Project description:MicroRNAs (miRNAs) are endogenous small RNAs that play important roles in various biological and metabolic processes in plants. Caragana intermedia is an important ecological and economic tree species that is prominent in the desert environment of west and northwest China. To date, no investigation into C. intermedia miRNAs has been reported. In this study, high-throughput sequencing of small RNAs was performed to identify both conserved and novel miRNAs, and also their target mRNA genes in C. intermedia. Based on sequence similarity and hairpin structure prediction, 132 putative conserved miRNAs (12 of which were confirmed to form hairpin precursors) belonging to 31 known miRNA families were identified. Ten novel miRNAs (including the miRNA* sequences of three novel miRNAs) were also discovered. The expression of 12 miRNAs was validated in different tissues, and the 12 miRNAs were further assessed by qRT-PCR after salt treatment. Furthermore, 36 potential target genes of 17 known miRNA families and two potential target genes of one novel miRNA were predicted, and some target genes were also assessed by qRT-PCR after salt treatment. Our study provides a basic catalog of miRNAs and their targets, which will promote further understanding of the important roles of miRNAs in C. intermedia and in other species of the leguminous genus, Caragana.

2015-12-31 | GSE44819 | GEO

Characterization of the O-Glycoproteome of Prevotella intermedia

Project description:Prevotella intermedia is a Gram-negative bacterium belonging to the Bacteroidetes phylum and is notably linked to periodontitis. Several other species within this phylum have been reported to possess the general O-glycosylation system, and the O-glycoproteome has been well characterized in Tannerella forsythia, Porphyromonas gingivalis, and Flavobacterium johnsoniae. In this study, we used electron cryotomography (cryoET) to view the ultrastructure of P. intermedia for the first time, revealing an electron dense surface layer surrounding both cells and outer membrane vesicles (OMVs). Interestingly, the OMVs were frequently large (>200 nm) and were of two types, with the lumens being either electron dense or translucent. LC-MS/MS analyses of OMVs and various cell fractions of P. intermedia resulted in the identification of 1655 proteins including 62 predicted T9SS cargo proteins. Consistent with the presence of large OMVs with electron dense lumens, periplasmic proteins contributed to nearly half the protein content of OMVs. For the glycoproteome, 445 unique O-glycosylation sites within 226 glycoproteins were identified. The O-glycosylation motif exhibited a much broader range than reported in other species, with O-glycosylation found at D(S/T)(A/I/L/M/T/V/S/C/G/F/N/E/Q/D/P). A single major O-glycan was identified of delta mass 1531.48 Da and its sequence was determined by MS2 and MS3 analyses using a combination of CID and HCD fragmentation modes. Following partial deglycosylation with trifluoromethanesulfonic acid, the O-glycan sequence was confirmed to be dHex-dHex-HexNAc(HPO3-C6H12O5)-dHex-Hex-HexA-Hex(dHex). Bioinformatic analyses of O-glycoprotein localization predicted 73 periplasmic proteins, 53 inner membrane proteins, 52 lipoproteins, 26 outer membrane proteins, and 14 proteins secreted by the T9SS.

2024-02-14 | PXD047143 | Pride

Identification of microRNAs in Caragana intermedia by high-throughput sequencing and expression analysis of 12 microRNAs and their targets under salt stress

2015-12-31 | E-GEOD-44819 | biostudies-arrayexpress