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Article ; Online: Shedding light on both ends: An update on analytical approaches for N- and C-terminomics.

Koudelka, Tomas / Winkels, Konrad / Kaleja, Patrick / Tholey, Andreas

Biochimica et biophysica acta. Molecular cell research

2021 Volume 1869, Issue 1, Page(s) 119137

Abstract: Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a limited substrate pool. This irreversible posttranslational modification modulates the ... ...

Abstract	Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a limited substrate pool. This irreversible posttranslational modification modulates the fate and activity of many proteins, making proteolytic processing a master switch in the regulation of e.g., the immune system, apoptosis and cancer progression. N- and C-terminomics, the identification of protein termini, has become indispensable in elucidating protease substrates and therefore protease function. Further, terminomics has the potential to identify yet unknown proteoforms, e.g. formed by alternative splicing or the recently discovered alternative ORFs. Different strategies and workflows have been developed that achieve higher sensitivity, a greater depth of coverage or higher throughput. In this review, we summarize recent developments in both N- and C-terminomics and include the potential of top-down proteomics which inherently delivers information on both ends of analytes in a single analysis.
MeSH term(s)	Animals ; Humans ; Proteolysis ; Proteome/chemistry ; Proteome/genetics ; Proteome/metabolism ; Proteomics/methods ; RNA Splicing
Chemical Substances	Proteome
Language	English
Publishing date	2021-10-06
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbamcr.2021.119137
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Article ; Online: Quantitative Top-Down Proteomics by Isobaric Labeling with Thiol-Directed Tandem Mass Tags.

Winkels, Konrad / Koudelka, Tomas / Tholey, Andreas

Journal of proteome research

2021 Volume 20, Issue 9, Page(s) 4495–4506

Abstract: While identification-centric (qualitative) top-down proteomics (TDP) has seen rapid progress in the recent past, the quantification of intact proteoforms within complex proteomes is still challenging. The by far mostly applied approach is label-free ... ...

Abstract	While identification-centric (qualitative) top-down proteomics (TDP) has seen rapid progress in the recent past, the quantification of intact proteoforms within complex proteomes is still challenging. The by far mostly applied approach is label-free quantification, which, however, provides limited multiplexing capacity, and its use in combination with multidimensional separation is encountered with a number of problems. Isobaric labeling, which is a standard quantification approach in bottom-up proteomics, circumvents these limitations. Here, we introduce the application of thiol-directed isobaric labeling for quantitative TDP. For this purpose, we analyzed the labeling efficiency and optimized tandem mass spectrometry parameters for optimal backbone fragmentation for identification and reporter ion formation for quantification. Two different separation schemes, gel-eluted liquid fraction entrapment electrophoresis × liquid chromatography-mass spectrometry (LC-MS) and high/low-pH LC-MS, were employed for the analyses of either
MeSH term(s)	Escherichia coli/genetics ; Proteome ; Proteomics ; Sulfhydryl Compounds ; Tandem Mass Spectrometry
Chemical Substances	Proteome ; Sulfhydryl Compounds
Language	English
Publishing date	2021-08-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00460
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Article ; Online: Regulation of microtubule detyrosination by Ca2+ and conventional calpains.

Bär, Julia / Popp, Yannes / Koudelka, Tomas / Tholey, Andreas / Mikhaylova, Marina

Journal of cell science

2022 Volume 135, Issue 9

Abstract: Detyrosination is a major post-translational modification of microtubules (MTs), which has significant impact on MT function in cell division, differentiation, growth, migration and intracellular trafficking. Detyrosination of α-tubulin occurs mostly via ...

Abstract	Detyrosination is a major post-translational modification of microtubules (MTs), which has significant impact on MT function in cell division, differentiation, growth, migration and intracellular trafficking. Detyrosination of α-tubulin occurs mostly via the recently identified complex of vasohibin 1 or 2 (VASH1 and VASH2, respectively) with small vasohibin binding protein (SVBP). However, there is still remaining detyrosinating activity in the absence of VASH1 and/or VASH2 and SVBP, and little is known about the regulation of detyrosination. Here, we found that intracellular Ca2+ is required for efficient MT detyrosination. Furthermore, we show that the Ca2+-dependent proteases calpains 1 and 2 (CAPN1 and CAPN2, respectively) regulate MT detyrosination in VASH1- and SVBP-overexpressing human embryonic kidney (HEK293T) cells. We identified new calpain cleavage sites in the N-terminal disordered region of VASH1. However, this cleavage did not affect the enzymatic activity of vasohibins. In conclusion, we suggest that the regulation of VASH1-mediated MT detyrosination by calpains could occur independently of vasohibin catalytic activity or via another yet unknown tubulin carboxypeptidase. Importantly, the Ca2+ dependency of calpains could allow a fine regulation of MT detyrosination. Thus, identifying the calpain-regulated pathway of MT detyrosination can be of major importance for basic and clinical research.
MeSH term(s)	Angiogenic Proteins/metabolism ; Calcium/metabolism ; Calpain/metabolism ; Carrier Proteins/metabolism ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; HEK293 Cells ; Humans ; Microtubules/metabolism ; Tubulin/metabolism
Chemical Substances	Angiogenic Proteins ; Carrier Proteins ; Cell Cycle Proteins ; SVBP protein, human ; Tubulin ; VASH1 protein, human ; VASH2 protein, human ; Calpain (EC 3.4.22.-) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2022-05-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.259108
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Article ; Online: Validation of Top-Down Proteomics Data by Bottom-Up-Based N-Terminomics Reveals Pitfalls in Top-Down-Based Terminomics Workflows.

Winkels, Konrad / Koudelka, Tomas / Kaulich, Philipp T / Leippe, Matthias / Tholey, Andreas

Journal of proteome research

2022 Volume 21, Issue 9, Page(s) 2185–2196

Abstract: Bottom-up proteomics (BUP)-based N-terminomics techniques have become standard to identify protein N-termini. While these methods rely on the identification of N-terminal peptides only, top-down proteomics (TDP) comes with the promise to provide ... ...

Abstract	Bottom-up proteomics (BUP)-based N-terminomics techniques have become standard to identify protein N-termini. While these methods rely on the identification of N-terminal peptides only, top-down proteomics (TDP) comes with the promise to provide additional information about post-translational modifications and the respective C-termini. To evaluate the potential of TDP for terminomics, two established TDP workflows were employed for the proteome analysis of the nematode
MeSH term(s)	Arginine ; DNA-Binding Proteins ; Protein Processing, Post-Translational ; Proteome/analysis ; Proteomics/methods ; Workflow
Chemical Substances	DNA-Binding Proteins ; Proteome ; Arginine (94ZLA3W45F)
Language	English
Publishing date	2022-08-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.2c00277
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Article ; Online: Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation.

Roske, Yvette / Cappel, Cedric / Cremer, Nils / Hoffmann, Patrick / Koudelka, Tomas / Tholey, Andreas / Heinemann, Udo / Daumke, Oliver / Damme, Markus

Nucleic acids research

2023 Volume 52, Issue 1, Page(s) 370–384

Abstract: The phospholipase D (PLD) family is comprised of enzymes bearing phospholipase activity towards lipids or endo- and exonuclease activity towards nucleic acids. PLD3 is synthesized as a type II transmembrane protein and proteolytically cleaved in ... ...

Abstract	The phospholipase D (PLD) family is comprised of enzymes bearing phospholipase activity towards lipids or endo- and exonuclease activity towards nucleic acids. PLD3 is synthesized as a type II transmembrane protein and proteolytically cleaved in lysosomes, yielding a soluble active form. The deficiency of PLD3 leads to the slowed degradation of nucleic acids in lysosomes and chronic activation of nucleic acid-specific intracellular toll-like receptors. While the mechanism of PLD phospholipase activity has been extensively characterized, not much is known about how PLDs bind and hydrolyze nucleic acids. Here, we determined the high-resolution crystal structure of the luminal N-glycosylated domain of human PLD3 in its apo- and single-stranded DNA-bound forms. PLD3 has a typical phospholipase fold and forms homodimers with two independent catalytic centers via a newly identified dimerization interface. The structure of PLD3 in complex with an ssDNA-derived thymidine product in the catalytic center provides insights into the substrate binding mode of nucleic acids in the PLD family. Our structural data suggest a mechanism for substrate binding and nuclease activity in the PLD family and provide the structural basis to design immunomodulatory drugs targeting PLD3.
MeSH term(s)	Humans ; Lysosomes/metabolism ; Phospholipase D/chemistry ; Phospholipases ; Exodeoxyribonucleases/chemistry
Chemical Substances	Phospholipase D (EC 3.1.4.4) ; Phospholipases (EC 3.1.-) ; PLD3 protein, human (EC 3.1.4.4) ; Exodeoxyribonucleases (EC 3.1.-)
Language	English
Publishing date	2023-11-23
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad1114
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Article ; Online: Recent Progress Concerning the

Oeser, Petr / Koudelka, Jakub / Petrenko, Artem / Tobrman, Tomáš

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 16

Abstract: This review summarizes the current state-of-the-art procedures in terms of the preparation ... ...

Abstract	This review summarizes the current state-of-the-art procedures in terms of the preparation of
Language	English
Publishing date	2021-08-22
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26165079
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Article ; Online: Protease-independent control of parthanatos by HtrA2/Omi.

Weiß, Jonas / Heib, Michelle / Korn, Thiemo / Hoyer, Justus / Fuchslocher Chico, Johaiber / Voigt, Susann / Koudelka, Tomas / Tholey, Andreas / Adam, Dieter

Cellular and molecular life sciences : CMLS

2023 Volume 80, Issue 9, Page(s) 258

Abstract: HtrA2/Omi is a mitochondrial serine protease with ascribed pro-apoptotic as well as pro-necroptotic functions. Here, we establish that HtrA2/Omi also controls parthanatos, a third modality of regulated cell death. Deletion of HtrA2/Omi protects cells ... ...

Abstract	HtrA2/Omi is a mitochondrial serine protease with ascribed pro-apoptotic as well as pro-necroptotic functions. Here, we establish that HtrA2/Omi also controls parthanatos, a third modality of regulated cell death. Deletion of HtrA2/Omi protects cells from parthanatos while reconstitution with the protease restores the parthanatic death response. The effects of HtrA2/Omi on parthanatos are specific and cannot be recapitulated by manipulating other mitochondrial proteases such as PARL, LONP1 or PMPCA. HtrA2/Omi controls parthanatos in a manner mechanistically distinct from its action in apoptosis or necroptosis, i.e., not by cleaving cytosolic IAP proteins but rather exerting its effects without exiting mitochondria, and downstream of PARP-1, the first component of the parthanatic signaling cascade. Also, previously identified or candidate substrates of HtrA2/Omi such as PDXDC1, VPS4B or moesin are not cleaved and dispensable for parthanatos, whereas DBC-1 and stathmin are cleaved, and thus represent potential parthanatic downstream mediators of HtrA2/Omi. Moreover, mass-spectrometric screening for novel parthanatic substrates of HtrA2/Omi revealed that the induction of parthanatos does not cause a substantial proteolytic cleavage or major alterations in the abundance of mitochondrial proteins. Resolving these findings, reconstitution of HtrA2/Omi-deficient cells with a catalytically inactive HtrA2/Omi mutant restored their sensitivity against parthanatos to the same level as the protease-active HtrA2/Omi protein. Additionally, an inhibitor of HtrA2/Omi's protease activity did not confer protection against parthanatic cell death. Our results demonstrate that HtrA2/Omi controls parthanatos in a protease-independent manner, likely via novel, unanticipated functions as a scaffolding protein and an interaction with so far unknown mitochondrial proteins.
MeSH term(s)	Parthanatos ; Serine Proteases/genetics ; Necroptosis ; Serine Endopeptidases/genetics ; Mitochondrial Proteins/genetics
Chemical Substances	Serine Proteases (EC 3.4.-) ; Serine Endopeptidases (EC 3.4.21.-) ; Mitochondrial Proteins
Language	English
Publishing date	2023-08-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-023-04904-7
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Article: Quantitative Top-Down Proteomics by Isobaric Labeling with Thiol-Directed Tandem Mass Tags

Winkels, Konrad / Koudelka, Tomas / Tholey, Andreas

Journal of proteome research. 2021 Aug. 02, v. 20, no. 9

2021

Abstract	While identification-centric (qualitative) top-down proteomics (TDP) has seen rapid progress in the recent past, the quantification of intact proteoforms within complex proteomes is still challenging. The by far mostly applied approach is label-free quantification, which, however, provides limited multiplexing capacity, and its use in combination with multidimensional separation is encountered with a number of problems. Isobaric labeling, which is a standard quantification approach in bottom-up proteomics, circumvents these limitations. Here, we introduce the application of thiol-directed isobaric labeling for quantitative TDP. For this purpose, we analyzed the labeling efficiency and optimized tandem mass spectrometry parameters for optimal backbone fragmentation for identification and reporter ion formation for quantification. Two different separation schemes, gel-eluted liquid fraction entrapment electrophoresis × liquid chromatography–mass spectrometry (LC–MS) and high/low-pH LC–MS, were employed for the analyses of either Escherichia coli (E. coli) proteomes or combined E. coli/yeast samples (two-proteome interference model) to study potential ratio compression. While the thiol-directed labeling introduces a bias in the quantifiable proteoforms, being restricted to Cys-containing proteoforms, our approach showed excellent accuracy in quantification, which is similar to that achievable in bottom-up proteomics. For example, 876 proteoforms could be quantified with high accuracy in an E. coli lysate. The LC–MS data were deposited to the ProteomeXchange with the dataset identifier PXD026310.
Keywords	Escherichia coli ; data collection ; electrophoresis ; liquid chromatography ; models ; proteome ; proteomics ; research ; tandem mass spectrometry ; yeasts
Language	English
Dates of publication	2021-0802
Size	p. 4495-4506.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00460
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Article ; Online: Formation of trisubstituted buta-1,3-dienes and α,β-unsaturated ketones

Oeser, Petr / Koudelka, Jakub / Dvořáková, Hana / Tobrman, Tomáš

RSC advances

2020 Volume 10, Issue 58, Page(s) 35109–35120

Abstract: We studied the reactions of vinyl phosphates and vinyl phosphordiamidates containing an ester functional group with organometallic reagents. We found that the functionalized vinyl phosphates were smoothly converted into tri- and tetrasubstituted buta-1,3- ...

Abstract	We studied the reactions of vinyl phosphates and vinyl phosphordiamidates containing an ester functional group with organometallic reagents. We found that the functionalized vinyl phosphates were smoothly converted into tri- and tetrasubstituted buta-1,3-dienes
Language	English
Publishing date	2020-09-22
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d0ra07472a
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Article ; Online: Phosphorylation of meprin β controls its cell surface abundance and subsequently diminishes ectodomain shedding.

Armbrust, Fred / Bickenbach, Kira / Koudelka, Tomas / Tholey, Andreas / Pietrzik, Claus / Becker-Pauly, Christoph

FASEB journal : official publication of the Federation of American Societies for Experimental Biology

2021 Volume 35, Issue 7, Page(s) e21677

Abstract: Meprin β is a zinc-dependent metalloprotease exhibiting a unique cleavage specificity with strong preference for acidic amino acids at the cleavage site. Proteomic studies revealed a diverse substrate pool of meprin β including the interleukin-6 receptor ...

Abstract	Meprin β is a zinc-dependent metalloprotease exhibiting a unique cleavage specificity with strong preference for acidic amino acids at the cleavage site. Proteomic studies revealed a diverse substrate pool of meprin β including the interleukin-6 receptor (IL-6R) and the amyloid precursor protein (APP). Dysregulation of meprin β is often associated with pathological conditions such as chronic inflammation, fibrosis, or Alzheimer's disease (AD). The extracellular regulation of meprin β including interactors, sheddases, and activators has been intensively investigated while intracellular regulation has been barely addressed in the literature. This study aimed to analyze C-terminal phosphorylation of meprin β with regard to cell surface expression and proteolytic activity. By immunoprecipitation of endogenous meprin β from the colon cancer cell line Colo320 and subsequent LC-MS analysis, we identified several phosphorylation sites in its C-terminal region. Here, T694 in the C-terminus of meprin β was the most preferred residue after phorbol 12-myristate 13-acetate (PMA) stimulation. We further demonstrated the role of protein kinase C (PKC) isoforms for meprin β phosphorylation and identified the involvement of PKC-α and PKC-β. As a result of phosphorylation, the meprin β activity at the cell surface is reduced and, consequently, the extent of substrate cleavage is diminished. Our data indicate that this decrease of the surface activity is caused by the internalization and degradation of meprin β.
MeSH term(s)	Cell Membrane/metabolism ; Colonic Neoplasms/metabolism ; Colonic Neoplasms/pathology ; Extracellular Space/metabolism ; Gene Expression Regulation ; Humans ; Metalloendopeptidases/genetics ; Metalloendopeptidases/metabolism ; Phosphorylation ; Protein Kinase C beta/genetics ; Protein Kinase C beta/metabolism ; Protein Kinase C-alpha/genetics ; Protein Kinase C-alpha/metabolism ; Proteolysis ; Tumor Cells, Cultured
Chemical Substances	Protein Kinase C beta (EC 2.7.11.13) ; Protein Kinase C-alpha (EC 2.7.11.13) ; Metalloendopeptidases (EC 3.4.24.-) ; meprin A (EC 3.4.24.18)
Language	English
Publishing date	2021-06-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639186-2
ISSN	1530-6860 ; 0892-6638
ISSN (online)	1530-6860
ISSN	0892-6638
DOI	10.1096/fj.202100271R
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