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Quantitative crotonylation proteomic analysis on Streptococcus pneumoniae

ABSTRACT: To further identify endogenous substrates of SPD_0839 and establish its regulatory network, quantitative proteomic analysis was performed on the spd_0839+ and p169 strains.

INSTRUMENT(S):

ORGANISM(S): Streptococcus Pneumoniae Serotype 2 (strain D39 / Nctc 7466)

SUBMITTER: Nan Li

LAB HEAD: xuesong sun

PROVIDER: PXD058867 | Pride | 2026-03-09

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	Kcr.tsv	Tabular
	checksum.txt	Txt
	p169KCR1.raw	Raw
	p169KCR2.raw	Raw
	p169KCR3.raw	Raw

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1 - 5 of 14

Publications

Crotonylation driving Streptococcus pneumoniae adaption and virulence.

Li Nan N Zhuang Jianpeng J Wu Jiayi J Xue Zhuoti Z Xu Jiayi J Fang Zuye Z Zheng Yundan Y Liu Yun Y Yang Yunpeng Y Ye Xinyu X He Qing-Yu QY Sun Xuesong X

Journal of advanced research 20250619

<h4>Introduction</h4>To cope with the host's stressful environment and immune clearance, some drug-resistant bacteria have reduced their virulence. Protein post-translational modifications (PTMs) are known to regulate numerous critical biological processes; however, their specific role in modulating bacterial virulence remains poorly understood.<h4>Objective</h4>This study seeks to elucidate the mechanistic role of lysine crotonylation (Kcr) in modulating Streptococcus pneumoniae virulence and a ...[more]

PMID: 40543838

Similar Datasets

Histone lysine acetylation, butyrylation, and crotonylation dynamics and functional interplay in rice under starvation and submergence

Project description:Histone lysine acylations are regulated by primary metabolism in animal cells. However, histone non-acetyl acylation is not yet studied in plants that have distinct primary metabolic pathways. In this work, we detected rice histone lysine butyrylation (Kbu) and crotonylation (Kcr) sites by mass spectrometry, and found both similar and specific acylation patterns compared with that in mammalian cells.

2018-09-06 | PXD009091 | Pride

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

Project description:We report the identification of 67 previously undescribed histone modifications, increasing the current number of known histone marks by about 70%. We further investigated one of the marks, lysine crotonylation (Kcr), confirming that it represents an evolutionarily-conserved histone posttranslational modification. The unique structure and genomic localization of histone Kcr suggest that it is mechanistically and functionally different from histone lysine acetylation (Kac). Specifically, in both human somatic and mouse male germ cell genomes, histone Kcr marks either active promoters or potential enhancers. In male germinal cells immediately following meiosis, Kcr is enriched on sex chromosomes and specifically marks testis-specific genes, including a significant proportion of X-linked genes that escape sex chromosome inactivation in haploid cells. These results therefore dramatically extend the repertoire of histone PTM sites and designate Kcr as a specific mark of active sex chromosome-linked genes in postmeiotic male germ cells. 2 histone marks (pan-lysine acetylation and pan-lysine crotonylation) were studied in 1 human cell type and 2 mouse cell types using ChIP-Seq. Input was sequenced for each cell type as a control. Pan-anti_Kac and pan-anti_Kcr antibodies were custom developed with PTM BioLab, Co., Ltd (Chicago, IL).

2011-10-06 | E-GEOD-32663 | biostudies-arrayexpress

Ku80 lysine crotonylation conversion to SUMOylation facilitates DNA non-homologous end joining and cellular resistance to radiation

Project description:A DNA double-strand break (DSB) is the most serious DNA damage and is also the principal molecular basis of radiotherapy. Upon DNA damage, the Ku80 is recruited and forms a critical DNA-PK complex at the DSB sites with Ku70 and the catalytic subunit (DNA-PKcs) to initiate DNA repair. How DNA-PK is assembled and activated is not fully understood. Based on the identification of radiation-reduced Ku80 K568 crotonylation through quantitative global lysine crotonylome analysis, we reveal that Ku80 K568 is crotonylated by p300-CBP-associated factor (PCAF). Upon DNA damage, the K568cr is decrotonylated by HDAC8. Decrotonylation of K568cr empties this site for the subsequent SUMOylation of Ku80 by CBX4.The conversion of Ku80 from K568 crotonylation to SUMOylation facilitates the assembly of DNA-PK complex and autophosphorylation of DNA-PKcs S2056, consequently activating the DSB repair. Moreover, mutation disrupting the post-translational modification (PTM) of Ku80 K568 site sensitizes cancer cells to radiotherapy in tumor-bearing nude mice models. Our findings provide fresh insights into the regulation of DNA-PK complex assembly and DSB repair. The conversion model between two different forms of post-translational modifications (PTMs) expands the atlas of therapeutic targets.

2025-05-07 | PXD061039 | Pride

Pneumococcus rolls epigenetic dice with a six phase random switch that controls virulence

Project description:We sequenced mRNA form 4 Streptococcus pneumoniae which expressed only a single HsdS variant of the phase variable type I restriction modification system. Samples were from mid log exponential growth phase in standard glucose containing growth medium. Examination of the mRNA profiles for evaluation of epigenetic regulation by a phase variable restriction modification system

2014-09-25 | E-GEOD-55182 | biostudies-arrayexpress

Global Proteomic Analysis of Lysine crotonylation in The Plant Pathogen Botrytis cinerea

Project description:Lysine crotonylation (Kcr), a recently discovered post-translational modification, plays a key role in the regulation of diverse cellular processes. Botrytis cinerea is a destructive necrotrophic fungal pathogen distributed worldwide with broad ranging hosts. However, the functions of Kcr are unknown in B. cinerea or any other plant fungal pathogens. Here, we comprehensively evaluated the crotonylation proteome of B. cinerea and identified 3967 Kcr sites in 1041 proteins, of which contained in 9 types of modification motifs. Our results show that although the crotonylation were largely conserved, different organisms contained distinct crotonylated proteins with unique functions. Bioinformatic analysis demonstrated that the majority of crotonylated proteins were distributed in cytoplasm (35%), mitochondria (26%) and nucleus (22%). The identified proteins were found to be involved in various metabolic and cellular processes, such as cytoplasmic translation and structural constituent of ribosome. Particularly, 26 crotonylated proteins participated in the pathogenicity of B. cinerea, suggesting a significant role for Kcr in this process. Protein interaction network analysis demonstrated that a mass of protein interactions are regulated by crotonylation. These data represent the ﬁrst report of the crotonylome of B. cinerea and provide a good foundation for further explorations of the role of Kcr in plant fungal pathogens.

2020-09-07 | PXD019358 | Pride

First comprehensive proteome analysis of lysine crotonylation in Streptococcus agalactiae, a pathogen causing meningoencephalitis in teleosts

Project description:In Homo sapiens, Streptococcus agalactiae is a common colonizer of the rectovaginal tract and a fundamental cause of neonatal and non-pregnant adults infectious diseases. It also causes infectious disease in fish which compromises food safety as well as possesses a zoonotic risk. Lysine crotonylation (Kcr) is a type of histone post-translational modifications discovered in 2011. Kcr dynamics are involved in active gene promoters and potential enhancers in yeast and mammalian. However, lysine crotonylation in S. agalactiae has not yet been studied. In the present study, we conducted the first proteome-wide profiling of Kcr in S. agalactiae and identified 241 Kcr sites on 675 proteins, representing the Kcr event in S. agalactiae. Bioinformatics analysis showed that 164 sequences were matched to a total of six definitively conserved motifs, and many of them were significantly enriched in metabolic processes, cellular process, and single-organism processes. Moreover, we found four crotonylation modified proteins predicted as quorum sensing system and virulence factors, which indicate the important role of PTM on bacterial QS system and virulence. These data represent the first report of a global crotonylation proteome and provide a promising starting point for further functional research of crotonylation in bacterial virulence in S. agalactiae.

2021-12-30 | PXD026445 | Pride

Identification and Tetramer Structure of SPD_0310 Hemin-storage Protein Linked to Streptococcus pneumoniae Iron Homeostasis and Virulence

Project description:We found that the homologous proteins of SPD_0310 of Streptococcus pneumoniae widely exists in Gram-positive bacteria. SPD_0310 has heme binding ability. In the GST pull-down experiment, we found that it can interact with several proteins.

2022-08-12 | PXD030298 | Pride

Proteomic investigation into the action mechanism of inhibitor ptsc1 against Streptococcus pneumoniae

Project description:Phenyl-thiazolylurea-sulfonamides compound 1 (ptsc1) is a new and efficient bacterial inhibitor. Although the inhibitor has antibacterial activity against several model bacteria, the details of its mechanism in Streptococcus pneumoniae (S. pneumoniae) have not been revealed. In the current study, we found that ptsc1 can significantly inhibit the growth of S. pneumoniae. To further investigate the molecular mechanism of its antibacterial effects, quantitative proteomics was performed to identify differential expressed proteins in S. pneumoniae. Compared with the normal group, the expression levels of 38 proteins were upregulated, whereas those of 88 proteins were downregulated (> 1.3 fold-change) in the experimental group (P < 0.05). KEGG pathways analysis revealed that ptsc1 regulated proteins were mainly involved in carbohydrate metabolism, DNA replication and repair, pyrimidine metabolism, fatty acid biosynthesis and oxidative phosphorylation pathways. The results of GO enrichment analysis showed that the inhibitor could lead to dysregulation of bacterial translation and energy metabolism, and cause intracellular oxidative stress.

2022-01-12 | PXD030534 | Pride

GlobaGlobal involvement of lysine crotonylation in protein modification and transcription regulation in ricel involvement of lysine crotonylation in protein modification and transcription regulation in rice

Project description:Lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. Here, we performed a global crotonylome analysis of rice (Oryza sativa L. japonica) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were predicted to be associated with chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins. Furthermore, to assess the relevance between histone Kcr and the genome, we performed a genomic localization analysis of histone Kcr by ChIP-seq analysis. Of the 10,923 identified peak regions, the majority (86.7%) of the enriched peaks were located in genes, especially exons. Furthermore, the degree of histone Kcr modification was positively correlated with gene expression in genic regions. Compared with other published histone modification data, the Kcr was co-located with the active histone modifications. Interestingly, histone Kcr facilitated expression of genes with existing active histone modifications. In addition, 77% of histone Kcr modifications overlapped with DNase hypersensitive sites (DHSs) in intergenic regions of the rice genome, and might mark other cis-regulatory DNA elements which are different from IPA1, a transcription activator in rice seedling. Overall, our results provide a comprehensive understanding of the biological functions of the crotonylome and new active histone modification in transcriptional regulation in plants.

2018-07-23 | PXD008716 | Pride

Klebsiella pneumoniae peptide hijacks a Streptococcus pneumoniae permease to subvert pneumococcal growth and colonization

Project description:Treatment of pneumococcal infections is limited by antibiotic resistance and exacerbation of disease by bacterial lysis releasing pneumolysin toxin and other inflammatory factors. We identified a novel peptide in the Klebsiella pneumoniae secretome, which enters Streptococcus pneumoniae via its AmiA-AliA/AliB permease. Subsequent downregulation of genes for amino acid biosynthesis and peptide uptake was associated with reduction of pneumococcal growth in defined medium and human cerebrospinal fluid, irregular cell shape, decreased chain length and decreased genetic transformation. The bacteriostatic effect was specific to S. pneumoniae and Streptococcus pseudopneumoniae with no effect on Streptococcus mitis, Haemophilus influenzae, Staphylococcus aureus or K. pneumoniae. Peptide sequence and length were crucial to growth suppression. The peptide reduced pneumococcal adherence to primary human airway epithelial cell cultures and colonization of rat nasopharynx, without toxicity. We also analysed the effect of peptide on the proteome of S. pneumoniae. We found alteration of the proteome by the peptide with some proteins turned on or off in line with the transcriptomic changes. We therefore identified a peptide with potential as a therapeutic for pneumococcal diseases suppressing growth of multiple clinical isolates, including antibiotic resistant strains, while avoiding bacterial lysis and dysbiosis.

2024-04-08 | PXD050408 | Pride

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