Bioinformatic identification of proteins with altered PTM levels in a mouse line established to study the mechanisms of the development of fibromuscular dysplasia
Data from a mass spectrometry experiment of a mouse line developed to study the mechanisms of fibromuscular dysplasia and deposited by d'Escamard et al. in ProteomeXchange (PXD051750) have been analyzed. Identification of peptides with post-translational modifications (PTMs) was repeated using more stringent conditions than in the original work. The following modifications were considered during analysis of changes in the PTM levels in experimental and control groups of mice: acetylation of lysine residue and N-terminal protein peptide, ubiquitination of lysine residue, phosphorylation of serine, threonine and tyrosine residues, and deamination of asparagine and glutamine residues. The multistage analysis resulted in selection of 23 proteins with PTMs for which different levels of modification between experimental and control groups could be assumed. These included six proteins with N-terminal protein acetylation, which were particularly interesting: P80318 (T-complex protein 1 subunit gamma), P43274 (Histone H1.4), P97823 (Acyl-protein thioesterase 1), P63242 (Eukaryotic translation initiation factor 5A-1), Q3UMT1 (Protein phosphatase 1 regulatory subunit 12C), Q9D8Y0 (EF-hand domain-containing protein D2). Thus, repeated bioinformatic analysis of the data deposited in the specialized databases resulted in detection of changes in the level of N-terminal acetylation of proteins that might be functionally significant in the mechanisms underlying the development of fibromuscular dysplasia.
Voronina A.I., Miroshnichenko Yu.V., Skvortsov V.S. (2024) Bioinformatic identification of proteins with altered PTM levels in a mouse line established to study the mechanisms of the development of fibromuscular dysplasia. Biomeditsinskaya Khimiya, 70(4), 248-255.
Voronina A.I. et al. Bioinformatic identification of proteins with altered PTM levels in a mouse line established to study the mechanisms of the development of fibromuscular dysplasia // Biomeditsinskaya Khimiya. - 2024. - V. 70. -N 4. - P. 248-255.
Voronina A.I. et al., "Bioinformatic identification of proteins with altered PTM levels in a mouse line established to study the mechanisms of the development of fibromuscular dysplasia." Biomeditsinskaya Khimiya 70.4 (2024): 248-255.
Voronina, A. I., Miroshnichenko, Yu. V., Skvortsov, V. S. (2024). Bioinformatic identification of proteins with altered PTM levels in a mouse line established to study the mechanisms of the development of fibromuscular dysplasia. Biomeditsinskaya Khimiya, 70(4), 248-255.
References
Knorre D.G., Kudryashova N.V., Godovikova T.S. (2009) Chemical and functional aspects of posttranslational modification of proteins. Acta Naturae, 1(3), 29–51. CrossRef Scholar google search
ProteomeXchange. Retrieved July 20, 2024, from: https://proteomecentral.proteomexchange.org. Scholar google search
Naryzhny S.N., Legina O.K. (2019) Structural-functional diversity of p53 proteoforms. Biomeditsinskaya Khimiya, 65(4), 263–276. CrossRef Scholar google search
Kisrieva Y.S., Petushkova N.A., Samenkova N.F., Kuznetsova G.P., Larina O.B., Teryaeva N.B., Usachev D.Yu., Zgoda V.G., Karuzina I.I. (2019) Comparative analysis of post-translational modifications in plasma proteome of patients with cerebral ischemia based on HPLC-MS/MS method. Biomeditsinskaya Khimiya, 65(3), 251–258. CrossRef Scholar google search
Skvortsov V.S., Ivanova Ya.O., Voronina A.I. (2021) The bioinformatic identification of proteins with varying levels of post-translational modifications in experimental ischemic stroke in mice. Biomeditsinskaya Khimiya, 67(6), 475–484. CrossRef Scholar google search
Simats A., Ramiro L., García-Berrocoso T., Briansó F., Gonzalo R., Martín L., Sabé A., Gill N., Penalba A., Colomé N., Sánchez A., Canals F., Bustamante A., Rosell A., Montaner J. (2020) A mouse brain-based multi-omics integrative approach reveals potential blood biomarkers for ischemic stroke. Mol. Cell. Proteomics, 19(12), 1921–1936. CrossRef Scholar google search
d’Escamard V., Lu S., Weiser-Evans M.C., Kovacic J. (2024) Integrative gene regulatory network analysis discloses key driver genes of fibromuscular dysplasia in females: The DEFINE-FMD study, accepted by Nature Cardiovascular Research. Scholar google search
Gornik H.L., Persu A., Adlam D., Aparicio L.S., Azizi M., Boulanger M., Bruno R.M., de Leeuw P., Fendrikova-Mahlay N., Froehlich J., Ganesh S.K., Gray B.H., Jamison C., Januszewicz A., Jeunemaitre X., Kadian-Dodov D., Kim E.S., Kovacic J.C., Mace P., Morganti A., Sharma A., Southerland A.M., Touzé E., van der Niepen P., Wang J., Weinberg I., Wilson S., Olin J.W., Plouin P.F. (2019) First international consensus on the diagnosis and management of fibromuscular dysplasia. Vas. Med., 24(2), 164–189. CrossRef Scholar google search
Yang-Jensen K.C., Sara M. Jørgensen S.M., Chuang C.Y., Davies M.J. (2024) Modification of extracellular matrix proteins by oxidants and electrophiles. Biochem. Soc. Trans., 52(3), 1199–1217. CrossRef Scholar google search
Ma B., Zhang K., Hendrie C., Liang C., Li M., Doherty-Kirby A., Lajoie G. (2003) PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom., 17(20), 2337–2342. CrossRef Scholar google search
The UniProt Consortium (2020) UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Res., 49(D1), D480–D489. CrossRef Scholar google search
Progenesis LC-MS version 4.0, Nonlinear Dynamics, Newcastle upon Tyne, UK. Scholar google search
Dutta B., Park J.E., Kumar S., Hao P., Gallart-Palau X., Serra A., Ren Y., Sorokin V., Lee C.N., Ho H.H., de Kleijn D., Sze S.K. (2017) Monocyte adhesion to atherosclerotic matrix proteins is enhanced by Asn-Gly-Arg deamidation. Sci. Rep., 7, 5765. CrossRef Scholar google search
