides were identical. We propose that BAP2 is not likely to be responsible for the apetalous mutation in B. rapa.

scholarly journals Two genes for ribosomal protein 51 of Saccharomyces cerevisiae complement and contribute to the ribosomes.

1984 ◽  
Vol 4 (9) ◽  
pp. 1871-1879 ◽  
Author(s):  
N Abovich ◽  
M Rosbash
Keyword(s):  
Ribosomal Protein ◽  
Dna Sequence ◽  
Open Reading Frames ◽  
Growth Defect ◽  
Wild Type ◽  
Coding Region ◽  
Insufficient Amount ◽  
The One ◽  
Carboxy Terminal ◽  
Reading Frames

We cloned and sequenced the second gene coding for yeast ribosomal protein 51 (RP51B). When the DNA sequence of this gene was compared with the DNA sequence of RP51A (J.L. Teem and M. Rosbash, Proc. Natl. Acad. Sci. U.S.A. 80:4403--4407, 1983), the following conclusions emerged: both genes code for a protein of 135 amino acids; both open reading frames are interrupted by a single intron which occurs directly after the initiating methionine; the open reading frames are 96% homologous and code for the same protein with the exception of the carboxy-terminal amino acid; DNA sequence homology outside of the coding region is extremely limited. The cloned genes, in combination with the one-step gene disruption techniques of Rothstein (R. J. Rothstein, Methods Enzymol. 101:202-211, 1983), were used to generate haploid strains containing mutations in the RP51A or RP51B genes or in both. Strains missing a normal RP51A gene grew poorly (180-min generation time versus 130 min for the wild type), whereas strains carrying a mutant RP51B were relatively normal. Strains carrying mutations in the two genes grew extremely poorly (6 to 9 h), which led us to conclude that RP51A and RP51B were both expressed. The results of Northern blot and primer extension experiments indicate that strains with a wild-type copy of the RP51B gene and a mutant (or deleted) RP51A gene grow slowly because of an insufficient amount of RP51 mRNA. The growth defect was completely rescued with additional copies of RP51B. The data suggest that RP51A contributes more RP51 mRNA (and more RP51 protein) than does RP51B and that intergenic dosage compensation, sufficient to rescue the growth defect of strains missing a wild-type RP51A gene, does not take place.

Characterization of transposable element-associated mutations that alter yeast alcohol dehydrogenase II expression

1983 ◽  
Vol 3 (1) ◽  
pp. 20-31
Author(s):  
V M Williamson ◽  
D Cox ◽  
E T Young ◽  
D W Russell ◽  
M Smith
Keyword(s):  
Alcohol Dehydrogenase ◽  
Dna Sequences ◽  
Target Sequence ◽  
Direct Repeats ◽  
Wild Type ◽  
Coding Region ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
Delta Sequence ◽  
Flanking Sequences

Seven cis-dominant, constitutively expressed mutations of the normally glucose-repressible isozyme of alcohol dehydrogenase (ADHII) from the yeast Saccharomyces cerevisiae are caused by insertion of transposable elements from the Ty1 family in front of the ADHII structural gene (ADR2) (V. M. Williamson, E. T. Young, and M. Ciriacy, Cell 23:605-614, 1981). We cloned ADR2 with its associated Ty1 element from five S. cerevisiae strains carrying these mutations. Comparison of the Ty1 elements by heteroduplex studies and restriction enzyme analyses indicated that four were very similar; the fifth, although the same size as the others (about 5.6 kilobases), differed by the presence of two large substitutions of approximately 1 and 2 kilobases. The DNA sequences of the terminal direct repeats (deltas) were very homologous but not identical and were similar to previously reported Ty1 element direct repeats. We determined the 5'-flanking sequences of the ADR2 gene isolated from a wild-type strain and from five Ty1-associated mutations. The 5-base pair target sequence at the site of Ty1 insertion was present at both ends of each Ty1 element. The sites of insertion of the elements were all different and occurred from 125 to 210 base pairs in front of the coding region of ADR2. The 5' end of the major transcript as determined by S1 mapping was the same in wild-type cells and in Ty1-associated constitutive mutants and was approximately 54 base pairs upstream from the coding region. ADR2 transcripts were not detected when a solo delta sequence was present in the 5'-flanking region of this gene.

scholarly journals DNA sequence of two linked actin genes of sea urchin.

1983 ◽  
Vol 3 (3) ◽  
pp. 448-456 ◽  
Author(s):  
M A Schuler ◽  
P McOsker ◽  
E B Keller
Keyword(s):  
Amino Acids ◽  
Dna Sequence ◽  
Sea Urchin ◽  
Dna Sequences ◽  
Coding Region ◽  
Slime Molds ◽  
Tandem Gene Duplication ◽  
Coding Regions ◽  
Actin Genes ◽  
Cytoplasmic Actin

DNA sequences have been determined for two actin genes which are closely linked in the genome of the sea urchin Strongylocentrotus purpuratus. The two genes have the same 5'-3' orientation; they were apparently formed originally by tandem gene duplication. The amino acids encoded by the two genes closely resemble those of cytoplasmic actins of mammals and slime molds and differ somewhat from those of mammalian muscle actin. Actin gene 1 had been tentatively identified earlier as the gene for an embryonic cytoplasmic actin by the homology of the 3' noncoding region with that of the cDNA of an embryonic actin mRNA from S. purpuratus. The DNA sequence of gene 1 shows presumptive signals for the initiation and termination of transcription which would govern the formation of a mature mRNA of 1.9 kilobases. Both actin genes 1 and 2 have introns in their coding regions at codons 121/122 and 204. These positions for actin introns have been reported so far only in the rat, not in lower organisms. The divergence of the sequences of these coding-region introns in the two actin genes is 66%, suggesting that the genes diverged about 90 million years ago. By contrast to the introns, the coding regions have been highly conserved; the amino acids of the two genes differ by only 1.3%, and the silent sites of the codons differ by only 12%.

Multi-Fractal Analysis for Feature Extraction from DNA Sequences

2010 ◽  
Vol 2 (2) ◽  
pp. 1-18 ◽  
Author(s):  
Witold Kinsner ◽  
Hong Zhang
Keyword(s):  
Feature Extraction ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Window Size ◽  
Signal Spectrum ◽  
Coding Region ◽  
Lévy Walk ◽  
Fractal Measures ◽  
Levy Walk ◽  
Biological Functionality

This paper presents estimations of multi-scale (multi-fractal) measures for feature extraction from deoxyribonucleic acid (DNA) sequences, and demonstrates the intriguing possibility of identifying biological functionality using information contained within the DNA sequence. We have developed a technique that seeks patterns or correlations in the DNA sequence at a higher level than the local base-pair structure. The technique has three main steps: (i) transforms the DNA sequence symbols into a modified Lévy walk, (ii) transforms the Lévy walk into a signal spectrum, and (iii) breaks the spectrum into sub-spectra and treats each of these as an attractor from which the multi-fractal dimension spectrum is estimated. An optimal minimum window size and volume element size are found for estimation of the multi-fractal measures. Experimental results show that DNA is multi-fractal, and that the multi-fractality changes depending upon the location (coding or non-coding region) in the sequence.

Two genes for ribosomal protein 51 of Saccharomyces cerevisiae complement and contribute to the ribosomes

1984 ◽  
Vol 4 (9) ◽  
pp. 1871-1879
Author(s):  
N Abovich ◽  
M Rosbash
Keyword(s):  
Ribosomal Protein ◽  
Dna Sequence ◽  
Open Reading Frames ◽  
Growth Defect ◽  
Wild Type ◽  
Coding Region ◽  
Insufficient Amount ◽  
The One ◽  
Carboxy Terminal ◽  
Reading Frames

We cloned and sequenced the second gene coding for yeast ribosomal protein 51 (RP51B). When the DNA sequence of this gene was compared with the DNA sequence of RP51A (J.L. Teem and M. Rosbash, Proc. Natl. Acad. Sci. U.S.A. 80:4403--4407, 1983), the following conclusions emerged: both genes code for a protein of 135 amino acids; both open reading frames are interrupted by a single intron which occurs directly after the initiating methionine; the open reading frames are 96% homologous and code for the same protein with the exception of the carboxy-terminal amino acid; DNA sequence homology outside of the coding region is extremely limited. The cloned genes, in combination with the one-step gene disruption techniques of Rothstein (R. J. Rothstein, Methods Enzymol. 101:202-211, 1983), were used to generate haploid strains containing mutations in the RP51A or RP51B genes or in both. Strains missing a normal RP51A gene grew poorly (180-min generation time versus 130 min for the wild type), whereas strains carrying a mutant RP51B were relatively normal. Strains carrying mutations in the two genes grew extremely poorly (6 to 9 h), which led us to conclude that RP51A and RP51B were both expressed. The results of Northern blot and primer extension experiments indicate that strains with a wild-type copy of the RP51B gene and a mutant (or deleted) RP51A gene grow slowly because of an insufficient amount of RP51 mRNA. The growth defect was completely rescued with additional copies of RP51B. The data suggest that RP51A contributes more RP51 mRNA (and more RP51 protein) than does RP51B and that intergenic dosage compensation, sufficient to rescue the growth defect of strains missing a wild-type RP51A gene, does not take place.

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