A combination of metabolome and transcriptome analyses reveals new targets of the Corynebacterium glutamicum nitrogen regulator AmtR

Buchinger, Sebastian; Strösser, Julia; Rehm, Nadine; Hänssler, Eva; Hans, Stephan; Bathe, Brigitte; Schomburg, Dietmar; Krämer, Reinhard; Burkovski, Andreas

doi:10.1016/j.jbiotec.2008.10.009

Cited by 37 publications

(33 citation statements)

References 35 publications

(22 reference statements)

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“…Its sevenfold increased expression in glutamine-grown cells might indicate that its activity with glutamine is lower than with ammonia. The pyrG gene could be a novel member of the AmtR regulon, as its expression was also threefold increased in a DamtR mutant compared with the wild-type (Buchinger et al, 2009). …”

Section: Discussionmentioning

confidence: 99%

“…Expression of nitrogencontrolled genes is regulated by the TetR-family protein AmtR (Jakoby et al, 2000), which blocks transcription of various genes during growth in nitrogen-rich medium. At least 35 genes are directly controlled by the AmtR repressor (Beckers et al, 2005;Buchinger et al, 2009) and these encode transporters and enzymes for ammonium assimilation (amtA, amtB, glnA, gltBD, dapA), creatinine (codA, crnT) and urea (urtABCDE, ureABCEFGD) metabolism, a number of biochemically uncharacterized enzymes and transport systems, as well as signal transduction proteins (glnD, glnK). In contrast with most TetR-type regulators, the dissociation of AmtR from its target promoters is not triggered by the binding of a low-molecular mass ligand, but by complex formation with the PII-type signal transduction protein GlnK (Beckers et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

“…Adenylylation is catalysed by the adenylyltransferase GlnD in response to nitrogen deprivation, but it is not yet clear how this is sensed by the enzyme. Global analyses on nitrogen metabolism focused on either AmtR (Buchinger et al, 2009) or the cell's response to ammonium limitation or starvation (Silberbach et al, 2005a, b).…”

Section: Introductionmentioning

confidence: 99%

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l-Glutamine as a nitrogen source for Corynebacterium glutamicum: derepression of the AmtR regulon and implications for nitrogen sensing

et al. 2010

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Corynebacterium glutamicum, a Gram-positive soil bacterium employed in the industrial production of various amino acids, is able to use a number of different nitrogen sources, such as ammonium, urea or creatinine. This study shows that l-glutamine serves as an excellent nitrogen source for C. glutamicum and allows similar growth rates in glucose minimal medium to those in ammonium. A transcriptome comparison revealed that the nitrogen starvation response was elicited when glutamine served as the sole nitrogen source, meaning that the target genes of the global nitrogen regulator AmtR were derepressed. Subsequent growth experiments with a variety of mutants defective in nitrogen metabolism showed that glutamate synthase is crucial for glutamine utilization, while a putative glutaminase is dispensable under the experimental conditions used. The gltBD operon encoding the glutamate synthase is a member of the AmtR regulon. The observation that the nitrogen starvation response was elicited at high intracellular l-glutamine levels has implications for nitrogen sensing. In contrast with other Gram-positive and Gram-negative bacteria such as Bacillus subtilis, Salmonella enterica serovar Typhimurium and Klebsiella pneumoniae, a drop in glutamine concentration obviously does not serve as a nitrogen starvation signal in C. glutamicum.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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l-Glutamine as a nitrogen source for Corynebacterium glutamicum: derepression of the AmtR regulon and implications for nitrogen sensing

et al. 2010

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“…Metabolomics can reveal the changes at metabolite level and reflect the phenotype directly, and therefore has been applied in a broad range of studies in various fields (Adamski and Suhre 2012;Putri et al 2013). Although more and more investigations are carried out to reveal the molecular mechanisms of cellular pathways in microbes using metabolomic technologies (Buchinger et al 2009;Yuan et al 2009), the metabolomic profilings of the host bacteria associated with the bacteriophage infection are still unclear.…”

Section: Introductionmentioning

confidence: 99%

The effect of tryptophol on the bacteriophage infection in high-temperature environment

Jin

Zhang

2015

Appl Microbiol Biotechnol

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Small metabolites can participate in the virus-host interactions in eukaryotes. However, little is known about roles of metabolites in the interactions between bacteria and bacteriophages. In this study, the metabolomic profilings of bacteriophage GVE2-infected and virus-free Geobacillus sp. E263, a thermophilic bacterium isolated from a deep-sea hydrothermal vent, were characterized. The results showed that metabolites tryptophol, adenine, and hydroxybenzylalcohol were significantly elevated in Geobacillus sp. E263 in response to the GVE2 infection. Furthermore, our data indicated that tryptophol was involved in the bacteriophage infection. Tryptophol could inhibit the infection/replication of GVE2 by interacting with the host's Clp protease. Therefore, our study revealed novel aspects of metabolites during the bacteriophage infection in high-temperature environment.

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“…For a rough microbial phenotyping, it could be sufficient to use qualitative and semiquantitative data if the expected difference in the metabolome of a mutant strain in reference to the parental strain is significant enough [12,13]. Nevertheless, the same information quality is usually not sufficient to serve for mathematical modeling and validation of a mechanistic metabolic model.…”

Section: Introductionmentioning

confidence: 99%

Metabolomics in Biotechnology (Microbial Metabolomics)

Oldiges

Noack

Paczia

2013

Metabolomics in Practice

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IntroductionThe first documentation of the term metabolomics goes back to two independent publications in 1998 and was used in the context of describing the metabolic behavior of microbial systems, showing a distinct phenotype regarding their physiology and extracellular metabolite spectrum [1,2]. For sure, these were not the first publications with such research activity, but these were the ones which obviously coined the term metabolomics. Later on, this term was picked up by the scientific community not only for the microbial field but also for many other scientific areas and paved its way to become one of the representatives of the omics era. In this sense, the suffix -ome is ''used to direct attention to holistic abstractions, an eventual goal, of which only a few parts may be initially in hand'' [3] and its origin goes back to the early twentieth century. Initially, the German botanist Hans Winkler is attributed to have coined the term genome by the combination of the terms gene and chromosome (Greek word soma = body) [4]. This keyword functioned as blueprint for the many other -omes that are currently investigated. Finally, they all go back to the Greek word soma and in opposite to the genome this term seems to be not precisely fitting for the metabolome, as the metabolites are not located or arranged in a body, but are distributed all over the system.Since 1998, the term metabolomics was increasingly used in the literature showing significant increase (Figure 15.1) and indicating the fast development of the field.The field of microbial metabolomics can be subdivided into the investigation of the endo-and exo-metabolome (intra-vs extracellular) as well as different approaches such as target analysis, metabolic profiling, and metabolic finger-/footprinting (Figure 15.2) [5,6]. On the one hand, the target analysis aims at the quantitative analysis of substrate and/or product metabolites of a given metabolic conversion, whereas metabolic profiling focuses on the quantitative analysis of a set of predefined metabolites belonging to a class of compounds or members of particular pathways or a linked group of metabolites (e.g., sugars, sugar phosphates, lipids, organic acids). On the other hand, metabolic Metabolomics in Practice: Successful Strategies to Generate and Analyze Metabolic Data, First Edition. Edited by Michael Lämmerhofer and Wolfram Weckwerth.

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A combination of metabolome and transcriptome analyses reveals new targets of the Corynebacterium glutamicum nitrogen regulator AmtR

Cited by 37 publications

References 35 publications

l-Glutamine as a nitrogen source for Corynebacterium glutamicum: derepression of the AmtR regulon and implications for nitrogen sensing

l-Glutamine as a nitrogen source for Corynebacterium glutamicum: derepression of the AmtR regulon and implications for nitrogen sensing

The effect of tryptophol on the bacteriophage infection in high-temperature environment

Metabolomics in Biotechnology (Microbial Metabolomics)

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