Tomas Fiedler

About Tomas Fiedler:

Postdoc @ Institute of Medical Microbiology, University of Rostock

SEEK ID: https://fairdomhub.org/people/57

Location:  Germany

Expertise: Microbiology, Biochemistry, Molecular Biology, Streptococcus pyogenes

Tools: DNA technology RNA technology Protein analysis Fermentation Mutagenesis

ORCID: Not specified

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SysMO

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep

Web page: http://sysmo.net/

SysMO-LAB

Comparative Systems Biology: Lactic Acid Bacteria

Programme: SysMO

Public web page: http://www.sysmo.net/index.php?index=57

University of Rostock

Country:  Germany

City: Rostock

Web page: http://www.uni-rostock.de

BIOLOG substrate utilization assay
SysMO-LAB

S. pyogenes M49 (591), E. faecalis V583, and L. lacis NZ9000 and their isogenic ldh deletion mutants were grown glucose free CDM-LAB medium in BIOLOG phenotype microarray plates PM01 and PM02. With this assay the abilitiy of the strains to grow on 190 different carbon sources was determined in 96 well format.

Submitter: Tomas Fiedler

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

A series of fermentor runs of M49 (591) wild type and ldh knock out mutant strains at different pH (6.5 and 7.5) and dilution rates (0.05 1/h and 0.15 1/h).
SysMO-LAB
No description specified

Creator: Tomas Fiedler

Submitter: The JERM Harvester

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Effect of growth rate and pH on pyruvate branching when L-LDH is knocked out
SysMO-LAB
No description specified

Creator: Tomas Fiedler

Submitter: The JERM Harvester

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Characterization of kinetics of the lactate dehydrogenase of S. pyogenes
SysMO-LAB

Measurements on Km, Vmax and allosteric activation or inhibition of the main L-lactate dehydrogenase

Creator: Tomas Fiedler

Submitter: Martijn Bekker

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Maximal specific growth rates of the three lactic acid bacteria and their ldh deletions.
SysMO-LAB

. L. lactis (NZ9000), E. faecalis (V538) and S. pyogenes (M49) wild type strain and their ldh- mutants were grown in batch cultures at 37°C in anaerobic 96 wells plates in either TH-broth supplemented with 0.5% (w/v) yeast (THY) or a chemically defined medium for LAB (pH 7.4) (CDM-LAB (10)). Both media were buffered with either 100 mM MES buffer or 100 mM MOPS buffer for growth at pH 6.5 and 7.5 respectively.

Creators: Martijn Bekker, Tomas Fiedler

Submitter: Martijn Bekker

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Characterization of flux distribution and general physiology of S. pyogenes in continuous cultures
SysMO-LAB

S. pyogenes was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05 and 0.15

Creators: Martijn Bekker, Tomas Fiedler

Submitter: Martijn Bekker

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The effects of fructose-1,6-bisphosphate, phosphate and ionic strength on enzyme activity differ for the three LDHs from three Lactic acid bacterias.
SysMO-LAB

Heterologous Expression of LDHs from different lactic acid bacteria in Escherichia coli DH5α.

Assessment of kinetic parameters of LDH to include in a catabolic model.

Creators: Silvio Hering, Tomas Fiedler

Submitter: Silvio Hering

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Measurement of LDH activity
SysMO-LAB
No description specified

Creator: Tomas Fiedler

Submitter: Tomas Fiedler

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Measurement of pyruvate kinase activity
SysMO-LAB
No description specified

Creator: Tomas Fiedler

Submitter: Tomas Fiedler

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Standard operating procedure to analyze the intracellular proteome of Clostridium acetobutylicum.
COSMIC
No description specified

Creators: Holger Janssen, Tomas Fiedler

Submitter: Holger Janssen

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Kinetic characterization of arginine deiminase and carbamate kinase from Streptococcus pyogenes M49
SysMO-LAB

Abstract (Expand)

Streptococcus pyogenes (group A Streptococcus, GAS) is an important human pathogen causing mild superficial infections of skin and mucous membranes, but also life-threatening systemic diseases. S. … pyogenes and other prokaryotic organisms use the arginine deiminase system (ADS) for survival in acidic environments. In this study, the arginine deiminase (AD), and carbamate kinase (CK) from S. pyogenes M49 strain 591 were heterologously expressed in E. coli DH5α, purified, and kinetically characterized. AD and CK from S. pyogenes M49 share high amino acid sequence similarity with the respective enzymes from Lactococcus lactis subsp. lactis IL1403 (45.6% and 53.5% identical amino acids) and Enterococcus faecalis V583 (66.8% and 66.8% identical amino acids). We found that the arginine deiminase of S. pyogenes is not allosterically regulated by the intermediates and products of the arginine degradation (E. g, ATP, citrulline, carbamoyl phosphate). The Km and Vmax values for arginine were 1.13±0.12 mM (mean ± SD) and 1.51±0.07 μmol/min/mg protein. The carbamate kinase is inhibited by ATP but unaffected by arginine and citrulline. The Km and Vmax values for ADP were 0.72±0.08 mM and 1.10±0.10 μmol/min/mg protein and the Km for carbamoyl phosphate was 0.65±0.07 mM. The optimum pH and temperature for both enzymes were 6.5 and 37°C, respectively.

Editor:

Date Published: 1st Jul 2013

Publication Type: Not specified

Regulation of the Activity of Lactate Dehydrogenases from Four Lactic Acid Bacteria
SysMO-LAB

Abstract

Not specified

Authors: , , H. Messiha, , , , , , ,

Date Published: 17th May 2013

Publication Type: Not specified

Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach
SysMO-LAB

Abstract (Expand)

Lactic acid-producing bacteria survive in distinct environments, but show common metabolic characteristics. Here we studied the dynamic interactions of the central metabolism in Lactococcus lactis, … extensively used as starter in dairy industry, and Streptococcus pyogenes, a human pathogen. Glucose-pulse experiments and enzymatic measurements were performed to parameterize kinetic models of glycolysis. Significant improvements were made to existing kinetic models for L. lactis, which subsequently accelerated the development of the first kinetic model of S. pyogenes glycolysis. The models revealed an important role for extracellular phosphate in regulation of central metabolism and the efficient use of glucose. Thus, phosphate which is rarely taken into account as an independent species in models of central metabolism has to be considered more thoroughly in the analysis of metabolic systems in the future. Insufficient phosphate supply can lead to a strong inhibition of glycolysis at high glucose concentration in both species, but more severely in S. pyogenes. S. pyogenes is more efficient in converting glucose to ATP, showing a higher tendency towards heterofermentative energy metabolism than L. lactis. Our comparative systems biology approach revealed that the glycolysis of L. lactis and S. pyogenes have similar characteristics, but are adapted to their individual natural habitats with respect to phosphate regulation. The mathematical models described here have been submitted to the Online Cellular Systems Modelling Database and can be accessed at http://jjj.biochem.sun.ac.za/database/levering/index.html free of charge.

Editor:

Date Published: 14th Feb 2012

Publication Type: Not specified

SABIO-RK--database for biochemical reaction kinetics.
SysMO-LAB

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible database storing comprehensive information about biochemical reactions and their kinetic properties. SABIO-RK offers standardized data manually … extracted from the literature and data directly submitted from lab experiments. The database content includes kinetic parameters in relation to biochemical reactions and their biological sources with no restriction on any particular set of organisms. Additionally, kinetic rate laws and corresponding equations as well as experimental conditions are represented. All the data are manually curated and annotated by biological experts, supported by automated consistency checks. SABIO-RK can be accessed via web-based user interfaces or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language), e.g. for import in modelling tools.

Authors: Ulrike Wittig, , Martin Golebiewski, , Lei Shi, Lenneke Jong, Enkhjargal Algaa, Andreas Weidemann, Heidrun Sauer-Danzwith, Saqib Mir, , Meik Bittkowski, Elina Wetsch, ,

Date Published: 22nd Nov 2011

Publication Type: Journal

Growth rate dependent control in Enterococcus faecalis: effects on the transcriptome, proteome and strong regulation of lactate dehydrogenase
SysMO-LAB

Abstract (Expand)

Enterococcus faecalis V583 was grown in a glucose-limited chemostat at three different (0.05 h(-1), 0.15 h(-1) and 0.4 h(-1)) growth rates. The fermentation pattern changed with growth rate, from a … mostly homolactic profile at high growth rate to a fermentation dominated by formate, acetate and ethanol production at low growth rate. A number of amino acids were consumed at the lower growth rates but not by fast growing cells. The change in metabolic profile was mainly caused by decreased flux through lactate dehydrogenase. Transcription of ldh-1, encoding the principal lactate dehydrogenase, showed very strong growth rate dependence and differed by three orders of magnitude between the highest and the lowest growth rates. Despite the increase in ldh-1 transcript, the content of the Ldh-1 protein was the same under all conditions. Using microarrays and qPCR the levels of 227 gene transcript were found to be affected by the growth rate, and 56 differentially expressed proteins were found by proteomic analyses. Few genes or proteins showed a growth rate-dependent increase or decrease in expression over the whole range of conditions, and many showed at maximum or minimum at the middle growth rate (D=0.15h(-1)). For many gene products a discrepancy between transcriptomic and proteomic data were seen, indicating post-transcriptional regulation of expression.

Authors: , Ellen M Faergestad, , Lars Snipen, ,

Date Published: 1st Nov 2011

Publication Type: Not specified

Transcriptome, proteome and metabolite analysis of a lactate dehydrogenase negative mutant of Enterococcus faecalis V583
SysMO-LAB

Abstract (Expand)

A constructed lactate dehydrogenase-negative mutant of Enterococcus faecalis V583 grows at the same rate as the wild type, but ferments glucose to ethanol, formate, and acetoin. Microrray analysis … showed that LDH deficiency had profound transcriptional effects, 43 genes in the mutant were found to be upregulated and 45 to be downregulated. Most of the upregulated genes encode enzymes of energy metabolism or transport. By 2D gel analysis 45 differentially expressed proteins were identified. A comparison of transcriptomic and proteomic data suggests that for several proteins the level of expression is regulated beyond the level of transcription. Pyruvate catabolic genes, including the truncated ldh, showed highly increased transcription in the mutant. These genes, along with a number of other differentially expressed genes, are preceded by sequences with homology to binding sites for the global redox-sensing repressor, Rex, of Staphylococcus aureus. The data indicate that the genes are transcriptionally regulated by the NADH/NAD ratio and that this ratio plays an important role in the regulatory network controlling energy metabolism in E. faecalis.

Authors: , , Ellen M Fergestad, Geir Mathiesen, ,

Date Published: 8th Feb 2011

Publication Type: Not specified

Insights into Streptococcus pyogenes pathogenesis from transcriptome studies
SysMO-LAB

Abstract (Expand)

Streptococcus pyogenes (group A Streptococcus [GAS]) is a major human pathogen, causing diseases ranging from mild superficial infections of the skin and pharyngeal mucosal membrane, up to severe … systemic and invasive diseases and autoimmune sequelae. The capability of GAS to cause this wide variety of infections is due to the expression of a large set of virulence factors, their concerted transcriptional regulation, and bacterial adaptation mechanisms to various host niches, which we are now beginning to understand on a molecular level. The addition of -omics technologies for GAS pathogenesis investigation, on top of traditional molecular methods, led to fast progress in understanding GAS pathogenesis mechanisms. This article focuses on differential transcriptional analysis performed on the bacterial side as well as on the host cell side. The microarray studies discussed provide new insight into the following five topics: gene-expression patterns under infection-relevant conditions, gene-expression patterns in mutant strains compared with wild-type strains, emergence of exceptionally fit GAS clones, gene-expression patterns of eukaryotic target and immune cells in response to GAS infection, and mechanisms underlying shifts from a pharyngeal to invasive GAS lifestyle.

Authors: , Venelina Sugareva, Nadja Patenge,

Date Published: 8th Dec 2010

Publication Type: Not specified

Physiological characterization of three lactic acid bacteria and their isogenic ldh deletion mutants shows that these organisms are optimized for Yatp and not ATP formation rates at their physiological pH
SysMO-LAB

Abstract (Expand)

Several lactic acid bacteria use homolactic fermentation for generation of ATP. Here we studied the role of the lactate dehydrogenase enzyme on the general physiology of the three homolactic acid … bacteria Lactococcus lactis, Enterococcus faecalis and Streptococcus pyogenes. Of note, deletion of the ldh genes hardly affected the growth rate in chemically defined medium in microaerophilic conditions. However, growth rate was affected in rich medium. Furthermore, deletion of ldh affected the ability for utilization of various substrates as a carbon source. A switch to mixed acid fermentation was observed in glucose-limited continuous growth and was dependent on the growth rate for S. pyogenes and dependent on the pH for E. faecalis. In S. pyogenes and L. lactis a change in pH resulted in a clear change in Yatp. The pH that showed the highest Yatp corresponded to the pH of the natural habitat of the organisms.

Authors: , , , , Anja Pritzschke, Nikolai Siemens, , ,

Date Published: 25th Nov 2010

Publication Type: Not specified

Copenhagen meeting 2012: Rostock presentation
SysMO-LAB
No description specified

Creator: Tomas Fiedler

Submitter: Tomas Fiedler

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SysMO-LAB2 Meeting Amsterdam 2013
No description specified

Start Date: 9th Jun 2013

End Date: 10th Jun 2013

Event Website: Not specified

Country:  Netherlands

City: Amsterdam

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