Dataset Information

Proteomic response to heat shock in males and females of a Baikal endemic amphipod Eulimnogammarus cyaneus (Dyb. 1874) (Crustacea: Amphipoda)

ABSTRACT: In this project we aimed to establish a proteome-based pipeline for a non-model Baikal endemic amphipod species Eulimnogammarus cyaneus (Dybowsky, 1874). We used next-generation transcriptome sequencing to create a database for protein identification and investigated the proteome of E. cyaneus with LC-MS with particular emphasis on sexual dimorphism and response to acute thermal stress. We were able to characterize ca. 1000 protein groups and found male- and female-specific proteins, as well as proteins specific for thermal stress conditions.

INSTRUMENT(S): LTQ Orbitrap XL ETD

ORGANISM(S): Eulimnogammarus Cyaneus

TISSUE(S): Whole Body

SUBMITTER: Polina Drozdova

LAB HEAD: Stefan Kalkhof

PROVIDER: PXD013237 | Pride | 2020-11-19

REPOSITORIES: Pride

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Publications

Proteomics reveals sex-specific heat shock response of Baikal amphipod Eulimnogammarus cyaneus.

Bedulina Daria D Drozdova Polina P Gurkov Anton A von Bergen Martin M Stadler Peter F PF Luckenbach Till T Timofeyev Maxim M Kalkhof Stefan S

The Science of the total environment 20201019

The ancient Lake Baikal is the largest source of liquid freshwater on Earth and home to a unique fauna. Several hundred mostly cold-adapted endemic amphipod species inhabit Baikal, an ecosystem that is already being influenced by global change. In this study, we characterized the core proteome and heat stress-induced changes in a temperature-tolerant endemic amphipod, Eulimnogammarus cyaneus, using a proteogenomic approach (PRIDE dataset PXD013237) to unravel the molecular mechanisms of the obse ...[more]

PMID: 33187699

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Project description:Purpose: Ribosome profiling and RNA-Seq were used to map the location and abundance of translating ribosomes on human skeletal muscle transcripts from a patient with Becker muscular dystrophy. Methods: Tissue homogenates were prepared from frozen sections of a muscle biopsy obtained from a patient with an NM_004006:c.40_41delGA dystrophin mutation and a normal control. Ribosome-protected fragments and total RNA were prepared from a single homogenate, so starting RNA populations for both libraries were closely matched. Homogenates were not clarified before RNase digestion to avoid loss of ribosomes associated with large molecular weight complexes and RNA-Seq libraries were prepared after rRNA subtraction to avoid positional loss of 5’ reads. RPF-Seq libraries were built using the TruSeq Small RNA Sample Preparation Kit (Illumina) and RNA-Seq libraries were built using the TruSeq RNA Sample Preparation v2 Kit (Illumina). RPF-Seq and RNA-Seq libraries were subjected to 50 cycles of single-end sequencing on an Illumina HiSeq 2000 instrument. Trimmed and filtered RPF- and RNA-Seq reads were mapped to RefSeq fasta sequences downloaded from the UCSC genome browser (hg19 assembly). Results: Most mutations that truncate the reading frame of the DMD gene result in loss of dystrophin expression and lead to Duchenne muscular dystrophy. However, amelioration of disease severity can result from alternate translation initiation beginning in DMD exon 6 that results in the expression of a highly functional N-truncated dystrophin. This novel isoform results from usage of an internal ribosome entry site (IRES) within exon 5 that is glucocorticoid-inducible. IRES activity is confirmed in patient muscle by both peptide sequencing and ribosomal profiling. Conclusions: Our results provide a molecular explanation for the rescue of 5’ truncating mutations via a heretofore undescribed mechanism of post-transcriptional regulation of dystrophin expression. The presence of a glucocorticoid-inducible IRES within a highly conserved region of the DMD sequence strongly suggests a programmed role for alternate translation initiation, and ongoing efforts to understand the relevant cell lineage-specific and/or conditional activation signals will shed light on underlying mechanisms of IRES control and elucidate potentially novel functions of dystrophin. Skeletal muscle ribosome-protected fragment and RNA-Seq profiles from a patient with an NM_004006:c.40_41delGA dystrophin mutation and a normal control were generated by deep sequencing using the Illumina HiSeq 2000.

Dataset Information

Proteomic response to heat shock in males and females of a Baikal endemic amphipod Eulimnogammarus cyaneus (Dyb. 1874) (Crustacea: Amphipoda)

Publications

Proteomics reveals sex-specific heat shock response of Baikal amphipod Eulimnogammarus cyaneus.

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