RESUMO
OBJECTIVE: The influence of the knockout of gene Fam20a on mice salivary glands was studied in this research, to provide a potential gene therapeutic target for salivary gland dysfunction. DESIGN: The control group with genotype Fam20af/f and conditional knockout (cKO) group with Fam20af/f;K14-Cre were constructed with Cre-Loxp. The influence of Fam20a on the salivary glands was studied in terms of morphology, functionality and molecular mechanism. RESULTS: In terms of morphology, the cross-sectional area ratio of ductal to the total was reduced in the cKO mice, while that of extracellular matrix to the total was increased. At the sub-microscopic level, the knockout of Fam20a led to abnormal sub-microscopic structure of the duct cells. Functionally, saliva flow rate was significantly reduced in cKO mice. The result was consistent with the change of acinar cell marker Aquaporin 5 which was abnormally diffusely expressed in the cytoplasm of acinar cells. Meanwhile, the expression of ductal cell markers Cytokeratin 7 and nerve growth factor ß were significantly decreased, suggesting the abnormal development and function of the duct cells. The research on the mechanism reveals that the loss of Fam20a led to the decreased expression and varied localization of bone morphogenetic protein 4 (BMP4), and a significant decrease of the proportion of phosphorylated extracellular signal-regulated protein1/2 (ERK1/2) to total ERK1/2. These changes suggested that the loss of Fam20a attenuated the activity of the BMP/ERK signaling pathway. CONCLUSIONS: Fam20a affects the morphology and function of salivary glands, probably by attenuating the activity of the BMP/ERK signaling pathway.
Assuntos
Proteínas do Esmalte Dentário , Glândulas Salivares , Células Acinares/metabolismo , Animais , Aquaporina 5 , Proteínas do Esmalte Dentário/metabolismo , Camundongos , Glândulas Salivares/crescimento & desenvolvimento , Glândulas Salivares/metabolismo , Transdução de SinaisRESUMO
The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified ("dark peptidome") by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.
Assuntos
Colite Ulcerativa , Microbiota , Cromatografia Líquida , Colite Ulcerativa/diagnóstico , Colite Ulcerativa/microbiologia , Endopeptidases , Fezes/microbiologia , Humanos , RNA Ribossômico 16S/genética , Serina , Espectrometria de Massas em TandemRESUMO
We designed a metaproteomic analysis method (ComPIL) to accommodate the ever-increasing number of sequences against which experimental shotgun proteomics spectra could be accurately and rapidly queried. Our objective was to create these large databases for the analysis of complex metasamples with unknown composition, including those derived from human, animal, and environmental microbiomes. The amount of high-throughput sequencing data has substantially increased since our original database was assembled in 2014. Here, we present a rebuild of the ComPIL libraries comprised of updated publicly disseminated sequence data as well as a modified version of the search engine ProLuCID-ComPIL optimized for querying experimental spectra. ComPIL 2.0 consists of 113 million protein records and roughly 4.8 billion unique tryptic peptide sequences and is 2.3 times the size of our original version. We searched a data set collected on a healthy human gut microbiome proteomic sample and compared the results to demonstrate that ComPIL 2.0 showed a substantial increase in the number of unique identified peptides and proteins compared to the first ComPIL version. The high confidence of protein identification and accuracy demonstrated by the use of ComPIL 2.0 may encourage the method's application for large-scale proteomic annotation of complex protein systems.
Assuntos
Misturas Complexas/análise , Bases de Dados de Proteínas , Proteômica/métodos , Sequência de Aminoácidos , Animais , Proteínas de Bactérias/análise , Microbioma Gastrointestinal , Humanos , Peptídeos/análise , Ferramenta de BuscaRESUMO
The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.
Assuntos
Bases de Dados de Proteínas/normas , Biblioteca de Peptídeos , Proteômica/métodos , Animais , Humanos , Espectrometria de Massas em Tandem/métodos , Fluxo de TrabalhoRESUMO
The lysis and extraction of soluble bacterial proteins from cells is a common practice for proteomics analyses, but insoluble bacterial biomasses are often left behind. Here, we show that with triflic acid treatment, the insoluble bacterial biomass of Gram- and Gram+ bacteria can be rendered soluble. We use LC-MS/MS shotgun proteomics to show that bacterial proteins in the soluble and insoluble postlysis fractions differ significantly. Additionally, in the case of Gram- Pseudomonas aeruginosa, triflic acid treatment enables the enrichment of cell-envelope-associated proteins. Finally, we apply triflic acid to a human microbiome sample to show that this treatment is robust and enables the identification of a new, complementary subset of proteins from a complex microbial mixture.
Assuntos
Bacillus subtilis/química , Proteínas de Bactérias/isolamento & purificação , Proteínas de Membrana/isolamento & purificação , Mesilatos/química , Proteômica/métodos , Pseudomonas aeruginosa/química , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Cromatografia Líquida , Misturas Complexas/química , Microbioma Gastrointestinal/genética , Humanos , Células Jurkat , Metagenoma , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/metabolismo , Sonicação/métodos , Espectrometria de Massas em TandemRESUMO
The secreted Streptococcus pyogenes cysteine protease SpeB is implicated in host immune system evasion and bacterial virulence. We present a small molecule inhibitor of SpeB 2477 identified from a high-throughput screen based on the hydrolysis of a fluorogenic peptide substrate Ac-AIK-AMC. 2477 inhibits other SpeB-related proteases but not human caspase-3, suggesting that the molecule targets proteases with the papain-like structural fold. A 1.59 Å X-ray crystal structure of 2477 bound to the SpeB active site reveals the mechanism of inhibition and the essential constituents of 2477 necessary for binding. An assessment against a panel of 2477 derivatives confirms our structural findings and shows that a carbamate and nitrile on 2477 are required for SpeB inhibition, as these moieties provide an extensive network of electrostatic and hydrogen-bonding interactions with SpeB active site residues. Surprisingly, despite 2477 having a reduced inhibitory potential against papain, the majority of 2477-related compounds inhibit papain to a much greater and broader extent than SpeB. These findings indicate that SpeB is more stringently selective than papain for this panel of small molecule inhibitors. On the basis of our structural and biochemical characterization, we propose modifications to 2477 for subsequent rounds of inhibitor design that will impart specificity to SpeB over other papain-like proteases, including alterations of the compound to exploit the differences in CA protease active site pocket sizes and electrostatics.