Dataset Information

Mass spec analysis of the sequences of proteins snFPITE-n1 and snFPITE-n2 from Sipunculus nudus

ABSTRACT: In this project, we purified proteins snFPITE-n1 and snFPITE-n2 from Sipunculus nudus, digested the proteins and determined the sequences of the proteins by Mass spec analysis. We have a database of the sequences of snFPITE proteins from Sipunculus nudus and we used the Mass spec results to search for the protein sequences from this database.

INSTRUMENT(S):

ORGANISM(S): Sipunculus Nudus

TISSUE(S): Whole Body

SUBMITTER: Xi Chen

LAB HEAD: Xi Chen

PROVIDER: PXD043675 | Pride | 2025-04-03

REPOSITORIES: Pride

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Publications

A facultative plasminogen-independent thrombolytic enzyme from Sipunculus nudus.

Tang Mingqing M Ma Guoxing G Xu Chunyan C Yang Hui H Lin Hongjun H Bian Chao C Hu Chengjia C Lu Meiling M Chen Lei L Jie Wencai W Yue Zhen Z Jian Jianbo J Sun Yuqing Y Yan Hui H Zhou Jingjing J Zhang Xianying X Liao Shengye S Li Zhaofa Z Cai Shuangfeng S Wu Yaqing Y Yang Kexin K Xiong Yanan Y Zhao Yonggang Y Lv Zhimin Z Xu Xiaoming X Liu Chuang C Xin Pengliang P Ye Lichao L Cui Xiuling X Shi Qiong Q Chen Xi X Xu Ruian R

Nature communications 20250424 1

Current thrombolytic therapies primarily function by converting plasminogen into plasmin, a process dependent on the fibrin-activator complex. This dependence, coupled with the substantial molecular size of plasmin, constrains its effectiveness in degrading D-dimer and restricts its diffusion within thrombi. Here, we introduce a small facultative plasminogen-independent thrombolytic enzyme, snFPITE, isolated from Sipunculus nudus. Compared to traditional thrombolytic agents, snFPITE does not req ...[more]

PMID: 40274794

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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.

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	1.xlsx	Xlsx
	2.msf	Msf
	2.raw	Raw

Dataset Information

Mass spec analysis of the sequences of proteins snFPITE-n1 and snFPITE-n2 from Sipunculus nudus

Dataset's files

Publications

A facultative plasminogen-independent thrombolytic enzyme from Sipunculus nudus.

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