Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels

Parras-Moltó, Marcos; Campos‐Laborie, Francisco J.; García-Diéguez, Juan; Rodríguez-Griñolo, M. Rosario; Pérez-Pulido, Antonio J.

doi:10.1186/1471-2105-14-229

Cited by 9 publications

(5 citation statements)

References 20 publications

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“…Emerging data on the cellular localization of proteins has exposed additional protein activity that occurs when a protein’s subcellular localization changes from the region where it is first destined. In a classical view, proteins are characterized by a single cellular compartment (cytoplasm, nucleus, plasma membrane, or extracellular region) in which each protein primarily resides and functions [86]. However, unexpected subcellular localization of such proteins challenges this classical view, and gives us one mechanism to explain a protein’s multifunctional ability.…”

Section: Introductionmentioning

confidence: 99%

Moonlighting proteins in cancer

2016

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Since the 1980s, growing evidence suggested that the cellular localization of proteins determined their activity and biological functions. In a classical view, a protein is characterized by the single cellular compartment where it primarily resides and functions. It is now believed that when proteins appear in different subcellular locations, the cells surpass the expected activity of proteins given the same genomic information to fulfill complex biological behavior. Many proteins are recognized for having the potential to exist in multiple locations in cells. Dysregulation of translocation may cause cancer or contribute to poorer cancer prognosis. Thus, quantitative and comprehensive assessment of dynamic proteins and associated protein movements could be a promising indicator in determining cancer prognosis and efficiency of cancer treatment and therapy. This review will summarize these so-called moonlighting proteins, in terms of a coupled intracellular cancer signaling pathway. Determination of the detailed biological intracellular and extracellular transit and regulatory activity of moonlighting proteins permits a better understanding of cancer and identification of potential means of molecular intervention.

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Section: Introductionmentioning

confidence: 99%

Moonlighting proteins in cancer

2016

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“…The subcellular localization of protein is closely related to its function (29,30). To gain insight into the function of ASAP, we performed gene ontology (GO) enrichment analysis on genes that are co-expressed with LINC00467 in TCGA COAD database.…”

Section: Asap Is An Inner Mitochondrial Membrane-associated Micropeptidementioning

confidence: 99%

Micropeptide ASAP encoded by LINC00467 promotes colorectal cancer progression by directly modulating ATP synthase activity

Ge¹,

Jia²,

Cen³

et al. 2021

Journal of Clinical Investigation

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Emerging evidence has shown that open reading frames inside lncRNA could encode micropeptides. However, their roles in cellular energy metabolism and tumor progression remain largely unknown. Here, we identified a 94-amino acid-length micropeptide encoded by lncRNA LINC00467 in colorectal cancer. We also characterized its conservation across higher mammals, localization to mitochondria, and the concerted local functions. This peptide enhanced the ATP synthase construction by interacting with the subunit α and γ (ATP5A and ATP5C), increased ATP synthase activity and mitochondrial oxygen consumption rate, and thereby promoted colorectal cancer cell proliferation. Hence, this micropeptide was termed as "ATP synthase associated peptide" (ASAP). Furthermore, loss of ASAP suppressed patient-derived xenograft growth with attenuated ATP synthase activity and mitochondrial ATP production. Clinically, high expression of ASAP and LINC00467 predicted poor prognosis of colorectal cancer patients. Taken together, our findings revealed a colorectal cancer-associated micropeptide as a vital player in mitochondrial metabolism and provided a therapeutic target for colorectal cancer.

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“…In addition, some features hidden in the TCR sequences may be difficult to extract due to the complexity of the structure and functions of the TCR. Examples include structural motifs, 3D conformations, and amino acid interactions ( Parras-Moltó et al, 2013 ; Stiffler et al, 2020 ). It is desirable to incorporate these hidden features in risk modeling to potentially improve the prediction accuracy.…”

Section: Introductionmentioning

confidence: 99%

TCRpred: incorporating T-cell receptor repertoire for clinical outcome prediction

Liu,

Hsu

et al. 2024

Front. Genet.

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T-cell receptor (TCR) plays critical roles in recognizing antigen peptides and mediating adaptive immune response against disease. High-throughput technologies have enabled the sequencing of TCR repertoire at the single nucleotide level, allowing researchers to characterize TCR sequences with high resolutions. The TCR sequences provide important information about patients’ adaptive immune system, and have the potential to improve clinical outcome prediction. However, it is challenging to incorporate the TCR repertoire data for prediction, because the data is unstructured, highly complex, and TCR sequences vary widely in their compositions and abundances across different individuals. We introduce TCRpred, an analytic tool for incorporating TCR repertoire for clinical outcome prediction. The TCRpred is able to utilize features that can be extracted from the TCR amino acid sequences, as well as features that are hidden in the TCR amino acid sequences and are hard to extract. Simulation studies show that the proposed approach has a good performance in predicting clinical outcome and tends to be more powerful than potential alternative approaches. We apply the TCRpred to real cancer datasets and demonstrate its practical utility in clinical outcome prediction.

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Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels

Cited by 9 publications

References 20 publications

Moonlighting proteins in cancer

Moonlighting proteins in cancer

Micropeptide ASAP encoded by LINC00467 promotes colorectal cancer progression by directly modulating ATP synthase activity

TCRpred: incorporating T-cell receptor repertoire for clinical outcome prediction

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