Genomics for Fungi

Bennett, Joan W.; Arnold, Jonathan

doi:10.1007/978-3-662-06101-5_13

Cited by 19 publications

(10 citation statements)

References 179 publications

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“…For the first time, scientists both in industry and research institutes can investigate the high ability of these organisms in product (acid) formation. Unlocking the biochemical networks and the regulatory mechanisms may provide an opportunity for their manipulation by amplifying or deleting critical steps in metabolism to improve acid production or to overproduce novel metabolites 73, 80, 81. The new information available will allow the application of systems biology in fungi, despite the present lack of databases for metabolite concentrations in cells 82.…”

Section: Perspectivesmentioning

confidence: 99%

Organic acids: old metabolites, new themes

Goldberg

Rokem

Pines

2006

J of Chemical Tech & Biotech

231

176

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Fumaric, L-malic and citric acids are intermediates of the oxidative tricarboxylic acid (TCA) cycle which in eukaryotes is localized in mitochondria. These organic acids are synthesized and accumulated in the medium to very high concentrations by filamentous fungi such as Aspergillus spp. and Rhizopus sp. This article reviews basic research on the unusual acid production capability and the associated metabolic pathways operating under defined stress conditions in these specific fungi. In particular, we describe and discuss the importance of the cytosolic reductive TCA pathway, which includes the cytosolic activities of pyruvate carboxylase, malate dehydrogenase and fumarase, for production of fumaric and L-malic acids. This article also describes the differences between fumaric acid, L-malic acid and citric acid production by different organisms (filamentous fungi, yeast, and higher eukaryotes), and the possible application of novel technologies (genetic engineering and bioinformatics) to fungal systems which may offer new industrial potential of filamentous fungi for the production of valuable metabolites.

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Section: Perspectivesmentioning

confidence: 99%

Organic acids: old metabolites, new themes

Goldberg

Rokem

Pines

2006

J of Chemical Tech & Biotech

231

176

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“…(1) Based on a typical fungal expressed sequence tag (EST) project with 5000 ESTs and a fungal genome with 8000-9000 genes (Bennett and Arnold 2001), the fraction of genes detected would be expected to be 1 Ϫ exp(Ϫ5000/8000) ϭ 0.46. (2) In addition, an empirical rule is that about 50% of fungal genes in EST collections will have fungal orthologs (Column 6 of Table 2 in Prade et al 2001).…”

Section: Resultsmentioning

confidence: 99%

“…The minimal gene complement of 256 genes essential to a bacterium, Mycoplasma genitalium with its about 700 kbp genome (one of the smallest), was recently identified by insertional mutagenesis (Hutchison et al 1999). The question is whether or not there is a counterpart to Mycoplasma among eukaryotes that could be exploited to identify the minimal complement of genes shared by most eukaryotes and necessary to build a eukaryotic system, i.e., the essential eukaryotic core (Bennett and Arnold 2001). Pneumocystis, the major AIDs-related pathogen, is unusual in its biology in several respects, and having a list of its essential genes would be useful in selecting new drug targets (Cushion 1998).…”

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confidence: 99%

Essential Eukaryotic Core

Strobel

Arnold

2004

Evolution

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Abstract. The AIDs-related fungal pathogen Pneumocystis carinii is unusual in having a remarkably compact genome of 7.7 megabase pairs (mbp) whose small size presents the opportunity to identify the essential eukaryotic core of genes. The essential eukaryotic core is defined to be a collection of essential genes shared by all eukaryotes. Sequencing the 3Ј ends of more than 5500 cDNAs from P. carinii allowed us to identify about 200 genes shared with its nearest known but distant relative, Schizosaccharomyces pombe and also Saccharomyces cerevisiae, and with homologs known to be essential in S. pombe or S. cerevisae. As the cDNA library contains about one half of the P. carinii genes, the size of the essential eukaryotic core (ϳ400) is slightly larger than the prokaryotic core (265-350) being identified by studies of the bacterial pathogen Mycoplasma genitalium. The collection of genes in the essential eukaryotic core may prove useful in identifying new broad spectrum antifungal drug targets. The minimal gene complement of 256 genes essential to a bacterium, Mycoplasma genitalium with its about 700 kbp genome (one of the smallest), was recently identified by insertional mutagenesis (Hutchison et al. 1999). The question is whether or not there is a counterpart to Mycoplasma among eukaryotes that could be exploited to identify the minimal complement of genes shared by most eukaryotes and necessary to build a eukaryotic system, i.e., the essential eukaryotic core (Bennett and Arnold 2001). Pneumocystis, the major AIDs-related pathogen, is unusual in its biology in several respects, and having a list of its essential genes would be useful in selecting new drug targets (Cushion 1998). It has a compact genome of 7.7 mbp (Cushion et al. 1993) and no close relatives outside the genus to highlight shared features with other fungi (Cushion 1998). Extensive sequence of this genome is accumulating as part of the Pneumocystis Genome project (Xu et al. 2003). The sequence of Pneumocystis carinii can be compared with several nearly fully sequenced fungal genomes (Goffeau et al. 1996;Galagan et al. 2003). Two of these relatives of P. carinii, Schizosaccharomyces pombe and S. cerevisiae, have extensive data identifying their essential fungal genes (Winzeler et al. 1999). In this report we infer the essential eukaryotic core by utilizing the small genome size of P. carinii, its isolated phylogenetic position as a basal ascomycete (Edman et al. 1988) and the partial sequences of about one half of its genes having homologs to essential genes in S. pombe or S. cerevisiae. MATERIALS AND METHODSBecause P. carinii is uncultivable, cosmid and cDNA libraries were derived from the karyotype of P. carinii form 1, extracted from the lungs of immunologically suppressed rats during fulminate infection (Xu et al. 2003). Library construction from this karyotype is detailed in Smulian et al. (2001) and at http://pneumocystis.uc.edu. The cDNA library used in this study is in the vector pSK11, and the entire cDNA library is available from the Ameri...

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“…Recent technological breakthroughs allow scientists to sequence and annotate genomes in a very short time frame. A combination of expressed sequence tags (EST), whole genome sequencing, and microarray technologies provides highthroughput capabilities (Bennett and Arnold 2001, Kim et al 2006, Payne et al 2006, Yu et al 2004a that can be applied to the identification of genes involved in aflatoxin production and for studying the regulatory mechanisms of gene expression (i.e., functional genomics).…”

Section: Genomics Of Aspergillus Flavusmentioning

confidence: 99%