Genomic response programs of Saccharomyces cerevisiae following protoplasting and regeneration

Castillo, Luis; Martínez, Ana Isabel; Gelis, Samuel; Ruíz-Herrera, José; Valentı́n, Eulogio; Sentandreu, Rafael

doi:10.1016/j.fgb.2007.10.002

Cited by 7 publications

(4 citation statements)

References 42 publications

(57 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…CaPIR1 showed a 2.7-fold increase in expression at 30 min and a 6-fold increase at 6 h during the regeneration process. A similar experiment with S. cerevisiae showed up-regulation of ScPIR1, ScPIR2, and ScPIR3 during protoplast regeneration (Castillo et al, 2008). Perhaps the Dpir1-1/Dpir1-2 Dpir32-1/Dpir32-2 strain described here would display defects during protoplast regeneration.…”

Section: Discussionsupporting

confidence: 62%

Peering Into Candida albicans Pir Protein Function and Comparative Genomics of the Pir Family

Kim

Rodriguez-Bobadilla

et al. 2022

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

The fungal cell wall, comprised primarily of protein and polymeric carbohydrate, maintains cell structure, provides protection from the environment, and is an important antifungal drug target. Pir proteins (proteins with internal repeats) are linked to cell wall β-1,3-glucan and are best studied in Saccharomyces cerevisiae. Sequential deletion of S. cerevisiae PIR genes produces strains with increasingly notable cell wall damage. However, a true null mutant lacking all five S. cerevisiae PIR genes was never constructed. Because only two PIR genes (PIR1, PIR32) were annotated in the Candida albicans genome, the initial goal of this work was to construct a true Δpir/Δpir null strain in this species. Unexpectedly, the phenotype of the null strain was almost indistinguishable from its parent, leading to the search for other proteins with Pir function. Bioinformatic approaches revealed nine additional C. albicans proteins that share a conserved Pir functional motif (minimally DGQ). Examination of the protein sequences revealed another conserved motif (QFQFD) toward the C-terminal end of each protein. Sequence similarities and presence of the conserved motif(s) were used to identify a set of 75 proteins across 16 fungal species that are proposed here as Pir proteins. The Pir family is greatly expanded in C. albicans and C. dubliniensis compared to other species and the orthologs are known to have specialized function during chlamydospore formation. Predicted Pir structures showed a conserved core of antiparallel beta-sheets and sometimes-extensive loops that contain amino acids with the potential to form linkages to cell wall components. Pir phylogeny demonstrated emergence of specific ortholog groups among the fungal species. Variation in gene expression patterns was noted among the ortholog groups during growth in rich medium. PIR allelic variation was quite limited despite the presence of a repeated sequence in many loci. Results presented here demonstrate that the Pir family is larger than previously recognized and lead to new hypotheses to test to better understand Pir proteins and their role in the fungal cell wall.

show abstract

Section: Discussionsupporting

confidence: 62%

Peering Into Candida albicans Pir Protein Function and Comparative Genomics of the Pir Family

Kim

Rodriguez-Bobadilla

et al. 2022

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

show abstract

“…However, the variety and movement of microbes are actually prone to various stresses counting chemical pollution [44]. The attendance of soil bacteria can improve the extent of pesticide degradation [15] as well as degradation of other organic pollutants [45].…”

Section: Pesticide Pcp Effect In Bacterial Ecological Systemmentioning

confidence: 99%

“…This can reduce the inhibition produced by the dechlorinated intermediates. The progressive mineralization of the component generates a series of microbial communities and enzymatic activities that enables an efficient dissipation of pesticides in soil and avoids metabolite accumulation [45].…”

Section: Some Enzymes Responsible For the Degradation Of Pcpmentioning

confidence: 99%

Effect of PCP Pesticide Contamination on Soil Quality

Ammeri¹,

Hidri²,

Hassen³

2021

Soil Contamination - Threats and Sustainable Solutions

View full text Add to dashboard Cite

In recent years, soil contamination with pesticides has become a crucial news issue with serious short- and long-term effects on human health and its environment. Pesticides play a significant role in the success of modern farming and food production. These compounds have potential for toxicity and adverse effects on human health and ecological soil systems. Pentachlorophenol (PCP) is one of the most recalcitrant chemicals polluting the environment for its stable aromatic ring system and chloride content. Nowadays, many sites are contaminated with this substance. In these areas, concentrations may stay high for a long time because of slow degradation in the soil due to the negative effects that PCP has on soil microbial populations. Bioremediation of PCP contaminated sites can be realized introducing directly, into a contaminated system, microorganisms able to consume selectively the target compound (bioaugmentation) or increasing the microbial indigenous population by addiction of nutrients in form of organic and/or inorganic fertilizers and biosolids (biostimulation). In the present chapter, we present an overview of the effect of PCP pesticide contamination on soil microbial populations (density and diversity), enzymatic activity and physicochemical parameters. Additionally, the bioremediation process will be detailed.

show abstract

“…When dealing with uncertainties in databases, fuzzy logic clustering algorithm can be utilized to cluster distinctive components of data into different membership levels relying upon their closeness [13].For instance, during the assessment of learning disabilities risk, sign and symptoms data may have some level of fluffiness when collecting data set such as mode of child not giving correct answer, not aware about LD, and Children of low socio-economic status and girls in general might be particularly under-enumerated by this type of general-data collection instrument. Censuses are particularly prone to underestimation [8].…”

Section: Fuzzy Logic K-mean Clusteringmentioning

confidence: 99%

Intelligent Predicting Learning Disabilities in School Going Children Using Fuzzy Logic K Mean Clustering in Machine Learning.

Mary. T,

2019

IJRTE

View full text Add to dashboard Cite

Learning disabilities (LD) is turning into a major issue in various nations around the globe which can even contrarily influence human common advancement. The undertaking of this work is to help the specialized programme network in their task to be with the standard. The underlying section of the paper gives a comprehensive investigation of the distinctive components of diagnosing learning disabilities. Despite the fact that LD can be analysed early - before 5 years of age, most youngsters were not determined to have LD until the age of nine on account of its unpredictable side effects and unclear indication in children disorder issue. Fuzzy logic K-means clustering has inspired a tremendous transformation in Machine learning and can take and able to resolve a variation of problems. This paper is the elaboration on the strategy for utilizing this mix to encourage the early analysis of LD. Since Fuzzy Logic clustering in Machine Learning is generally considered and connected in different areas of science, we invite all the related analysts from the fields of computer science, engineering, statistics, social sciences, healthcare, and so on, etc. The result of the paper demonstrates that the previously mentioned methodology can possibly be the potential of the supporting decision-making system in LD investigating and diagnosing.

show abstract

Genomic response programs of Saccharomyces cerevisiae following protoplasting and regeneration

Cited by 7 publications

References 42 publications

Peering Into Candida albicans Pir Protein Function and Comparative Genomics of the Pir Family

Peering Into Candida albicans Pir Protein Function and Comparative Genomics of the Pir Family

Effect of PCP Pesticide Contamination on Soil Quality

Intelligent Predicting Learning Disabilities in School Going Children Using Fuzzy Logic K Mean Clustering in Machine Learning.

Contact Info

Product

Resources

About