Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Apilactobacillus kunkeei releases RNA-associated membrane vesicles and proteinaceous nanoparticles

ABSTRACT: 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.

ORGANISM(S): Apilactobacillus kunkeei

PROVIDER: GSE205998 | GEO | 2023/06/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Characterization and composition of membrane vesicles and secreted proteins in Apilactobacillus kunkeei

Project description:Secreted particles, including membrane vesicles, have increasingly been recognized as important for bacterial community functions and host-interaction processes, but their specific compositions and functional roles are debated. In this study, we have characterized the secreted particles of Apilactobacillus kunkeei, a defensive symbiont of honeybees. We cultivated A. kunkeei strains A1401 and A0901 and separated the secreted protein particles from the extracellular membrane vesicles using density gradient ultracentrifugation. A proteomics analyses identified more than 500 proteins in each strain, of which 27 to 45 proteins were relatively more abundant in the cell-free supernatant, including glycoside hydrolases and peptidases. The extracellular transcriptome associated with the membrane vesicles contained a relatively higher fraction of mRNAs derived from highly transcribed operons such as those for ribosomal proteins and ATP synthase subunits, whereas highly expressed tRNAs were relatively more abundant in the cellular fraction. Based on these results, we propose that mRNAs for highly expressed proteins are overproduced and that superfluous mRNAs are fragmented, packaged into membrane vesicles and secreted. The results have implications for the utilization of membrane vesicles in A. kunkeei as a delivery tool for small RNA molecules, while also providing more general insights into the role of membrane vesicles in bacteria.

2023-09-07 | PXD034473 | Pride

Characterization and composition of membrane vesicles and secreted proteins in Apilactobacillus kunkeei

2023-09-07 | PXD034474 | Pride

Fluidigm Biomark 96.96 nanofluidic arrays for qRT-PCR of 93 miRNAs: salivary extracellular vesicles

2016-08-01 | GSE78763 | GEO

Yeast Membrane Bound Polysome

Project description:Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. mRNA species bound to membrane-associated polysomes were separated from other mRNAs by sedimentation equilibrium or sedimentation velocity. The distribution of individual transcripts in the 'membrane-bound' and 'cytosolic' fractions was quantitated for thousands of genes by hybridization to DNA microarrays. Transcripts known to encode secreted or membrane proteins were enriched in the membrane-bound fractions, whereas those known to encode cytoplasmic proteins were enriched in the fractions containing mRNAs associated with free and cytoplasmic ribosomes. On this basis, we identified over 275 human genes and 285 yeast genes that are likely to encode previously unrecognized secreted or membrane proteins. Keywords: Logical Set

2005-08-24 | GSE3180 | GEO

Yeast Membrane Bound Polysome

2005-08-24 | E-GEOD-3180 | biostudies-arrayexpress

RIP-Seq and RNA-Seq of an RNA-binding protein secreted by Listeria monocytogenes which activates RIG-I signaling

Project description:Secreted bacterial RNAs have recently emerged as a novel host-pathogen interaction mode. Naked RNA molecules are highly labile in the extracellular environment and must be protected by packaging into membrane vesicles or into complexes with RNA binding proteins. RNA secretion through membrane vesicles has been shown for several bacterial species but, surprisingly, proteins that bind and stabilize bacterial RNAs in the extracellular environment have not been reported yet. Here, we show that the bacterial pathogen L. monocytogenes secretes a small RNA binding protein that we named Zea. We show that Zea binds and stabilizes a subset of L. monocytogenes RNA, causing its accumulation in the extracellular medium. Zea modulates L. monocytogenes in vivo. Furthemore, Zea binds the mammalian non-self-RNA innate immunity sensor RIG-I and potentiates RIG-I-signaling during infection. This study provides a mechanism for the stability of extracellular RNA and unveils how secreted bacterial RNAs participate in the host-pathogen crosstalk.

2019-10-16 | E-MTAB-7665 | biostudies-arrayexpress

MicroRNA analysis of breast cancer cell lines

Project description:Membrane vesicles released by neoplastic cells into extracellular medium contain potential of carrying arrays of oncogenic molecules including proteins and microRNAs (miRNA). Extracellular (exosome-like) vesicles play a major role in cell-to-cell communication. Thus, the characterization of miRNAs of exosome-like vesicles is imperative in clarifying intercellular signaling as well as identifying disease markers. microarray analysis identified several oncogenic miRNA between the two types vesicles.

2013-11-28 | GSE52802 | GEO

MicroRNA analysis of breast cancer cell lines

2013-11-28 | GSE52802 | GEO

Fluidigm Biomark 96.96 nanofluidic arrays for qRT-PCR of 93 miRNAs: salivary extracellular vesicles

Project description:Crude extracellular vesicles (EVs) from eight healthy volunteers were separated into 6 fractions based on their densities by using the iodixanol-based density gradient centrifugation method. To determine the distribution of miRNAs among these fractions, quantities of 93 miRNAs were quantified by the TaqMan real time PCR method using the BioMark HD system (Fluidigm) equipped with 96.96 dynamic array (Fluidigm). Six samples were fractionated from a crude EVs by density gradient centrifugation. Total of 48 samples were prepared from 8 healthy volunteers. Technical replicate of 4 gave 8 x 6 x 4 x 93 = 17,856 data. As control Tris-HCl EDTA buffer (TE) was used.

2016-08-01 | E-GEOD-78763 | biostudies-arrayexpress

Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing [total RNA]

Project description:Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.

2016-10-31 | GSE88753 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data