Two Duplicated Genes DDI2 and DDI3 in Budding Yeast Encode a Cyanamide Hydratase and Are Induced by Cyanamide

Li, Jia; Biss, Michael; Fu, Yu; Xu, Xin; Moore, Stanley A.; Xiao, Wei

doi:10.1074/jbc.m115.645408

Cited by 16 publications

(26 citation statements)

References 53 publications

(36 reference statements)

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“…Since ferulic acid, p -coumaric acid, and related aromatic lignin degradation products are among the most toxic fermentation inhibitors in ACSH and many other lignocellulosic hydrolysates ( Piotrowski et al 2014 ), genes that reduce aromatic aldehydes into their less toxic alcohols may be beneficial. We also found two nonsyntenic homologs of DDI2 and DDI3 , which were recently shown to encode identical cyanamide hydratases in S288c ( Li et al 2015 ). If their activity is broader or the divergent (88% identical) homolog ( DDI72 ) present in Y22-3 has novel activities, these genes might also metabolize other amides present in ACSH, such as acetamide, feruloyl amide, and p -coumaroyl amide ( Chundawat et al 2010 ).…”

Section: Resultsmentioning

confidence: 51%

Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain ofSaccharomyces cerevisiaeUsed in Biofuels Research

McIlwain

Peris

Sardi

et al. 2016

G3 Genes|Genomes|Genetics

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The genome sequences of more than 100 strains of the yeast Saccharomyces cerevisiae have been published. Unfortunately, most of these genome assemblies contain dozens to hundreds of gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few strains have been chosen for genome sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe the nearly complete genome sequence of GLBRCY22-3 (Y22-3), a strain of S. cerevisiae derived from the stress-tolerant wild strain NRRL YB-210 and subsequently engineered for xylose metabolism. After benchmarking several genome assembly approaches, we developed a pipeline to integrate Pacific Biosciences (PacBio) and Illumina sequencing data and achieved one of the highest quality genome assemblies for any S. cerevisiae strain. Specifically, the contig N50 is 693 kbp, and the sequences of most chromosomes, the mitochondrial genome, and the 2-micron plasmid are complete. Our annotation predicts 92 genes that are not present in the reference genome of the laboratory strain S288c, over 70% of which were expressed. We predicted functions for 43 of these genes, 28 of which were previously uncharacterized and unnamed. Remarkably, many of these genes are predicted to be involved in stress tolerance and carbon metabolism and are shared with a Brazilian bioethanol production strain, even though the strains differ dramatically at most genetic loci. The Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.

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Section: Resultsmentioning

confidence: 51%

Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain ofSaccharomyces cerevisiaeUsed in Biofuels Research

McIlwain

Peris

Sardi

et al. 2016

G3 Genes|Genomes|Genetics

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“…Furthermore, two genes encoding the enzyme cyanamide hydratase are uniquely present in Bb8028. Cyanamide hydratase converts cyanamide into urea, and has been studied in relation to fungal survival in the soil since cyanamide is used as a fertilizer and is also synthesized by vetch species [55, 56]. Bb8028 also contains 13 unique genes involved in transport processes, of which five belong to the major facilitator (MFS) superfamily, four to the family of ATP-binding cassette (ABC) transporters, and the remaining four are dedicated siderophore and dicarboxylate transporters, as well as a sodium/proton antiporter.…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics of Beauveria bassiana: uncovering signatures of virulence against mosquitoes

et al. 2016

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BackgroundEntomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence.ResultsA high-quality, near-complete genome assembly was achieved for the highly virulent isolate Bb8028, which was compared to the assemblies of the four other isolates. Whole genome analysis showed a high level of genetic diversity between the five isolates (2.85–16.8 SNPs/kb), which grouped into two distinct phylogenetic clusters. Mating type gene analysis revealed the presence of either the MAT1–1–1 or the MAT1–2–1 gene. Moreover, a putative new MAT gene (MAT1-2–8) was detected in the MAT1–2 locus. Comparative genome analysis revealed that Bb8028 contains 163 genes exclusive for this isolate. These unique genes have a tendency to cluster in the genome and to be often located near the telomeres. Among the genes unique to Bb8028 are a Non-Ribosomal Peptide Synthetase (NRPS) secondary metabolite gene cluster, a polyketide synthase (PKS) gene, and five genes with homology to bacterial toxins. A survey of candidate virulence genes for B. bassiana is presented.ConclusionsOur results indicate several genes and molecular processes that may underpin virulence towards mosquitoes. Thus, the genome sequences of five isolates of B. bassiana provide a better understanding of the natural variation in virulence and will offer a major resource for future research on this important biological control agent.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3339-1) contains supplementary material, which is available to authorized users.

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“…They displayed the highest induction (>100-fold) after treatment with a sublethal dose of MMS ( Fu et al, 2008 ), and was named after DDI1 ( Liu and Xiao, 1997 ). It turns out that DDI2/3 encodes a cyanamide hydratase ( Li et al, 2015 ). Interestingly, the DDI2/3 gene is also highly induced after treatment with cyanamide (CY), as measured by a lacZ reporter assay ( Li et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

“…It turns out that DDI2/3 encodes a cyanamide hydratase ( Li et al, 2015 ). Interestingly, the DDI2/3 gene is also highly induced after treatment with cyanamide (CY), as measured by a lacZ reporter assay ( Li et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

“…Firstly, the DDI2 gene expression is barely detectable under normal culture conditions and can be highly induced by CY or MMS. Secondly, the induction appears to be rapid and reproducible, and in a linear relationship within a broad range of CY and MMS doses, as judged by the lacZ reporter assay ( Li et al, 2015 ). Thirdly, as CY is a simple compound and has been used as crop fertilizer, it is inexpensive and hence can be applied to large-scale production.…”

Section: Introductionmentioning

confidence: 99%

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Utilization of a Strongly Inducible DDI2 Promoter to Control Gene Expression in Saccharomyces cerevisiae

et al. 2018

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Regulating target gene expression is a common method in yeast research. In Saccharomyces cerevisiae, there are several widely used regulated expression systems, such as the GAL and Tet-off systems. However, all current expression systems possess some intrinsic deficiencies. We have previously reported that the DDI2 gene can be induced to very high levels upon cyanamide or methyl methanesulfonate treatment. Here we report the construction of gene expression systems based on the DDI2 promoter in both single- and multi-copy plasmids. Using GFP as a reporter gene, it was demonstrated that the target gene expression could be increased by up to 2,000-fold at the transcriptional level by utilizing the above systems. In addition, a DDI2-based construct was created for promoter shuffling in the budding yeast genome to control endogenous gene expression. Overall, this study offers a set of convenient and highly efficient experimental tools to control target gene expression in budding yeast.

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Two Duplicated Genes DDI2 and DDI3 in Budding Yeast Encode a Cyanamide Hydratase and Are Induced by Cyanamide

Cited by 16 publications

References 53 publications

Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain ofSaccharomyces cerevisiaeUsed in Biofuels Research

Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain ofSaccharomyces cerevisiaeUsed in Biofuels Research

Comparative genomics of Beauveria bassiana: uncovering signatures of virulence against mosquitoes

Utilization of a Strongly Inducible DDI2 Promoter to Control Gene Expression in Saccharomyces cerevisiae

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