scholarly journals Imbalance between Expression of FOXC2 and Its lncRNA in Lymphedema-Distichiasis Caused by Frameshift Mutations

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 650
Author(s):  
Sara Missaglia ◽  
Daniela Tavian ◽  
Sandro Michelini ◽  
Paolo Enrico Maltese ◽  
Andrea Bonanomi ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Healthy Subjects ◽  
Lymphatic System ◽  
System Development ◽  
Bioinformatic Analysis ◽  
Wild Type ◽  
Mutant Proteins ◽  
Frameshift Mutations ◽  
Forkhead Box ◽  
Frameshift Mutant

Forkhead-box C2 (FOXC2) is a transcription factor involved in lymphatic system development. FOXC2 mutations cause Lymphedema-distichiasis syndrome (LD). Recently, a natural antisense was identified, called lncRNA FOXC2-AS1, which increases FOXC2 mRNA stability. No studies have evaluated FOXC2 and FOXC2-AS1 blood expression in LD and healthy subjects. Here, we show that FOXC2 and FOXC-AS1 expression levels were similar in both controls and patients, and a significantly higher amount of both RNAs was observed in females. A positive correlation between FOXC2 and FOXC2-AS1 expression was found in both controls and patients, excluding those with frameshift mutations. In these patients, the FOXC2-AS1/FOXC2 ratio was about 1:1, while it was higher in controls and patients carrying other types of mutations. The overexpression or silencing of FOXC2-AS1 determined a significant increase or reduction in FOXC2 wild-type and frameshift mutant proteins, respectively. Moreover, confocal and bioinformatic analysis revealed that these variations caused the formation of nuclear proteins aggregates also involving DNA. In conclusion, patients with frameshift mutations presented lower values of the FOXC2-AS1/FOXC2 ratio, due to a decrease in FOXC2-AS1 expression. The imbalance between FOXC2 mRNA and its lncRNA could represent a molecular mechanism to reduce the amount of FOXC2 misfolded proteins, protecting cells from damage.

scholarly journals Expression of a Mutant kcnj2 Gene Transcript in Zebrafish

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Ivone U. S. Leong ◽  
Jonathan R. Skinner ◽  
Andrew N. Shelling ◽  
Donald R. Love
Keyword(s):  
Mouse Models ◽  
Muscle Development ◽  
Bioinformatic Analysis ◽  
Periodic Paralysis ◽  
Dominant Negative ◽  
Gene Transcript ◽  
Wild Type ◽  
Autosomal Dominant Disorder ◽  
Mutant Proteins ◽  
Inwardly Rectifying

Long QT 7 syndrome (LQT7, also known as Andersen-Tawil syndrome) is a rare autosomal-dominant disorder that causes cardiac arrhythmias, periodic paralysis, and dysmorphic features. Mutations in the human KCNJ2 gene, which encodes for the subunit of the potassium inwardly-rectifying channel (IK1), have been associated with the disorder. The majority of mutations are considered to be dominant-negative as mutant proteins interact to limit the function of wild type KCNJ2 proteins. Several LQT7 syndrome mouse models have been created that vary in the physiological similarity to the human disease. To complement the LQT7 mouse models, we investigated the usefulness of the zebrafish as an alternative model via a transient approach. Initial bioinformatic analysis identified the zebrafish orthologue of the human KCNJ2 gene, together with a spatial expression profile that was similar to that of human. The expression of a kcnj2-12 transcript carrying an in-frame deletion of critical amino acids identified in human studies resulted in embryos that exhibited defects in muscle development, thereby affecting movement, a decrease in jaw size, pupil-pupil distance, and signs of scoliosis. These defects correspond to some phenotypes expressed by human LQT7 patients.

scholarly journals Genome wide effects of oleic acid on cultured bovine granulosa cells: evidence for the activation of pathways favoring folliculo-luteal transition

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Vengala Rao Yenuganti ◽  
Dirk Koczan ◽  
Jens Vanselow
Keyword(s):  
Oleic Acid ◽  
Granulosa Cells ◽  
System Development ◽  
Circulatory System ◽  
Bioinformatic Analysis ◽  
Negative Energy ◽  
Tissue Remodelling ◽  
Gonadotropin Secretion ◽  
Genome Wide

Abstract Background Metabolic stress, as negative energy balance on one hand or obesity on the other hand can lead to increased levels of free fatty acids in the plasma and follicular fluid of animals and humans. In an earlier study, we showed that increased oleic acid (OA) concentrations affected the function of cultured bovine granulosa cells (GCs). Here, we focus on genome wide effects of increased OA concentrations. Results Our data showed that 413 genes were affected, of which 197 were down- and 216 up-regulated. Specifically, the expression of FSH-regulated functional key genes, CCND2, LHCGR, INHA and CYP19A1 and 17-β-estradiol (E2) production were reduced by OA treatment, whereas the expression of the fatty acid transporter CD36 was increased and the morphology of the cells was changed due to lipid droplet accumulation. Bioinformatic analysis revealed that associated pathways of the putative upstream regulators “FSH” and “Cg (choriogonadotropin)” were inhibited and activated, respectively. Down-regulated genes are over-represented in GO terms “reproductive structure/system development”, “ovulation cycle process”, and “(positive) regulation of gonadotropin secretion”, whereas up-regulated genes are involved in “circulatory system development”, “vasculature development”, “angiogenesis” or “extracellular matrix/structure organization”. Conclusions From these data we conclude that besides inhibiting GC functionality, increased OA levels seemingly promote angiogenesis and tissue remodelling, thus suggestively initiating a premature fulliculo-luteal transition. In vivo this may lead to impeded folliculogenesis and ovulation, and cause sub-fertility.

scholarly journals Investigation of the Stability of Yeast rad52 Mutant Proteins Uncovers Post-translational and Transcriptional Regulation of Rad52p

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 91-101 ◽  
Author(s):  
Erin N Asleson ◽  
Dennis M Livingston
Keyword(s):  
Half Life ◽  
Translational Regulation ◽  
Cellular Level ◽  
Missense Mutations ◽  
Wild Type ◽  
Mutant Proteins ◽  
Gal1 Promoter ◽  
Rad52 Protein ◽  
The Stability ◽  
Mutant Forms

Abstract We investigated the stability of the Saccharomyces cerevisiae Rad52 protein to learn how a cell controls its quantity and longevity. We measured the cellular levels of wild-type and mutant forms of Rad52p when expressed from the RAD52 promoter and the half-lives of the various forms of Rad52p when expressed from the GAL1 promoter. The wild-type protein has a half-life of 15 min. rad52 mutations variably affect the cellular levels of the protein products, and these levels correlate with the measured half-lives. While missense mutations in the N terminus of the protein drastically reduce the cellular levels of the mutant proteins, two mutations—one a deletion of amino acids 210-327 and the other a missense mutation of residue 235—increase the cellular level and half-life more than twofold. These results suggest that Rad52p is subject to post-translational regulation. Proteasomal mutations have no effect on Rad52p half-life but increase the amount of RAD52 message. In contrast to Rad52p, the half-life of Rad51p is >2 hr, and RAD51 expression is unaffected by proteasomal mutations. These differences between Rad52p and Rad51p suggest differential regulation of two proteins that interact in recombinational repair.

Mismatch repair of heteroduplex DNA intermediates of extrachromosomal recombination in mammalian cells

1994 ◽  
Vol 14 (1) ◽  
pp. 400-406
Author(s):  
W P Deng ◽  
J A Nickoloff
Keyword(s):  
Dna Replication ◽  
Mismatch Repair ◽  
Mammalian Cells ◽  
Strand Break ◽  
Wild Type ◽  
Heteroduplex Dna ◽  
Frameshift Mutations ◽  
Single Strand Annealing ◽  
Extrachromosomal Recombination ◽  
Strand Annealing

Previous work indicated that extrachromosomal recombination in mammalian cells could be explained by the single-strand annealing (SSA) model. This model predicts that extrachromosomal recombination leads to nonconservative crossover products and that heteroduplex DNA (hDNA) is formed by annealing of complementary single strands. Mismatched bases in hDNA may subsequently be repaired to wild-type or mutant sequences, or they may remain unrepaired and segregate following DNA replication. We describe a system to examine the formation and mismatch repair of hDNA in recombination intermediates. Our results are consistent with extrachromosomal recombination occurring via SSA and producing crossover recombinant products. As predicted by the SSA model, hDNA was present in double-strand break-induced recombination intermediates. By placing either silent or frameshift mutations in the predicted hDNA region, we have shown that mismatches are efficiently repaired prior to DNA replication.

scholarly journals Requirement of PKR Dimerization Mediated by Specific Hydrophobic Residues for Its Activation by Double-Stranded RNA and Its Antigrowth Effects in Yeast

1998 ◽  
Vol 18 (12) ◽  
pp. 7009-7019 ◽  
Author(s):  
Rekha C. Patel ◽  
Ganes C. Sen
Keyword(s):  
Helical Structure ◽  
Wild Type ◽  
Dimerization Domain ◽  
Double Stranded Rna ◽  
Mutant Proteins ◽  
Hydrophobic Residues ◽  
Dsrna Binding ◽  
Dependent Protein ◽  
Substitution Mutations

ABSTRACT The roles of protein dimerization and double-stranded RNA (dsRNA) binding in the biochemical and cellular activities of PKR, the dsRNA-dependent protein kinase, were investigated. We have previously shown that both properties of the protein are mediated by the same domain. Here we show that dimerization is mediated by hydrophobic residues present on one side of an amphipathic α-helical structure within this domain. Appropriate substitution mutations of residues on that side produced mutants with increased or decreased dimerization activities. Using these mutants, we demonstrated that dimerization is not essential for dsRNA binding. However, enhancing dimerization artificially, by providing an extraneous dimerization domain, increased dsRNA binding of both wild-type and mutant proteins. In vitro, the dimerization-defective mutants could not be activated by dsRNA but were activated normally by heparin. In Saccharomyces cerevisiae, unlike wild-type PKR, these mutants could not inhibit cell growth and the dsRNA-binding domain of the dimerization-defective mutants could not prevent the antigrowth effect of wild-type PKR. These results demonstrate the biological importance of the dimerization properties of PKR.

scholarly journals Helicase Motif Ia Is Involved in Single-Strand DNA-Binding and Helicase Activities of the Herpes Simplex Virus Type 1 Origin-Binding Protein, UL9

2003 ◽  
Vol 77 (4) ◽  
pp. 2477-2488 ◽  
Author(s):  
Boriana Marintcheva ◽  
Sandra K. Weller
Keyword(s):  
Herpes Simplex ◽  
Atpase Activity ◽  
Structural Information ◽  
Origin Of Replication ◽  
Wild Type ◽  
Mutant Proteins ◽  
Ssdna Binding ◽  
Simplex Virus ◽  
Hsv 1

ABSTRACT UL9 is a multifunctional protein essential for herpes simplex virus type 1 (HSV-1) replication in vivo. UL9 is a member of the superfamily II helicases and exhibits helicase and origin-binding activities. It is thought that UL9 binds the origin of replication and unwinds it in the presence of ATP and the HSV-1 single-stranded DNA (ssDNA)-binding protein. We have previously characterized the biochemical properties of mutants in all helicase motifs except for motif Ia (B. Marintcheva and S. Weller, J. Biol. Chem. 276:6605-6615, 2001). Structural information for other superfamily I and II helicases indicates that motif Ia is involved in ssDNA binding. By analogy, we hypothesized that UL9 motif Ia is important for the ssDNA-binding function of the protein. On the basis of sequence conservation between several UL9 homologs within the Herpesviridae family and distant homology with helicases whose structures have been solved, we designed specific mutations in motif Ia and analyzed them genetically and biochemically. Mutant proteins with residues predicted to be involved in ssDNA binding (R112A and R113A/F115A) exhibited wild-type levels of intrinsic ATPase activity and moderate to severe defects in ssDNA-stimulated ATPase activity and ssDNA binding. The S110T mutation targets a residue not predicted to contact ssDNA directly. The mutant protein with this mutation exhibited wild-type levels of intrinsic ATPase activity and near wild-type levels of ssDNA-stimulated ATPase activity and ssDNA binding. All mutant proteins lack helicase activity but were able to dimerize and bind the HSV-1 origin of replication as well as wild-type UL9. Our results indicate that residues from motif Ia contribute to the ssDNA-binding and helicase activities of UL9 and are essential for viral growth. This work represents the successful application of an approach based on a combination of bioinformatics and structural information from related proteins to deduce valuable information about a protein of interest.

scholarly journals Analysis of Genomes Changes in Pseudomonas Chlororaphis Subsp. Aurantiaca Strains Producing Phenazines

2021 ◽  
Author(s):  
Anastasia I. Liaudanskaya ◽  
Natalia P. Maximova ◽  
Katsiaryna G. Verameyenka
Keyword(s):  
Mutant Strain ◽  
Phenylalanine Hydroxylase ◽  
Response Regulator ◽  
Trna Genes ◽  
Type I ◽  
Pseudomonas Chlororaphis ◽  
Wild Type ◽  
Mutant Proteins ◽  
Domain Structures ◽  
Genome Annotations

Abstract Genomes of three strains – phenazine producers – Pseudomonas chlororaphis subsp. aurantiaca (B-162 (wild-type), mutant strain B-162/255 and its derivatives B-162/17) were sequenced and compared. All genome annotations revealed 6347 CDS, 5 rRNA clusters (5S, 16S, 23S) and 59 tRNA genes. Comparison analysis of wild-type strain and B-162/255 mutant strain genomes allowed revealing 32 mutations. 19 new mutations were detected upon comparison of genomes strains B-162/255 and B-162/17. Further bioinformatics analysis allowed predicting mutant proteins` functions and secondary structures of five gene products, mutations in which might potentially have influence on phenazine synthesis and secretion in Pseudomonas bacteria. These genes are phenylalanine hydroxylase transcriptional activator PhhR, type I secretion system ATPase, transcriptional regulator MvaT, GacA response regulator and histidine kinase. Amino acid substitutions were located in domain structures of corresponding proteins.

scholarly journals Mutant tryptophan aporepressors with altered specificities of corepressor recognition.

Genetics ◽  
1991 ◽  
Vol 128 (1) ◽  
pp. 29-35
Author(s):  
D N Arvidson ◽  
M Shapiro ◽  
P Youderian
Keyword(s):  
Dna Binding ◽  
Binding Pocket ◽  
Side Chain ◽  
Wild Type ◽  
Mutant Proteins ◽  
Naturally Occurring ◽  
Repressor Complex ◽  
Genes Encoding ◽  
Active Repressor

Abstract The Escherichia coli trpR gene encodes tryptophan aporepressor, which binds the corepressor ligand, L-tryptophan, to form an active repressor complex. The side chain of residue valine 58 of Trp aporepressor sits at the bottom of the corepressor (L-tryptophan) binding pocket. Mutant trpR genes encoding changes of Val58 to the other 19 naturally occurring amino acids were made. Each of the mutant proteins requires a higher intracellular concentration of tryptophan for activation of DNA binding than wild-type aporepressor. Whereas wild-type aporepressor is activated better by 5-methyltryptophan (5-MT) than by tryptophan, Ile58 and other mutant aporepressors prefer tryptophan to 5-MT as corepressor, and Ala58 and Gly58 prefer 5-MT much more strongly than wild-type aporepressor in vivo. These mutant aporepressors are the first examples of DNA-binding proteins with altered specificities of cofactor recognition.

scholarly journals Plasmodium falciparum Kelch13 and its artemisinin-resistant mutants assemble as hexamers in solution: a SAXS data driven shape restoration study

2021 ◽  
Author(s):  
Nainy Goel ◽  
Kanika Dhiman ◽  
Nidhi Kalidas ◽  
Anwesha Mukhopadhyay ◽  
Ashish ◽  
...  
Keyword(s):  
Artemisinin Resistance ◽  
Resistant Mutant ◽  
Data Driven ◽  
Wild Type ◽  
Saxs Data ◽  
Mutant Proteins ◽  
X Ray ◽  
X Ray Scattering ◽  
Shape Restoration ◽  
Spatial Positioning

AbstractArtemisinin-resistant mutations in PfKelch13 identified worldwide are mostly confined to its BTB/POZ and KRP domains. To date, only two crystal structures of the BTB/POZ-KRP domains as tight dimers are available, which limits structure-based interpretations of its functionality. Our solution Small-Angle X-ray Scattering (SAXS) data driven shape restoration of larger length of protein brought forth that: i) PfKelch13 forms a stable hexamer in P6 symmetry, ii) interactions of the N-termini drive the hexameric assembly, and iii) the six KRP domains project independently in space, forming a cauldron-like architecture. While artemisinin-sensitive mutant A578S packed like the wild-type, hexameric assemblies of dominant artemisinin-resistant mutant proteins R539T and C580Y displayed detectable differences in spatial positioning of their BTB/POZ-KRP domains. Lastly, mapping of mutations known to enable artemisinin resistance explained that most mutations exist mainly in these domains because they are non-detrimental to assembly of mutant PfKelch13 and yet can alter the flux of downstream events essential for susceptibility to artemisinin.

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