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Article ; Online: Systems biology: current status and challenges.

Zupanic, Anze / Bernstein, Hans C / Heiland, Ines

Cellular and molecular life sciences : CMLS

2020 Volume 77, Issue 3, Page(s) 379–380

Abstract: We put together a special issue on current approaches in systems biology with a focus on mathematical modeling of metabolic networks. Mathematical models have increasingly been used to unravel molecular mechanisms of complex dynamic biological processes. ...

Abstract	We put together a special issue on current approaches in systems biology with a focus on mathematical modeling of metabolic networks. Mathematical models have increasingly been used to unravel molecular mechanisms of complex dynamic biological processes. We here provide a short introduction into the topics covered in this special issue, highlighting current developments and challenges.
MeSH term(s)	Humans ; Metabolic Networks and Pathways/physiology ; Models, Theoretical ; Systems Biology/methods
Language	English
Publishing date	2020-01-13
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-019-03410-z
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Article ; Online: The evolution of the plastid phosphate translocator family.

Bockwoldt, Mathias / Heiland, Ines / Fischer, Karsten

Planta

2019 Volume 250, Issue 1, Page(s) 245–261

Abstract: Main conclusion: The plastid phosphate translocators evolved in algae but diversified into several groups, which adopted different physiological functions by extensive gene duplications and losses in Streptophyta. The plastid phosphate translocators ( ... ...

Abstract	Main conclusion: The plastid phosphate translocators evolved in algae but diversified into several groups, which adopted different physiological functions by extensive gene duplications and losses in Streptophyta. The plastid phosphate translocators (pPT) are a family of transporters involved in the exchange of metabolites and inorganic phosphate between stroma and cytosol. Based on their substrate specificities, they were divided into four subfamilies named TPT, PPT, GPT and XPT. To analyse the occurrence of these transporters in different algae and land plant species, we identified 652 pPT genes in 101 sequenced genomes for phylogenetic analysis. The first three subfamilies are found in all species and evolved before the split of red and green algae while the XPTs were derived from the duplication of a GPT gene at the base of Streptophyta. The analysis of the intron-exon structures of the pPTs corroborated these findings. While the number and positions of introns are conserved within each subfamily, they differ between the subfamilies suggesting an insertion of the introns shortly after the three subfamilies evolved. During angiosperm evolution, the subfamilies further split into different groups (TPT1-2, PPT1-3, GPT1-6). Angiosperm species differ significantly in the total number of pPTs, with many species having only a few, while several plants, especially crops, have a higher number, pointing to the importance of these transporters for improved source-sink strength and yield. The differences in the number of pPTs can be explained by several small-scale gene duplications and losses in plant families or single species, but also by whole genome duplications, for example, in grasses. This work could be the basis for a comprehensive analysis of the molecular and physiological functions of this important family of transporters.
MeSH term(s)	Chromosome Mapping ; Evolution, Molecular ; Exons/genetics ; Gene Duplication ; Genome, Plant/genetics ; Introns/genetics ; Magnoliopsida/genetics ; Magnoliopsida/metabolism ; Membrane Transport Proteins/genetics ; Membrane Transport Proteins/metabolism ; Phosphates/metabolism ; Phylogeny ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plants/genetics ; Plants/metabolism ; Plastids/metabolism
Chemical Substances	Membrane Transport Proteins ; Phosphates ; Plant Proteins
Language	English
Publishing date	2019-04-16
Publishing country	Germany
Document type	Journal Article
ZDB-ID	208909-9
ISSN	1432-2048 ; 0032-0935 ; 1866-2749
ISSN (online)	1432-2048
ISSN	0032-0935 ; 1866-2749
DOI	10.1007/s00425-019-03161-y
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Article ; Online: Welcome to the Family: Identification of the NAD

Ziegler, Mathias / Monné, Magnus / Nikiforov, Andrey / Agrimi, Gennaro / Heiland, Ines / Palmieri, Ferdinando

Biomolecules

2021 Volume 11, Issue 6

Abstract: Subcellular compartmentation is a fundamental property of eukaryotic cells. Communication and metabolic and regulatory interconnectivity between organelles require that solutes can be transported across their surrounding membranes. Indeed, in mammals, ... ...

Abstract	Subcellular compartmentation is a fundamental property of eukaryotic cells. Communication and metabolic and regulatory interconnectivity between organelles require that solutes can be transported across their surrounding membranes. Indeed, in mammals, there are hundreds of genes encoding solute carriers (SLCs) which mediate the selective transport of molecules such as nucleotides, amino acids, and sugars across biological membranes. Research over many years has identified the localization and preferred substrates of a large variety of SLCs. Of particular interest has been the SLC25 family, which includes carriers embedded in the inner membrane of mitochondria to secure the supply of these organelles with major metabolic intermediates and coenzymes. The substrate specificity of many of these carriers has been established in the past. However, the route by which animal mitochondria are supplied with NAD
MeSH term(s)	Biological Transport/genetics ; Humans ; Mitochondria/genetics ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/genetics ; Mitochondrial Membrane Transport Proteins/metabolism ; NAD/genetics ; NAD/metabolism ; Solute Carrier Proteins/genetics ; Solute Carrier Proteins/metabolism
Chemical Substances	Mitochondrial Membrane Transport Proteins ; Solute Carrier Proteins ; NAD (0U46U6E8UK)
Language	English
Publishing date	2021-06-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom11060880
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Article: Early Evolutionary Selection of NAD Biosynthesis Pathway in Bacteria.

Sharma, Suraj / Hsieh, Yin-Chen / Dietze, Jörn / Bockwoldt, Mathias / Strømland, Øyvind / Ziegler, Mathias / Heiland, Ines

Metabolites

2022 Volume 12, Issue 7

Abstract: Bacteria use two alternative pathways to synthesize nicotinamide adenine dinucleotide (NAD) from nicotinamide (Nam). A short, two-step route proceeds through nicotinamide mononucleotide (NMN) formation, whereas the other pathway, a four-step route, ... ...

Abstract	Bacteria use two alternative pathways to synthesize nicotinamide adenine dinucleotide (NAD) from nicotinamide (Nam). A short, two-step route proceeds through nicotinamide mononucleotide (NMN) formation, whereas the other pathway, a four-step route, includes the deamidation of Nam and the reamidation of nicotinic acid adenine dinucleotide (NAAD) to NAD. In addition to having twice as many enzymatic steps, the four-step route appears energetically unfavourable, because the amidation of NAAD includes the cleavage of ATP to AMP. Therefore, it is surprising that this pathway is prevalent not only in bacteria but also in yeast and plants. Here, we demonstrate that the considerably higher chemical stability of the deamidated intermediates, compared with their amidated counterparts, might compensate for the additional energy expenditure, at least at elevated temperatures. Moreover, comprehensive bioinformatics analyses of the available >6000 bacterial genomes indicate that an early selection of one or the other pathway occurred. The mathematical modelling of the NAD pathway dynamics supports this hypothesis, as there appear to be no advantages in having both pathways.
Language	English
Publishing date	2022-06-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo12070569
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Article ; Online: Natural isotope correction improves analysis of protein modification dynamics.

Dietze, Jörn / van Pijkeren, Alienke / Egger, Anna-Sophia / Ziegler, Mathias / Kwiatkowski, Marcel / Heiland, Ines

Analytical and bioanalytical chemistry

2021 Volume 413, Issue 30, Page(s) 7333–7340

Abstract: Stable isotope labelling in combination with high-resolution mass spectrometry approaches are increasingly used to analyze both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics, it is critical to ... ...

Abstract	Stable isotope labelling in combination with high-resolution mass spectrometry approaches are increasingly used to analyze both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics, it is critical to correct the measured values for naturally occurring stable isotopes, a process commonly called isotopologue correction or deconvolution. While the importance of isotopologue correction is well recognized in metabolomics, it has received far less attention in proteomics approaches. Although several tools exist that enable isotopologue correction of mass spectrometry data, the majority is tailored for the analysis of low molecular weight metabolites. We here present PICor which has been developed for isotopologue correction of complex isotope labelling experiments in proteomics or metabolomics and demonstrate the importance of appropriate correction for accurate determination of protein modifications dynamics, using histone acetylation as an example.
MeSH term(s)	Acetyl Coenzyme A/analysis ; Acetylation ; Animals ; Chromatography, Liquid/methods ; HEK293 Cells ; Humans ; Isotope Labeling/methods ; Mice ; Molecular Weight ; Protein Processing, Post-Translational ; Proteins/chemistry ; Proteomics ; RAW 264.7 Cells ; Tandem Mass Spectrometry/methods
Chemical Substances	Proteins ; Acetyl Coenzyme A (72-89-9)
Language	English
Publishing date	2021-10-27
Publishing country	Germany
Document type	Journal Article
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-021-03732-7
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Article ; Online: Dynamics of NAD-metabolism: everything but constant.

Opitz, Christiane A / Heiland, Ines

Biochemical Society transactions

2015 Volume 43, Issue 6, Page(s) 1127–1132

Abstract: NAD, as well as its phosphorylated form, NADP, are best known as electron carriers and co-substrates of various redox reactions. As such they participate in approximately one quarter of all reactions listed in the reaction database KEGG. In metabolic ... ...

Abstract	NAD, as well as its phosphorylated form, NADP, are best known as electron carriers and co-substrates of various redox reactions. As such they participate in approximately one quarter of all reactions listed in the reaction database KEGG. In metabolic pathway analysis, the total amount of NAD is usually assumed to be constant. That means that changes in the redox state might be considered, but concentration changes of the NAD moiety are usually neglected. However, a growing number of NAD-consuming reactions have been identified, showing that this assumption does not hold true in general. NAD-consuming reactions are common characteristics of NAD(+)-dependent signalling pathways and include mono- and poly-ADP-ribosylation of proteins, NAD(+)-dependent deacetylation by sirtuins and the formation of messenger molecules such as cyclic ADP-ribose (cADPR) and nicotinic acid (NA)-ADP (NAADP). NAD-consuming reactions are thus involved in major signalling and gene regulation pathways such as DNA-repair or regulation of enzymes central in metabolism. All known NAD(+)-dependent signalling processes include the release of nicotinamide (Nam). Thus cellular NAD pools need to be constantly replenished, mostly by recycling Nam to NAD(+). This process is, among others, regulated by the circadian clock, causing complex dynamic changes in NAD concentration. As disturbances in NAD homoeostasis are associated with a large number of diseases ranging from cancer to diabetes, it is important to better understand the dynamics of NAD metabolism to develop efficient pharmacological invention strategies to target this pathway.
MeSH term(s)	Acetylation ; Animals ; Biosynthetic Pathways ; Circadian Clocks/physiology ; Feedback, Physiological/physiology ; Humans ; Models, Biological ; NAD/metabolism ; Oxidation-Reduction ; Sirtuin 1/metabolism
Chemical Substances	NAD (0U46U6E8UK) ; Sirtuin 1 (EC 3.5.1.-)
Language	English
Publishing date	2015-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20150133
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Article: Natural isotope correction improves analysis of protein modification dynamics

Dietze, Jörn / van Pijkeren, Alienke / Egger, Anna-Sophia / Ziegler, Mathias / Kwiatkowski, Marcel / Heiland, Ines

Analytical and bioanalytical chemistry. 2021 Dec., v. 413, no. 30

2021

Abstract	Stable isotope labelling in combination with high-resolution mass spectrometry approaches are increasingly used to analyze both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics, it is critical to correct the measured values for naturally occurring stable isotopes, a process commonly called isotopologue correction or deconvolution. While the importance of isotopologue correction is well recognized in metabolomics, it has received far less attention in proteomics approaches. Although several tools exist that enable isotopologue correction of mass spectrometry data, the majority is tailored for the analysis of low molecular weight metabolites. We here present PICor which has been developed for isotopologue correction of complex isotope labelling experiments in proteomics or metabolomics and demonstrate the importance of appropriate correction for accurate determination of protein modifications dynamics, using histone acetylation as an example.
Keywords	acetylation ; analytical chemistry ; histones ; mass spectrometry ; metabolites ; metabolomics ; molecular weight ; proteomics ; stable isotopes
Language	English
Dates of publication	2021-12
Size	p. 7333-7340.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ISSN	1618-2642
DOI	10.1007/s00216-021-03732-7
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Article: The evolution of the plastid phosphate translocator family

Bockwoldt, Mathias / Fischer, Karsten / Heiland, Ines

Planta. 2019 July, v. 250, no. 1

2019

Abstract: MAIN CONCLUSION: The plastid phosphate translocators evolved in algae but diversified into several groups, which adopted different physiological functions by extensive gene duplications and losses in Streptophyta. The plastid phosphate translocators (pPT) ...

Abstract	MAIN CONCLUSION: The plastid phosphate translocators evolved in algae but diversified into several groups, which adopted different physiological functions by extensive gene duplications and losses in Streptophyta. The plastid phosphate translocators (pPT) are a family of transporters involved in the exchange of metabolites and inorganic phosphate between stroma and cytosol. Based on their substrate specificities, they were divided into four subfamilies named TPT, PPT, GPT and XPT. To analyse the occurrence of these transporters in different algae and land plant species, we identified 652 pPT genes in 101 sequenced genomes for phylogenetic analysis. The first three subfamilies are found in all species and evolved before the split of red and green algae while the XPTs were derived from the duplication of a GPT gene at the base of Streptophyta. The analysis of the intron–exon structures of the pPTs corroborated these findings. While the number and positions of introns are conserved within each subfamily, they differ between the subfamilies suggesting an insertion of the introns shortly after the three subfamilies evolved. During angiosperm evolution, the subfamilies further split into different groups (TPT1-2, PPT1-3, GPT1-6). Angiosperm species differ significantly in the total number of pPTs, with many species having only a few, while several plants, especially crops, have a higher number, pointing to the importance of these transporters for improved source–sink strength and yield. The differences in the number of pPTs can be explained by several small-scale gene duplications and losses in plant families or single species, but also by whole genome duplications, for example, in grasses. This work could be the basis for a comprehensive analysis of the molecular and physiological functions of this important family of transporters.
Keywords	algae ; Angiospermae ; Chlorophyta ; crops ; cytosol ; gene duplication ; grasses ; introns ; metabolites ; phosphates ; phylogeny ; substrate specificity ; transporters
Language	English
Dates of publication	2019-07
Size	p. 245-261.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	208909-9
ISSN	1432-2048 ; 0032-0935 ; 1866-2749
ISSN (online)	1432-2048
ISSN	0032-0935 ; 1866-2749
DOI	10.1007/s00425-019-03161-y
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Multi-scale modeling of drug binding kinetics to predict drug efficacy.

Clarelli, Fabrizio / Liang, Jingyi / Martinecz, Antal / Heiland, Ines / Abel Zur Wiesch, Pia

Cellular and molecular life sciences : CMLS

2019 Volume 77, Issue 3, Page(s) 381–394

Abstract: Optimizing drug therapies for any disease requires a solid understanding of pharmacokinetics (the drug concentration at a given time point in different body compartments) and pharmacodynamics (the effect a drug has at a given concentration). Mathematical ...

Abstract	Optimizing drug therapies for any disease requires a solid understanding of pharmacokinetics (the drug concentration at a given time point in different body compartments) and pharmacodynamics (the effect a drug has at a given concentration). Mathematical models are frequently used to infer drug concentrations over time based on infrequent sampling and/or in inaccessible body compartments. Models are also used to translate drug action from in vitro to in vivo conditions or from animal models to human patients. Recently, mathematical models that incorporate drug-target binding and subsequent downstream responses have been shown to advance our understanding and increase predictive power of drug efficacy predictions. We here discuss current approaches of modeling drug binding kinetics that aim at improving model-based drug development in the future. This in turn might aid in reducing the large number of failed clinical trials.
MeSH term(s)	Animals ; Drug Delivery Systems/methods ; Drug Design ; Humans ; Kinetics ; Models, Theoretical ; Pharmaceutical Preparations/metabolism
Chemical Substances	Pharmaceutical Preparations
Language	English
Publishing date	2019-11-25
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-019-03376-y
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Article ; Online: Identification of evolutionary and kinetic drivers of NAD-dependent signaling.

Bockwoldt, Mathias / Houry, Dorothée / Niere, Marc / Gossmann, Toni I / Reinartz, Ines / Schug, Alexander / Ziegler, Mathias / Heiland, Ines

Proceedings of the National Academy of Sciences of the United States of America

2019 Volume 116, Issue 32, Page(s) 15957–15966

Abstract: Nicotinamide adenine dinucleotide (NAD) provides an important link between metabolism and signal transduction and has emerged as central hub between bioenergetics and all major cellular events. NAD-dependent signaling (e.g., by sirtuins and poly- ... ...

Abstract	Nicotinamide adenine dinucleotide (NAD) provides an important link between metabolism and signal transduction and has emerged as central hub between bioenergetics and all major cellular events. NAD-dependent signaling (e.g., by sirtuins and poly-adenosine diphosphate [ADP] ribose polymerases [PARPs]) consumes considerable amounts of NAD. To maintain physiological functions, NAD consumption and biosynthesis need to be carefully balanced. Using extensive phylogenetic analyses, mathematical modeling of NAD metabolism, and experimental verification, we show that the diversification of NAD-dependent signaling in vertebrates depended on 3 critical evolutionary events: 1) the transition of NAD biosynthesis to exclusive usage of nicotinamide phosphoribosyltransferase (NamPT); 2) the occurrence of nicotinamide N-methyltransferase (NNMT), which diverts nicotinamide (Nam) from recycling into NAD, preventing Nam accumulation and inhibition of NAD-dependent signaling reactions; and 3) structural adaptation of NamPT, providing an unusually high affinity toward Nam, necessary to maintain NAD levels. Our results reveal an unexpected coevolution and kinetic interplay between NNMT and NamPT that enables extensive NAD signaling. This has implications for therapeutic strategies of NAD supplementation and the use of NNMT or NamPT inhibitors in disease treatment.
MeSH term(s)	Amino Acid Sequence ; Animals ; Biological Evolution ; Biosynthetic Pathways ; HeLa Cells ; Humans ; Kinetics ; NAD/metabolism ; Nicotinamide N-Methyltransferase ; Nicotinamide Phosphoribosyltransferase/chemistry ; Nicotinamide Phosphoribosyltransferase/metabolism ; Phylogeny ; Signal Transduction ; Substrate Specificity ; Vertebrates/metabolism
Chemical Substances	NAD (0U46U6E8UK) ; Nicotinamide N-Methyltransferase (EC 2.1.1.1) ; Nicotinamide Phosphoribosyltransferase (EC 2.4.2.12)
Language	English
Publishing date	2019-07-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1902346116
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