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Book: Cellular and molecular biology of filamentous fungi

Borkovich, Katherine A.

2010

Author's details	ed. by Katherine A. Borkovich
Language	English
Size	XIII, 788 S. : Ill., graph. Darst.
Publisher	ASM Press
Publishing place	Washington, DC
Publishing country	United States
Document type	Book
HBZ-ID	HT016477742
ISBN	978-1-55581-473-1 ; 1-55581-473-5
Database	Catalogue ZB MED Nutrition, Environment, Agriculture

In stock of ZB MED Bonn / Germany

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114/71	available for loan (reading room)	Freihandmagazin (U1)

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Article: "Yes, indeed, the Lord made only one Katie!" --The journeys of the unsinkable Katherine H. Borkovich, MD: an exclusive profile/interview by Blaine Taylor. Interview by Blaine Taylor.

Borkovich, K H

Maryland state medical journal

1980 Volume 29, Issue 7, Page(s) 35–49

MeSH term(s)	History, 20th Century ; Internal Medicine/history ; Maryland ; Travel
Language	English
Publishing date	1980-07
Publishing country	United States
Document type	Biography ; Historical Article ; Interview
ZDB-ID	414335-8
ISSN	0025-4363
ISSN	0025-4363
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Article ; Online: Heterotrimeric G-Protein Signaling Is Required for Cellulose Degradation in Neurospora crassa.

Collier, Logan A / Ghosh, Arit / Borkovich, Katherine A

mBio

2020 Volume 11, Issue 6

Abstract: The filamentous ... ...

Abstract	The filamentous fungus
MeSH term(s)	Biodegradation, Environmental ; Carbohydrate Metabolism ; Cellulase/genetics ; Cellulase/metabolism ; Cellulose/metabolism ; Fungal Proteins/metabolism ; GTP-Binding Proteins/chemistry ; GTP-Binding Proteins/genetics ; GTP-Binding Proteins/metabolism ; Gene Expression Regulation, Fungal ; Multigene Family ; Mutation ; Neurospora crassa/physiology ; Protein Multimerization ; Signal Transduction
Chemical Substances	Fungal Proteins ; Cellulose (9004-34-6) ; Cellulase (EC 3.2.1.4) ; GTP-Binding Proteins (EC 3.6.1.-)
Language	English
Publishing date	2020-11-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.02419-20
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Article ; Online: Multiple calcium signaling genes play a role in the circadian period of Neurospora crassa.

Baruah, Darshana / Marak, Christy Noche K / Roy, Avishek / Gohain, Dibakar / Kumar, Ajeet / Das, Pallavi / Borkovich, Katherine A / Tamuli, Ranjan

FEMS microbiology letters

2023 Volume 370

Abstract: The Ca2+ signaling genes cpe-1, plc-1, ncs-1, splA2, camk-1, camk-2, camk-3, camk-4, cmd, and cnb-1 are necessary for a normal circadian period length in Neurospora crassa. In addition, the Q10 values ranged between 0.8 and 1.2 for the single mutants ... ...

Abstract	The Ca2+ signaling genes cpe-1, plc-1, ncs-1, splA2, camk-1, camk-2, camk-3, camk-4, cmd, and cnb-1 are necessary for a normal circadian period length in Neurospora crassa. In addition, the Q10 values ranged between 0.8 and 1.2 for the single mutants lacking cpe-1, splA2, camk-1, camk-2, camk-3, camk-4, and cnb-1, suggesting that the circadian clock exhibits standard temperature compensation. However, the Q10 value for the ∆plc-1 mutant was 1.41 at 25 and 30 °C, 1.53 and 1.40 for the ∆ncs-1 mutant at 20 and 25 °C, and at 20 and 30 °C, respectively, suggesting a partial loss of temperature compensation in these two mutants. Moreover, expression of frq, a regulator of the circadian period, and the blue light receptor wc-1, were increased >2-fold in the Δplc-1, ∆plc-1; ∆cpe-1, and the ∆plc-1; ∆splA2 mutants at 20 °C. The frq mRNA level was increased >2-fold in the Δncs-1 mutant compared to the ras-1bd strain at 20 °C. Therefore, multiple Ca2+ signaling genes regulate the circadian period, by influencing expression of the frq and wc-1 genes that are critical for maintaining the normal circadian period length in N. crassa.
MeSH term(s)	Neurospora crassa/genetics ; Neurospora crassa/metabolism ; Circadian Rhythm/genetics ; Calcium Signaling ; Calcium-Calmodulin-Dependent Protein Kinase Type 4/metabolism ; Calcium/metabolism ; Phospholipases A2, Secretory/metabolism ; Fungal Proteins/genetics ; Fungal Proteins/metabolism
Chemical Substances	Calcium-Calmodulin-Dependent Protein Kinase Type 4 (EC 2.7.11.17) ; Calcium (SY7Q814VUP) ; Phospholipases A2, Secretory (EC 3.1.1.4) ; Fungal Proteins
Language	English
Publishing date	2023-05-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	752343-9
ISSN	1574-6968 ; 0378-1097
ISSN (online)	1574-6968
ISSN	0378-1097
DOI	10.1093/femsle/fnad044
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Article ; Online: Targeted Metabolomics Using LC-MS in Neurospora crassa.

Carrillo, Alexander J / Halilovic, Lida / Hur, Manhoi / Kirkwood, Jay S / Borkovich, Katherine A

Current protocols

2022 Volume 2, Issue 5, Page(s) e454

Abstract: The filamentous fungus Neurospora crassa has historically been a model for understanding the relationship between genes and metabolism-auxotrophic mutants of N. crassa were used by Beadle and Tatum to develop the one-gene-one-enzyme hypothesis for which ... ...

Abstract	The filamentous fungus Neurospora crassa has historically been a model for understanding the relationship between genes and metabolism-auxotrophic mutants of N. crassa were used by Beadle and Tatum to develop the one-gene-one-enzyme hypothesis for which they earned the Nobel Prize in 1958. In the ensuing decades, several techniques have been developed for the systematic analysis of metabolites in N. crassa and other fungi. Untargeted and targeted approaches have been used, with a focus on secondary metabolites over primary metabolism. Here, we describe a pipeline for sample preparation, metabolite extraction, Liquid Chromatography-Mass Spectrometry (LC-MS), and data analysis that can be used for targeted metabolomics of primary metabolites in N. crassa. Liquid cultures are grown with shaking in a defined minimal medium and then collected using filtration. Samples are lyophilized for 2 days at -80°C, pulverized, and mixed with a solution to extract polar metabolites. The metabolites are separated and identified using LC-MS, with downstream analysis using Skyline interpretive software. Relative levels of hundreds of metabolites can be detected and compared across strains. © 2022 Wiley Periodicals LLC. Basic Protocol: Metabolite extraction and detection from Neurospora crassa cell cultures using Liquid Chromatography-Mass Spectrometry.
MeSH term(s)	Chromatography, Liquid/methods ; Metabolome ; Metabolomics/methods ; Neurospora crassa ; Tandem Mass Spectrometry
Language	English
Publishing date	2022-05-26
Publishing country	United States
Document type	Journal Article
ISSN	2691-1299
ISSN (online)	2691-1299
DOI	10.1002/cpz1.454
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Article ; Online: Small RNA Isolation and Library Construction for Expression Profiling of Small RNAs from Neurospora crassa and Fusarium oxysporum and Analysis of Small RNAs in Fusarium oxysporum-Infected Plant Root Tissue.

Ouyang, Shou-Qiang / Park, Gyungsoon / Ji, Hui-Min / Borkovich, Katherine A

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

2020 Volume 2170, Page(s) 199–212

Abstract: Due to crucial roles in gene regulation, noncoding small RNAs (sRNAs) of 20-30 nucleotides (nt) have been intensively studied in mammals and plants and are implicated in significant diseases and metabolic disorders. Elucidation of biogenesis mechanisms ... ...

Abstract	Due to crucial roles in gene regulation, noncoding small RNAs (sRNAs) of 20-30 nucleotides (nt) have been intensively studied in mammals and plants and are implicated in significant diseases and metabolic disorders. Elucidation of biogenesis mechanisms and functional characterization of sRNAs is often achieved using tools such as separation of small-sized RNA and deep sequencing. Although RNA interference pathways, such as quelling and meiotic silencing, have been well-described in Neurospora crassa, knowledge of sRNAs in other filamentous fungi is still limited compared to other eukaryotes. As a prerequisite for study, isolation and sequence analysis of sRNAs is necessary. We developed a protocol for isolation and library construction of sRNAs of 20-30 nt for deep sequencing in two filamentous fungi, N. crassa and Fusarium oxysporum f.sp. lycopersici. Using 200-300 μg total RNA, sRNA was isolated by size-fractionation and ligated with adapters and amplified by RT-PCR for deep sequencing. Sequence analysis of several cDNA clones showed that the cloned sRNAs were not tRNAs and rRNAs and were fungal genome-specific. In order to validate fungal miRNAs that were imported into the host cell, we developed a straightforward method to isolate protoplasts from tomato roots infected by Fusarium oxysporum f.sp. lycopersici using enzymatic digestion.
MeSH term(s)	DNA, Complementary/genetics ; DNA, Complementary/metabolism ; Fusarium/genetics ; Fusarium/pathogenicity ; Gene Expression Regulation, Fungal/genetics ; Gene Expression Regulation, Fungal/physiology ; Neurospora crassa/genetics ; Neurospora crassa/pathogenicity ; Protoplasts/metabolism
Chemical Substances	DNA, Complementary
Language	English
Publishing date	2020-08-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-0743-5_14
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Article ; Online: Regulator of G Protein Signaling Proteins Control Growth, Development and Cellulase Production in

Cabrera, Ilva E / Oza, Yagna / Carrillo, Alexander J / Collier, Logan A / Wright, Sara J / Li, Liande / Borkovich, Katherine A

Journal of fungi (Basel, Switzerland)

2022 Volume 8, Issue 10

Abstract: Heterotrimeric (αβγ) G protein signaling pathways are critical environmental sensing systems found in eukaryotic cells. Exchange of GDP for GTP on the Gα subunit leads to its activation. In contrast, GTP hydrolysis on the Gα is accelerated by Regulator ... ...

Abstract	Heterotrimeric (αβγ) G protein signaling pathways are critical environmental sensing systems found in eukaryotic cells. Exchange of GDP for GTP on the Gα subunit leads to its activation. In contrast, GTP hydrolysis on the Gα is accelerated by Regulator of G protein Signaling (RGS) proteins, resulting in a return to the GDP-bound, inactive state. Here, we analyzed growth, development and extracellular cellulase production in strains with knockout mutations in the seven identified RGS genes (
Language	English
Publishing date	2022-10-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2784229-0
ISSN	2309-608X ; 2309-608X
ISSN (online)	2309-608X
ISSN	2309-608X
DOI	10.3390/jof8101076
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Article ; Online: Calcineurin Subunits A and B Interact to Regulate Growth and Asexual and Sexual Development in Neurospora crassa.

Tamuli, Ranjan / Deka, Rekha / Borkovich, Katherine A

PloS one

2016 Volume 11, Issue 3, Page(s) e0151867

Abstract: Calcineurin is a calcium/calmodulin dependent protein phosphatase in eukaryotes that consists of a catalytic subunit A and a regulatory subunit B. Previous studies in the filamentous fungus Neurospora crassa had suggested that the catalytic subunit of ... ...

Abstract	Calcineurin is a calcium/calmodulin dependent protein phosphatase in eukaryotes that consists of a catalytic subunit A and a regulatory subunit B. Previous studies in the filamentous fungus Neurospora crassa had suggested that the catalytic subunit of calcineurin might be an essential protein. We generated N. crassa strains expressing the A (cna-1) and B (cnb-1) subunit genes under the regulation of Ptcu-1, a copper-responsive promoter. In these strains, addition of bathocuproinedisulfonic acid (BCS), a copper chelator, results in induction of cna-1 and cnb-1, while excess Cu2+ represses gene expression. Through analysis of these strains under repressing and inducing conditions, we found that the calcineurin is required for normal growth, asexual development and female fertility in N. crassa. Moreover, we isolated and analyzed cnb-1 mutant alleles generated by repeat-induced point mutation (RIP), with the results further supporting roles for calcineurin in growth and fertility in N. crassa. We demonstrated a direct interaction between the CNA-1 and CNB-1 proteins using an assay system developed to study protein-protein interactions in N. crassa.
MeSH term(s)	Calcineurin/chemistry ; Calcineurin/genetics ; Calcineurin/metabolism ; Copper/chemistry ; Copper/metabolism ; Fungal Proteins/chemistry ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Gene Expression Regulation, Fungal/drug effects ; Genetic Vectors/genetics ; Genetic Vectors/metabolism ; Hyphae/growth & development ; Hyphae/metabolism ; Immunoprecipitation ; Neurospora crassa/growth & development ; Neurospora crassa/metabolism ; Phenanthrolines/pharmacology ; Point Mutation ; Promoter Regions, Genetic ; Protein Subunits/chemistry ; Protein Subunits/genetics ; Protein Subunits/metabolism
Chemical Substances	Fungal Proteins ; Phenanthrolines ; Protein Subunits ; bathocuproine sulfonate (73348-75-1) ; Copper (789U1901C5) ; Calcineurin (EC 3.1.3.16)
Language	English
Publishing date	2016-03-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0151867
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Article ; Online: The SNARE protein FolVam7 mediates intracellular trafficking to regulate conidiogenesis and pathogenicity in Fusarium oxysporum f. sp. lycopersici.

Li, Bing / Gao, Ying / Mao, Hui-Ying / Borkovich, Katherine A / Ouyang, Shou-Qiang

Environmental microbiology

2019 Volume 21, Issue 8, Page(s) 2696–2706

Abstract: Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are conserved in fungi, plants and animals. The Vam7 gene encodes a v-SNARE protein that involved in vesicle trafficking in fungi. Here, we identified and characterized the ... ...

Abstract	Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are conserved in fungi, plants and animals. The Vam7 gene encodes a v-SNARE protein that involved in vesicle trafficking in fungi. Here, we identified and characterized the function of FolVam7, a homologue of the yeast SNARE protein Vam7p in Fusarium oxysporum f. sp. lycopersici (Fol), a fungal pathogen of tomato. FolVam7 contains SNARE and PX (Phox homology) domains that are indispensable for normal localization and function of FolVam7. Targeted gene deletion showed that FolVam7-mediated vesicle trafficking is important for vegetative growth, asexual development, conidial morphology and plant infection. Further cytological examinations revealed that FolVam7 is localized to vesicles and vacuole membranes in the hyphae stage. Moreover, the ΔFolvam7 mutant is insensitive to salt and osmotic stresses and hypersensitive to cell wall stressors. Taken together, our results suggested that FolVam7-mediated vesicle trafficking promotes vegetative growth, conidiogenesis and pathogenicity of Fol.
MeSH term(s)	Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Fusarium/genetics ; Fusarium/growth & development ; Fusarium/pathogenicity ; Fusarium/physiology ; Hyphae/metabolism ; Lycopersicon esculentum/microbiology ; Plant Diseases/microbiology ; Protein Transport ; SNARE Proteins/genetics ; SNARE Proteins/metabolism ; Spores, Fungal/metabolism ; Vacuoles/metabolism ; Virulence/genetics
Chemical Substances	Fungal Proteins ; SNARE Proteins
Language	English
Publishing date	2019-03-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.14585
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Article ; Online: Small RNA isolation and library construction for expression profiling of small RNAs from Neurospora and Fusarium using illumina high-throughput deep sequencing.

Park, Gyungsoon / Borkovich, Katherine A

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

2012 Volume 883, Page(s) 155–164

Abstract: Due to crucial roles in gene regulation, noncoding small RNAs (smRNAs) of 20-30 nucleotides (nt) have been intensively studied in mammals and plants, and are known to be implicated in significant diseases and metabolic disorders. Elucidation of ... ...

Abstract	Due to crucial roles in gene regulation, noncoding small RNAs (smRNAs) of 20-30 nucleotides (nt) have been intensively studied in mammals and plants, and are known to be implicated in significant diseases and metabolic disorders. Elucidation of biogenesis mechanisms and functional characterization of smRNAs are often achieved using tools, such as separation of small-sized RNA and high-throughput sequencing. Although RNA interference pathways such as quelling and meiotic silencing have been well described in Neurospora crassa, knowledge of smRNAs in filamentous fungi is still limited compared to other eukaryotes. As a prerequisite for study, isolation and sequence analysis of smRNAs are necessary. We developed a protocol for isolation and library construction of smRNAs of 20-30 nt for Solexa sequencing in two -filamentous fungi, N. crassa and Fusarium oxysporum f.sp. lycopersici. Using 200-300 μg total RNA, smRNA was isolated by size fractionation, ligated with adapters, and amplified by RT-PCR for Solexa sequencing. Sequence analysis of several cDNA clones showed that the cloned smRNAs were not tRNAs and rRNAs and were fungal genome specific.
MeSH term(s)	Buffers ; Culture Techniques ; Electrophoresis, Polyacrylamide Gel/methods ; Fusarium/genetics ; Gene Expression Profiling/methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Neurospora crassa/genetics ; Phenol/chemistry ; RNA, Fungal/genetics ; RNA, Fungal/isolation & purification ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/isolation & purification ; Reverse Transcriptase Polymerase Chain Reaction ; Solvents/chemistry
Chemical Substances	Buffers ; RNA, Fungal ; RNA, Small Untranslated ; Solvents ; Phenol (339NCG44TV)
Language	English
Publishing date	2012
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-61779-839-9_12
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