Systems Analysis Unfolds the Relationship between the Phosphoketolase Pathway and Growth in Aspergillus nidulans

Panagiotou, Gianni; Andersen, Mikael Rørdam; Grotkjær, Thomas; Regueira, Torsten Ulrik Bak; Hofmann, Gerald; Nielsen, Jens; Olsson, Lisbeth

doi:10.1371/journal.pone.0003847

Cited by 40 publications

(33 citation statements)

References 31 publications

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“…To the best of our knowledge, this is the first time that the in vivo activity of the phosphoketolase pathway in clostridia has been revealed. So far, the existence of the phosphoketolase pathway has been described only for the lactic acid bacteria (3), bifidobacteria (22), and yeast and filamentous fungi (28,36).…”

Section: Discussionmentioning

confidence: 99%

Phosphoketolase Pathway for Xylose Catabolism in Clostridium acetobutylicum Revealed by ¹³ C Metabolic Flux Analysis

et al. 2012

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b Solvent-producing clostridia are capable of utilizing pentose sugars, including xylose and arabinose; however, little is known about how pentose sugars are catabolized through the metabolic pathways in clostridia. In this study, we identified the xylose catabolic pathways and quantified their fluxes in Clostridium acetobutylicum based on [1-13 C]xylose labeling experiments. The phosphoketolase pathway was found to be active, which contributed up to 40% of the xylose catabolic flux in C. acetobutylicum. The split ratio of the phosphoketolase pathway to the pentose phosphate pathway was markedly increased when the xylose concentration in the culture medium was increased from 10 to 20 g liter ؊1 . To our knowledge, this is the first time that the in vivo activity of the phosphoketolase pathway in clostridia has been revealed. A phosphoketolase from C. acetobutylicum was purified and characterized, and its activity with xylulose-5-P was verified. The phosphoketolase was overexpressed in C. acetobutylicum, which resulted in slightly increased xylose consumption rates during the exponential growth phase and a high level of acetate accumulation. Substrate cost is a major factor impacting the economics of fermentative solvent production by clostridia (7, 21). To reduce the substrate cost, abundant and inexpensive lignocellulosic materials could be used, and one of their major components is pentose-rich hemicellulose (15). Solventogenic clostridia, including Clostridium acetobutylicum and Clostridium beijerinckii, are capable of utilizing the hemicellulosic pentoses xylose and arabinose (25). However, knowledge of clostridial pentose metabolism is very limited.Recently, our group has characterized two key enzymes in the xylose utilization pathway of C. acetobutylicum, xylose isomerase and xylulokinase, which convert xylose to xylulose-5-P (14). In many bacteria such as Escherichia coli, xylulose-5-P is further catabolized to form the central intermediate glyceraldehyde-3-P by the pentose phosphate pathway enzymes, including transketolase and transaldolase. Another xylose catabolic pathway through the phosphoketolase is found to be present in heterofermentative and facultative homofermentative lactic acid bacteria (19, 37). The thiamine diphosphate-dependent phosphoketolases (EC 4.1.2.9) cleave xylulose-5-P into acetyl-P and glyceraldehyde-3-P. In bifidobacteria, phosphoketolases are key enzymes of the fructose-6-P shunt to convert fructose-6-P to acetyl-P and erythrose-4-P (12, 34).Little is known about how xylose is metabolized through the metabolic pathways in solventogenic clostridia. Recent studies have shown that genes of the pentose phosphate pathway and a putative phosphoketolase-encoding gene in C. acetobutylicum are induced by pentose sugars (13, 33). However, the contribution of individual pathways to clostridial xylose catabolism has not been analyzed. To manipulate clostridia for efficient xylose utilization, it is important to gain insight into the responses of xylose catabolic pathways to environmental an...

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Section: Discussionmentioning

confidence: 99%

Phosphoketolase Pathway for Xylose Catabolism in Clostridium acetobutylicum Revealed by ¹³ C Metabolic Flux Analysis

et al. 2012

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“…However, a recent study on Aspergillus nidulans suggests that XFP provides greater flexibility to central metabolism: higher specific growth rates and growth yields were observed with xylose, glycerol or ethanol when XFP was overexpressed in A. nidulans . Moreover, the overexpression of XFP resulted in high conversion yields of sugars to secondary metabolites originating from acetyl-CoA at the expense of a lower flux through glycolysis [Panagiotou et al, 2008]. Theoretically, the degradation of pentoses through XFP would be energetically advantageous over the classical pentose phosphate pathway since an additional ATP can be gained from degradation of acetyl-P to acetate [Wolfe, 2005].…”

Section: Discussionmentioning

confidence: 99%

Bacterial and Eukaryotic Phosphoketolases: Phylogeny, Distribution and Evolution

et al. 2010

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Phosphoketolases (XFPs) are glycolytic enzymes present in several organisms belonging to the Eukarya and Bacteria domains. A total of 151 putative xfp genes were detected in 650 complete genomes available in public databases. Elimination of redundant sequences and pseudogenes rendered a final data set of 128 phosphoketolases, which was analyzed by phylogenetic methods. The distribution of xfp genes was uneven in most taxonomic groups, with the exception of the taxonomical division Lactobacillaceae, in which all the species studied harbored a putative xfp gene. Putative xfp genes were also present predominantly in Rhizobiales and Actinobacteria divisions, in which 23 out of 28 genomes and 23 out of 41 genomes contained at least one putative xfp homolog, respectively. Phylogenetic analyses showed clear discordance with the expected order of organismal descent even in groups where xfp is prevalent, such as Lactobacillaceae. The presence of putative paralogs in some organisms cannot account for these discrepancies; instead, these paralogs are most possibly xenologs. The results of the phylogenetic analyses, the distribution of xfp genes and the location of some xfp genes in plasmids are independent pieces of evidence that point to horizontal gene transfer as a major driving force in the evolution of phosphoketolases.

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“…Carbon sources used were glucose monohydrate or glycerol (15 g L ¡1 ). A. nidulans batch cultivation medium is reported in Panagiotou et al (2008).…”

Section: Growth Mediummentioning

confidence: 99%

Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis

et al. 2009

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Glycerol is catabolized by a wide range of microorganisms including Aspergillus species. To identify the transcriptional regulation of glycerol metabolism in Aspergillus, we analyzed data from triplicate batch fermentations of three different Aspergilli (Aspergillus nidulans, Aspergillus oryzae and Aspergillus niger) with glucose and glycerol as carbon sources. Protein comparisons and cross-analysis with gene expression data of all three species resulted in the identification of 88 genes having a conserved response across the three Aspergilli. A promoter analysis of the up-regulated genes led to the identification of a conserved binding site for a putative regulator to be 5'-TGCGGGGA-3', a binding site that is similar to the binding site for Adr1 in yeast and humans. We show that this Adr1 consensus binding sequence was over-represented on promoter regions of several genes in A. nidulans, A. oryzae and A. niger. Our transcriptome analysis indicated that genes involved in ethanol, glycerol, fatty acid, amino acids and formate utilization are putatively regulated by Adr1 in Aspergilli as in Saccharomyces cerevisiae and this transcription factor therefore is likely to be cross-species conserved among Saccharomyces and distant Ascomycetes. Transcriptome data were further used to evaluate the high osmolarity glycerol pathway. All the components of this pathway present in yeast have orthologues in the three Aspergilli studied and its gene expression response suggested that this pathway functions as in S. cerevisiae. Our study clearly demonstrates that cross-species evolutionary comparisons among filamentous fungi, using comparative genomics and transcriptomics, are a powerful tool for uncovering regulatory systems.

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Systems Analysis Unfolds the Relationship between the Phosphoketolase Pathway and Growth in Aspergillus nidulans

Cited by 40 publications

References 31 publications

Phosphoketolase Pathway for Xylose Catabolism in Clostridium acetobutylicum Revealed by ¹³ C Metabolic Flux Analysis

Phosphoketolase Pathway for Xylose Catabolism in Clostridium acetobutylicum Revealed by ¹³ C Metabolic Flux Analysis

Bacterial and Eukaryotic Phosphoketolases: Phylogeny, Distribution and Evolution

Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis

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Systems Analysis Unfolds the Relationship between the Phosphoketolase Pathway and Growth in Aspergillus nidulans

Cited by 40 publications

References 31 publications

Phosphoketolase Pathway for Xylose Catabolism in Clostridium acetobutylicum Revealed by 13 C Metabolic Flux Analysis

Phosphoketolase Pathway for Xylose Catabolism in Clostridium acetobutylicum Revealed by 13 C Metabolic Flux Analysis

Bacterial and Eukaryotic Phosphoketolases: Phylogeny, Distribution and Evolution

Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis

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Phosphoketolase Pathway for Xylose Catabolism in Clostridium acetobutylicum Revealed by ¹³ C Metabolic Flux Analysis

Phosphoketolase Pathway for Xylose Catabolism in Clostridium acetobutylicum Revealed by ¹³ C Metabolic Flux Analysis