Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulation of acetate tolerance by unannotated small open reading frame (smORF) polypeptides in Methylomonas sp. DH-1

ABSTRACT: Regulation of acetate tolerance by unannotated small open reading frame (smORF) polypeptides in Methylomonas sp. DH-1

PROVIDER: PRJNA849630 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19664800_1.fastq.gz	Fastqsanger.gz
	SRR19664800_2.fastq.gz	Fastqsanger.gz
	SRR19664801_1.fastq.gz	Fastqsanger.gz
	SRR19664801_2.fastq.gz	Fastqsanger.gz
	SRR19664802_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 22

Similar Datasets

Regulation of acetate tolerance by unannotated small open reading frame (smORF) polypeptides in Methylomonas sp. DH-1

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-08-08 | GSE206217 | GEO

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

Project description:Computational, genomic, and proteomic approaches have been used to discover nonannotated proteincoding small open reading frames (smORFs). Some novel smORFs have crucial biological roles in cells and organisms, which motivates the search for additional smORFs. Proteomic smORF discovery methods are advantageous because they detect smORF-encoded polypeptides (SEPs) to validate smORF translation and SEP stability. Because SEPs are shorter and less abundant than average proteins, SEP detection using proteomics faces unique challenges. Here, we optimize several steps in the SEP discovery workflow to improve SEP isolation and identification. These changes have led to the detection of several new human SEPs (novel human genes), improved confidence in the SEP assignments, and enabled quantification of SEPs under different cellular conditions. These improvements will allow faster detection and characterization of new SEPs and smORFs.

2017-10-17 | PXD005643 | Pride

smORF atlas

Project description:smORF atlas

| PRJNA756021 | ENA

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

2019-06-26 | MSV000084014 | MassIVE

A coding sequence-embedded principle governs translational reading frame fidelity

Project description:Upon initiation at an AUG start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. Although some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known how the ribosome normally prevents spontaneous frameshift errors. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3’ end of 18S rRNA to scan the AUG-like codons after the decoding process. The internal mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a post-decoding mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like “sticky” codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes codon “stickiness”. Further supporting the role of “sticky” sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes by minimizing the appearance of AUG-like codons in the frame 2. These results suggest an important layer of information embedded within the protein coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.

2016-04-12 | GSE80156 | GEO

Expression and strain variation of the novel "small open reading frame" (smorf) multigene family in Babesia bovis.

Project description:Small open reading frame (smorf) genes comprise the second largest Babesia bovis multigene family. All known 44 variant smorf genes are located in close chromosomal proximity to ves1 genes, which encode proteins that mediate cytoadhesion and contribute to immune evasion. In this study, we characterised the general topology of smorf genes and investigated the gene repertoire, transcriptional profile and SMORF expression in two distinct strains, T2Bo and Mo7. Sequence analysis using degenerate primers identified additional smorf genes in each strain and demonstrated that the smorf gene repertoire varies between strains, with conserved and unique genes in both. Smorf genes have multiple semi-conserved and variable blocks, and a large hypervariable insertion in 20 of the 44 genes defines two major branches of the family, termed smorf A and smorf B. A total of 32 smorf genes are simultaneously transcribed in T2Bo strain B. bovis merozoites obtained from deep brain tissue of an acutely infected animal. SMORF peptide-specific antiserum bound in immunoblots to multiple proteins with a range of sizes predicted by smorf genes, confirming translation of smorf gene products from these transcripts. These results indicate that the smorf multigene family is larger than previously described and demonstrate that smorf genes are expressed and are undergoing variation, both within strains and in a lineage-specific pattern independent of strain specificity. The function of these novel proteins is unknown.

| S-EPMC3459096 | biostudies-literature

smORF atlas (part 1-RiboSeq)

Project description:smORF atlas (part 1-RiboSeq)

| PRJNA756018 | ENA

smORF atlas (part 2-RNASeq)

Project description:smORF atlas (part 2-RNASeq)

| PRJNA756023 | ENA

Methylomonas koyamae

Project description:Methylomonas koyamae overview

| PRJNA315326 | ENA

Identification of putative encoding smORF genes in drosophila imaginal discs

Project description:We aim to identify the genes that encode for putatives smORF peptides in imaginal leg disc at larval and pupal stages