Genetics and some characteristics of acetate-requiring strains in Neurospora crassa.

Kuwana, Homare; Okumura, Ryota

doi:10.1266/jjg.54.235

Cited by 13 publications

(11 citation statements)

References 25 publications

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“…According to experimental observation, mutants in ace-2 , ace-3 and ace - 4 can grow in acetate minimal media, because the enzymes in the glyoxysome are induced when extracellular acetate is present in the medium [83]. Conversely, ace-2 , ace-3 and ace-4 mutants cannot grow in sucrose minimal media, even though sucrose can be converted to acetate intracellularly, because the glyoxysomal enzymes are not expressed in this condition [1].…”

Section: Resultsmentioning

confidence: 99%

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

et al. 2013

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The filamentous fungus Neurospora crassa played a central role in the development of twentieth-century genetics, biochemistry and molecular biology, and continues to serve as a model organism for eukaryotic biology. Here, we have reconstructed a genome-scale model of its metabolism. This model consists of 836 metabolic genes, 257 pathways, 6 cellular compartments, and is supported by extensive manual curation of 491 literature citations. To aid our reconstruction, we developed three optimization-based algorithms, which together comprise Fast Automated Reconstruction of Metabolism (FARM). These algorithms are: LInear MEtabolite Dilution Flux Balance Analysis (limed-FBA), which predicts flux while linearly accounting for metabolite dilution; One-step functional Pruning (OnePrune), which removes blocked reactions with a single compact linear program; and Consistent Reproduction Of growth/no-growth Phenotype (CROP), which reconciles differences between in silico and experimental gene essentiality faster than previous approaches. Against an independent test set of more than 300 essential/non-essential genes that were not used to train the model, the model displays 93% sensitivity and specificity. We also used the model to simulate the biochemical genetics experiments originally performed on Neurospora by comprehensively predicting nutrient rescue of essential genes and synthetic lethal interactions, and we provide detailed pathway-based mechanistic explanations of our predictions. Our model provides a reliable computational framework for the integration and interpretation of ongoing experimental efforts in Neurospora, and we anticipate that our methods will substantially reduce the manual effort required to develop high-quality genome-scale metabolic models for other organisms.

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Section: Resultsmentioning

confidence: 99%

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

et al. 2013

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“…The first eucaryotic complex mutant, a strain carryingpdhAl (linkage group I), was described by Romano and Kornberg (16), and Payton et al (12) found a second and unlinked gene pdhB (linkage group V). Isolation ofpdh mutants has also recently been reported for N. crassa (6). The present paper reports the isolation of a third unlinked gene for the complex pdhC (linkage group VIII).…”

mentioning

confidence: 55%

A third unlinked gene controlling the pyruvate dehydrogenase complex in Aspergillus nidulans

Bos¹,

Slakhorst²,

Visser³

et al. 1981

J Bacteriol

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Pyruvate dehydrogenase complex mutants of Aspergillus nidulans were obtained by ultraviolet treatment and enrichment procedures. Among 160 glycolytic mutants, 86 pyruvate dehydrogenase complex mutants (including some temperature-sensitive mutants) were found. In addition to genespdhA and pdhB, which are described in previous studies, a third gene, pdhC, controlling the function of the enzyme complex, was identified. The three genes were not linked and were mapped in the following linkage groups: pdhA in group I, pdhB in group V, and pdhC in group VIII, where it was the first marker on the left arm.

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“…col-k: colonial, lethal ascospore See le-l. com: compact IIIR. Between ace-2 (5%) and ad4 (<1 to 5%) (578,814).…”

Section: Aza: Azapurine Resistantmentioning

confidence: 99%

“…Between cut (4 to 10%) and pyr-i (12 to 19%) (PB). Right of ace4 (10 to 17%) (578). (812) Produces exudate in fissures formed under the agar and on the surface.…”

Section: Er: Eruptmentioning

confidence: 99%

Chromosomal loci of Neurospora crassa

Perkins¹,

Radford²,

Newmeyer³

et al. 1982

Microbiol Rev

263

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I I ' ~~~~T h Ñ CiOr(r r N z ADDITIONAL LOCI IN LINKAGE GROUP ILinked to mt (8 to 12%) Linked to mt, acr-3 (5%) Right of arg-i (5/29) Linked to so and aro-8 Right of un-18 Between ad-5 and the centromere Between arg-i (4%) and his-3 (I to 2%) Between In(H4250) and T(39311) Left of mt (23%) Linked to mt (2%) and aza-i (39%o) Left of nit-2 (30%) Left of mt (14%) Linked to un-i (9%), probably to the right Linked to hom (1%), probably to the right Linked to mt (17 to 22%) Between T(NM103) and al-2 (18%) Between T(4540) and cr-2Between thi-i (12 to 20%/6) and ad-9 (5%) Linked to ad-5 (1/54), probably to the left Linked to mt (6%) Linked to cys-5 (<1%), probably to the right Right of ad-9 (12%), linked to al (0/76) Right of his-3 (2%) Between the T(AR173) breakpoints Linked to al-2 (10%) and nic-i (1 to 5%) Linked to ad-9 (0/44); right of thi-i (2%) Linked to mt (5%), probably to the left Linked to al-I (10%) Right of os-i (3%) Between nit,i (5 to 19%) and al-I (6 to 19%io) Linked near arg-i Left of al-2 (25%o) Left of mt (16%) Right of nic-2 (6%) Linked to ad-9 (2%), probably to the right Left of cr-i (15%) Left of mt (10%) Probably between his-2 (3%) and cr-i (3%) Between T(NM103) and the right tip Between mt (20%) and arg-i (1%) Between ad-3 (6%) and al-i (16%) Between his-3 and nic-2 Between cyh-i (5%) and al-I (7%) Linked to cyh-i (18%), al-i (2%), and mb-2 (6%) Between arg-i (3%) and T(39311) Between tre (41%) and ad-9 Linked to mt (9%) Linked to mt (20%) Complex phenotype. Alternative requirements: 2-acetylaminofluorine, certain azo dyes, or certain single amino acids. Cold sensitive. Originated among progeny of a rib-i strain that had become tolerant to 2-acetylaminofluorine.

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Genetics and some characteristics of acetate-requiring strains in Neurospora crassa.

Cited by 13 publications

References 25 publications

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

A third unlinked gene controlling the pyruvate dehydrogenase complex in Aspergillus nidulans

Chromosomal loci of Neurospora crassa

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