Posttranslational modifications in systems biology

Aggarwal, Suruchi; Tolani, Priya; Gupta, Srishti; Yadav, Amit Kumar

doi:10.1016/bs.apcsb.2021.03.005

Cited by 17 publications

(11 citation statements)

References 136 publications

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“…Proteins posttranslational modifications (PTMs) play a crucial role in regulating various biological processes, which can modulate the structure, activity and function of proteins by introducing new functional groups. 12 , 13 Lysine acetylation (Kac) is an essential posttranslational modification discovered in histones in the 1960s. 14 This modification regulates many biological functions (such as chromatin remodelling, gene expression regulation, protein stability, cytoskeletal dynamics and cellular metabolic state) and is closely linked to cardiovascular diseases.…”

Section: Introductionmentioning

confidence: 99%

“… 6 Quantitative analysis and PTMs of proteins are essential for understanding biological complexity. 12 , 18 To better understand the pathogenesis of PE, we integrated proteome and acetyl proteome (acetylome) systematically to analyse the vital features of placental proteins in pregnant women with PE and provided a landscape of acetylation in PE, which may contribute to developing valuable novel biomarkers for PE.…”

Section: Introductionmentioning

confidence: 99%

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Systematic proteomics analysis of lysine acetylation reveals critical features of placental proteins in pregnant women with preeclampsia

Shangguan

Wang

Shi

et al. 2021

J Cellular Molecular Medi

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Preeclampsia (PE) is a dangerous hypertensive disorder that occurs during pregnancy. The specific aetiology and pathogenesis of PE have yet to be clarified. To better reveal the specific pathogenesis of PE, we characterized the proteome and acetyl proteome (acetylome) profile of placental tissue from PE and normal‐term pregnancy by label‐free quantification proteomics technology and PRM analysis. In this research, 373 differentially expressed proteins (DEPs) were identified by proteome analysis. Functional enrichment analysis revealed significant enrichment of DEPs related to angiogenesis and the immune system. COL12A1, C4BPA and F13A1 may be potential biomarkers for PE diagnosis and new therapeutic targets. Additionally, 700 Kac sites were identified on 585 differentially acetylated proteins (DAPs) by acetylome analyses. These DAPs may participate in the occurrence and development of PE by affecting the complement and coagulation cascades pathway, which may have important implications for better understand the pathogenesis of PE. In conclusion, this study systematically analysed the reveals critical features of placental proteins in pregnant women with PE, providing a resource for exploring the contribution of lysine acetylation modification to PE.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Systematic proteomics analysis of lysine acetylation reveals critical features of placental proteins in pregnant women with preeclampsia

Shangguan

Wang

Shi

et al. 2021

J Cellular Molecular Medi

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“…Despite these significant advances, we have a limited understanding regarding the complete architecture of these signaling networks, and how they interplay with each other ( Djouder et al, 2010 ; Bosch et al, 2020b ). Reflecting the increasing complexity found in combinatorial PTM-driven signaling and proteome regulation ( Aggarwal et al, 2021 ), recent studies confirm that LD proteins are substrates for, and/or regulators of, acetylation ( Qian et al, 2017 ; Nguyen et al, 2019 ), palmitoylation ( Suzuki et al, 2015 ), ubiquitylation ( Zhang et al, 2018 ; BasuRay et al, 2019 ; Sugihara et al, 2019 ), ISGylation ( Thery et al, 2021 ), or UFMylation ( Eck et al, 2020 ). Proteomics procedures hold a key to globally understand the dynamics and function of these PTMs, but a majority of strategies have relied on the affinity purification of peptides bearing a specific PTM before its analysis by mass spectrometry ( Murray et al, 2019 ; Nelson et al, 2021 ; Paulo and Schweppe, 2021 ; Rivera et al, 2021 ; Hsieh et al, 2022 ).…”

Section: Future Directionsmentioning

confidence: 99%

Insights Into the Biogenesis and Emerging Functions of Lipid Droplets From Unbiased Molecular Profiling Approaches

Sánchez-Álvarez

Pozo

Bosch

et al. 2022

Front. Cell Dev. Biol.

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Lipid droplets (LDs) are spherical, single sheet phospholipid-bound organelles that store neutral lipids in all eukaryotes and some prokaryotes. Initially conceived as relatively inert depots for energy and lipid precursors, these highly dynamic structures play active roles in homeostatic functions beyond metabolism, such as proteostasis and protein turnover, innate immunity and defense. A major share of the knowledge behind this paradigm shift has been enabled by the use of systematic molecular profiling approaches, capable of revealing and describing these non-intuitive systems-level relationships. Here, we discuss these advances and some of the challenges they entail, and highlight standing questions in the field.

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“…In evaluating the virulence of fungal pathogens, epigenetic modifications are a more direct and rapid response to stress. Epigenetic modifications that have received wide attention include PTMs, such as phosphorylation, ubiquitination, and acetylation ( Table 1 ) ( Aggarwal et al., 2021 ; Zhang Y. et al., 2021 ). Phosphorylation regulates kinase pathways during fungal infection.…”

Section: Posttranslational Modifications In Fungal Pathogenesismentioning

confidence: 99%

“…Over past decades, application of MS-based proteomics has expanded rapidly, especially in studies of proteomes and posttranslational modifications (PTMs), such as acetylation, phosphorylation, succinylation, and crotonylation ( Figure 1A ) ( Aggarwal et al., 2021 ). Application in studies of microbiological pathogenesis and interactions between pathogens and hosts has led to the discovery of many novel mechanisms of host–fungus interactions ( Toor et al., 2018 ; Khan et al., 2019 ; Li Y. et al., 2019 ; Zamith-Miranda et al., 2019 ; Bruno et al., 2020 ; Machata et al., 2020 ; Thak et al., 2020 ; Zhou et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Pathogen-Host Interaction Repertoire at Proteome and Posttranslational Modification Levels During Fungal Infections

Sun

et al. 2021

Front. Cell. Infect. Microbiol.

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Prevalence of fungal diseases has increased globally in recent years, which often associated with increased immunocompromised patients, aging populations, and the novel Coronavirus pandemic. Furthermore, due to the limitation of available antifungal agents mortality and morbidity rates of invasion fungal disease remain stubbornly high, and the emergence of multidrug-resistant fungi exacerbates the problem. Fungal pathogenicity and interactions between fungi and host have been the focus of many studies, as a result, lots of pathogenic mechanisms and fungal virulence factors have been identified. Mass spectrometry (MS)-based proteomics is a novel approach to better understand fungal pathogenicities and host–pathogen interactions at protein and protein posttranslational modification (PTM) levels. The approach has successfully elucidated interactions between pathogens and hosts by examining, for example, samples of fungal cells under different conditions, body fluids from infected patients, and exosomes. Many studies conclude that protein and PTM levels in both pathogens and hosts play important roles in progression of fungal diseases. This review summarizes mass spectrometry studies of protein and PTM levels from perspectives of both pathogens and hosts and provides an integrative conceptual outlook on fungal pathogenesis, antifungal agents development, and host–pathogen interactions.

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Posttranslational modifications in systems biology

Cited by 17 publications

References 136 publications

Systematic proteomics analysis of lysine acetylation reveals critical features of placental proteins in pregnant women with preeclampsia

Systematic proteomics analysis of lysine acetylation reveals critical features of placental proteins in pregnant women with preeclampsia

Insights Into the Biogenesis and Emerging Functions of Lipid Droplets From Unbiased Molecular Profiling Approaches

Pathogen-Host Interaction Repertoire at Proteome and Posttranslational Modification Levels During Fungal Infections

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