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Series GSE205998 Query DataSets for GSE205998
Status Public on Jun 09, 2023
Title Apilactobacillus kunkeei releases RNA-associated membrane vesicles and proteinaceous nanoparticles
Organism Apilactobacillus kunkeei
Experiment type Expression profiling by high throughput sequencing
Summary Extracellularly released particles, including membrane vesicles, have increasingly been recognized as important for bacterial community functions and host-interaction processes, but their compositions and functional roles differ between species and also between strains of the same species. In this study, we have determined the composition of membrane vesicles and protein particles identified in the cell-free pellets of two strains of Apilactobacillus kunkeei, a defensive symbiont of honeybees. The membrane vesicles were separated from the extracellular particles using density gradient ultracentrifugation. The peaks of the RNA and protein distributions were separated from each other and the highest concentration of RNA was observed in the fractions that contained the membrane vesicles while the highest protein concentration coincided with the fractions that contained extracellular particles. A comparative proteomics analysis by LC-MS/MS showed that 37 proteins with type-I signal peptides were consistently identified across the fractionated samples obtained from the cell-free pellets, of which 29 were orthologs detected in both strains. Functional predictions of the extracellular proteins revealed the presence of glycoside hydrolases, glycosyltransferases, giant proteins and peptidases. The extracellular transcriptomes mapped to a broad set of genes with a similar functional profile as the whole cell transcriptome. This study provides insights into the composition of membrane vesicles and extracellular proteins of a bee-associated symbiont.
Overall design The RNA associated with cell-free pellets (CFP) from Apilactobacillus kunkeei strain A1401 was compared with RNA extracted from whole cell lysates (WCL). Biological replicates were prepared and paired CFP and WCL samples were obtained from each biological replicate.
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Contributor(s) Seeger C, Dyrhage K, Näslund K, Andersson SG
Citation(s) 37705871
Submission date Jun 13, 2022
Last update date Sep 15, 2023
Contact name Siv Andersson
Organization name Uppsala University
Street address Husargatan 3
City Uppsala
ZIP/Postal code 752 37
Country Sweden
Platforms (1)
GPL32344 Illumina MiSeq (Apilactobacillus kunkeei)
Samples (6)
GSM6238831 CFP, rep1
GSM6238832 CFP, rep2
GSM6238833 CFP, rep3
BioProject PRJNA848781

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Supplementary file Size Download File type/resource
GSE205998_A1401.gff.gz 509.7 Kb (ftp)(http) GFF
GSE205998_RNAseq.DESeq2.csv.gz 66.4 Kb (ftp)(http) CSV 32.3 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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