A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability

Schmid, Amy K.; Reiss, David J; Pan, Min; Koide, Tie; Baliga, Nitin S.

doi:10.1038/msb.2009.40

Cited by 58 publications

(145 citation statements)

References 53 publications

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“…Although all genes required for a functional spED pathway as well as gluconeogenesis via the EMP pathway were identified in the genome of Hbt. salinarum, no growth with glucose as the sole carbon source has been reported so far (180,369,397,562). For a functional npED pathway, only GK is missing (252).…”

Section: Fig 27mentioning

confidence: 99%

“…furiosus) (for review and literature, see references 27 and 28). This exciting progress allowed the unraveling of protein function in vivo and qualifies Archaea as model organisms for synthetic biology and systems biology (303,397,398). Thus, within the last years, the first genome-wide metabolic models, flux balance analysis (FBA), as well as first detailed reaction kinetic models were established for Archaea (338,(399)(400)(401)(402)(403)(404).…”

Section: Metabolic and Regulatory Characteristics Of Well-studied Arcmentioning

confidence: 99%

“…salinarum is not able to utilize glucose as the sole carbon source, glucose seems to play an important role in Hbt. salinarium cell metabo-lism, as concluded from studies of the TrmB family transcription factor (VNG1451C; TrmBL1 homolog) and its regulatory function by using a systems biology approach (397). A VNG1451C deletion strain was constructed and phenotypically characterized.…”

Section: Fig 27mentioning

confidence: 99%

“…Transcriptomic studies as well as genome-wide promoter binding studies (chromatin immunoprecipitation with microarray technology [ChIP-chip]) and promoter-reporter fusion assays for selected genes were performed with the ⌬trmB mutant in comparison to the parent strain. Finally, computational integration was used to construct transcriptional and metabolic networks regulated by the TrmB family transcription factor (397). In summary, binding of the TrmB-like protein to 113 promoters {cis-regulatory element [TA CT-N (7)(8) GAGTA]} was found but only in the absence of glucose and glycerol.…”

Section: Fig 27mentioning

confidence: 99%

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Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

265

286

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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Section: Fig 27mentioning

confidence: 99%

Section: Metabolic and Regulatory Characteristics Of Well-studied Arcmentioning

confidence: 99%

Section: Fig 27mentioning

confidence: 99%

Section: Fig 27mentioning

confidence: 99%

See 2 more Smart Citations

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

265

286

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show abstract

“…Molecular data pertaining to haloarchaeal transcriptional regulation, specifically regulators of carbon utilization, are severely limited. Only a few global regulators, namely, transcription factors (8,11,36), have been implicated in regulating carbon utilization in haloarchaea. Specifically, in Halobacterium salinarium, pairs of general transcription factors TBP and TFB control gene clusters (8,11), and transcription factor TrmB regulates diverse metabolic pathways in response to nutrient limitation (36).…”

mentioning

confidence: 99%

GlpR Represses Fructose and Glucose Metabolic Enzymes at the Level of Transcription in the HaloarchaeonHaloferax volcanii

2010

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In this study, a DeoR/GlpR-type transcription factor was investigated for its potential role as a global regulator of sugar metabolism in haloarchaea, using Haloferax volcanii as a model organism. Common to a number of haloarchaea and Gram-positive bacterial species, the encoding glpR gene was chromosomally linked with genes of sugar metabolism. In H. volcanii, glpR was cotranscribed with the downstream phosphofructokinase (PFK; pfkB) gene, and the transcript levels of this glpR-pfkB operon were 10-to 20-fold higher when cells were grown on fructose or glucose than when they were grown on glycerol alone. GlpR was required for repression on glycerol based on significant increases in the levels of PFK (pfkB) transcript and enzyme activity detected upon deletion of glpR from the genome. Deletion of glpR also resulted in significant increases in both the activity and the transcript (kdgK1) levels of 2-keto-3-deoxy-D-gluconate kinase (KDGK), a key enzyme of haloarchaeal glucose metabolism, when cells were grown on glycerol, compared to the levels obtained for media with glucose. Promoter fusions to a ␤-galactosidase bgaH reporter revealed that transcription of glpR-pfkB and kdgK1 was modulated by carbon source and GlpR, consistent with quantitative reverse transcription-PCR (qRT-PCR) and enzyme activity assays. The results presented here provide genetic and biochemical evidence that GlpR controls both fructose and glucose metabolic enzymes through transcriptional repression of the glpR-pfkB operon and kdgK1 during growth on glycerol.The archaeal basal transcriptional machinery closely resembles the eucaryal RNA polymerase II (RNAP II) apparatus. Along with a multisubunit RNAP (46), archaea encode two basal transcription factors, TATA-binding protein (TBP) and transcription factor B (TFB), which are homologs of the eucaryal TBP and general transcription factor TFIIB, respectively (5, 39). Although archaeal transcriptional components are fundamentally eukaryote-like in nature (35), the majority of candidate transcriptional regulators are homologous to bacterial activators and repressors (2, 26). Only a few archaeal candidate regulators resemble eukaryotic gene-specific transcription factors, one of the best characterized of which is GvpE, an activator of gas vesicle biosynthesis in haloarchaea which resembles the eukaryotic basic leucine zipper proteins (25, 31). While bioinformatics predicts many candidate archaeal regulators, only a limited number have been characterized at the molecular level, most of which are from hyperthermophiles (4,13,23,24,27,42). Molecular data pertaining to haloarchaeal transcriptional regulation, specifically regulators of carbon utilization, are severely limited. Only a few global regulators, namely, transcription factors (8, 11, 36), have been implicated in regulating carbon utilization in haloarchaea. Specifically, in Halobacterium salinarium, pairs of general transcription factors TBP and TFB control gene clusters (8, 11), and transcription factor TrmB regulates diverse metabolic pathwa...

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Extremozymes: Biocatalysts From Extremophilic Microorganisms and Their Relevance in Current Biotechnology

Singh

Ray

2021

Environmental and Agricultural Microbiology

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A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability

Cited by 58 publications

References 53 publications

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

GlpR Represses Fructose and Glucose Metabolic Enzymes at the Level of Transcription in the HaloarchaeonHaloferax volcanii

Extremozymes: Biocatalysts From Extremophilic Microorganisms and Their Relevance in Current Biotechnology

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