scholarly journals Structure and function of Pif1 helicase

2017 ◽  
Vol 45 (5) ◽  
pp. 1159-1171 ◽  
Author(s):  
Alicia K. Byrd ◽  
Kevin D. Raney
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Replication Fork ◽  
Rdna Locus ◽  
Multiple Roles ◽  
Trna Genes ◽  
Helicase Domain ◽  
Biological Studies ◽  
Okazaki Fragment Processing ◽  
And Function ◽  
Pif1 Helicase

Pif1 family helicases have multiple roles in the maintenance of nuclear and mitochondrial DNA in eukaryotes. Saccharomyces cerevisiae Pif1 is involved in replication through barriers to replication, such as G-quadruplexes and protein blocks, and reduces genetic instability at these sites. Another Pif1 family helicase in S. cerevisiae, Rrm3, assists in fork progression through replication fork barriers at the rDNA locus and tRNA genes. ScPif1 (Saccharomyces cerevisiae Pif1) also negatively regulates telomerase, facilitates Okazaki fragment processing, and acts with polymerase δ in break-induced repair. Recent crystal structures of bacterial Pif1 helicases and the helicase domain of human PIF1 combined with several biochemical and biological studies on the activities of Pif1 helicases have increased our understanding of the function of these proteins. This review article focuses on these structures and the mechanism(s) proposed for Pif1's various activities on DNA.

scholarly journals Pif1-family helicases cooperate to suppress widespread replication fork arrest at tRNA genes

2016 ◽  
Author(s):  
Joseph S. Osmundson ◽  
Jayashree Kumar ◽  
Rani Yeung ◽  
Duncan J. Smith
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Damage ◽  
Dna Polymerase ◽  
Replication Fork ◽  
Trna Genes ◽  
Strand Displacement ◽  
Dna Polymerase Δ ◽  
Replication Fork Arrest ◽  
Nuclear Processes ◽  
Lagging Strand

ABSTRACTSaccharomyces cerevisiaeencodes two distinct Pif1-family helicases – Pif1 and Rrm3 – which have been reported to play distinct roles in numerous nuclear processes. Here, we systematically characterize the roles of Pif1 helicases in replisome progression and lagging-strand synthesis inS. cerevisiae. We demonstrate that either Pif1 or Rrm3 redundantly stimulate strand-displacement by DNA polymerase δ during lagging-strand synthesis. By analyzing replisome mobility inpif1andrrm3mutants, we show that Rrm3, with a partially redundant contribution from Pif1, suppresses widespread terminal arrest of the replisome at tRNA genes. Although both head-on and codirectional collisions induce replication fork arrest at tRNA genes, head-on collisions arrest a higher proportion of replisomes; consistent with this observation, we find that head-on collisions between tRNA transcription and replisome progression are under-represented in theS. cerevisiaegenome. Further, we demonstrate that tRNA-mediated arrest is R-loop independent, and propose that replisome arrest and DNA damage are mechanistically separable.

scholarly journals Determinants of Replication-Fork Pausing at tRNA Genes in Saccharomyces cerevisiae

Genetics ◽  
2020 ◽  
Vol 214 (4) ◽  
pp. 825-838
Author(s):  
Rani Yeung ◽  
Duncan J. Smith
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Repair ◽  
Transcription Factor ◽  
Rna Polymerase ◽  
Replication Fork ◽  
Rna Polymerase Iii ◽  
Trna Genes ◽  
Link Type ◽  
Replication Fork Progression ◽  
Polymerase Iii

Transfer RNA (tRNA) genes are widely studied sites of replication-fork pausing and genome instability in the budding yeast Saccharomyces cerevisiae. tRNAs are extremely highly transcribed and serve as constitutive condensin binding sites. tRNA transcription by RNA polymerase III has previously been identified as stimulating replication-fork pausing at tRNA genes, but the nature of the block to replication has not been incontrovertibly demonstrated. Here, we describe a systematic, genome-wide analysis of the contributions of candidates to replication-fork progression at tDNAs in yeast: transcription factor binding, transcription, topoisomerase activity, condensin-mediated clustering, and Rad18-dependent DNA repair. We show that an asymmetric block to replication is maintained even when tRNA transcription is abolished by depletion of one or more subunits of RNA polymerase III. By contrast, analogous depletion of the essential transcription factor TFIIIB removes the obstacle to replication. Therefore, our data suggest that the RNA polymerase III transcription complex itself represents an asymmetric obstacle to replication even in the absence of RNA synthesis. We additionally demonstrate that replication-fork progression past tRNA genes is unaffected by the global depletion of condensin from the nucleus, and can be stimulated by the removal of topoisomerases or Rad18-dependent DNA repair pathways.

Taxonomic characterization and identification of Saccharomyces cerevisiae D8 for brandy production from pineapple

2018 ◽  
Vol 39 (4) ◽  
pp. 474-482
Author(s):  
Hoang Thi Le Thuong ◽  
Nguyen Quang Hao ◽  
Tran Thi Thuy
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Low Ph ◽  
Yeast Strains ◽  
Biological Studies ◽  
Taxonomic Characterization

Eight yeast strains (denoted as D1 to D8) were isolated from samples of natural fermented pineapple. Strain D8 showed highest alcoholic production at low pH and special aroma of pineapple has been chosen for further study. Taxonomic characterization of strain D8 using morphological, biochemical and molecular biological studies confirmed that strain D8  belong to Saccharomycetaceae family, Saccharomycetales order and Saccharomyces cerevisiae species. Therefore, we named this strain as Saccharomyces cerevisiae D8 for further study on Brandy production from pineapple. Citation: Hoang Thi Le Thuong, Nguyen Quang Hao, Tran Thi Thuy, 2017. Taxonomic characterization and identification of Saccharomyces cerevisiae D8 for brandy production from pineapple. Tap chi Sinh hoc, 39(4): 474- 482. DOI: 10.15625/0866-7160/v39n4.10864.*Corresponding author: [email protected] Received 5 December 2016, accepted 12 August 2017

scholarly journals Distribution of a Limited Sir2 Protein Pool Regulates the Strength of Yeast rDNA Silencing and Is Modulated by Sir4p

Genetics ◽  
1998 ◽  
Vol 149 (3) ◽  
pp. 1205-1219 ◽  
Author(s):  
Jeffrey S Smith ◽  
Carrie Baker Brachmann ◽  
Lorraine Pillus ◽  
Jef D Boeke
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Simple Model ◽  
Regulatory Mechanism ◽  
Transcriptional Silencing ◽  
Rdna Locus ◽  
Genetic Manipulations ◽  
Protein Levels ◽  
Endogenous Level ◽  
Protein Pool ◽  
Negative Effect

Abstract Transcriptional silencing in Saccharomyces cerevisiae occurs at the silent mating-type loci HML and HMR, at telomeres, and at the ribosomal DNA (rDNA) locus RDN1. Silencing in the rDNA occurs by a novel mechanism that depends on a single Silent Information Regulator (SIR) gene, SIR2. SIR4, essential for other silenced loci, paradoxically inhibits rDNA silencing. In this study, we elucidate a regulatory mechanism for rDNA silencing based on the finding that rDNA silencing strength directly correlates with cellular Sir2 protein levels. The endogenous level of Sir2p was shown to be limiting for rDNA silencing. Furthermore, small changes in Sir2p levels altered rDNA silencing strength. In rDNA silencing phenotypes, sir2 mutations were shown to be epistatic to sir4 mutations, indicating that SIR4 inhibition of rDNA silencing is mediated through SIR2. Furthermore, rDNA silencing is insensitive to SIR3 overexpression, but is severely reduced by overexpression of full-length Sir4p or a fragment of Sir4p that interacts with Sir2p. This negative effect of SIR4 overexpression was overridden by co-overexpression of SIR2, suggesting that SIR4 directly inhibits the rDNA silencing function of SIR2. Finally, genetic manipulations of SIR4 previously shown to promote extended life span also resulted in enhanced rDNA silencing. We propose a simple model in which telomeres act as regulators of rDNA silencing by competing for limiting amounts of Sir2 protein.

scholarly journals Targeting Pin1 for Modulation of Cell Motility and Cancer Therapy

Biomedicines ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 359
Author(s):  
Hsiang-Hao Chuang ◽  
Yen-Yi Zhen ◽  
Yu-Chen Tsai ◽  
Cheng-Hao Chuang ◽  
Ming-Shyan Huang ◽  
...  
Keyword(s):  
Cancer Therapy ◽  
Tumor Suppressors ◽  
Protein Conformation ◽  
Genome Stability ◽  
Recent Progress ◽  
Multiple Roles ◽  
Cancer Development ◽  
Cancer Hallmarks ◽  
Underlying Mechanisms ◽  
And Function

Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) specifically binds and isomerizes the phosphorylated serine/threonine-proline (pSer/Thr-Pro) motif, which leads to changes in protein conformation and function. Pin1 is widely overexpressed in cancers and plays an important role in tumorigenesis. Mounting evidence has revealed that targeting Pin1 is a potential therapeutic approach for various cancers by inhibiting cell proliferation, reducing metastasis, and maintaining genome stability. In this review, we summarize the underlying mechanisms of Pin1-mediated upregulation of oncogenes and downregulation of tumor suppressors in cancer development. Furthermore, we also discuss the multiple roles of Pin1 in cancer hallmarks and examine Pin1 as a desirable pharmaceutical target for cancer therapy. We also summarize the recent progress of Pin1-targeted small-molecule compounds for anticancer activity.

scholarly journals The Schizosaccharomyces pombe cho1+ Gene Encodes a Phospholipid Methyltransferase

Genetics ◽  
1998 ◽  
Vol 150 (2) ◽  
pp. 553-562
Author(s):  
Margaret I Kanipes ◽  
John E Hill ◽  
Susan A Henry
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Sequence Analysis ◽  
Schizosaccharomyces Pombe ◽  
Gene Disruption ◽  
Structure And Function ◽  
Biosynthetic Enzyme ◽  
Gene Encoding ◽  
Complementation Groups ◽  
Eukaryotic Organisms ◽  
And Function

Abstract The isolation of mutants of Schizosaccharomyces pombe defective in the synthesis of phosphatidylcholine via the methylation of phosphatidylethanolamine is reported. These mutants are choline auxotrophs and fall into two unlinked complementation groups, cho1 and cho2. We also report the analysis of the cho1+ gene, the first structural gene encoding a phospholipid biosynthetic enzyme from S. pombe to be cloned and characterized. The cho1+ gene disruption mutant (cho1Δ) is viable if choline is supplied and resembles the cho1 mutants isolated after mutagenesis. Sequence analysis of the cho1+ gene indicates that it encodes a protein closely related to phospholipid methyltransferases from Saccharomyces cerevisiae and rat. Phospholipid methyltransferases encoded by a rat liver cDNA and the S. cerevisiae OPI3 gene are both able to complement the choline auxotrophy of the S. pombe cho1 mutants. These results suggest that both the structure and function of the phospholipid N-methyltransferases are broadly conserved among eukaryotic organisms.

scholarly journals Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo.

1986 ◽  
Vol 6 (7) ◽  
pp. 2663-2673 ◽  
Author(s):  
M C Strobel ◽  
J Abelson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Trna Gene ◽  
Nuclear Extract ◽  
Nonsense Suppression ◽  
Trna Genes ◽  
Suppressor Activity ◽  
Specific Sequence ◽  
Made In

The Saccharomyces cerevisiae leucine-inserting amber suppressor tRNA gene SUP53 (a tRNALeu3 allele) was used to investigate the relationship between precursor tRNA structure and mature tRNA function. This gene encodes a pre-tRNA which contains a 32-base intron. The mature tRNASUP53 contains a 5-methylcytosine modification of the anticodon wobble base. Mutations were made in the SUP53 intron. These mutant genes were transcribed in an S. cerevisiae nuclear extract preparation. In this extract, primary tRNA gene transcripts are end-processed and base modified after addition of cofactors. The base modifications made in vitro were examined, and the mutant pre-tRNAs were analyzed for their ability to serve as substrates for partially purified S. cerevisiae tRNA endonuclease and ligase. Finally, the suppressor function of these mutant tRNA genes was assayed after their integration into the S. cerevisiae genome. Mutant analysis showed that the totally intact precursor tRNA, rather than any specific sequence or structure of the intron, was necessary for efficient nonsense suppression by tRNASUP53. Less efficient suppressor activity correlated with the absence of the 5-methylcytosine modification. Most of the intron-altered precursor tRNAs were successfully spliced in vitro, indicating that modifications are not critical for recognition by the tRNA endonuclease and ligase.

Enzymatic Synthesis of Glycosphingolipids: A Review

Synthesis ◽  
2021 ◽  
Author(s):  
Qingjiang Li ◽  
Zhongwu Guo
Keyword(s):  
Signal Transduction ◽  
Enzymatic Synthesis ◽  
Biological Activities ◽  
Cell Interaction ◽  
Glycosidic Linkage ◽  
The Past ◽  
Biological Studies ◽  
Hydrophobic Lipid ◽  
Synthetic Methodologies ◽  
And Function

Glycosphingolipids (GSLs) are the major vertebrate glycolipids, which contain two distinctive moieties, a glycan and a ceramide, stitched together by a β-glycosidic linkage. The hydrophobic lipid chains of ceramide can insert into the cell membrane to form “lipid rafts” and anchor the hydrophilic glycan onto the cell surface to generate microdomains and function as signaling molecules. GSLs mediate signal transduction, cell interaction, and many other biological activities, and are also related to many diseases. To meet the need of biological studies, chemists have developed various synthetic methodologies to access GSLs. Among them, the application of enzymes to GSL synthesis has witnessed significant advancements in the past decades. This review summarizes briefly the history and progress of enzymatic GSL synthesis.

scholarly journals Saccharomyces cerevisiae Expresses Three Functionally Distinct Homologues of the Nramp Family of Metal Transporters

2000 ◽  
Vol 20 (21) ◽  
pp. 7893-7902 ◽  
Author(s):  
Matthew E. Portnoy ◽  
Xiu Fen Liu ◽  
Valeria Cizewski Culotta
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Yeast Cells ◽  
Manganese Ions ◽  
Iron Starvation ◽  
Metal Transporters ◽  
Cellular Accumulation ◽  
Metal Treatment ◽  
Intracellular Vesicles ◽  
And Function ◽  
Cellular Compartments

ABSTRACT The baker's yeast Saccharomyces cerevisiae expresses three homologues of the Nramp family of metal transporters: Smf1p, Smf2p, and Smf3p, encoded by SMF1, SMF2, andSMF3, respectively. Here we report a comparative analysis of the yeast Smf proteins at the levels of localization, regulation, and function of the corresponding metal transporters. Smf1p and Smf2p function in cellular accumulation of manganese, and the two proteins are coregulated by manganese ions and the BSD2 gene product. Under manganese-replete conditions, Bsd2p facilitates trafficking of Smf1p and Smf2p to the vacuole, where these transport proteins are degraded. However, Smf1p and Smf2p localize to distinct cellular compartments under metal starvation: Smf1p accumulates at the cell surface, while Smf2p is restricted to intracellular vesicles. The third Nramp homologue, Smf3p, is quite distinctive. Smf3p is not regulated by Bsd2p or by manganese ions and is not degraded in the vacuole. Instead, Smf3p is down-regulated by iron through a mechanism that does not involve transcription or protein stability. Smf3p localizes to the vacuolar membrane independently of metal treatment, and yeast cells lacking Smf3p show symptoms of iron starvation. We propose that Smf3p helps to mobilize vacuolar stores of iron.

scholarly journals The fate and function of glycosphingolipid glucosylceramide

2003 ◽  
Vol 358 (1433) ◽  
pp. 869-873 ◽  
Author(s):  
Gerrit van Meer ◽  
Jasja Wolthoorn ◽  
Sophie Degroote
Keyword(s):  
Cellular Differentiation ◽  
Membrane Lipids ◽  
Early Stage ◽  
Cellular Level ◽  
Mature Stage ◽  
Storage Diseases ◽  
Head Groups ◽  
Biological Studies ◽  
Intracellular Membrane Transport ◽  
And Function

In higher eukaryotes, glucosylceramide is the simplest member and precursor of a fascinating class of membrane lipids, the glycosphingolipids. These lipids display an astounding variation in their carbohydrate head groups, suggesting that glycosphingolipids serve specialized functions in recognition processes. It is now realized that they are organized in signalling domains on the cell surface. They are of vital importance as, in their absence, embryonal development is inhibited at an early stage. Remarkably, individual cells can live without glycolipids, perhaps because their survival does not depend on glycosphingolipid–mediated signalling mechanisms. Still, these cells suffer from defects in intracellular membrane transport. Various membrane proteins do not reach their intracellular destination, and, indeed, some intracellular organelles do not properly differentiate to their mature stage. The fact that glycosphingolipids are required for cellular differentiation suggests that there are human diseases resulting from defects in glycosphingolipid synthesis. In addition, the same cellular differentiation processes may be affected by defects in the degradation of glycosphingolipids. At the cellular level, the pathology of glycosphingolipid storage diseases is not completely understood. Cell biological studies on the intracellular fate and function of glycosphingolipids may open new ways to understand and defeat not only lipid storage diseases, but perhaps other diseases that have not been connected to glycosphingolipids so far.

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