scholarly journals Human to yeast pathway transplantation: cross-species dissection of the adenine de novo pathway regulatory node

2017 ◽  
Author(s):  
Neta Agmon ◽  
Jasmine Temple ◽  
Zuojian Tang ◽  
Tobias Schraink ◽  
Maayan Baron ◽  
...  
Keyword(s):  
Yeast Strain ◽  
Transcriptional Control ◽  
De Novo ◽  
Enzyme Level ◽  
Yeast Cells ◽  
Protein Coding ◽  
Coding Regions ◽  
Human Proteins ◽  
Human Ortholog ◽  
Yeast Genes

AbstractPathway transplantation from one organism to another represents a means to a more complete understanding of a biochemical or regulatory process. The purine biosynthesis pathway, a core metabolic function, was transplanted from human to yeast. We replaced the entireSaccharomyces cerevisiaeadenine de novo pathway with the cognate human pathway components. A yeast strain was “humanized” for the full pathway by deleting all relevant yeast genes completely and then providing the human pathway in trans using a neochromosome expressing the human protein coding regions under the transcriptional control of their cognate yeast promoters and terminators. The “humanized” yeast strain grows in the absence of adenine, indicating complementation of the yeast pathway by the full set of human proteins. While the strain with the neochromosome is indeed prototrophic, it grows slowly in the absence of adenine. Dissection of the phenotype revealed that the human ortholog ofADE4, PPAT, shows only partial complementation. We have used several strategies to understand this phenotype, that point toPPAT/ADE4as the central regulatory node. Pathway metabolites are responsible for regulatingPPAT’sprotein abundance through transcription and proteolysis as well as its enzymatic activity by allosteric regulation in these yeast cells. Extensive phylogenetic analysis of PPATs from diverse organisms hints at adaptations of the enzyme-level regulation to the metabolite levels in the organism. Finally, we isolated specific mutations in PPAT as well as in other genes involved in the purine metabolic network that alleviate incomplete complementation byPPATand provide further insight into the complex regulation of this critical metabolic pathway.

scholarly journals Dysregulated Transcriptional Control in Prostate Cancer

2019 ◽  
Vol 20 (12) ◽  
pp. 2883 ◽  
Author(s):  
Simon J. Baumgart ◽  
Ekaterina Nevedomskaya ◽  
Bernard Haendler
Keyword(s):  
Prostate Cancer ◽  
Drug Targets ◽  
Transcriptional Control ◽  
Regulatory Elements ◽  
Protein Coding ◽  
Coding Regions ◽  
Super Enhancer ◽  
Position Coding ◽  
Transcription Dysregulation ◽  
Dna Regulatory Elements

Recent advances in whole-genome and transcriptome sequencing of prostate cancer at different stages indicate that a large number of mutations found in tumors are present in non-protein coding regions of the genome and lead to dysregulated gene expression. Single nucleotide variations and small mutations affecting the recruitment of transcription factor complexes to DNA regulatory elements are observed in an increasing number of cases. Genomic rearrangements may position coding regions under the novel control of regulatory elements, as exemplified by the TMPRSS2-ERG fusion and the amplified enhancer identified upstream of the androgen receptor (AR) gene. Super-enhancers are increasingly found to play important roles in aberrant oncogenic transcription. Several players involved in these processes are currently being evaluated as drug targets and may represent new vulnerabilities that can be exploited for prostate cancer treatment. They include factors involved in enhancer and super-enhancer function such as bromodomain proteins and cyclin-dependent kinases. In addition, non-coding RNAs with an important gene regulatory role are being explored. The rapid progress made in understanding the influence of the non-coding part of the genome and of transcription dysregulation in prostate cancer could pave the way for the identification of novel treatment paradigms for the benefit of patients.

scholarly journals Pandoravirus celtis illustrates the microevolution processes at work in the giant Pandoraviridae genomes

2018 ◽  
Author(s):  
Matthieu Legendre ◽  
Jean-Marie Alempic ◽  
Nadège Philippe ◽  
Audrey Lartigue ◽  
Sandra Jeudy ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Repertoire ◽  
Protein Coding ◽  
Genomic Changes ◽  
Coding Regions ◽  
Protein Coding Genes ◽  
Intergenic Regions ◽  
Mere Existence ◽  
Increasing Functions ◽  
Similar Gene

AbstractWith genomes of up to 2.7 Mb propagated in µm-long oblong particles and initially predicted to encode more than 2000 proteins, members of the Pandoraviridae family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution. A previous analysis of six newly available isolates, independently confirmed by a study including 3 others, established that the Pandoraviridae pan-genome is open, meaning that each new strain exhibits protein-coding genes not previously identified in other family members. With an average increment of about 60 proteins, the gene repertoire shows no sign of reaching a limit and remains largely coding for proteins without recognizable homologs in other viruses or cells (ORFans). To explain these results, we proposed that most new protein-coding genes were created de novo, from pre-existing non-coding regions of the G+C rich pandoravirus genomes. The comparison of the gene content of a new isolate, P. celtis, closely related (96% identical genome) to the previously described P. quercus is now used to test this hypothesis by studying genomic changes in a microevolution range. Our results confirm that the differences between these two similar gene contents mostly consist of protein-coding genes without known homologs (ORFans), with statistical signatures close to that of intergenic regions. These newborn proteins are under slight negative selection, perhaps to maintain stable folds and prevent protein aggregation pending the eventual emergence of fitness-increasing functions. Our study also unraveled several insertion events mediated by a transposase of the hAT family, 3 copies of which are found in P. celtis and are presumably active. Members of the Pandoraviridae are presently the first viruses known to encode this type of transposase.

scholarly journals Coenzyme Q10 deficiencies: pathways in yeast and humans

2018 ◽  
Vol 62 (3) ◽  
pp. 361-376 ◽  
Author(s):  
Agape M. Awad ◽  
Michelle C. Bradley ◽  
Lucía Fernández-del-Río ◽  
Anish Nag ◽  
Hui S. Tsui ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
De Novo ◽  
Human Gene ◽  
Coenzyme Q ◽  
Human Cells ◽  
Yeast Cells ◽  
Gene Products ◽  
Functional Conservation ◽  
Hydrophobic Lipid ◽  
Yeast Genes

Coenzyme Q (ubiquinone or CoQ) is an essential lipid that plays a role in mitochondrial respiratory electron transport and serves as an important antioxidant. In human and yeast cells, CoQ synthesis derives from aromatic ring precursors and the isoprene biosynthetic pathway. Saccharomyces cerevisiae coq mutants provide a powerful model for our understanding of CoQ biosynthesis. This review focusses on the biosynthesis of CoQ in yeast and the relevance of this model to CoQ biosynthesis in human cells. The COQ1–COQ11 yeast genes are required for efficient biosynthesis of yeast CoQ. Expression of human homologs of yeast COQ1–COQ10 genes restore CoQ biosynthesis in the corresponding yeast coq mutants, indicating profound functional conservation. Thus, yeast provides a simple yet effective model to investigate and define the function and possible pathology of human COQ (yeast or human gene involved in CoQ biosynthesis) gene polymorphisms and mutations. Biosynthesis of CoQ in yeast and human cells depends on high molecular mass multisubunit complexes consisting of several of the COQ gene products, as well as CoQ itself and CoQ intermediates. The CoQ synthome in yeast or Complex Q in human cells, is essential for de novo biosynthesis of CoQ. Although some human CoQ deficiencies respond to dietary supplementation with CoQ, in general the uptake and assimilation of this very hydrophobic lipid is inefficient. Simple natural products may serve as alternate ring precursors in CoQ biosynthesis in both yeast and human cells, and these compounds may act to enhance biosynthesis of CoQ or may bypass certain deficient steps in the CoQ biosynthetic pathway.

scholarly journals De novo, systemic, deleterious amino acid substitutions are common in large cytoskeleton-related protein coding regions

2016 ◽  
Vol 6 (2) ◽  
pp. 211-216
Author(s):  
Rebecca J. Stoll ◽  
Grace R. Thompson ◽  
Mohammad D. Samy ◽  
George Blanck
Keyword(s):  
Amino Acid ◽  
De Novo ◽  
Amino Acid Substitutions ◽  
Related Protein ◽  
Protein Coding ◽  
Coding Regions

scholarly journals Identification of novel CSNK2A1 variants and the genotype–phenotype relationship in patients with Okur–Chung neurodevelopmental syndrome: a case report and systematic literature review

2021 ◽  
Vol 49 (5) ◽  
pp. 030006052110170
Author(s):  
Ruo-hao Wu ◽  
Wen-ting Tang ◽  
Kun-yin Qiu ◽  
Xiao-juan Li ◽  
Dan-xia Tang ◽  
...  
Keyword(s):  
De Novo ◽  
Facial Dysmorphism ◽  
Comprehensive Overview ◽  
Protein Coding ◽  
Coding Regions ◽  
Gtp Binding ◽  
Phenotypic Spectrum ◽  
Whole Exome ◽  
First Time ◽  
Binding Loop

De novo germline variants of the casein kinase 2α subunit (CK2α) gene ( CSNK2A1) have been reported in individuals with the congenital neuropsychiatric disorder Okur–Chung neurodevelopmental syndrome (OCNS). Here, we report on two unrelated children with OCNS and review the literature to explore the genotype–phenotype relationship in OCNS. Both children showed facial dysmorphism, growth retardation, and neuropsychiatric disorders. Using whole-exome sequencing, we identified two novel de novo CSNK2A1 variants: c.479A>G p.(H160R) and c.238C>T p.(R80C). A search of the literature identified 12 studies that provided information on 35 CSNK2A1 variants in various protein-coding regions of CK2α. By quantitatively analyzing data related to these CSNK2A1 variants and their corresponding phenotypes, we showed for the first time that mutations in protein-coding CK2α regions appear to influence the phenotypic spectrum of OCNS. Mutations altering the ATP/GTP-binding loop were more likely to cause the widest range of phenotypes. Therefore, any assessment of clinical spectra for this disorder should be extremely thorough. This study not only expands the mutational spectrum of OCNS, but also provides a comprehensive overview to improve our understanding of the genotype–phenotype relationship in OCNS.

scholarly journals Extreme purifying selection against point mutations in the human genome

2021 ◽  
Author(s):  
Noah Dukler ◽  
Mehreen R Mughal ◽  
Ritika Ramani ◽  
Yi-Fei Huang ◽  
Adam Siepel
Keyword(s):  
Human Genome ◽  
De Novo ◽  
Point Mutations ◽  
Purifying Selection ◽  
Selection Coefficient ◽  
Sequencing Data ◽  
Protein Coding ◽  
Coding Regions ◽  
Protein Coding Genes ◽  
Selective Effects

Genome sequencing of tens of thousands of human individuals has recently enabled the measurement of large selective effects for mutations to protein-coding genes. Here we describe a new method, called ExtRaINSIGHT, for measuring similar selective effects at individual sites in noncoding as well as in coding regions of the human genome. ExtRaINSIGHT estimates the prevalance of strong purifying selection, or "ultraselection" (λs), as the fractional depletion of rare single-nucleotide variants (minor allele frequency <0.1%) in a target set of genomic sites relative to matched sites that are putatively neutrally evolving, in a manner that controls for local variation and neighbor-dependence in mutation rate. We show using simulations that, above an appropriate threshold, λs is closely related to the average site-specific selection coefficient against heterozygous point mutations, as predicted at mutation-selection balance. Applying ExtRaINSIGHT to 71,702 whole genome sequences from gnomAD v3, we find particularly strong evidence of ultraselection in evolutionarily ancient miRNAs and neuronal protein-coding genes, as well as at splice sites. Moreover, our estimated selection coefficient against heterozygous amino-acid replacements across the genome (at 1.4%) is substantially larger than previous estimates based on smaller sample sizes. By contrast, we find weak evidence of ultraselection in other noncoding RNAs and transcription factor binding sites, and only modest evidence in ultraconserved elements and human accelerated regions. We estimate that ~0.3-0.5% of the human genome is ultraselected, with one third to one half of ultraselected sites falling in coding regions. These estimates suggest ~0.3-0.4 lethal or nearly lethal de novo mutations per potential human zygote, together with ~2 de novo mutations that are more weakly deleterious. Overall, our study sheds new light on the genome-wide distribution of fitness effects for new point mutations by combining deep new sequencing data sets and classical theory from population genetics.

scholarly journals NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome

2010 ◽  
Vol 2010 ◽  
pp. 1-10 ◽  
Author(s):  
Jan-Hendrik Teune ◽  
Gerhard Steger
Keyword(s):  
Noncoding Rna ◽  
De Novo ◽  
Plant Genome ◽  
Messenger Rnas ◽  
Protein Coding ◽  
Rna Molecules ◽  
Coding Regions ◽  
Mirna Genes ◽  
Genomic Scale ◽  
Eukaryotic Genomes

MicroRNAs (miRNA) are small regulatory, noncoding RNA molecules that are transcribed as primary miRNAs (pri-miRNA) from eukaryotic genomes. At least in plants, their regulatory activity is mediated through base-pairing with protein-coding messenger RNAs (mRNA) followed by mRNA degradation or translation repression. We describeNOVOMIR, a program for the identification of miRNA genes in plant genomes. It uses a series of filter steps and a statistical model to discriminate a pre-miRNA from other RNAs and does rely neither on prior knowledge of a miRNA target nor on comparative genomics. The sensitivity and specificity ofNOVOMIR for detection of premiRNAs fromArabidopsis thalianais ~0.83 and ~0.99, respectively. Plant pre-miRNAs are more heterogeneous with respect to size and structure than animal pre-miRNAs. Despite these difficulties,NOVOMIR is well suited to perform searches for pre-miRNAs on a genomic scale.NOVOMIR is written in Perl and relies on two additional, free programs for prediction of RNA secondary structure (RNALFOLD, RNASHAPES).

scholarly journals The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): comparative analysis with related Mimosoid species

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ueric José Borges de Souza ◽  
Rhewter Nunes ◽  
Cíntia Pelegrineti Targueta ◽  
José Alexandre Felizola Diniz-Filho ◽  
Mariana Pires de Campos Telles
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Reconstruction ◽  
Single Copy ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Coding Regions ◽  
Phylogenetic Studies ◽  
Rna Genes ◽  
Small Single Copy

Abstract Stryphnodendron adstringens is a medicinal plant belonging to the Leguminosae family, and it is commonly found in the southeastern savannas, endemic to the Cerrado biome. The goal of this study was to assemble and annotate the chloroplast genome of S. adstringens and to compare it with previously known genomes of the mimosoid clade within Leguminosae. The chloroplast genome was reconstructed using de novo and referenced-based assembly of paired-end reads generated by shotgun sequencing of total genomic DNA. The size of the S. adstringens chloroplast genome was 162,169 bp. This genome included a large single-copy (LSC) region of 91,045 bp, a small single-copy (SSC) region of 19,014 bp and a pair of inverted repeats (IRa and IRb) of 26,055 bp each. The S. adstringens chloroplast genome contains a total of 111 functional genes, including 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. A total of 137 SSRs and 42 repeat structures were identified in S. adstringens chloroplast genome, with the highest proportion in the LSC region. A comparison of the S. adstringens chloroplast genome with those from other mimosoid species indicated that gene content and synteny are highly conserved in the clade. The phylogenetic reconstruction using 73 conserved coding-protein genes from 19 Leguminosae species was supported to be paraphyletic. Furthermore, the noncoding and coding regions with high nucleotide diversity may supply valuable markers for molecular evolutionary and phylogenetic studies at different taxonomic levels in this group.

scholarly journals Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme.

1997 ◽  
Vol 17 (3) ◽  
pp. 1160-1169 ◽  
Author(s):  
X Shi ◽  
M Chang ◽  
A J Wolf ◽  
C H Chang ◽  
A A Frazer-Abel ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Nuclear Protein ◽  
Elongation Factor ◽  
Yeast Cells ◽  
Temperature Sensitive ◽  
Protein Coding ◽  
Initiation Factors ◽  
Yeast Genes

The products of the yeast CDC73 and PAF1 genes were originally identified as RNA polymerase II-associated proteins. Paf1p is a nuclear protein important for cell growth and transcriptional regulation of a subset of yeast genes. In this study we demonstrate that the product of CDC73 is a nuclear protein that interacts directly with purified RNA polymerase II in vitro. Deletion of CDC73 confers a temperature-sensitive phenotype. Combination of the cdc73 mutation with the more severe paf1 mutation does not result in an enhanced phenotype, indicating that the two proteins may function in the same cellular processes. To determine the relationship between Cdc73p and Paf1p and the recently described holoenzyme form of RNA polymerase II, we created yeast strains containing glutathione S-transferase (GST)-tagged forms of CDC73, PAF1, and TFG2 functionally replacing the chromosomal copies of the genes. Isolation of GST-tagged Cdc73p and Paf1p complexes has revealed a unique form of RNA polymerase II that contains both Cdc73p and Paf1p but lacks the Srbps found in the holoenzyme. The Cdc73p-Paf1p-RNA polymerase II-containing complex also includes Gal11p, and the general initiation factors TFIIB and TFIIF, but lacks TBP, TFIIH, and transcription elongation factor TFIIS as well as the Srbps. The Srbp-containing holoenzyme does not include either Paf1p or Cdc73p, demonstrating that these two forms of RNA polymerase II are distinct. In confirmation of the hypothesis that the two forms coexist in yeast cells, we found that a TFIIF-containing complex isolated via the GST-tagged Tfg2p construct contains both (i) the Srbps and (ii) Cdc73p and Paf1p. The Srbps and Cdc73p-Paf1p therefore appear to define two complexes with partially redundant, essential functions in the yeast cell. Using the technique of differential display, we have identified several genes whose transcripts require Cdc73p and/or Paf1p for normal levels of expression. Our analysis suggests that there are multiple RNA polymerase II-containing complexes involved in the expression of different classes of protein-coding genes.

scholarly journals Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data

2018 ◽  
Author(s):  
Xiaomeng Tian ◽  
Ran Li ◽  
Weiwei Fu ◽  
Yan Li ◽  
Xihong Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
De Novo ◽  
3D Structure ◽  
Regulatory Elements ◽  
Protein Coding ◽  
Web Based ◽  
Coding Regions ◽  
Pan Genome ◽  
Enhanced Resolution ◽  
Genome Assemblies

AbstractPigs (Sus scrofa) exhibit diverse phenotypes in different breeds shaped by the combined effects of various local adaptation and artificial selection. To comprehensively characterize the genetic diversity of pigs, we construct a pig pan-genome by comparing genome assemblies of 11 representative pig breeds with the reference genome (Sscrofa11.1). Approximately 72.5 Mb non-redundant sequences were identified as pan-sequences which were absent from the Sscrofa11.1. On average, 41.7 kb of spurious heterozygous SNPs per individual are removed and 12.9 kb novel SNPs per individual are recovered using pan-genome as the reference for SNP calling, thereby providing enhanced resolution for genetic diversity in pigs. Homolog annotation and analysis using RNA-seq and Hi-C data indicate that these pan-sequences contain protein-coding regions and regulatory elements. These pan-sequences can further improve the interpretation of local 3D structure. The pan-genome as well as the accompanied web-based database will serve as a primary resource for exploration of genetic diversity and promote pig breeding and biomedical research.

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