| 1. |
- Astromskas, Eimantas, et al.
(författare)
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Ends-in vs. ends-out targeted insertion mutagenesis in Saccharomyces castellii.
- 2009
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Ingår i: Current Genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 55:3, s. 339-347
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Tidskriftsartikel (refereegranskat)abstract
- Gene replacement (knock-out) is a major tool for the analysis of gene function. However, the efficiency of correct targeting varies between species, and is dependent on the structure of the DNA construct. We analyzed the targeted insertion mutagenesis method in the budding yeast Saccharomyces castellii, phylogenetically positioned after the whole genome duplication event in the Saccharomyces lineage. We compared the targeting efficiency for target DNA constructs in the respective ends-in and ends-out form. For some of the constructs S. castellii showed a similar high degree of homologous recombination as S. cerevisiae. In agreement with S. cerevisiae, a higher targeting efficiency was seen for the diploid strain than for the haploid. Surprisingly, a higher degree of targeting efficiency was seen for ends-out constructs compared to ends-in constructs. This result may have been influenced by the difference in the length of the homologous target sequences used, although long homology regions of 300 bp-1 kb were used in all constructs. Remarkably, very short regions of cohesive heterologous sequences at the ends of the constructs highly stimulated random illegitimate integration, suggesting that the pathway of non-homologous end joining is highly active in S. castellii.
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| 2. |
- Berghoff, Bork A., et al.
(författare)
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RNA-based regulation in type I toxin-antitoxin systems and its implication for bacterial persistence
- 2017
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Ingår i: Current Genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 63:6, s. 1011-1016
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Forskningsöversikt (refereegranskat)abstract
- Bacterial dormancy is a valuable survival strategy upon challenging environmental conditions. Dormant cells tolerate the consequences of high stress levels and may re-populate the environment upon return to favorable conditions. Antibiotic-tolerant bacteria-termed persisters-regularly cause relapsing infections, increase the likelihood of antibiotic resistance, and, therefore, earn increasing attention. Their generation often depends on toxins from chromosomal toxin-antitoxin systems. Here, we review recent insights concerning RNA-based control of toxin synthesis, and discuss possible implications for persister generation.
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| 3. |
- Chowdhury, Md Jamil, et al.
(författare)
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Fluorescent protein expression in the ectomycorrhizal fungus Laccaria bicolor: a plasmid toolkit for easy use of fluorescent markers in basidiomycetes
- 2020
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Ingår i: Current Genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 66, s. 791-811
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Tidskriftsartikel (refereegranskat)abstract
- For long time, studies on ectomycorrhiza (ECM) have been limited by inefficient expression of fluorescent proteins (FPs) in the fungal partner. To convert this situation, we have evaluated the basic requirements of FP expression in the model ECM homobasidiomycete Laccaria bicolor and established eGFP and mCherry as functional FP markers. Comparison of intron-containing and intronless FP-expression cassettes confirmed that intron-processing is indispensable for efficient FP expression in Laccaria. Nuclear FP localization was obtained via in-frame fusion of FPs between the intron-containing genomic gene sequences of Laccaria histone H2B, while cytosolic FP expression was produced by incorporating the intron-containing 5 ' fragment of the glyceraldehyde-3-phosphate dehydrogenase encoding gene. In addition, we have characterized the consensus Kozak sequence of strongly expressed genes in Laccaria and demonstrated its boosting effect on transgene mRNA accumulation. Based on these results, an Agrobacterium-mediated transformation compatible plasmid set was designed for easy use of FPs in Laccaria. The four cloning plasmids presented here allow fast and highly flexible construction of C-terminal in-frame fusions between the sequences of interest and the two FPs, expressed either from the endogenous gene promoter, allowing thus evaluation of the native regulation modes of the gene under study, or alternatively, from the constitutive Agaricus bisporus gpdII promoter for enhanced cellular protein localization assays. The molecular tools described here for cell-biological studies in Laccaria can also be exploited in studies of other biotrophic or saprotrophic basidiomycete species susceptible to genetic transformation.
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| 4. |
- Cohn, Marita, et al.
(författare)
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Telomeric sequence diversity within the genus Saccharomyces
- 1998
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Ingår i: Current Genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 33:2, s. 83-91
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Tidskriftsartikel (refereegranskat)abstract
- Conservation of telomeric DNA repeat sequences has been found across evolutionarily diverse eukaryotes. Here we report on a marked telomeric sequence diversity within the budding yeast genus Saccharomyces. Cloning and sequencing of telomeric repeat units from S. castellii, S. dairensis, S. exiguus and S. kluyveri showed a length variation between 8 and 26 bp, as well as a distinct variation in the degree of homogeneity, among the species. In S. castellii and S. dairensis, TCTGGGTG constituted a majority of the telomeric repeat units. However, the character of the variant repeats differed: in S. castellii the major class of variant repeats contained additional TG dinucleotides per repeat unit, [TCTGGGTG(TG)(1-3)], whereas in S. dairensis the major variant repeat is the shorter, uniform sequence TCTGGG. This result suggests mechanistic differences in the action of the telomerases of these closely related yeasts. Despite their length and homogeneity differences, all the Saccharomyces telomeric sequences show a conserved core which is also shared by the Candida glabrata telomeric sequence. This evolutionary similarity may be partly explained by the preservation of a binding site for the RAP1 protein.
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| 5. |
- Derouiche, Abderahmane, 1980, et al.
(författare)
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Evolution and tinkering: what do a protein kinase, a transcriptional regulator and chromosome segregation/cell division proteins have in common?
- 2016
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Ingår i: Current Genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 62:1, s. 67-70
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Forskningsöversikt (refereegranskat)abstract
- In this study, we focus on functional interactions among multi-domain proteins which share a common evolutionary origin. The examples we develop are four Bacillus subtilis proteins, which all possess an ATP-binding Walker motif: the bacterial tyrosine kinase (BY-kinase) PtkA, the chromosome segregation protein Soj (ParA), the cell division protein MinD and a transcription regulator SalA. These proteins have arisen via duplication of the ancestral ATP-binding domain, which has undergone fusions with other functional domains in the process of divergent evolution. We point out that these four proteins, despite having very different physiological roles, engage in an unusually high number of binary functional interactions. Namely, MinD attracts Soj and PtkA to the cell pole, and in addition, activates the kinase function of PtkA. SalA also activates the kinase function of PtkA, and it gets phosphorylated by PtkA as well. The consequence of this phosphorylation is the activation of SalA as a transcriptional repressor. We hypothesize that these functional interactions remain preserved during divergent evolution and represent a constraint on the process of evolutionary "tinkering", brought about by fusions of different functional domains.
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| 6. |
- Finlay, Roger
(författare)
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Fungal stress biology: a preface to the Fungal Stress Responses special edition
- 2015
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Ingår i: Current Genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 61, s. 231-238
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Tidskriftsartikel (refereegranskat)abstract
- There is currently an urgent need to increase global food security, reverse the trends of increasing cancer rates, protect environmental health, and mitigate climate change. Toward these ends, it is imperative to improve soil health and crop productivity, reduce food spoilage, reduce pesticide usage by increasing the use of biological control, optimize bioremediation of polluted sites, and generate energy from sustainable sources such as biofuels. This review focuses on fungi that can help provide solutions to such problems. We discuss key aspects of fungal stress biology in the context of the papers published in this Special Issue of Current Genetics. This area of biology has relevance to pure and applied research on fungal (and indeed other) systems, including biological control of insect pests, roles of saprotrophic fungi in agriculture and forestry, mycotoxin contamination of the food-supply chain, optimization of microbial fermentations including those used for bioethanol production, plant pathology, the limits of life on Earth, and astrobiology.
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| 7. |
- Finlay, Roger
(författare)
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The International Symposium on Fungal Stress: ISFUS
- 2015
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Ingår i: Current Genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 61, s. 479-487
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Tidskriftsartikel (refereegranskat)abstract
- Fungi play central roles in many biological processes, influencing soil fertility, decomposition, cycling of minerals, and organic matter, plant health, and nutrition. They produce a wide spectrum of molecules, which are exploited in a range of industrial processes to manufacture foods, food preservatives, flavoring agents, and other useful biological products. Fungi can also be used as biological control agents of microbial pathogens, nematodes or insect pests, and affect plant growth, stress tolerance, and nutrient acquisition. Successful exploitation of fungi requires better understanding of the mechanisms that fungi use to cope with stress as well as the way in which they mediate stress tolerance in other organisms. It is against this backdrop that a scientific meeting on fungal stress was held in So Jos, dos Campos, Brazil, in October 2014. The meeting, hosted by Drauzio E. N. Rangel and Alene E. Alder-Rangel, and supported by the So Paulo Research Foundation (FAPESP), brought together more than 30 young, mid-career, and highly accomplished scientists from ten different countries. Here we summarize the highlights of the meeting.
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| 8. |
- Georgiev, Alexander, et al.
(författare)
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Characterization of MYR1, a dosage suppressor of YPT6 and RIC1 deficient mutants
- 2008
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Ingår i: Current Genetics. - Berlin : Springer. - 0172-8083 .- 1432-0983. ; 53:4, s. 235-47
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Tidskriftsartikel (refereegranskat)abstract
- Membrane traffic is tightly regulated and the Rab protein family of small GTPases plays a central role in this regulation. One member of this family is the Saccharomyces cerevisae protein Ypt6. To search for new genes interacting with Ypt6-related pathways, we performed a genetic screen for high copy suppressors of ypt6Delta temperature sensitivity at 35 degrees C. Among the suppressors, MYR1 was also able to suppress the temperature sensitive mutant lacking Ric1, a subunit of the Ypt6 guanine exchanging factor complex Ric1/Rgp1. Myr1 is characterized by a coiled coil region and a GYF domain, a protein module binding proline-rich sequences. Myr1 is able to bind membranes but is also associated with larger structures insoluble in Triton X-100. By immunofluorescence, Myr1 shows a network-like pattern as well as small foci. Overexpression of Myr1 influences nuclear envelope morphology and high levels are lethal. This lethality is rescued when the N-terminal region, containing the GYF domain, is deleted. The transcription profile of a myr1Delta strain shows effects on genes involved in nuclear migration, Ras signalling and transcription. Taken together, these results suggest that Myr1 is a novel factor linked to the secretory pathway and important cellular regulatory mechanisms.
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| 9. |
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| 10. |
- Himmelstrand, Kajsa, et al.
(författare)
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Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes
- 2014
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Ingår i: Current Genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 60, s. 303-313
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Tidskriftsartikel (refereegranskat)abstract
- Sizes of mitochondrial genomes vary extensively between fungal species although they typically contain a conserved set of core genes. We have characterised the mitochondrial genome of the conifer root rot pathogen Heterobasidion irregulare and compared the size, gene content and structure of 20 Basidiomycete mitochondrial genomes. The mitochondrial genome of H. irregulare was 114, 193 bp and contained a core set of 15 protein coding genes, two rRNA genes and 26 tRNA genes. In addition, we found six non-conserved open reading frames (ORFs) and four putative plasmid genes clustered in three separate regions together with 24 introns and 14 intronic homing endonuclease genes, unequally spread across seven of the core genes. The size differences among the 20 Basidiomycetes can largely be explained by length variation of intergenic regions and introns. The Agaricomycetes contained the nine largest mitochondrial genomes in the Basidiomycete group and Agaricomycete genomes are significantly (p < 0.001) larger than the other Basidiomycetes. A feature of the Agaricomycete mitochondrial genomes in this study was the simultaneous occurrence of putative plasmid genes and non-conserved ORFs, with Cantharellus cibarius as only exception, where no non-conserved ORF was identified. This indicates a mitochondrial plasmid origin of the non-conserved ORFs or increased mitochondrial genome dynamics of species harbouring mitochondrial plasmids. We hypothesise that two independent factors are the driving forces for large mitochondrial genomes: the homing endonuclease genes in introns and integration of plasmid DNA.
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