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Article: David D. Perkins (1919-2007): a lifetime of Neurospora genetics.

Raju, Namboori B

2007 Volume 86, Issue 2, Page(s) 177–186

MeSH term(s)	Genetics/history ; History, 20th Century ; History, 21st Century ; Neurospora/genetics
Language	English
Publishing date	2007-10-29
Publishing country	India
Document type	Bibliography ; Biography ; Historical Article ; Journal Article ; Portrait
ZDB-ID	3039-9
ISSN	0973-7731 ; 0022-1333 ; 0958-8361
ISSN (online)	0973-7731
ISSN	0022-1333 ; 0958-8361
DOI	10.1007/s12041-007-0024-9
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Article: Neurospora as a model fungus for studies in cytogenetics and sexual biology at Stanford.

Raju, Namboori B

Journal of biosciences

2009 Volume 34, Issue 1, Page(s) 139–159

Abstract: Dodge's early work (1927-1940) on Neurospora genetics and sexual biology inspired Beadle and Tatum at Stanford to use N.crassa for their landmark discovery that genes specify enzymes. Neurospora has since become a model organism for numerous genetic, ... ...

Abstract	Dodge's early work (1927-1940) on Neurospora genetics and sexual biology inspired Beadle and Tatum at Stanford to use N.crassa for their landmark discovery that genes specify enzymes. Neurospora has since become a model organism for numerous genetic, cytogenetic, biochemical, molecular and population biology studies. Neurospora is haploid in the vegetative phase with a transient diploid sexual phase. Its meiotic cells (asci) are large, allowing easy examination of dividing nuclei and chromosomes under a light microscope. The haploid meiotic products are themselves the sexual progeny that grow into vegetative cultures, thus avoiding the cumbersome testcrosses and complex dominance -recessive relationships, as in diploid organisms.The Perkins'laboratory at Stanford (1949-2007) played a pivotal role in advancing our knowledge of Neurospora genetics, sexual biology, cytogenetics and population biology. Since 1974, I have taken advantage of various chromosome-staining methods to examine ascus and ascospore development in wild type and in numerous mutant strains. In addition,I have used GFP-tagged genes to visualize the expression or silencing of unpaired genes in a post-transcriptional gene silencing process (meiotic silencing by unpaired DNA) that operates specifically during meiosis. The genome of N. crassa contains over 10 000 protein- coding genes. Gene knockouts or mutations in specific sequences may now be readily correlated with the observed cytological defects in the sexual stage, thus advancing our molecular understanding of complex processes during ascus and ascospore development.
MeSH term(s)	California ; Epigenesis, Genetic ; Fungal Proteins/genetics ; Gene Rearrangement ; Gene Silencing ; Haploidy ; Meiosis ; Models, Genetic ; Mutation ; Neurospora/genetics ; Neurospora/growth & development ; Neurospora/physiology ; Reproduction/physiology ; Spores, Fungal/genetics ; Spores, Fungal/growth & development ; Spores, Fungal/physiology ; Universities
Chemical Substances	Fungal Proteins
Language	English
Publishing date	2009-05-08
Publishing country	India
Document type	Journal Article ; Review
ZDB-ID	756157-x
ISSN	0250-5991
ISSN	0250-5991
DOI	10.1007/s12038-009-0015-5
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Article ; Online: Meiosis and ascospore development in Cochliobolus heterostrophus.

Raju, Namboori B

Fungal genetics and biology : FG & B

2008 Volume 45, Issue 4, Page(s) 554–564

Abstract: Cochliobolus heterostrophus produces eight filiform ascospores per ascus, following meiosis and a postmeiotic mitosis. Early ascus development and nuclear divisions in C. heterostrophus resemble those of the prototypic Pyrenomycete Neurospora crassa. ... ...

Abstract	Cochliobolus heterostrophus produces eight filiform ascospores per ascus, following meiosis and a postmeiotic mitosis. Early ascus development and nuclear divisions in C. heterostrophus resemble those of the prototypic Pyrenomycete Neurospora crassa. However, the two fungi differ in several important details owing to differences in ascus and ascospore shape, spindle pole body (SPB) behavior during spore delimitation, and ascospore development. In C. heterostrophus, the two spindles at meiosis II, and the four spindles at the postmeiotic mitosis are aligned irregularly, unlike the tandem or ladder rung-like orientation of spindles of N. crassa. Prior to ascospore delimitation, all eight nuclei reorient themselves and their SPB plaques migrate toward the base of the ascus. The SPB plaques facilitate demarcation of the lower end of each incipient ascospore. The filiform ascospores are uninucleate and unsegmented at inception but they become highly multinucleate, multisegmented, and helically coiled when mature. An account of ascus development, nuclear divisions, and ascospore delimitation and maturation is presented here and supported by a series of photomicrographs.
MeSH term(s)	Ascomycota/cytology ; Ascomycota/genetics ; Ascomycota/physiology ; Meiosis ; Neurospora crassa/physiology ; Organelles ; Spores, Fungal/genetics
Language	English
Publishing date	2008-04
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1319820-8
ISSN	1096-0937 ; 1087-1845 ; 0147-5975
ISSN (online)	1096-0937
ISSN	1087-1845 ; 0147-5975
DOI	10.1016/j.fgb.2007.08.007
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Article: Meiosis and ascospore development in nonlinear asci of Neurospora pannonica.

Raju, Namboori B

Mycologia

2002 Volume 94, Issue 1, Page(s) 99–104

Abstract: Neurospora pannonica is homothallic, with 8-spored asci. Immature asci are usually swollen and noncylindrical while the mature asci are narrow and cylindrical. The two meiotic divisions resemble those of other Neurospora species. However, the orientation ...

Abstract	Neurospora pannonica is homothallic, with 8-spored asci. Immature asci are usually swollen and noncylindrical while the mature asci are narrow and cylindrical. The two meiotic divisions resemble those of other Neurospora species. However, the orientation of third-division mitotic spindles and the distribution of nuclei in the swollen asci are irregular. Ascospores are arranged irregularly at first, but as the ascospores enlarge and mature the asci gradually become cylindrical, with the ascospores aligned in single file. The asci cannot be considered ordered tetrads, because ascospore order does not reliably reflect the assortment of chromosomes at the first and second meiotic divisions. Contrary to the original species description, ascospores require heat shock for germination and hyphae are sent out at both ends of germinating ascospores.
Language	English
Publishing date	2002-01
Publishing country	England
Document type	Journal Article
ZDB-ID	281335-x
ISSN	1557-2536 ; 0027-5514
ISSN (online)	1557-2536
ISSN	0027-5514
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Article: Abnormal ascospore morphology in the bud mutant of Neurospora tetrasperma.

Raju, Namboori B / Burk, Anna G

Fungal genetics and biology : FG & B

2004 Volume 41, Issue 6, Page(s) 582–589

Abstract: A recessive ascospore mutant of Neurospora tetrasperma, named bud, was isolated from a wild-collected heterokaryotic strain with four different nuclear components. bud segregates as a single mendelian gene. When bud is homozygous, meiosis is apparently ... ...

Abstract	A recessive ascospore mutant of Neurospora tetrasperma, named bud, was isolated from a wild-collected heterokaryotic strain with four different nuclear components. bud segregates as a single mendelian gene. When bud is homozygous, meiosis is apparently normal but postmeiotic events are not. Abnormal orientation of spindles at the postmeiotic mitosis often results in failed pair-wise association of nuclei and their irregular distribution along the length of the ascus prior to spore delimitation. Consequently, many asci cut out more than four ascospores; some contain no nuclei while others contain more than two. The most dramatic effect of bud is on ascospore delimitation itself. Many ascospores are irregularly shaped and are often interconnected, because of incomplete spore delimitation. Ascospores also show one or two lobes or bud-like extensions of varying sizes. Over 75% of ascospores from bud x bud remain white or tan and are inviable. The interaction of bud with a dominant Eight-spore mutant (E) was examined in both heterozygous and homozygous crosses. When both bud and E are heterozygous, bud has no effect on ascospore delimitation or on the phenotype of E because bud is recessive; many asci produce 5-8 ascospores just as in E x E(+). And when bud is homozygous and E is heterozygous, ascospore delimitation is less affected than when E is absent. Moreover, when both bud and E are homozygous, the effect on ascospore development is less extreme than when E is homozygous singly.
MeSH term(s)	Crosses, Genetic ; Culture Media ; Heterozygote ; Homozygote ; Mutation ; Neurospora/genetics ; Neurospora/growth & development ; Neurospora/physiology ; Spores, Fungal/physiology ; Spores, Fungal/ultrastructure
Chemical Substances	Culture Media
Language	English
Publishing date	2004-06
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1319820-8
ISSN	1096-0937 ; 1087-1845 ; 0147-5975
ISSN (online)	1096-0937
ISSN	1087-1845 ; 0147-5975
DOI	10.1016/j.fgb.2004.01.007
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Article ; Online: Evidence for the absence of meiotic silencing by unpaired DNA in Neurospora tetrasperma.

Jacobson, David J / Raju, Namboori B / Freitag, Michael

Fungal genetics and biology : FG & B

2008 Volume 45, Issue 3, Page(s) 351–362

Abstract: Meiotic silencing by unpaired DNA is a posttranscriptional gene silencing process in Neurospora crassa. Any gene without a homolog in the same chromosomal position during meiotic prophase generates a sequence-specific signal that prevents expression of ... ...

Abstract	Meiotic silencing by unpaired DNA is a posttranscriptional gene silencing process in Neurospora crassa. Any gene without a homolog in the same chromosomal position during meiotic prophase generates a sequence-specific signal that prevents expression of all copies of that gene, but only during meiosis. Meiotic silencing is epigenetic and involves components of a meiosis-specific RNA silencing machinery. Although N. tetrasperma is closely related to N. crassa, its sexual biology is significantly different. N. tetrasperma was used here to evaluate both the generality of meiotic silencing within the genus and its possible evolutionary significance. A reporter gene for meiotic silencing, a histone H1-GFP fusion construct, was introgressed from N. crassa into various chromosome locations in N. tetrasperma. Whereas we did not observe meiotic silencing in four out of five introgression series, we obtained inconclusive results in the fifth series. Thus, we propose that meiotic silencing in N. tetrasperma is either absent or is substantially reduced when compared to N. crassa, possibly because the sad-1 gene (RNA-directed RNA polymerase, RdRP) is naturally unsynapsed (although "paired") and self-silenced during meiosis by structural differences between N. tetrasperma mating-type chromosomes. In N. crassa, wild-type sad-1 function is essential for meiotic silencing. Many point mutations in or deletion of sad-1 result in self-silencing of RdRP, and consequently suppression of meiotic silencing in heterozygous asci. The apparent absence or reduced meiotic silencing in N. tetrasperma raises the possibility that this form of silencing is not necessarily a major genome defense mechanism or responsible for reproductive isolation among the species of the genus Neurospora.
MeSH term(s)	Chromosome Pairing/genetics ; DNA, Fungal/genetics ; Gene Silencing ; Genes, Fungal ; Genes, Mating Type, Fungal/genetics ; Green Fluorescent Proteins/genetics ; Green Fluorescent Proteins/metabolism ; Histones/genetics ; Histones/metabolism ; Meiosis/genetics ; Models, Biological ; Mutation ; Neurospora/genetics ; Neurospora/growth & development
Chemical Substances	DNA, Fungal ; Histones ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2008-03
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	1319820-8
ISSN	1096-0937 ; 1087-1845 ; 0147-5975
ISSN (online)	1096-0937
ISSN	1087-1845 ; 0147-5975
DOI	10.1016/j.fgb.2007.09.014
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Article: Neurospora spore killers Sk-2 and Sk-3 suppress meiotic silencing by unpaired DNA.

Raju, Namboori B / Metzenberg, Robert L / Shiu, Patrick K T

Genetics

2007 Volume 176, Issue 1, Page(s) 43–52

Abstract: In Neurospora crassa, pairing of homologous DNA segments is monitored during meiotic prophase I. Any genes not paired with a homolog, as well as any paired homologs of that gene, are silenced during the sexual phase by a mechanism known as meiotic ... ...

Abstract	In Neurospora crassa, pairing of homologous DNA segments is monitored during meiotic prophase I. Any genes not paired with a homolog, as well as any paired homologs of that gene, are silenced during the sexual phase by a mechanism known as meiotic silencing by unpaired DNA (MSUD). Two genes required for MSUD have been described previously: sad-1 (suppressor of ascus dominance), encoding an RNA-directed RNA polymerase, and sad-2, encoding a protein that controls the perinuclear localization of SAD-1. Inactivation of either sad-1 or sad-2 suppresses MSUD. We have now shown that MSUD is also suppressed by either of two Spore killer strains, Sk-2 and Sk-3. These were both known to contain a haplotype segment that behaves as a meiotic drive element in heterozygous crosses of killer x sensitive. Progeny ascospores not carrying the killer element fail to mature and are inviable. Crosses homozygous for either of the killer haplotypes suppress MSUD even though ascospores are not killed. The killer activity maps to the same 30-unit-long region within which recombination is suppressed in killer x sensitive crosses. We suggest that the region contains a suppressor of MSUD.
MeSH term(s)	Chromosome Pairing/genetics ; DNA, Fungal/genetics ; Diploidy ; Gene Silencing ; Genes, Fungal ; Genetic Linkage ; Green Fluorescent Proteins/metabolism ; Heterozygote ; Histones/metabolism ; Meiosis/genetics ; Neurospora/cytology ; Neurospora/genetics ; Recombinant Fusion Proteins/metabolism ; Regulatory Sequences, Nucleic Acid ; Spores, Fungal/cytology ; Spores, Fungal/genetics ; Suppression, Genetic ; Tubulin/metabolism
Chemical Substances	DNA, Fungal ; Histones ; Recombinant Fusion Proteins ; Tubulin ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2007-05
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.106.069161
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Article: Meiotic silencing in the homothallic fungus Gibberella zeae.

Son, Hokyoung / Min, Kyunghun / Lee, Jungkwan / Raju, Namboori B / Lee, Yin-Won

Fungal biology

2011 Volume 115, Issue 12, Page(s) 1290–1302

Abstract: The homothallic ascomycete fungus Gibberella zeae is an important pathogen on major cereal crops. The objective of this study was to determine whether meiotic silencing occurs in G. zeae. Cytological studies demonstrated that GFP and RFP-fusion proteins ... ...

Abstract	The homothallic ascomycete fungus Gibberella zeae is an important pathogen on major cereal crops. The objective of this study was to determine whether meiotic silencing occurs in G. zeae. Cytological studies demonstrated that GFP and RFP-fusion proteins were not detected during meiosis, both in heterozygous outcrosses and homozygous selfings. The deletion of rsp-1, a homologue used for studies on meiotic silencing of Neurospora crassa, triggered abnormal ascospores from selfing, but outcrosses between the mutant and wild-type strain resulted in some ascospores with mutant phenotype (low occurrence of ascus dominance). When the ectopic mutants that carried an additional copy of rsp-1 were selfed, they primarily produced ascospores with normal shape but a few ascospores (0.23 %) were abnormal, in which both endogenous and ectopically integrated genes contained numerous point mutations. The ectopic mutants showed low occurrence of ascus dominance in outcrosses with strains that carried the wild-type allele. Approximately 10 % of ascospores were abnormal but all of the single-ascospore isolates produced normal-shaped ascospores from selfing. However, no ascus dominance was observed when the mutants were outcrossed with a sad-1 deletion mutant, which lacks the putative RNA-dependent RNA polymerase essential for meiotic silencing in N. crassa. All results were consistent with those generated from an additional gene, roa, required for ascospore morphogenesis. This study demonstrated that G. zeae possesses a functional meiotic silencing mechanism which is triggered by unpaired DNA, as in N. crassa.
MeSH term(s)	Fungal Proteins/genetics ; Gene Expression Regulation, Fungal ; Gene Silencing ; Gibberella/cytology ; Gibberella/genetics ; Meiosis ; Spores, Fungal/cytology ; Spores, Fungal/genetics
Chemical Substances	Fungal Proteins
Language	English
Publishing date	2011-12
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2532164-X
ISSN	1878-6162 ; 1878-6146
ISSN (online)	1878-6162
ISSN	1878-6146
DOI	10.1016/j.funbio.2011.09.006
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Article: Meiotic silencing in the homothallic fungus Gibberella zeae

Son, Hokyoung / Min, Kyunghun / Lee, Jungkwan / Raju, Namboori B / Lee, Yin-Won

Fungal biology. 2011 Dec., v. 115, no. 12

2011

Abstract	The homothallic ascomycete fungus Gibberella zeae is an important pathogen on major cereal crops. The objective of this study was to determine whether meiotic silencing occurs in G. zeae. Cytological studies demonstrated that GFP and RFP-fusion proteins were not detected during meiosis, both in heterozygous outcrosses and homozygous selfings. The deletion of rsp-1, a homologue used for studies on meiotic silencing of Neurospora crassa, triggered abnormal ascospores from selfing, but outcrosses between the mutant and wild-type strain resulted in some ascospores with mutant phenotype (low occurrence of ascus dominance). When the ectopic mutants that carried an additional copy of rsp-1 were selfed, they primarily produced ascospores with normal shape but a few ascospores (0.23 %) were abnormal, in which both endogenous and ectopically integrated genes contained numerous point mutations. The ectopic mutants showed low occurrence of ascus dominance in outcrosses with strains that carried the wild-type allele. Approximately 10 % of ascospores were abnormal but all of the single-ascospore isolates produced normal-shaped ascospores from selfing. However, no ascus dominance was observed when the mutants were outcrossed with a sad-1 deletion mutant, which lacks the putative RNA-dependent RNA polymerase essential for meiotic silencing in N. crassa. All results were consistent with those generated from an additional gene, roa, required for ascospore morphogenesis. This study demonstrated that G. zeae possesses a functional meiotic silencing mechanism which is triggered by unpaired DNA, as in N. crassa.
Keywords	DNA ; DNA-directed RNA polymerase ; Gibberella zeae ; Neurospora crassa ; ascospores ; fungi ; genes ; grain crops ; meiosis ; morphogenesis ; mutants ; pathogens ; phenotype ; point mutation ; proteins ; selfing
Language	English
Dates of publication	2011-12
Size	p. 1290-1302.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2532164-X
ISSN	1878-6162 ; 1878-6146
ISSN (online)	1878-6162
ISSN	1878-6146
DOI	10.1016/j.funbio.2011.09.006
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Article: SAD-2 is required for meiotic silencing by unpaired DNA and perinuclear localization of SAD-1 RNA-directed RNA polymerase.

Shiu, Patrick K T / Zickler, Denise / Raju, Namboori B / Ruprich-Robert, Gwenael / Metzenberg, Robert L

Proceedings of the National Academy of Sciences of the United States of America

2006 Volume 103, Issue 7, Page(s) 2243–2248

Abstract: A gene unpaired during the meiotic homolog pairing stage in Neurospora generates a sequence-specific signal that silences the expression of all copies of that gene. This process is called Meiotic Silencing by Unpaired DNA (MSUD). Previously, we have ... ...

Abstract	A gene unpaired during the meiotic homolog pairing stage in Neurospora generates a sequence-specific signal that silences the expression of all copies of that gene. This process is called Meiotic Silencing by Unpaired DNA (MSUD). Previously, we have shown that SAD-1, an RNA-directed RNA polymerase (RdRP), is required for MSUD. We isolated a second gene involved in this process, sad-2. Mutated Sad-2 (RIP) alleles, like those of Sad-1, are dominant and suppress MSUD. Crosses homozygous for Sad-2 are blocked at meiotic prophase. SAD-2 colocalizes with SAD-1 in the perinuclear region, where small interfering RNAs have been shown to reside in mammalian cells. A functional sad-2(+) gene is necessary for SAD-1 localization, but the converse is not true. The data suggest that SAD-2 may function to recruit SAD-1 to the perinuclear region, and that the proper localization of SAD-1 is important for its activity.
MeSH term(s)	Base Pair Mismatch/genetics ; Chromosome Pairing ; DNA, Fungal/metabolism ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Gene Silencing ; Genes, Dominant ; Genes, Fungal ; Meiosis/genetics ; Molecular Sequence Data ; Mutation ; Neurospora/enzymology ; Neurospora/genetics ; Neurospora/physiology ; Nuclear Envelope/enzymology ; Nuclear Envelope/metabolism ; RNA Replicase/analysis ; RNA Replicase/metabolism ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; Reproduction/genetics ; Spores, Fungal/genetics
Chemical Substances	DNA, Fungal ; Fungal Proteins ; RNA, Small Interfering ; RNA Replicase (EC 2.7.7.48)
Language	English
Publishing date	2006-02-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.0508896103
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