SAD-3, a Putative Helicase Required for Meiotic Silencing by Unpaired DNA, Interacts with Other Components of the Silencing Machinery

Hammond, Thomas M.; Xiao, Hua; Boone, Erin C.; Perdue, Tony D.; Pukkila, Patricia J.; Shiu, Patrick

doi:10.1534/g3.111.000570

Cited by 47 publications

(79 citation statements)

References 23 publications

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“…A VanGuard 1274ZH microscope (equipped with a Canon Power Shot S3 IS digital camera) was used to examine and photograph the collected asci under magnification. Visual examination of ascospore production, using fluffy (fl) strains as designated females, was performed as previously described (35).…”

Section: Methodsmentioning

confidence: 99%

Molecular dissection of Neurospora Spore killer meiotic drive elements

Hammond

Rehard

Xiao

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Meiotic drive is a non-Mendelian inheritance phenomenon in which certain selfish genetic elements skew sexual transmission in their own favor. In some cases, progeny or gametes carrying a meiotic drive element can survive preferentially because it causes the death or malfunctioning of those that do not carry it. In Neurospora, meiotic drive can be observed in fungal spore killing. In a cross of Spore killer (Sk) × WT (Sk-sensitive), the ascospores containing the Spore killer allele survive, whereas the ones with the sensitive allele degenerate. Sk-2 and Sk-3 are the most studied meiotic drive elements in Neurospora, and they each theoretically contain two essential components: a killer element and a resistance gene. Here we report the identification and characterization of the Sk resistance gene, rsk (resistant to Spore killer). rsk seems to be a fungal-specific gene, and its deletion in a killer strain leads to self-killing. Sk-2, Sk-3, and naturally resistant isolates all use rsk for resistance. In each killer system, rsk sequences from an Sk strain and a resistant isolate are highly similar, suggesting that they share the same origin. Sk-2, Sk-3, and sensitive rsk alleles differ from each other by their unique indel patterns. Contrary to long-held belief, the killer targets not only late but also early ascospore development. The WT RSK protein is dispensable for ascospore production and is not a target of the spore-killing mechanism. Rather, a resistant version of RSK likely neutralizes the killer element and prevents it from interfering with ascospore development.intragenomic conflict | segregation distortion | selfish elements I n fungi, plants, and animals, not all genes follow the Mendelian pattern of inheritance. Meiotic drive, sometimes referred to as segregation distortion, describes the phenomenon in which certain "cheating" alleles are recovered in more than half of the progeny (1). Two well-known examples are the segregation distorter (SD) in Drosophila and the t haplotype in Mus. In these cases, sperm not carrying the aggressive allele (the drive element) either degenerate (in flies) or become functionally impaired (in mice) (2, 3). In fungi, meiotic drive can be observed as spore killing, in which ascospores (sexual spores) that carry the "Spore killer" element survive preferentially (4). Examples of spore killing can be found in Neurospora sitophila, Neurospora intermedia, Podospora anserina, Gibberella fujikuroi, and Cochliobolus heterostrophus.Spore killer-2 (Sk-2) and Spore killer-3 (Sk-3), which behave similarly, are the most studied distortion elements in Neurospora (5). Originally discovered in N. intermedia, the two spore-killing factors have been introgressed into Neurospora crassa for extensive genetic studies. In a Spore killer (Sk) × WT (Sk-sensitive or Sk S ) cross, regardless of which acts as the female, the four Skcontaining spores are black (B) and viable, whereas the four Sksensitive spores are white (W) and inviable. Manifestation of killing does not occur until late ascospore de...

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Section: Methodsmentioning

confidence: 99%

Molecular dissection of Neurospora Spore killer meiotic drive elements

Hammond

Rehard

Xiao

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…Further screens for meiotic silencing factors identified two RNAi-related genes in addition to Sad-1: an Argonaute-like protein, suppressor of meiotic silencing-2 (Sms-2; Lee et al 2003); and a Dicer-like protein, suppressor of meiotic silencing-3 (Dcl-1/Sms-3; Alexander et al 2008). In addition, the involvement of a putative helicase, Sad-3, has been reported (Hammond et al 2011). Several other Sms mutants have also been identified (DW Lee and R Aramayo, pers.…”

Section: R Aramayo and Eu Selkermentioning

confidence: 99%

Neurospora crassa, a Model System for Epigenetics Research

Aramayo

Selker

2013

Cold Spring Harbor Perspectives in Biology

133

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SUMMARYThe filamentous fungus Neurospora crassa has provided a rich source of knowledge on epigenetic phenomena that would have been difficult or impossible to gain from other systems. Neurospora sports features found in higher eukaryotes but absent in both budding and fission yeast, including DNA methylation and H3K27 methylation, and also has distinct RNA interference (RNAi)-based silencing mechanisms operating in mitotic and meiotic cells. This has provided an unexpected wealth of information on gene silencing systems. One silencing mechanism, named repeat-induced point mutation (RIP), has both epigenetic and genetic aspects and provided the first example of a homology-based genome defense system. A second silencing mechanism, named quelling, is an RNAi-based mechanism that results in silencing of transgenes and their native homologs. A third, named meiotic silencing, is also RNAi-based but is distinct from quelling in its time of action, targets, and apparent purpose.Outline

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“…This approach has since been adapted for use with the N. crassa knockout collection (Colot et al 2006). Essentially, strains from the collection are put through crosses where asm-1 + or r + is unpaired during meiosis (Hammond et al 2011a). The production of phenotypically normal ascospores in such crosses suggests that the knockout (i.e., deleted gene) suppresses MSUD, typically because the deleted gene encodes a necessary component of the MSUD machinery.…”

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“…sad-6 transcripts were at relatively high levels in both vegetative and sexual RNAs (10.93 and 22.61 RPKM), demonstrating that sad-6's expression pattern is more like those of quelling genes than of MSUD-specific genes. Its pattern is also similar to that of mus-25 (6.56 and 13.51 RPKM), which is known to Overall, sad-6's expression pattern suggests that it has roles in both vegetative and sexual processes.Characterization of basic developmental processes in sad-6 D strains Deletion or mutation of MSUD genes has not been observed to affect vegetative growth processes, such as growth rate, conidia production, or overall appearance under standard growth conditions (e.g., Hammond et al 2011aHammond et al , 2013b. We therefore performed assays to determine whether sad-6 D would be the first sad mutant associated with such defects.…”

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confidence: 99%

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Efficient Detection of Unpaired DNA Requires a Member of the Rad54-Like Family of Homologous Recombination Proteins

et al. 2014

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Meiotic silencing by unpaired DNA (MSUD) is a process that detects unpaired regions between homologous chromosomes and silences them for the duration of sexual development. While the phenomenon of MSUD is well recognized, the process that detects unpaired DNA is poorly understood. In this report, we provide two lines of evidence linking unpaired DNA detection to a physical search for DNA homology. First, we have found that a putative SNF2-family protein (SAD-6) is required for efficient MSUD in Neurospora crassa. SAD-6 is closely related to Rad54, a protein known to facilitate key steps in the repair of double-strand breaks by homologous recombination. Second, we have successfully masked unpaired DNA by placing identical transgenes at slightly different locations on homologous chromosomes. This masking falls apart when the distance between the transgenes is increased. We propose a model where unpaired DNA detection during MSUD is achieved through a spatially constrained search for DNA homology. The identity of SAD-6 as a Rad54 paralog suggests that this process may be similar to the searching mechanism used during homologous recombination. MEIOSIS is fundamental to sexual reproduction. During meiosis, chromosomes are replicated, aligned, recombined, and segregated to nuclei that will develop into gametes. Two of these key processes, alignment and recombination, likely require a search for DNA homology between chromosomes (Barzel and Kupiec 2008;Moore and Shaw 2009). Such homology searching is necessary because sexual organisms inherit a copy of each chromosome from each of its parents. These chromosomes, referred to as homologs, must somehow find each other so that alignment, recombination, and segregation can occur.Although recent research has improved our understanding of homology search mechanisms (Forget and Kowalczykowski 2012;Renkawitz et al. 2013), there are many questions that remain unanswered. The filamentous fungus Neurospora crassa may be useful for investigating the unknowns of homology searching because it possesses a genetically tractable phenomenon called meiotic silencing by unpaired DNA (MSUD) (Aramayo and Selker 2013;Billmyre et al. 2013). MSUD scans pairs of homologs for segments of DNA that are not accurately paired between them. If improper pairing (i.e., unpairing) is identified, the offending sequences are silenced for the duration of sexual development. For example, if a hypothetical gene called "gene A" is on the left arm of one chromosome but on the right arm of its homolog, it will be silenced. The same holds true if gene A has been lost from one of the homologs.A functional MSUD response can be easily detected with alleles that affect ascospore (sexual spore) color or shape. Indeed, MSUD was discovered during studies of ascospore maturation-1 (asm-1), a gene required for the production of pigmented (black) ascospores . A cross between an asm-1 + strain and an asm-1 D strain produces mostly unpigmented (white) ascospores. This is because MSUD silences the unpaired asm-1 + all...

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SAD-3, a Putative Helicase Required for Meiotic Silencing by Unpaired DNA, Interacts with Other Components of the Silencing Machinery

Cited by 47 publications

References 23 publications

Molecular dissection of Neurospora Spore killer meiotic drive elements

Molecular dissection of Neurospora Spore killer meiotic drive elements

Neurospora crassa, a Model System for Epigenetics Research

Efficient Detection of Unpaired DNA Requires a Member of the Rad54-Like Family of Homologous Recombination Proteins

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