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Journal of proteomics
Elsevier
Journal of proteomics

Elsevier

1874-3919

Journal of proteomics/Journal Journal of proteomicsSCIISTP
正式出版
收录年代

    Salt stress downregulates 2-hydroxybutyrylation in Arabidopsis siliques

    Geriqiqige HongXiaoyi SuKe XuBin Liu...
    1页
    查看更多>>摘要：Lysine 2-hydroxyisobutyrylation (Khib) is one of the newly discovered post-translational modifications (PTMs) through protein acylation. It has been reported to be widely distributed in both eukaryotes and prokaryotes, and plays an important role in chromatin conformation change, gene transcription, protein subcellular localization, protein-protein interaction, signal transduction, and cellular proliferation. In this study, the Khib modification proteome of siliques from A. thaliana under salt stress (Ss) and those in the control (Cs) were compared. The results showed that Khib modification was abundant in siliques. Totally 3810 normalized Khib sites on 1254 proteins were identified, and the Khib modification showed a downregulation trend dramatically: it was down-regulated at 282 sites on 205 proteins while was up-regulated at 96 sites on 78 proteins in Ss siliques (Data are available via ProteomeXchange with identifier PXD028116 and PXD026643). Among them, 13 proteins, including F4IVN6, Q9M1P5, and Q9LF33, had sites with the most significant regulation of Khib modification. Bioinformatics analysis suggested that the differentially Khib-regulated proteins mainly participated in glycol-ysis/gluconeogenesis and endocytosis. In particular, there were differentially1 17 Khib-regulated proteins that were mapped to the protein-protein interaction database. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism. Overall, our work reveals the first systematic analysis of Khib proteome in Arabidopsis siliques under salt stress, and sheds a light on the future studies on the regulatory mechanisms of Khib during the salt stress response of plants.Significance: In this study, we found the Khib-modified proteins in silique under salt stress and described the enrichment of Khib-modified proteins involved in the biological processes and cellular localization. Proteins undergoing 2-hydroxyisobutylation were mainly involved in the gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism, suggesting that 2-hydroxyisobutylation affects the energy metabolic pathway, and thus the development of the plant. In addition, specific candidate proteins that may affect plant development under salt stress were selected. This study will provide a theoretical basis for revealing the function and mechanism of these proteins and their 2-hydroxyisobutyryl modifications during the development of silique under salt stress.
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    Leveraging homologies for cross-species plasma proteomics in ungulates using data-independent acquisition

    Zainab NooraSelvam ParamasivanbPriya GhodasaraSaul Chemonges...
    1页
    查看更多>>摘要：The collection of blood plasma is minimally invasive, and the fluid is a rich source of proteins for biomarker studies in both humans and animals. Plasma protein analysis by mass spectrometry (MS) can be challenging, though modern data acquisition strategies, such as sequential window acquisition of all theoretical fragment ion spectra (SWATH), enable reproducible quantitation of hundreds of proteins in non-depleted plasma from humans and laboratory model animals. Although there is strong potential to enhance veterinary and translational research, SWATH-based plasma proteomics in non-laboratory animals is virtually non-existent. One limitation to date is the lack of comprehensively annotated genomes to aid protein identification. The current study established plasma peptide spectral repositories for sheep and cattle that enabled quantification of over 200 proteins in non-depleted plasma using SWATH approach. Moreover, bioinformatics pipeline was developed to leverage inter-species homologies to enhance the depth of baseline libraries and plasma protein quantification in bovids. Finally, the practical utility of using bovid libraries for SWATH data extraction in taxonomically related non-domestic ungulate species (giraffe) has been demonstrated.Significance: Ability to quickly generate comprehensive spectral libraries is limiting the applicability of data-independent acquisition, such as SWATH, to study proteomes of non-laboratory animals. We describe an approach to obtain relatively shallow foundational plasma repositories from domestic ruminants and employ homology searches to increase the depth of data, which we subsequently extend to unsequenced ungulates using SWATH method. When applied to cross-species proteomics, the number of proteins quantified by our approach far exceeds what is traditionally used in plasma protein tests.
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    TMT-based quantitative proteomic analysis of the effects of novel antimicrobial peptide AMP-17 against Candida albicans

    Long-Bing YangGuo GuoZhu-Qing TianLuo-Xiong Zhou...
    1页
    查看更多>>摘要：Candida albicans is the most common human fungal pathogen in immunocompromised individuals. With the emergence of clinical fungal resistance, there is an urgent need to develop novel antifungal agents. AMP-17, a novel antimicrobial peptide from Musca domestica, has an antifungal effect against C. albicans, but its mechanism of antifungal action remains unclear. In the current study, we performed a proteomics analysis in C. albicans using TMT technique under the treatment of AMP-17. A total of 3931 proteins were identified, of which 3600 included quantitative information. With a 1.5-fold change threshold and a t-testp-value < 0.05 as standard, 423 differentially expressed proteins (DEPs) were up-regulated and 180 DEPs were down-regulated in the AMP-17/ control. Notably, GO enrichment revealed that DEPs associated with the cell wall, RNA and oxidative stress were significantly up-regulated, while DEPs involved in ergosterol metabolism and membrane were significantly down-regulated in the AMP-17/control. KEGG pathway enrichment revealed that DEPs involved seven significant metabolic pathways, mainly involved oxidative phosphorylation, RNA degradation, propanoate metabolism and fatty acid metabolism. These results show that AMP-17 induces a complex organism response in C. albicans, indicating that AMP-17 may inhibit growth by affecting multiple targets in C. albicans cells. Significance: Antimicrobial peptides (AMPs) are an important part of the innate immune system of organisms and having broad range of activity against fungi, bacteria and viruses. These AMPs are considered as probable candidate for forthcoming drugs, due to their broad range of activity, lesser toxicity and decreased resistance development by target cells. AMP-17, a novel antimicrobial peptide from M. domestica, has significant antifungal activity against C. albicans. It has been confirmed that AMP-17 can play an antifungal effect by destroying the cell wall and cell membrane of C. albicans in previous studies, but its mechanism of action at the protein level is currently unclear. In the current study, using the TMT-based quantitative proteomics method, 603 differentially expressed proteins were identified in the cells of C. albicans treated with AMP-17 for 12 h, and these DEPs were closely related to cell wall, cell membrane, RNA degradation and oxidative stress. The results provide new insights into the potential mechanism of action of AMP- 17 against C. albicans. Meanwhile, it provides certain technical support and theoretical basis for the research and development of novel peptide drugs.
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    StatsPro: Systematic integration and evaluation of statistical approaches for detecting differential expression in label-free quantitative proteomics

    Yin YangJingqiu ChengShisheng WangHao Yang...
    1页
    查看更多>>摘要：Quantitative label-free mass spectrometry (MS) is an increasingly powerful technology for profiling thousands of proteins from complex biological samples. One of the primary goals of analyses performed on such proteomics data is to detect differentially expressed proteins (DEPs) under different experimental conditions. Many statistical methods have been developed and assessed for DEP detection in various proteomics studies. However, it remains a challenge for many proteomics scientists to choose an appropriate statistical procedure. Therefore, in this study, we organized 12 common testing algorithms and 6 P-value combination methods and further provided Cohen's d effect size for every protein and three evaluation criteria to help proteomics scientists investigate their influence on DEP detection in a systematic manner. To promote the widespread use of these methods, we developed a user-friendly web tool, StatsPro, and presented two case studies involving label-free quantitative proteomics data obtained using data-dependent acquisition and data-independent acquisition to illustrate its practicability. This tool is freely available in our GitHub repository (https://github.com/YanglabWCH/StatsPro/ ).Significance: One of the primary goals of analyses performed on liquid chromatography-mass spectrometry (LC-MS) based proteomics data is to detect differentially expressed proteins (DEPs) under different experimental conditions. Despite of many research efforts have been proposed to detect DEPs, to date, there is a scarcity of efficient, systematic, and easy-to-handle tools that are tailored for proteomics scientists to choose an appropriate statistical procedure. Herein, we present a new tool, StatsPro, to enable implementation and evaluation of different statistical methods for proteomics scientists. This tool has two significant advances compared to existing software: a) It integrates up to 18 common statistical approaches (12 statistical tests and 6 P-value combination strategies) and performs Cohen's d effect size systematically for users, moreover, it provides a web-based interface and can be quite conveniently operated by users, even those with less profound computational background, b) It supports three performance evaluation criteria (e.g. number of DEPs, correlation coefficient between P-values and effect sizes, Area under the ROC curve) for users to review the final statistical results, which may guide the method selection for DEPs detection.
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    The global proteome and ubiquitinome of bacterial and viral co-infected bronchial epithelial cells

    Thomas SuraSurabhi SurabhiSra Maa?Sven Hammerschmidt...
    1页
    查看更多>>摘要：Viral infections facilitate bacterial trafficking to the lower respiratory tract resulting in bacterial-viral co-infections. Bacterial dissemination to the lower respiratory tract is enhanced by influenza A virus induced epithelial cell damage and dysregulation of immune responses. Epithelial cells act as a line of defense and detect pathogens by a high variety of pattern recognition receptors. The post-translational modification ubiquitin is involved in almost every cellular process. Moreover, ubiquitination contributes to the regulation of host immune responses, influenza A virus uncoating and transport within host cells. We applied proteomics with a special focus on ubiquitination to assess the impact of single bacterial and viral as well as bacterial-viral co-infections on bronchial epithelial cells. We used Tandem Ubiquitin Binding Entities to enrich polyubiquitinated proteins and assess changes in the ubiquitinome. Infecting 16HBE cells with Streptococcus pyogenes led to an increased abundance of proteins related to mitochondrial translation and energy metabolism in proteome and ubiquitinome. In contrast, influenza A virus infection mainly altered the ubiquitinome. Co-infections had no additional impact on protein abundances or affected pathways. Changes in protein abundance and enriched pathways were assigned to imprints of both infecting pathogens.Significance: Viral and bacterial co-infections of the lower respiratory tract are a burden for health systems worldwide. Therefore, it is necessary to elucidate the complex interplay between the host and the infecting pathogens. Thus, we analyzed the proteome and the ubiquitinome of co-infected bronchial epithelial cells to elaborate a potential synergism of the two infecting organisms. The results presented in this work can be used as a starting point for further analyses.
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    Deep impact of the inactivation of the SecA2-only protein export pathway on the proteosurfaceome of Listeria monocytogenes

    Ingrid ChafseyRafal OstrowskiMorgan GuilbaudPilar Teixeira...
    1页
    查看更多>>摘要：Listeria monocytogenes presents a dimorphism associated to the SecA2 activity with cells having a normal rod shape or a dysmorphic elongated filamentous form. Besides variation of the cell and colony morphotype, this cell differentiation has profound ecophysiological and physiopathological implications with collateral effects on virulence and patho-genicity, biotope colonisation, bacterial adhesion and biofilm formation. This suggests the SecA2-only protein export could influence the listerial cell surface, which was investigated first by characterising its properties in L. monocytogenes wt and ΔsecA2. The degree of hydrophilicity and Lewis acid-base properties appeared significantly affected upon SecA2 inactivation. As modification of electrostatic properties would owe to modification in the composition of cell-surface proteins, the proteosurfaceome was further investigated by shotgun label-free proteomic analysis with a comparative relative quantitative approach. Following secretomic analysis, the protein secretion routes of the identified proteins were mapped considering the cognate transport and post-translocational maturation systems, as well as protein categories and subcellular localisation. Differential protein abundance profiles coupled to network analysis revealed the SecA2 dependence of 48 proteins, including some related to cell envelope biogenesis, translation and protein export, which could account for modifications of adhesion and surface properties of L. monocytogenes upon SecA2 inactivation. This investigation unravelled the profound influence of SecA2 activity on the cell surface properties and proteosurfaceome of L. monocytogenes, which provides advanced insights about its ecophysiopathology. Significance: L. monocytogenes is a foodborne zoonotic pathogen and etiological agent of human listeriosis. This species presents a cellular dimorphism associated to the SecA2 activity that has profound physiopathological and ecophysiological implications with collateral effects on bacterial virulence and colonisation. To explore the influence of the SecA2-only protein export on the listerial cell, the surface properties of L. monocytogenes expressing or depleted of SecA2 was characterised by microelectrophoresis, microbial affinity to solvents and contact angles analyses. As modifications of hydrophilicity and Lewis acid-base electrostatic properties would owe to modification in the composition of cell-surface proteins, the proteinaceous subset of the surfaceome, i.e. the proteosurfaceome, was investigated further by shotgun label-free proteomic analysis. This subproteome appeared quite impacted upon SecA2 inactivation with the identification of proteins accounting for modifications in the cell surface properties. The profound influence of SecA2 activity on the cell surface of L. monocytogenes was unravelled, which provides advanced insights about its ecophysiopathology.
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    Proteomic analysis of Rhodospirillum rubrum after carbon monoxide exposure reveals an important effect on metallic cofactor biosynthesis

    Christine CavazzaVeronique Collin-FaureJulien PerardHelene Diemer...
    1页
    查看更多>>摘要：Some carboxydotrophs like Rhodospirillum rubrum are able to grow with CO as their sole source of energy using a Carbone monoxide dehydrogenase (CODH) and an Energy conserving hydrogenase (ECH) to perform anaero-bically the so called water-gas shift reaction (WGSR) (CO + H2O -> CO2 + H2). Several studies have focused at the biochemical and biophysical level on this enzymatic system and a few OMICS studies on CO metabolism. Knowing that CO is toxic in particular due to its binding to heme iron atoms, and is even considered as a potential antibacterial agent, we decided to use a proteomic approach in order to analyze R. rubrum adaptation in term of metabolism and management of the toxic effect. In particular, this study allowed highlighting a set of proteins likely implicated in ECH maturation, and important perturbations in term of cofactor biosynthesis, especially metallic cofactors. This shows that even this CO tolerant microorganism cannot avoid completely CO toxic effects associated with its interaction with metallic ions.Significance: This proteomic study highlights the fact that even in a microorganism able to handle carbon monoxide and in some way detoxifying it via the intrinsic action of the carbon monoxide dehydrogenase (CODH), CO has important effects on metal homeostasis, metal cofactors and metalloproteins. These effects are direct or indirect via transcription regulation, and amplified by the high interdependency of cofactors biosynthesis.
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    Corrigendum to: "Venomics of the poorly studied hognosed pitvipers Porthidium arcosae and Porthidium volcanicum"

    Marco Ruiz-CamposLibia SanzFabian BonillaMahmood Sasa...
    1页
    查看更多>>摘要：An older version of Panel A of Fig. 3 was inadvertently published in page 7 of Journal of Proteomics 249 (2021) 104379. The correct figure shown here differs from the published one only in the molecular mass markers (lanes labelled "S") displayed in the SDS-PAGE inset.
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    PROTREC: A probability-based approach for recovering missing proteins based on biological networks

    Weijia KongBertr Jern Han WongHuanhuan GaoTiannan Guo...
    1页
    查看更多>>摘要：A novel network-based approach for predicting missing proteins (MPs) is proposed here. This approach, PROTREC (short for PROtein RECovery), dominates existing network-based methods - such as Functional Class Scoring (FCS), Hypergeometric Enrichment (HE), and Gene Set Enrichment Analysis (GSEA) - across a variety of proteomics datasets derived from different proteomics data acquisition paradigms: Higher PROTREC scores are much more closely correlated with higher recovery rates of MPs across sample replicates. The PROTREC score, unlike methods reporting p-values, can be directly interpreted as the probability that an unreported protein in a proteomic screen is actually present in the sample being screened.Significance: Mass spectrometry (MS) has developed rapidly in recent years; however, an obvious proportion of proteins is still undetected, leading to missing protein problems. A few existing protein recovery methods are based on biological networks, but the performance is not satisfactory. We propose a new protein recovery method, PROTREC, a Bayesian-inspired approach based on biological networks, which shows exceptional performance across multiple validation strategies. It does not rely on peptide information, so it avoids the ambiguity issue that most protein assembly methods face.
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    • NSTL