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Article ; Online: Drosophila

Chen, Shu-Fen / Hsien, Hsin-Lun / Wang, Ting-Fang / Lin, Ming-Der

International journal of molecular sciences

2023 Volume 24, Issue 14

Abstract: Establishing apicobasal polarity, involving intricate interactions among polarity regulators, is key for epithelial cell function. Though phosphatase of regenerating liver (PRL) proteins are implicated in diverse biological processes, including cancer, ... ...

Abstract	Establishing apicobasal polarity, involving intricate interactions among polarity regulators, is key for epithelial cell function. Though phosphatase of regenerating liver (PRL) proteins are implicated in diverse biological processes, including cancer, their developmental role remains unclear. In this study, we explore the role of
MeSH term(s)	Animals ; Drosophila/metabolism ; Drosophila Proteins/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Photoreceptor Cells, Invertebrate/metabolism ; Liver/metabolism ; Cell Polarity/genetics
Chemical Substances	Drosophila Proteins ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
Language	English
Publishing date	2023-07-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241411501
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Article ; Online: PacBio Long-Read Sequencing, Assembly, and Funannotate Reannotation of the Complete Genome of Trichoderma reesei QM6a.

Li, Wan-Chen / Wang, Ting-Fang

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2234, Page(s) 311–329

Abstract: Single-molecule real-time (SMRT) sequencing developed by Pacific BioSciences (PacBio) offers three major advantages compared to second-generation sequencing: long read length and high consensus accuracy, and a low degree of bias. Together with high ... ...

Abstract	Single-molecule real-time (SMRT) sequencing developed by Pacific BioSciences (PacBio) offers three major advantages compared to second-generation sequencing: long read length and high consensus accuracy, and a low degree of bias. Together with high sequencing coverage, these advantages overcome the difficulty of sequencing genomic regions such as long AT-rich islands and repeated regions (e.g., ribosomal DNA) in the genome of Trichoderma reesei QM6a. Herein, we describe a protocol for preparing high-quality, high molecular weight genomic DNA for PacBio long-read sequencing, de novo assembly and streamlined annotation of the QM6a genome.
MeSH term(s)	DNA, Fungal/isolation & purification ; Genome, Fungal ; Hypocreales/genetics ; Molecular Sequence Annotation ; Molecular Weight ; RNA, Fungal/isolation & purification ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Software
Chemical Substances	DNA, Fungal ; RNA, Fungal
Language	English
Publishing date	2020-11-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1048-0_21
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Article ; Online: Budding yeast Rad51: a paradigm for how phosphorylation and intrinsic structural disorder regulate homologous recombination and protein homeostasis.

Woo, Tai-Ting / Chuang, Chi-Ning / Wang, Ting-Fang

Current genetics

2021 Volume 67, Issue 3, Page(s) 389–396

Abstract: The RecA-family recombinase Rad51 is the central player in homologous recombination (HR), the faithful pathway for repairing DNA double-strand breaks (DSBs) during both mitosis and meiosis. The behavior of Rad51 protein in vivo is fine-tuned via ... ...

Abstract	The RecA-family recombinase Rad51 is the central player in homologous recombination (HR), the faithful pathway for repairing DNA double-strand breaks (DSBs) during both mitosis and meiosis. The behavior of Rad51 protein in vivo is fine-tuned via posttranslational modifications conducted by multiple protein kinases in response to cell cycle cues and DNA lesions. Unrepaired DSBs and ssDNA also activate Mec1
MeSH term(s)	DNA Damage/genetics ; Homeostasis/genetics ; Homologous Recombination/genetics ; Humans ; Intracellular Signaling Peptides and Proteins/genetics ; Meiosis/genetics ; Mitosis/genetics ; Protein-Serine-Threonine Kinases/genetics ; Rad51 Recombinase/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics
Chemical Substances	Intracellular Signaling Peptides and Proteins ; Saccharomyces cerevisiae Proteins ; MEC1 protein, S cerevisiae (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; TEL1 protein, S cerevisiae (EC 2.7.11.1) ; RAD51 protein, S cerevisiae (EC 2.7.7.-) ; RAD51 protein, human (EC 2.7.7.-) ; Rad51 Recombinase (EC 2.7.7.-)
Language	English
Publishing date	2021-01-12
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	282876-5
ISSN	1432-0983 ; 0172-8083
ISSN (online)	1432-0983
ISSN	0172-8083
DOI	10.1007/s00294-020-01151-2
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Article ; Online: Correction to: Budding yeast Rad51: a paradigm for how phosphorylation and intrinsic structural disorder regulate homologous recombination and protein homeostasis.

Woo, Tai-Ting / Chuang, Chi-Ning / Wang, Ting-Fang

Current genetics

2021 Volume 67, Issue 3, Page(s) 397–398

Language	English
Publishing date	2021-02-20
Publishing country	United States
Document type	Published Erratum
ZDB-ID	282876-5
ISSN	1432-0983 ; 0172-8083
ISSN (online)	1432-0983
ISSN	0172-8083
DOI	10.1007/s00294-021-01161-8
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Article ; Online: Noncanonical usage of stop codons in ciliates expands proteins with structurally flexible Q-rich motifs.

Chuang, Chi-Ning / Liu, Hou-Cheng / Woo, Tai-Ting / Chao, Ju-Lan / Chen, Chiung-Ya / Hu, Hisao-Tang / Hsueh, Yi-Ping / Wang, Ting-Fang

eLife

2024 Volume 12

Abstract: Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein ... ...

Abstract	Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein phosphorylation and protein-protein interactions. PolyQ and polyQ/N tracts are structurally flexible sequences that trigger protein aggregation. We report that due to their high percentages of STQ or STQN amino acid content, four SCDs and three prion-causing Q/N-rich motifs of yeast proteins possess autonomous protein expression-enhancing activities. Since these Q-rich motifs can endow proteins with structural and functional plasticity, we suggest that they represent useful toolkits for evolutionary novelty. Comparative Gene Ontology (GO) analyses of the near-complete proteomes of 26 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, including
MeSH term(s)	Animals ; Mice ; Codon, Terminator/metabolism ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Dictyostelium/genetics ; Fungal Proteins/metabolism ; Glutamine/metabolism
Chemical Substances	Codon, Terminator ; Fungal Proteins ; Glutamine (0RH81L854J)
Language	English
Publishing date	2024-02-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.91405
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Article ; Online: TSETA: A Third-Generation Sequencing-Based Computational Tool for Mapping and Visualization of SNPs, Meiotic Recombination Products, and RIP Mutations.

Liu, Hou-Cheng / Li, Wan-Chen / Wang, Ting-Fang

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2234, Page(s) 331–361

Abstract: TSETA (Third-generation Sequencing to Enable Tetrad Analysis) is a fungus-centric software pipeline that utilizes chromosome-level sequence assembly for genome-wide and single-nucleotide-resolution mapping of single-nucleotide polymorphisms (SNPs), ... ...

Abstract	TSETA (Third-generation Sequencing to Enable Tetrad Analysis) is a fungus-centric software pipeline that utilizes chromosome-level sequence assembly for genome-wide and single-nucleotide-resolution mapping of single-nucleotide polymorphisms (SNPs), meiotic recombination products, illegitimate mutations (IMs) and repeat-induced point (RIP) mutations. It utilizes a newly invented algorithm (i.e., BLASTN-guided sectional MAFFT) to perform fast, accurate, and low-cost multiple genome sequence alignments. This new algorithm outcompetes next-generation sequencing (NGS)-based variant-calling approaches for accurate and comprehensive identification of single-nucleotide variants (SNVs) and insertion/deletion mutations (Indels) among the near-complete genome sequences of any two or more intraspecific strains, as well as sequences before and after meiosis, with single-nucleotide precision. TSETA also has a powerful tool for the visualization of the results from the scale of the chromosomal landscape to individual nucleotides. The data output files are user-friendly for researchers and students lacking computational expertise to analyze and reason about data and evidence.
MeSH term(s)	Algorithms ; Base Sequence ; Computational Biology/methods ; Genetic Markers ; High-Throughput Nucleotide Sequencing/methods ; Meiosis/genetics ; Point Mutation/genetics ; Polymorphism, Single Nucleotide/genetics ; Recombination, Genetic/genetics ; Software
Chemical Substances	Genetic Markers
Language	English
Publishing date	2020-11-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1048-0_22
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Article: Budding yeast Rad51: a paradigm for how phosphorylation and intrinsic structural disorder regulate homologous recombination and protein homeostasis

Woo, Tai-Ting / Chuang, Chi-Ning / Wang, Ting-Fang

Current genetics. 2021 June, v. 67, no. 3

2021

Abstract	The RecA-family recombinase Rad51 is the central player in homologous recombination (HR), the faithful pathway for repairing DNA double-strand breaks (DSBs) during both mitosis and meiosis. The behavior of Rad51 protein in vivo is fine-tuned via posttranslational modifications conducted by multiple protein kinases in response to cell cycle cues and DNA lesions. Unrepaired DSBs and ssDNA also activate Mec1ᴬᵀᴿ and Tel1ᴬᵀᴹ family kinases to initiate the DNA damage response (DDR) that safeguards genomic integrity. Defects in HR and DDR trigger genome instability and result in cancer predisposition, infertility, developmental defects, neurological diseases or premature aging. Intriguingly, yeast Mec1ᴬᵀᴿ- and Tel1ᴬᵀᴹ-dependent phosphorylation promotes Rad51 protein stability during DDR, revealing how Mec1ᴬᵀᴿ can alleviate proteotoxic stress. Moreover, Mec1ᴬᵀᴿ- and Tel1ᴬᵀᴹ-dependent phosphorylation also occurs on DDR-unrelated proteins, suggesting that Mec1ᴬᵀᴿ and Tel1ᴬᵀᴹ have a DDR-independent function in protein homeostasis. In this minireview, we first describe how human and budding yeast Rad51 are phosphorylated by multiple protein kinases at different positions to promote homology-directed DNA repair and recombination (HDRR). Then, we discuss recent findings showing that intrinsic structural disorder and Mec1ᴬᵀᴿ/Tel1ᴬᵀᴹ-dependent phosphorylation are coordinated in yeast Rad51 to regulate both HR and protein homeostasis.
Keywords	DNA damage ; DNA repair ; genetic instability ; genomics ; homeostasis ; homologous recombination ; humans ; meiosis ; mitosis ; phosphorylation ; protein kinases ; recombinases ; yeasts
Language	English
Dates of publication	2021-06
Size	p. 389-396.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	NAL-AP-2-clean ; Review
ZDB-ID	282876-5
ISSN	1432-0983 ; 0172-8083
ISSN (online)	1432-0983
ISSN	0172-8083
DOI	10.1007/s00294-020-01151-2
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Repeat-induced point (RIP) mutation in the industrial workhorse fungus Trichoderma reesei.

Li, Wan-Chen / Chen, Chia-Ling / Wang, Ting-Fang

Applied microbiology and biotechnology

2018 Volume 102, Issue 4, Page(s) 1567–1574

Abstract: Trichoderma reesei (syn. Hypocrea jecorina) is a filamentous ascomycete. Due to its capability of producing large amounts of lignocellulolytic enzymes and various heterologous proteins, this fungus has been widely used for industrial applications for ... ...

Abstract	Trichoderma reesei (syn. Hypocrea jecorina) is a filamentous ascomycete. Due to its capability of producing large amounts of lignocellulolytic enzymes and various heterologous proteins, this fungus has been widely used for industrial applications for over 70 years. It is also a model organism for lignocellulosic biomass degradation and metabolic engineering. Recently, we experimentally and computationally demonstrated that Trichoderma reesei exhibits high homology pairing and repeat-induced point (RIP) mutation activities at a premeiotic stage, i.e., between fertilization and karyogamy or premeiotic DNA replication. The discovery of RIP in Trichoderma reesei not only reveals significant impacts of sexual reproduction on evolution and chromosome architecture but also provides intriguing perspectives for industrial strain improvement. This review emphasizes two major points about RIP and RIP-like processes in Pezizomycotina fungi. First, the molecular mechanisms of RIP and RIP-like processes in Trichoderma reesei and other Pezizomycotina fungi are apparently distinct from those originally described in the model fungus Neurospora crassa. Second, orthologs of the rid1 (deficient in RIP-1) DNA methyltransferase gene were shown to be essential for sexual development in at least four Pezizomycotina fungi, including Trichoderma reesei. In contrast, rid1 is dispensable for Neurospora crassa sexual development. We suggest that the rid1-like gene products and/or their DNA methyltransferase activities play critical roles in promoting fungal sexual development. The Neurospora crassa rid1 gene might have lost this evolutionarily conserved function.
MeSH term(s)	DNA Modification Methylases/genetics ; DNA Modification Methylases/metabolism ; Homologous Recombination ; Meiosis ; Point Mutation ; Repetitive Sequences, Nucleic Acid ; Trichoderma/genetics ; Trichoderma/growth & development
Chemical Substances	DNA Modification Methylases (EC 2.1.1.-)
Language	English
Publishing date	2018-02
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-017-8731-5
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Zs.A 2229: Show issues

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Article ; Online: Third-generation sequencing-based mapping and visualization of single nucleotide polymorphism, meiotic recombination, illegitimate mutation and repeat-induced point mutation.

Li, Wan-Chen / Liu, Hou-Cheng / Lin, Ying-Jyun / Tung, Shu-Yun / Wang, Ting-Fang

NAR genomics and bioinformatics

2020 Volume 2, Issue 3, Page(s) lqaa056

Abstract: Generation of new genetic diversity by crossover (CO) and non-crossover (NCO) is a fundamental process in eukaryotes. Fungi have played critical roles in studying this process because they permit tetrad analysis, which has been used by geneticists for ... ...

Abstract	Generation of new genetic diversity by crossover (CO) and non-crossover (NCO) is a fundamental process in eukaryotes. Fungi have played critical roles in studying this process because they permit tetrad analysis, which has been used by geneticists for several decades to determine meiotic recombination products. New genetic variations can also be generated in zygotes via illegitimate mutation (IM) and repeat-induced point mutation (RIP). RIP is a genome defense mechanism for preventing harmful expansion of transposable elements or duplicated sequences in filamentous fungi. Although the exact mechanism of RIP is unknown, the C:G to T:A mutations might result from DNA cytosine methylation. A comprehensive approach for understanding the molecular mechanisms underlying these important processes is to perform high-throughput mapping of CO, NCO, RIP and IM in zygotes bearing large numbers of heterozygous variant markers. To this aim, we developed 'TSETA', a versatile and user-friendly pipeline that utilizes high-quality and chromosome-level genome sequences involved in a single meiotic event of the industrial workhorse fungus
Language	English
Publishing date	2020-07-29
Publishing country	England
Document type	Journal Article
ISSN	2631-9268
ISSN (online)	2631-9268
DOI	10.1093/nargab/lqaa056
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Article ; Online: Dual roles of yeast Rad51 N-terminal domain in repairing DNA double-strand breaks.

Woo, Tai-Ting / Chuang, Chi-Ning / Higashide, Mika / Shinohara, Akira / Wang, Ting-Fang

Nucleic acids research

2020 Volume 48, Issue 15, Page(s) 8474–8489

Abstract: Highly toxic DNA double-strand breaks (DSBs) readily trigger the DNA damage response (DDR) in cells, which delays cell cycle progression to ensure proper DSB repair. In Saccharomyces cerevisiae, mitotic S phase (20-30 min) is lengthened upon DNA damage. ... ...

Abstract	Highly toxic DNA double-strand breaks (DSBs) readily trigger the DNA damage response (DDR) in cells, which delays cell cycle progression to ensure proper DSB repair. In Saccharomyces cerevisiae, mitotic S phase (20-30 min) is lengthened upon DNA damage. During meiosis, Spo11-induced DSB onset and repair lasts up to 5 h. We report that the NH2-terminal domain (NTD; residues 1-66) of Rad51 has dual functions for repairing DSBs during vegetative growth and meiosis. Firstly, Rad51-NTD exhibits autonomous expression-enhancing activity for high-level production of native Rad51 and when fused to exogenous β-galactosidase in vivo. Secondly, Rad51-NTD is an S/T-Q cluster domain (SCD) harboring three putative Mec1/Tel1 target sites. Mec1/Tel1-dependent phosphorylation antagonizes the proteasomal degradation pathway, increasing the half-life of Rad51 from ∼30 min to ≥180 min. Our results evidence a direct link between homologous recombination and DDR modulated by Rad51 homeostasis.
MeSH term(s)	DNA Breaks, Double-Stranded ; DNA Damage/genetics ; DNA Repair/genetics ; DNA-Binding Proteins/genetics ; Endodeoxyribonucleases/genetics ; Gene Expression Regulation, Fungal/genetics ; Intracellular Signaling Peptides and Proteins/genetics ; Meiosis/genetics ; Phosphorylation/genetics ; Proteasome Endopeptidase Complex/genetics ; Protein Domains/genetics ; Protein-Serine-Threonine Kinases/genetics ; Proteolysis ; Rad51 Recombinase/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; beta-Galactosidase/genetics
Chemical Substances	DNA-Binding Proteins ; Intracellular Signaling Peptides and Proteins ; Saccharomyces cerevisiae Proteins ; MEC1 protein, S cerevisiae (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; TEL1 protein, S cerevisiae (EC 2.7.11.1) ; RAD51 protein, S cerevisiae (EC 2.7.7.-) ; Rad51 Recombinase (EC 2.7.7.-) ; Endodeoxyribonucleases (EC 3.1.-) ; Spo11 protein, S cerevisiae (EC 3.1.-) ; beta-Galactosidase (EC 3.2.1.23) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2020-07-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa587
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