scholarly journals De Novo Development of mtDNA Deletion Due to Decreased POLG and SSBP1 Expression in Humans

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 284
Author(s):  
Yeonmi Lee ◽  
Taeho Kim ◽  
Miju Lee ◽  
Seongjun So ◽  
Mustafa Zafer Karagozlu ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
De Novo ◽  
Wild Type Allele ◽  
Wild Type ◽  
Factors Associated ◽  
Mtdna Deletions ◽  
Nuclear Factors ◽  
Mtdna Deletion ◽  
In The Wild ◽  
Mtdna Replication

Defects in the mitochondrial genome (mitochondrial DNA (mtDNA)) are associated with both congenital and acquired disorders in humans. Nuclear-encoded DNA polymerase subunit gamma (POLG) plays an important role in mtDNA replication, and proofreading and mutations in POLG have been linked with increased mtDNA deletions. SSBP1 is also a crucial gene for mtDNA replication. Here, we describe a patient diagnosed with Pearson syndrome with large mtDNA deletions that were not detected in the somatic cells of the mother. Exome sequencing was used to evaluate the nuclear factors associated with the patient and his family, which revealed a paternal POLG mutation (c.868C > T) and a maternal SSBP1 mutation (c.320G > A). The patient showed lower POLG and SSBP1 expression than his healthy brothers and the general population of a similar age. Notably, c.868C in the wild-type allele was highly methylated in the patient compared to the same site in both his healthy brothers. These results suggest that the co- deficient expression of POLG and SSBP1 genes could contribute to the development of mtDNA deletion.

scholarly journals SPO71 Encodes a Developmental Stage-Specific Partner for Vps13 in Saccharomyces cerevisiae

2013 ◽  
Vol 12 (11) ◽  
pp. 1530-1537 ◽  
Author(s):  
Jae-Sook Park ◽  
Yuuya Okumura ◽  
Hiroyuki Tachikawa ◽  
Aaron M. Neiman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Ectopic Expression ◽  
Membrane Vesicles ◽  
Specific Gene ◽  
Wild Type ◽  
Protein Mutation ◽  
Prospore Membrane ◽  
In The Wild ◽  
Membrane Morphogenesis

ABSTRACT The creation of haploid gametes in yeast, termed spores, requires the de novo formation of membranes within the cytoplasm. These membranes, called prospore membranes, enclose the daughter nuclei generated by meiosis. Proper growth and closure of prospore membranes require the highly conserved Vps13 protein. Mutation of SPO71 , a meiosis-specific gene first identified as defective in spore formation, was found to display defects in membrane morphogenesis very similar to those seen in vps13 Δ cells. Specifically, prospore membranes are smaller than in the wild type, they fail to close, and membrane vesicles are present within the prospore membrane lumen. As in vps13 Δ cells, the levels of phophatidylinositol-4-phosphate are reduced in the prospore membranes of spo71 Δ cells. SPO71 is required for the translocation of Vps13 from the endosome to the prospore membrane, and ectopic expression of SPO71 in vegetative cells results in mislocalization of Vps13. Finally, the two proteins can be coprecipitated from sporulating cells. We propose that Spo71 is a sporulation-specific partner for Vps13 and that they act in concert to regulate prospore membrane morphogenesis.

scholarly journals Improving 3-methylphenol (m-cresol) production in yeast via in vivo glycosylation or methylation

2020 ◽  
Vol 20 (8) ◽  
Author(s):  
Julia Hitschler ◽  
Eckhard Boles
Keyword(s):  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Wild Type ◽  
Biotechnological Production ◽  
Yeast Saccharomyces Cerevisiae ◽  
In Situ Extraction ◽  
Methylsalicylic Acid Synthase ◽  
In The Wild

ABSTRACT Heterologous expression of 6-methylsalicylic acid synthase (MSAS) together with 6-MSA decarboxylase enables de novo production of the platform chemical and antiseptic additive 3-methylphenol (3-MP) in the yeast Saccharomyces cerevisiae. However, toxicity of 3-MP prevents higher production levels. In this study, we evaluated in vivo detoxification strategies to overcome limitations of 3-MP production. An orcinol-O-methyltransferase from Chinese rose hybrids (OOMT2) was expressed in the 3-MP producing yeast strain to convert 3-MP to 3-methylanisole (3-MA). Together with in situ extraction by dodecane of the highly volatile 3-MA this resulted in up to 211 mg/L 3-MA (1.7 mM) accumulation. Expression of a UDP-glycosyltransferase (UGT72B27) from Vitis vinifera led to the synthesis of up to 533 mg/L 3-MP as glucoside (4.9 mM). Conversion of 3-MP to 3-MA and 3-MP glucoside was not complete. Finally, deletion of phosphoglucose isomerase PGI1 together with methylation or glycosylation and feeding a fructose/glucose mixture to redirect carbon fluxes resulted in strongly increased product titers, with up to 897 mg/L 3-MA/3-MP (9 mM) and 873 mg/L 3-MP/3-MP as glucoside (8.1 mM) compared to less than 313 mg/L (2.9 mM) product titers in the wild type controls. The results show that methylation or glycosylation are promising tools to overcome limitations in further enhancing the biotechnological production of 3-MP.

scholarly journals Expression of Mutated Paramecium Telomerase RNAs In Vivo Leads to Templating Errors That Resemble Those Made by Retroviral Reverse Transcriptase

1999 ◽  
Vol 19 (4) ◽  
pp. 2887-2894 ◽  
Author(s):  
Amanda J. Ye ◽  
W. John Haynes ◽  
Daniel P. Romero
Keyword(s):  
Reverse Transcriptase ◽  
De Novo ◽  
Telomerase Rna ◽  
Paramecium Tetraurelia ◽  
Wild Type ◽  
Telomeric Dna ◽  
Telomeric Repeats ◽  
Immunodeficiency Virus ◽  
In The Wild

ABSTRACT Telomeric DNA consists of short, tandemly repeated sequences at the ends of chromosomes. Telomeric DNA in the ciliate Paramecium tetraurelia is synthesized by an error-prone telomerase with an RNA template specific for GGGGTT repeats. We have previously shown that misincorporation of TTP residues at the telomerase RNA templating nucleotide C52 accounts for the 30% GGGTTT repeats randomly distributed in wild-type telomeres. To more completely characterize variable repeat synthesis in P. tetraurelia, telomerase RNA genes mutated at C52 (A, U, and G) were expressed in vivo. De novo telomeric repeats from transformants indicate that the predominant TTP misincorporation error seen in the wild-type telomerase is dependent on the presence of a C residue at template position 52. Paradoxically, the effects of various other telomerase RNA template and alignment region mutations on de novo telomeres include significant changes in fidelity, as well as the synthesis of aberrant, 5-nucleotide telomeric repeats. The occurrence of deletion errors and the altered fidelity of mutatedP. tetraurelia telomerase, in conjunction with misincorporation by the wild-type enzyme, suggest that the telomerase RNA template domain may be analogous to homopolymeric mutational hot spots that lead to similar errors by the human immunodeficiency virus proofreading-deficient reverse transcriptase.

scholarly journals Whole-Genome Expression Profiling Defines the HrpL Regulon of Pseudomonas syringae pv. tomato DC3000, Allows de novo Reconstruction of the Hrp cis Element, and Identifies Novel Coregulated Genes

2006 ◽  
Vol 19 (11) ◽  
pp. 1167-1179 ◽  
Author(s):  
Adriana O. Ferreira ◽  
Christopher R. Myers ◽  
Jeffrey S. Gordon ◽  
Gregory B. Martin ◽  
Monica Vencato ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
De Novo ◽  
Effector Proteins ◽  
Iterative Refinement ◽  
Host Cells ◽  
Whole Genome ◽  
Wild Type ◽  
Tomato Dc3000 ◽  
Type Iii ◽  
In The Wild

Pseudomonas syringae pv. tomato DC3000 is a model pathogen of tomato and Arabidopsis that uses a hypersensitive response and pathogenicity (Hrp) type III secretion system (T3SS) to deliver virulence effector proteins into host cells. Expression of the Hrp system and many effector genes is activated by the HrpL alternative sigma factor. Here, an open reading frame-specific whole-genome microarray was constructed for DC3000 and used to comprehensively identify genes that are differentially expressed in wild-type and ΔhrpL strains. Among the genes whose differential regulation was statistically significant, 119 were upregulated and 76 were downregulated in the wild-type compared with the ΔhrpL strain. Hierarchical clustering revealed a subset of eight genes that were upregulated particularly rapidly. Gibbs sampling of regions upstream of HrpL-activated op-erons revealed the Hrp promoter as the only identifiable regulatory motif and supported an iterative refinement involving real-time polymerase chain reaction testing of additional HrpL-activated genes and refinements in a hidden Markov model that can be used to predict Hrp promoters in P. syringae strains. This iterative bioinformatic-experimental approach to a comprehensive analysis of the HrpL regulon revealed a mix of genes controlled by HrpL, including those encoding most type III effectors, twin-arginine transport (TAT) substrates, other regulatory proteins, and proteins involved in the synthesis or metabolism of phyto-hormones, phytotoxins, and myo-inositol. This analysis provides an extensively verified, robust method for predicting Hrp promoters in P. syringae genomes, and it supports subsequent identification of effectors and other factors that likely are important to the host-specific virulence of P. syringae.

scholarly journals Error-Prone Polymerase, DNA Polymerase IV, Is Responsible for Transient Hypermutation during Adaptive Mutation in Escherichia coli

2003 ◽  
Vol 185 (11) ◽  
pp. 3469-3472 ◽  
Author(s):  
Joshua D. Tompkins ◽  
Jennifer L. Nelson ◽  
Jill C. Hazel ◽  
Stacy L. Leugers ◽  
Jeffrey D. Stumpf ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Polymerase ◽  
Type Strain ◽  
Wild Type Strain ◽  
Adaptive Mutation ◽  
Wild Type ◽  
Pol Iv ◽  
In The Wild ◽  
Dna Polymerase Iv

ABSTRACT The frequencies of nonselected mutations among adaptive Lac+ revertants of Escherichia coli strains with and without the error-prone DNA polymerase IV (Pol IV) were compared. This frequency was more than sevenfold lower in the Pol IV-defective strain than in the wild-type strain. Thus, the mutations that occur during hypermutation are due to Pol IV.

scholarly journals Fitness effects ofcis-regulatory variants in theSaccharomyces cerevisiae TDH3promoter

2017 ◽  
Author(s):  
Fabien Duveau ◽  
William Toubiana ◽  
Patricia J. Wittkopp
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Wild Type Allele ◽  
Wild Type ◽  
Fitness Effects ◽  
Regulatory Variants ◽  
Fitness Consequences ◽  
Regulatory Mutations ◽  
Affect Cell Growth

AbstractVariation in gene expression is widespread within and between species, but fitness consequences of this variation are generally unknown. Here we use mutations in theSaccharomyces cerevisiae TDH3promoter to assess how changes inTDH3expression affect cell growth. From these data, we predict the fitness consequences ofde novomutations and natural polymorphisms in theTDH3promoter. Nearly all mutations and polymorphisms in theTDH3promoter were found to have no significant effect on fitness in the environment assayed, suggesting that the wild type allele of this promoter is robust to the effects of most newcis-regulatory mutations.

scholarly journals OS10.5 Outcome of unresectable de novo IDH wild-type GBM: A decade analysis of factors influencing survival

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii21-iii21
Author(s):  
A Hamdan ◽  
K Homyer ◽  
G Swan ◽  
G Bankov ◽  
S Alfadhel ◽  
...  
Keyword(s):  
Multivariate Analysis ◽  
Adjuvant Treatment ◽  
De Novo ◽  
Performance Status ◽  
Univariate Analysis ◽  
Treatment Modalities ◽  
Poor Performance Status ◽  
Wild Type ◽  
Factors Associated ◽  
Good Performance Status

Abstract BACKGROUND Patients with unresectable GBM represent an understudied and underpowered disease subgroup for which limited outcome data exist to support treatment recommendations. In this study, we present a ten-year analysis on outcome of unresectable GBM patients at our unit. MATERIAL AND METHODS We collected data for all consecutive adult de novo IDH wild-type (IDHwt) GBM patients who had undergone biopsy at our unit (2009–18, N= 177) and analysed those that had complete data on performance status, radiology, MGMT status, and adjuvant treatment (N= 156). We used step-wise cox proportional hazards regression to analyse factors associated with survival and outcomes. RESULTS Of 156 patients, mean age was 60.8 years old (range 19–89, 34/21.8% >69 years old), 63 (40.4%) were females, and 50 (32.1%), 26 (16.7%) and 12 (7.7%) had multifocal, butterfly or both lesion types respectively. 101 (64.7%) patients had good performance status (ECOG 0–1), and 49 (31.4%) had methylated MGMT lesions. Adjuvant treatment modalities were best supportive care (41, 26.3%), RT only (33, 21.2%), TMZ only (20, 12.8%), RT and TMZ (10, 6.4%), concurrent TMZ/RT only (29, 18.6%) and concurrent TMZ/RT plus adjuvant TMZ [TMZ/RT+TMZ] (23, 14.7%). Median OS was 6.1 months (range 0–50.7), with 22% and 2% 1- and 2-year OS respectively. Patients who were MGMT methylated, had good performance status, and received TMZ/RT+TMZ had the highest survival (median OS 18.7 vs 5.5 months, P<0.0001). Multivariate analysis revealed factors associated with worse OS; these include male sex (HR 1.6, 95%CI 1.1–2.2), unmethylated MGMT (1.8, 1.3–2.8), poor performance status ie ECOG>1 (2.4, 1.6–3.3), not receiving TMZ/RT+TMZ (3.1, 1.8–5.1). In addition, univariate analysis initially revealed that older age (>69yrs) was significantly associated with poorer outcome, however in multivariate analysis, this effect was obliterated (HR 1.3, 95%CI 0.9–2.1). CONCLUSION In this study, we provide one of the largest series of unresectable IDHwt GBM outcome in the literature. Survival of patients harbouring unresectable IDHwt GBM can be unexpectedly long, and may even reach nearly twice that of the unselected, biopsy-only GBM patients receiving TMZ/RT+TMZ studied in the original Stupp trial (median OS of 9.4 months). For this subgroup of IDHwt GBM patients, advanced age may not necessarily predict poor outcome, once adjusted for other outcome predictors. Future randomised trials looking into unresectable IDHwt GBM should stratify patients according to the factors revealed above.

scholarly journals Candida albicans Uses Multiple Mechanisms To Acquire the Essential Metabolite Inositol during Infection

2008 ◽  
Vol 76 (6) ◽  
pp. 2793-2801 ◽  
Author(s):  
Ying-Lien Chen ◽  
Sarah Kauffman ◽  
Todd B. Reynolds
Keyword(s):  
Candida Albicans ◽  
Mouse Model ◽  
Double Mutant ◽  
De Novo ◽  
Systemic Infection ◽  
Bloodstream Infections ◽  
Wild Type Allele ◽  
Transporter Gene ◽  
Wild Type ◽  
Life Threatening

ABSTRACT Candida albicans is an important cause of life-threatening systemic bloodstream infections in immunocompromised patients. In order to cause infections, C. albicans must be able to synthesize the essential metabolite inositol or acquire it from the host. Based on the similarity of C. albicans to Saccharomyces cerevisiae, it was predicted that C. albicans may generate inositol de novo, import it from the environment, or both. The C. albicans inositol synthesis gene INO1 (orf19.7585) and inositol transporter gene ITR1 (orf19.3526) were each disrupted. The ino1Δ/ino1Δ mutant was an inositol auxotroph, and the itr1Δ/itr1Δ mutant was unable to import inositol from the medium. Each of these mutants was fully virulent in a mouse model of systemic infection. It was not possible to generate an ino1Δ/ino1Δ itr1Δ/itr1Δ double mutant, suggesting that in the absence of these two genes, C. albicans could not acquire inositol and was nonviable. A conditional double mutant was created by replacing the remaining wild-type allele of ITR1 in an ino1Δ/ino1Δ itr1Δ/ITR1 strain with a conditionally expressed allele of ITR1 driven by the repressible MET3 promoter. The resulting ino1Δ/ino1Δ itr1Δ/PMET3 ::ITR1 strain was found to be nonviable in medium containing methionine and cysteine (which represses the PMET3 promoter), and it was avirulent in the mouse model of systemic candidiasis. These results suggest a model in which C. albicans has two equally effective mechanisms for obtaining inositol while in the host. It can either generate inositol de novo through Ino1p, or it can import it from the host through Itr1p.

scholarly journals Metabolome and Transcriptome Association Analysis Reveals Regulation of Flavonoid Biosynthesis by Overexpression of LaMIR166a in Larix kaempferi (Lamb.) Carr

Forests ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1367
Author(s):  
Yanru Fan ◽  
Zhexin Li ◽  
Lifeng Zhang ◽  
Suying Han ◽  
Liwang Qi
Keyword(s):  
Cell Lines ◽  
Association Analysis ◽  
De Novo ◽  
Embryonic Cell ◽  
Flavonoid Biosynthesis ◽  
Larix Kaempferi ◽  
Wild Type ◽  
Transgenic Cell ◽  
In The Wild ◽  
Embryonic Cell Lines

Somatic embryogenesis is an ideal model process for studying early plant development. Embryonic cell lines of Larix kaempferi (Lamb.) Carr overexpressing LaMIR166a were obtained in our previous study. Here, a combination of de novo transcriptomics and extensively targeted metabolomics was used to study the transcriptional profiles and metabolic changes in wild-type and LaMIR166a-overexpressed embryonic cell lines. A total of 459 metabolites were found in the wild-type and transgenic cell lines. Compared to those in the wild-type cell lines, transcripts and metabolites were significantly altered in the LaMIR166a-overexpressed cell lines. Among differentially expressed genes (DEGs), phenylalanine and flavonoid synthesis genes were significantly enriched, and among differentially accumulated metabolites (DAMs), phenolic acids and flavonoids accumulated in particularly high amounts. Thus, the flavonoid biosynthetic pathway seems to be the most abundant pathway in response to LaMIR166a overexpression. Based on the Kyoto Encyclopedia of Genes and Genomes database, the association analysis of metabolome and transcriptome data showed that flavonoid biosynthesis and plant hormone signal transduction processes were significantly changed in miR166a-overexpression lines, suggesting that miR166 might be involved in these processes. The present study identified a number of potential metabolites associated with LaMIR166a overexpression, providing a significant foundation for a better understanding of the regulatory mechanisms underlying miR166.

scholarly journals Targeted transformation of Ascobolus immersus and de novo methylation of the resulting duplicated DNA sequences.

1989 ◽  
Vol 9 (7) ◽  
pp. 2818-2827 ◽  
Author(s):  
C Goyon ◽  
G Faugeron
Keyword(s):  
Dna Sequences ◽  
Cytosine Methylation ◽  
De Novo ◽  
Wild Type Allele ◽  
Wild Type ◽  
Single Stranded Dna ◽  
Type Allele ◽  
Double Stranded Dna ◽  
Ascobolus Immersus

To develop a method to modify genomic sequences in Ascobolus immersus by precisely reintroducing defined DNA segments previously manipulated in vitro, we investigated the effect of transforming DNA conformation on recombination with chromosomal sequences. Circular single-stranded DNA carrying the met2 gene and double-stranded DNA linearized by cutting within the met2 gene both transformed protoplasts of a met2 mutant strain of A. immersus to prototrophy. In contrast to the equivalent circular double-stranded DNA, which chiefly integrated at nonhomologous chromosomal sites, single-stranded and double-stranded cut DNAs recombined primarily with the homologous chromosomal met2 sequence. Of the single-stranded DNA transformants, 65% resulted from replacement of the resident met2 mutation by the exogenous wild-type allele. In 70% of the double-stranded-cut DNA transformants, one or more copies of the transforming DNA had integrated at the met2 locus, leading to tandem duplications of the met2 target region separated by plasmid DNA. These duplicated sequences could recombine, leading to progeny containing only one copy of the met2 region. This resulted in a precise gene replacement if the wild-type allele had been retained. In addition, we show that newly duplicated sequences were most often de novo methylated at the cytosine residues during the sexual phase. Cytosine methylation was associated with inactivation of the integrated met2 gene(s) in segregants of crosses. However, methylation was not accurately maintained at each DNA replication cycle, so that Met- segregants recovered a wild-type phenotype through successive mitotic divisions. This finding indicated that met2 genes were silenced by methylation alone.

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