scholarly journals Microhomology Selection for Microhomology Mediated End Joining in Saccharomyces cerevisiae

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 284 ◽  
Author(s):  
Kihoon Lee ◽  
Jae-Hoon Ji ◽  
Kihoon Yoon ◽  
Jun Che ◽  
Ja-Hwan Seol ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Budding Yeast ◽  
Product Formation ◽  
Dna Breaks ◽  
End Joining ◽  
Base Pairs ◽  
Circular Chromosome ◽  
Proximal Side ◽  
Selection For ◽  
Insight Into

Microhomology-mediated end joining (MMEJ) anneals short, imperfect microhomologies flanking DNA breaks, producing repair products with deletions in a Ku- and RAD52-independent fashion. Puzzlingly, MMEJ preferentially selects certain microhomologies over others, even when multiple microhomologies are available. To define rules and parameters for microhomology selection, we altered the length, the position, and the level of mismatches to the microhomologies flanking homothallic switching (HO) endonuclease-induced breaks and assessed their effect on MMEJ frequency and the types of repair product formation. We found that microhomology of eight to 20 base pairs carrying no more than 20% mismatches efficiently induced MMEJ. Deletion of MSH6 did not impact MMEJ frequency. MMEJ preferentially chose a microhomology pair that was more proximal from the break. Interestingly, MMEJ events preferentially retained the centromere proximal side of the HO break, while the sequences proximal to the telomere were frequently deleted. The asymmetry in the deletional profile among MMEJ products was reduced when HO was induced on the circular chromosome. The results provide insight into how cells search and select microhomologies for MMEJ in budding yeast.

scholarly journals A New Saccharomyces cerevisiae Strain with a Mutant Smt3-Deconjugating Ulp1 Protein Is Affected in DNA Replication and Requires Srs2 and Homologous Recombination for Its Viability

2004 ◽  
Vol 24 (12) ◽  
pp. 5130-5143 ◽  
Author(s):  
Christine Soustelle ◽  
Laurence Vernis ◽  
Karine Fréon ◽  
Anne Reynaud-Angelin ◽  
Roland Chanet ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Homologous Recombination ◽  
Nonhomologous End Joining ◽  
End Joining ◽  
Recombination Mechanism ◽  
Growth Defects ◽  
Protein Conjugates ◽  
Synthetically Lethal ◽  
Mutant Cells ◽  
Insight Into

ABSTRACT The Saccharomyces cerevisiae Srs2 protein is involved in DNA repair and recombination. In order to gain better insight into the roles of Srs2, we performed a screen to identify mutations that are synthetically lethal with an srs2 deletion. One of them is a mutated allele of the ULP1 gene that encodes a protease specifically cleaving Smt3-protein conjugates. This allele, ulp1-I615N, is responsible for an accumulation of Smt3-conjugated proteins. The mutant is unable to grow at 37°C. At permissive temperatures, it still shows severe growth defects together with a strong hyperrecombination phenotype and is impaired in meiosis. Genetic interactions between ulp1 and mutations that affect different repair pathways indicated that the RAD51-dependent homologous recombination mechanism, but not excision resynthesis, translesion synthesis, or nonhomologous end-joining processes, is required for the viability of the mutant. Thus, both Srs2, believed to negatively control homologous recombination, and the process of recombination per se are essential for the viability of the ulp1 mutant. Upon replication, mutant cells accumulate single-stranded DNA interruptions. These structures are believed to generate different recombination intermediates. Some of them are fixed by recombination, and others require Srs2 to be reversed and fixed by an alternate pathway.

scholarly journals Filamentous growth of the budding yeast Saccharomyces cerevisiae induced by overexpression of the WHI2 gene

Microbiology ◽  
1997 ◽  
Vol 143 (6) ◽  
pp. 1867-1876 ◽  
Author(s):  
P. A. Radcliffe ◽  
K. M. Binley ◽  
J. Trevethick ◽  
M. Hall ◽  
P. E. Sudbery
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Budding Yeast ◽  
Filamentous Growth ◽  
Yeast Saccharomyces Cerevisiae

Communities ready for takeoff

2017 ◽  
Vol 36 (1) ◽  
pp. 14-26 ◽  
Author(s):  
Sanne A. M. Rijkhoff ◽  
Season A. Hoard ◽  
Michael J. Gaffney ◽  
Paul M. Smith
Keyword(s):  
Site Selection ◽  
Science Literature ◽  
Location Selection ◽  
Community Assets ◽  
Selection Decisions ◽  
The Social ◽  
Selection For ◽  
Insight Into ◽  
New Infrastructure ◽  
Take All

Although much of the social science literature supports the importance of community assets for success in many policy areas, these assets are often overlooked when selecting communities for new infrastructure facilities. Extensive collaboration is crucial for the success of environmental and economic projects, yet it often is not adequately addressed when making siting decisions for new projects. This article develops a social asset framework that includes social, creative, and human capital to inform site-selection decisions. This framework is applied to the Northwest Advanced Renewables Alliance project to assess community suitability for biofuel-related developments. This framework is the first to take all necessary community assets into account, providing insight into successful site selection beyond current models. The framework not only serves as a model for future biorefinery projects but also guides tasks that depend on informed location selection for success.

scholarly journals Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
So-Ra Han ◽  
Byeollee Kim ◽  
Jong Hwa Jang ◽  
Hyun Park ◽  
Tae-Jin Oh
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cold Adaptation ◽  
Gc Content ◽  
Glycogen Metabolism ◽  
Extreme Environment ◽  
Circular Chromosome ◽  
Cold Regions ◽  
Insight Into

Abstract Background The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. Results Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. Conclusions We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

scholarly journals Competition Between Adjacent Meiotic Recombination Hotspots in the Yeast Saccharomyces cerevisiae

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 661-670 ◽  
Author(s):  
Qing-Qing Fan ◽  
Fei Xu ◽  
Michael A White ◽  
Thomas D Petes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Meiotic Recombination ◽  
Telomeric Sequence ◽  
Coding Region ◽  
Dna Breaks ◽  
Local Formation ◽  
Yeast Saccharomyces Cerevisiae ◽  
Recombination Hotspots ◽  
Double Strand Dna Breaks ◽  
His4 Gene

In a wild-type strain of Saccharomyces cerevisiae, a hotspot for meiotic recombination is located upstream of the HIS4 gene. An insertion of a 49-bp telomeric sequence into the coding region of HIS4 strongly stimulates meiotic recombination and the local formation of meiosis-specific double-strand DNA breaks (DSBs). When strains are constructed in which both hotspots are heterozygous, hotspot activity is substantially less when the hotspots are on the same chromosome than when they are on opposite chromosomes.

A Requirement for Recombinational Repair in Saccharomyces cerevisiae Is Caused by DNA Replication Defects of mec1 Mutants

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 595-605 ◽  
Author(s):  
Bradley J Merrill ◽  
Connie Holm
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Dna Synthesis ◽  
Synthetic Lethality ◽  
Velocity Sedimentation ◽  
Recombinational Repair ◽  
Repair Pathway ◽  
Dna Breaks ◽  
Single Stranded Dna ◽  
Double Stranded Dna

Abstract To examine the role of the RAD52 recombinational repair pathway in compensating for DNA replication defects in Saccharomyces cerevisiae, we performed a genetic screen to identify mutants that require Rad52p for viability. We isolated 10 mec1 mutations that display synthetic lethality with rad52. These mutations (designated mec1-srf for synthetic lethality with rad-fifty-two) simultaneously cause two types of phenotypes: defects in the checkpoint function of Mec1p and defects in the essential function of Mec1p. Velocity sedimentation in alkaline sucrose gradients revealed that mec1-srf mutants accumulate small single-stranded DNA synthesis intermediates, suggesting that Mec1p is required for the normal progression of DNA synthesis. sml1 suppressor mutations suppress both the accumulation of DNA synthesis intermediates and the requirement for Rad52p in mec1-srf mutants, but they do not suppress the checkpoint defect in mec1-srf mutants. Thus, it appears to be the DNA replication defects in mec1-srf mutants that cause the requirement for Rad52p. By using hydroxyurea to introduce similar DNA replication defects, we found that single-stranded DNA breaks frequently lead to double-stranded DNA breaks that are not rapidly repaired in rad52 mutants. Taken together, these data suggest that the RAD52 recombinational repair pathway is required to prevent or repair double-stranded DNA breaks caused by defective DNA replication in mec1-srf mutants.

Incentives for Using LEIM in the Investigation of Corrosion Initiation on Organic Coated Alloys

2001 ◽  
Vol 699 ◽  
Author(s):  
S. R. Taylor ◽  
A.M. Mierisch
Keyword(s):  
Electrochemical Impedance ◽  
Numerical Models ◽  
Physical Phenomenon ◽  
Product Formation ◽  
Coated Metal ◽  
Aqueous Environments ◽  
Damage Process ◽  
Experimental Process ◽  
Measurement Artifact ◽  
Insight Into

AbstractLocal electrochemical impedance mapping and spectroscopy (LEIM/S) have become important tools for the investigation of local electrochemical breakdown events associated with the degradation of organically coated metals in aqueous environments. LEIM/S of organic coated metal substrates has revealed local degradation events that are distributed spatially and temporally. These observations provide support to a number of long-standing theories, as well as provide new insight into the damage process. The local changes in impedance observed at early stages of immersion support the presence of virtual pores, while the metastability of impedance peaks representing the local changes provide evidence of healing via corrosion product formation. Each of these are long-standing theories used to explain global electrochemical impedance measurements. This paper will provide an overview of some of the events observed using LEIM and examine these results in the context of recent analytical and numerical models. Models used to predict the electric field above an equipotential disk electrode support the interpretation of most experimental LEI data as being representative of chemical and physical phenomenon and not a result of measurement artifact. However, certain features may be an artifact of the finite nature of the experimental process. The interpretation of LEIM events in view of current experimental and modeling results will be discussed.

scholarly journals DNA damage and heat shock dually regulate genes in Saccharomyces cerevisiae.

1986 ◽  
Vol 6 (1) ◽  
pp. 90-96 ◽  
Author(s):  
T McClanahan ◽  
K McEntee
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Damage ◽  
Heat Shock ◽  
Shock Treatment ◽  
Northern Hybridization ◽  
Heat Shock Treatment ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Hsp70 Family ◽  
Transcriptional Start Sites

Two Saccharomyces cerevisiae genes isolated in a differential hybridization screening for DNA damage regulation (DDR genes) were also transcriptionally regulated by heat shock treatment. A 0.45-kilobase transcript homologous to the DDRA2 gene and a 1.25-kilobase transcript homologous to the DDR48 gene accumulated after exposure of cells to 4-nitroquinoline-1-oxide (NQO; 1 to 1.5 microgram/ml) or brief heat shock (20 min at 37 degrees C). The DDRA2 transcript, which was undetectable in untreated cells, was induced to high levels by these treatments, and the DDR48 transcript increased more than 10-fold as demonstrated by Northern hybridization analysis. Two findings argue that dual regulation of stress-responsive genes is not common in S. cerevisiae. First, two members of the heat shock-inducible hsp70 family of S. cerevisiae, YG100 and YG102, were not induced by exposure to NQO. Second, at least one other DNA-damage-inducible gene, DIN1, was not regulated by heat shock treatment. We examined the structure of the induced RNA homologous to DDRA2 after heat shock and NQO treatments by S1 nuclease protection experiments. Our results demonstrated that the DDRA2 transcript initiates equally frequently at two sites separated by 5 base pairs. Both transcriptional start sites were utilized when cells were exposed to either NQO or heat shock treatment. These results indicate that DDRA2 and DDR48 are members of a unique dually regulated stress-responsive family of genes in S. cerevisiae.

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