Papers by Piotr Mieczkowski
Additional file 15: of Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
Data bank genome access of Sordariomycetes used in comparative studies. (PDF 70 kb)
Additional file 14: of Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
C. cacaofunesta GPI-anchored proteins _Effectors CSEP. (XLSX 34 kb)
Additional file 13: of Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
Blast proteins form True Vascular fungi against C. cacaofunesta proteome. (XLSX 11 kb)
Additional file 11: of Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
Complete phylogenic analysis of Ceratocystis PI-PLCs. (PDF 1635 kb)
Additional file 10: of Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
C. cacaofunesta PI-PLCs Identification_Genomic Distribution_GC content in PI-PLC clusters. (XLSX ... more C. cacaofunesta PI-PLCs Identification_Genomic Distribution_GC content in PI-PLC clusters. (XLSX 26 kb)
Additional file 7: of Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
Gene family analysis in Ceratocystis. (PDF 680 kb)
This article cites 59 articles, 25 of which can be accessed free
Additional file 2: of Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
GO classification and KEGG annotation of C. cacaofunesta and C. fimbriata predicted proteins. (PD... more GO classification and KEGG annotation of C. cacaofunesta and C. fimbriata predicted proteins. (PDF 1084 kb)
Nucleic Acids Research, 2021
Iron-sulfur clusters (4Fe–4S) exist in many enzymes concerned with DNA replication and repair. Th... more Iron-sulfur clusters (4Fe–4S) exist in many enzymes concerned with DNA replication and repair. The contribution of these clusters to enzymatic activity is not fully understood. We identified the MET18 (MMS19) gene of Saccharomyces cerevisiae as a strong mutator on GC-rich genes. Met18p is required for the efficient insertion of iron-sulfur clusters into various proteins. met18 mutants have an elevated rate of deletions between short flanking repeats, consistent with increased DNA polymerase slippage. This phenotype is very similar to that observed in mutants of POL3 (encoding the catalytic subunit of Pol δ) that weaken binding of the iron-sulfur cluster. Comparable mutants of POL2 (Pol ϵ) do not elevate deletions. Further support for the conclusion that met18 strains result in impaired DNA synthesis by Pol δ are the observations that Pol δ isolated from met18 strains has less bound iron and is less processive in vitro than the wild-type holoenzyme.
ABSTRACTAgaves, which have been grown commercially for fiber or alcoholic beverages, are emerging... more ABSTRACTAgaves, which have been grown commercially for fiber or alcoholic beverages, are emerging as a candidate crop for biochemicals and biofuels production in semiarid regions because of their high productivity in low rainfall areas, drought tolerance, and low lignin content.In this work, we present the transcriptomic atlas of Agave sisalana, Agave fourcroydes, and agave hybrid 11648 (A. amaniensis x A. angustifolia) under prolonged drought in field conditions. Leaf, stem, and root tissues were sequenced, and gene expression profiles were correlated with biomass composition, enzymatic hydrolysis of cell wall carbohydrates, histochemical analysis, and non-structural carbohydrates content.Differences in biomass accessibility were attributed to either lignin content or lignin composition, possibly through modification of s/g ratio promoted by changes in Caffeic Acid 3-O-Methyltransferase (COMT) transcript abundance. Unlike most plants, the most highly expressed transcripts do not en...
DNA Research, 2019
The Polyploid Gene Assembler (PGA), developed and tested in this study, represents a new strategy... more The Polyploid Gene Assembler (PGA), developed and tested in this study, represents a new strategy to perform gene-space assembly from complex genomes using low coverage DNA sequencing. The pipeline integrates reference-assisted loci and de novo assembly strategies to construct high-quality sequences focused on gene content. Pipeline validation was conducted with wheat (Triticum aestivum), a hexaploid species, using barley (Hordeum vulgare) as reference, that resulted in the identification of more than 90% of genes and several new genes. Moreover, PGA was used to assemble gene content in Saccharum spontaneum species, a parental lineage for hybrid sugarcane cultivars. Saccharum spontaneum gene sequence obtained was used to reference-guided transcriptome analysis of six different tissues. A total of 39,234 genes were identified, 60.4% clustered into known grass gene families. Thirty-seven gene families were expanded when compared with other grasses, three of them highlighted by the number of gene copies potentially involved in initial development and stress response. In addition, 3,108 promoters (many showing tissue specificity) were identified in this work. In summary, PGA can reconstruct high-quality gene sequences from polyploid genomes, as shown for wheat and S. spontaneum species, and it is more efficient than conventional genome assemblers using low coverage DNA sequencing.
G3 (Bethesda, Md.), Nov 6, 2018
The strain JAY270/PE2 is a highly efficient biocatalyst used in the production of bioethanol from... more The strain JAY270/PE2 is a highly efficient biocatalyst used in the production of bioethanol from sugarcane feedstock. This strain is heterothallic and diploid, and its genome is characterized by abundant structural and nucleotide polymorphisms between homologous chromosomes. One of the reasons it is favored by many distilleries is that its cells do not normally aggregate, a trait that facilitates cell recycling during batch-fed fermentations. However, long-term propagation makes the yeast population vulnerable to the effects of genomic instability, which may trigger the appearance of undesirable phenotypes such as cellular aggregation. In pure cultures of JAY270, we identified the recurrent appearance of mutants displaying a mother-daughter cell separation defect resulting in rough colonies in agar media and fast sedimentation in liquid culture. We investigated the genetic basis of the colony morphology phenotype and found that JAY270 is heterozygous for a frameshift mutation in th...
DNA repair, May 21, 2017
Variations in mutation rates across the genome have been demonstrated both in model organisms and... more Variations in mutation rates across the genome have been demonstrated both in model organisms and in cancers. This phenomenon is largely driven by the damage specificity of diverse mutagens and the differences in DNA repair efficiency in given genomic contexts. Here, we demonstrate that the single-strand DNA-specific cytidine deaminase APOBEC3B (A3B) damages tRNA genes at a 1000-fold higher efficiency than other non-tRNA genomic regions in budding yeast. We found that A3B-induced lesions in tRNA genes were predominantly located on the non-transcribed strand, while no transcriptional strand bias was observed in protein coding genes. Furthermore, tRNA gene mutations were exacerbated in cells where RNaseH expression was completely abolished (Δrnh1Δrnh35). These data suggest a transcription-dependent mechanism for A3B-induced tRNA gene hypermutation. Interestingly, in strains proficient in DNA repair, only 1% of the abasic sites formed upon excision of A3B-deaminated cytosines were not ...
Proceedings of the National Academy of Sciences of the United States of America, Dec 13, 2016
DNA replication stress (DRS)-induced genomic instability is an important factor driving cancer de... more DNA replication stress (DRS)-induced genomic instability is an important factor driving cancer development. To understand the mechanisms of DRS-associated genomic instability, we measured the rates of genomic alterations throughout the genome in a yeast strain with lowered expression of the replicative DNA polymerase δ. By a genetic test, we showed that most recombinogenic DNA lesions were introduced during S or G2 phase, presumably as a consequence of broken replication forks. We observed a high rate of chromosome loss, likely reflecting a reduced capacity of the low-polymerase strains to repair double-stranded DNA breaks (DSBs). We also observed a high frequency of deletion events within tandemly repeated genes such as the ribosomal RNA genes. By whole-genome sequencing, we found that low levels of DNA polymerase δ elevated mutation rates, both single-base mutations and small insertions/deletions. Finally, we showed that cells with low levels of DNA polymerase δ tended to accumula...
PLoS genetics, Oct 1, 2016
Accumulation of somatic changes, due to environmental and endogenous lesions, in the human genome... more Accumulation of somatic changes, due to environmental and endogenous lesions, in the human genome is associated with aging and cancer. Understanding the impacts of these processes on mutagenesis is fundamental to understanding the etiology, and improving the prognosis and prevention of cancers and other genetic diseases. Previous methods relying on either the generation of induced pluripotent stem cells, or sequencing of single-cell genomes were inherently error-prone and did not allow independent validation of the mutations. In the current study we eliminated these potential sources of error by high coverage genome sequencing of single-cell derived clonal fibroblast lineages, obtained after minimal propagation in culture, prepared from skin biopsies of two healthy adult humans. We report here accurate measurement of genome-wide magnitude and spectra of mutations accrued in skin fibroblasts of healthy adult humans. We found that every cell contains at least one chromosomal rearrangement and 600-13,000 base substitutions. The spectra and correlation of base substitutions with epigenomic features resemble many cancers. Moreover, because biopsies were taken from body parts differing by sun exposure, we can delineate the precise contributions of environmental and endogenous factors to the accrual of genetic changes within the same individual. We show here that UV-induced and endogenous DNA damage can have a comparable impact on the somatic mutation loads in skin fibroblasts.
Cell, 2016
To provide a detailed analysis of the molecular components and underlying mechanisms associated w... more To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSC). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease such as how different copy number alternations influence the proteome, the proteins associated with chromosomal instability, the sets of signaling pathways that diverse genome rearrangements converge on, as well as the ones most associated with short overall survival. Specific protein acetylations associated with homologous recombination deficiency suggest a potential means for stratifying patients for therapy. In addition to providing a valuable resource, these findings provide a view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in HGSC.
PLoS genetics, 2015
Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidi... more Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Ma...
An integrated pipeline for transcriptional profile of an industrial Saccharomyces cerevisiae strain during alcoholic fermentation
The bioethanol production system used in Brazil is based on the alcoholic fermentation of sucrose... more The bioethanol production system used in Brazil is based on the alcoholic fermentation of sucrose derived from sugarcane feedstock by highly adapted strains of the yeast Saccharomyces cerevisiae. PE-2 and CAT-1 are the most productive and widely adopted S. cerevisiae strains used by distilleries in Brazil. Due to no sterile condition at industrial scale, the process carries a variety of bacterial contaminants that are regularly related to yeast-bacteria co-aggregation phenotype, decreasing bioethanol yield. In this study we investigate the molecular physiology of the main S. cerevisiae commercial strain (PE-2) used on Brazilian bioethanol process under two distinct conditions: typical fermentation and flocculated (co-aggregated) fermentation. We collected samples on 13 time-points (6 time-points of typical fermentation and 7 time-points of flocculated fermentation) on sugarcane mills. Transcriptional machinery of PE-2 was assessed by high throughput sequencing-based methods (RNA-seq...
BMC Plant Biology, 2014
Background: Nitrogen (N) is a main nutrient required for tree growth and biomass accumulation. In... more Background: Nitrogen (N) is a main nutrient required for tree growth and biomass accumulation. In this study, we analyzed the effects of contrasting nitrogen fertilization treatments on the phenotypes of fast growing Eucalyptus hybrids (E. urophylla x E. grandis) with a special focus on xylem secondary cell walls and global gene expression patterns. Results: Histological observations of the xylem secondary cell walls further confirmed by chemical analyses showed that lignin was reduced by luxuriant fertilization, whereas a consistent lignin deposition was observed in trees grown in N-limiting conditions. Also, the syringyl/guaiacyl (S/G) ratio was significantly lower in luxuriant nitrogen samples. Deep sequencing RNAseq analyses allowed us to identify a high number of differentially expressed genes (1,469) between contrasting N treatments. This number is dramatically higher than those obtained in similar studies performed in poplar but using microarrays. Remarkably, all the genes involved the general phenylpropanoid metabolism and lignin pathway were found to be down-regulated in response to high N availability. These findings further confirmed by RT-qPCR are in agreement with the reduced amount of lignin in xylem secondary cell walls of these plants. Conclusions: This work enabled us to identify, at the whole genome level, xylem genes differentially regulated by N availability, some of which are involved in the environmental control of xylogenesis. It further illustrates that N fertilization can be used to alter the quantity and quality of lignocellulosic biomass in Eucalyptus, offering exciting prospects for the pulp and paper industry and for the use of short coppices plantations to produce second generation biofuels.
BMC plant biology, Jan 19, 2014
Background Eucalyptus species are the most widely planted hardwood species in the world and are r... more Background Eucalyptus species are the most widely planted hardwood species in the world and are renowned for their rapid growth and adaptability. In Brazil, one of the most widely grown Eucalyptus cultivars is the fast-growing Eucalyptus urophylla x Eucalyptus grandis hybrid. In a previous study, we described a chemical characterization of these hybrids when subjected to flavonoid supplementation on 2 distinct timetables, and our results revealed marked differences between the wood composition of the treated and untreated trees.ResultsIn this work, we report the transcriptional responses occurring in these trees that may be related to the observed chemical differences. Gene expression was analysed through mRNA-sequencing, and notably, compared to control trees, the treated trees display differential down-regulation of cell wall formation pathways such as phenylpropanoid metabolism as well as differential expression of genes involved in sucrose, starch and minor CHO metabolism and ge...
Uploads
Papers by Piotr Mieczkowski