Ontology highlight
ABSTRACT:
PROVIDER: PRJNA719468 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14169803.fastq.gz | Fastqsanger.gz | |||
| SRR14169804.fastq.gz | Fastqsanger.gz | |||
| SRR14169805.fastq.gz | Fastqsanger.gz | |||
| SRR14169806.fastq.gz | Fastqsanger.gz | |||
| SRR14169807.fastq.gz | Fastqsanger.gz |
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Project description:Microbes in biofilms face the challenge of substrate limitation. In particular, cells in Pseudomonas aeruginosa biofilms growing in the laboratory or during host colonization often become limited for oxygen. Previously we found that phenazines, antibiotics produced by P. aeruginosa, balance the intracellular redox state for cells in biofilms. Here, we show that genes involved in denitrification are induced in phenazine-null (Δphz) mutant biofilms grown under an aerobic atmosphere, even in the absence of nitrate. This finding suggests that resident cells employ a bet-hedging strategy to anticipate the potential availability of nitrate and counterbalance their highly reduced redox state. Consistent with our previous characterization of aerobically-grown colonies supplemented with nitrate, we find that the pathway that is induced in Δphz colonies combines the nitrate reductase activity of the periplasmic enzyme Nap with downstream reduction of nitrite to nitrogen gas catalyzed by the enzymes Nir, Nor, and Nos. This regulatory relationship differs from the denitrification pathway that functions under anaerobic growth with nitrate as the terminal electron acceptor, which depends on the membrane-associated nitrate reductase Nar. We identify sequences in the promoter regions of the nap and nir operons that are required for the effects of phenazines on expression. We also show that specific phenazines have differential effects on nap gene expression. Finally, we provide evidence that individual steps of the denitrification pathway are catalyzed at different depths within aerobically grown biofilms, suggesting metabolic cross-feeding between community subpopulations. (corresponding publication)
2018-10-19 | PXD008924 | Pride
Project description:Small proteins (SPs) are defined as peptides of 100 amino acids or less encoded by short open reading frames (sORFs). Recent studies have shown that SPs are involved in many important biological processes, including cell signaling, metabolism, growth and so on. However, most of the annotated SPs in almost all species are currently lacking the evidence for protein existence and are regard as missing proteins (MPs). In addition, more and more mis-annotated sORFs have been discovered by proteogenomic methods in human, mice and even the well-characterised Saccharomyces cerevisiae. This reveals a blind spot in traditional gene annotation technology for those SPs-encoding genes. Because SPs are short and generally low abundant, SPs identification using proteomics faces challenges. A deeper coverage of SPs identification may help validate more MPs and discover more potential mis-annotated sORFs. Here, we applied a SPs enrichment-based proteogenomic strategy to Saccharomyces cerevisiae. By integrating four different SPs enrichment methods, we have successfully validated 31 MPs and discovered 3 novel sORFs (YKL104W-A, YHR052C-B and YHR054C-B) which were verified by novel peptide synthesis. In-depth analysis of our SPs enrichment datasets also reveals a series of special physicochemical and biological characteristics of SPs and particular rules of SPs identification. Based on these, we then systematically conclude the difficulties, causes and solutions in SPs identification.
2018-06-15 | PXD008586 | Pride
Project description:How to separate hydrophobic peptides and to prevent loss of such peptides, nevertheless, have not been drawn enough attention (19). As a membrane protein possesses higher hydrophobicity, especially for one with multiple bilayer-exposed domains, efficient detection of hydrophobic peptides becomes a critical issue for its identification. It is generally recognized that MPs have two characteristics, relatively shorter sequences of amino acids and higher hydrophobicity.
2018-10-24 | PXD010630 | Pride
Project description:In recent years, high-throughput technologies have contributed to development a more precise picture of the human proteome. However, 2,129 proteins remain listed as missing proteins (MPs) in the newest neXtProt release (2019-02). The main reasons for MPs are a low abundance, low-molecular-weight (LMW), unexpected modifications, membrane characteristics, etc. Moreover, more than 50% of the MS/MS data have not been successfully identified in shotgun proteomics. Open-pFind, an efficient open search engine, recently released by the pFind group in China, presents an opportunity to identify these buried MPs in complex samples. Proteins and potential MPs were identified using Open-pFind and three other search engines to compare their performance and efficiency with three large-scale datasets digested by different enzymes. Our results demonstrated that Open-pFind identified 29.9-47.5% more peptide-spectrum matches (PSMs), 48.0-63.9% more peptides sequences (with modifications) and 22.7-38.1% more peptide sequences (regardless of modifications) than those identified by the second-best search engine. As a result, Open-pFind detected 7.5-19.3% more candidate MPs than those by the second-best search engine. In total, 5 (PE2) of the 150 candidate MPs identified by Open-pFind were verified from two unique peptides containing more than 9 amino acids (AA) by using spectrum theoretical prediction with pDeep, and synthesized peptide matching with pBuild, after spectrum quality analysis, isobaric post-translational modification, and single amino acid variant (SAAV) filtering. These five verified MPs can be ranked in the PE1 level. In addition, three other candidate MPs were verified with two unique peptides (one peptide containing more than 9 AA) and the other containing only 8 AA), which were slightly lower than the criteria listed by C-HPP, and required additional verification information. More importantly, unexpected modifications were detected in these MPs. Another 141 MPs were listed as candidates, but required additional verification information.
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Project description:The intricate molecular environment of the native membrane profoundly influences every aspect of membrane protein (MP) biology. Despite this, the most prevalent method of studying MPs uses detergent-like molecules that disrupt and remove this vital local membrane context. This severely impedes our ability to quantitatively decipher the local molecular context and comprehend its regulatory role in the structure, function, and biogenesis of MPs. Using a library of membrane-active polymers we have developed a platform for the high-throughput analysis of the membrane proteome. The platform enables near-complete spatially resolved extraction of target MPs directly from their endogenous membranes into native nanodiscs that maintain the local membrane context. We accompany this advancement with an open-access quantitative database that provides the most efficient extraction conditions of 2065 unique mammalian MPs. Our method enables rapid and near-complete extraction and purification of target MPs directly from their endogenous organellar membranes at physiological expression levels while maintaining the nanoscale local membrane environment. Going beyond the plasma membrane proteome, our platform enables extraction from any target organellar membrane including the endoplasmic reticulum, mitochondria, lysosome, Golgi, and even transient organelles such as the autophagosome. To further validate this platform we took several independent MPs and demonstrated how our resource can enable rapid extraction and purification of target MPs from different organellar membranes with high efficiency and purity. Further, taking two synaptic vesicle MPs, we show how the database can be extended to capture multiprotein complexes between overexpressed MPs. We expect these publicly available resources to empower researchers across disciplines to capture membrane ‘nano-scoops’ containing a target MP efficiently and interface with structural, functional, and other bioanalytical approaches. We demonstrate an example of this by combining our extraction platform with single-molecule TIRF imaging to demonstrate how it can enable rapid determination of homo-oligomeric states of target MPs in native cell membranes.
2024-08-23 | PXD052184 | Pride
Project description:The epidermis, the most superficial layer of human skin, serves a critical barrier function, protecting the body from external pathogens and allergens. Dysregulation in the epidermal differentiation process contributes to barrier dysfunction and is implicated in the pathology of various dermatological diseases, including atopic dermatitis (AD). Mucopolysaccharide polysulfate (MPS) is used as a moisturizing agent for xerosis in AD patients. However, its mechanism of action on keratinocytes, the main constituent of the epidermis, remains unclear. In this study, we investigated the impact of MPS on keratinocytes by subjecting adult human epidermal keratinocyte (HEKa) cells and three-dimensional cultured keratinocytes to MPS treatment, followed by transcriptome analysis. The analysis revealed that MPS treatment enhances keratinocyte differentiation and suppresses proliferation. We focused on amphiregulin (AREG), a membrane protein that belongs to the epidermal growth factor (EGF) family and possesses a heparin-binding domain, as a significant target of the MPS among the genes altered by MPS. It is revealed that MPS exerts an inhibitory effect directly on AREG, rather than on the EGF receptor or other members of the EGF family. Furthermore, it is suggested that AREG leads to a reduction in epidermal barrier function, whereas MPS contributes to barrier enhancement through AREG inhibition. Collectively, these findings suggest that MPS modulates barrier function through the inhibition of AREG, offering insights into potential therapeutic strategies for skin barrier restoration.
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Project description:It has been proved that intramuscular fat (IMF) or marbling in beef improves palatability. Recently, consumers have considered not only the degree of marbling but also the size and distribution of marbling flecks for their health and appetizing looking of beef. Computer image analysis (CIA) systems have been developed to assess various characteristics of marbling particles (MPs) such as the number, size, and distribution (fineness or coarseness) objectively. Some CIA indexes about MPs indicating how MPs are distributed evenly had significant positive relationship with price which represents consumers’ interest. RNA-seq research about formation of fine MPs in the longissimus thoracis (LT) muscle tissue of cattle have not yet been tried in transcriptome level. This study was conducted to reveal the DEGs between groups which have high or low number of fine MPs in the Longissimus thoracis muscle of Korean beef cattle and to understand molecular events associated with marbling fineness.
2021-07-20 | GSE166206 | GEO