The analysis of a large number of human and mouse genes codifying for a populated cluster of transmembrane proteins revealed that some of the genes significantly vary in their primary nucleotide sequence inter-species and also intra-species. In spite of that divergence and of the fact that all these genes share a common parental function we asked the question of whether at DNA level they have some kind of common compositional structure, not evident from the analysis of their primary nucleotide sequence. To reveal the existence of gene clusters not based on primary sequence relationships we have analyzed 13574 human and 14047 mouse genes by the composon-clustering methodology. The data presented show that most of the genes from each one of the samples are distributed in 18 clusters sharing the common compositional features between the particular human and mouse clusters. It was observed, in addition, that between particular human and mouse clusters having similar composon-profiles large variations in gene population were detected as an indication that a significant amount of orthologs between both species differs in compositional features. A gene cluster containing exclusively genes codifying for transmembrane proteins, an important fraction of which belongs to the Rhodopsin G-protein coupled receptor superfamily, was also detected. This indicates that even though some of them display low sequence similarity, all of them, in both species, participate with similar compositional features in terms of composons. We conclude that in this family of transmembrane proteins in general and in the Rhodopsin G-protein coupled receptor in particular, the composon-clustering reveals the existence of a type of common compositional structure underlying the primary nucleotide sequence closely correlated to function.
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http://dx.doi.org/10.1007/s00239-016-9763-7 | DOI Listing |
J Cell Biol
March 2025
Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, USA.
While membrane proteins such as ion channels continuously turn over and require replacement, the mechanisms of specificity of efficient channel delivery to appropriate membrane subdomains remain poorly understood. GJA1-20k is a truncated Connexin43 (Cx43) isoform arising from translation initiating at an internal start codon within the same parent GJA1 mRNA and is requisite for full-length Cx43 trafficking to cell borders. GJA1-20k does not have a full transmembrane domain, and it is not known how GJA1-20k enables forward delivery of Cx43 hemichannels.
View Article and Find Full Text PDFFront Immunol
December 2024
Department of Otolaryngology, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China.
Background: B-cell receptor-associated protein 31 (BCAP31) is a widely expressed transmembrane protein primarily located in the endoplasmic reticulum (ER), including the ER-mitochondria associated membranes. Emerging evidence suggests that BCAP31 may play a role in cancer development and progression, although its specific effects across different cancer types remain incompletely understood.
Methods: The raw data on BCAP31 expression in tumor and adjacent non-tumor (paracancerous) samples were obtained from the Broad Institute Cancer Cell Line Encyclopedia (CCLE) and UCSC databases.
Cancer Metab
December 2024
Department of Obstetrics and Gynecology, First Affiliated Hospital, Shihezi University, Shihezi, China.
Clin Mol Hepatol
December 2024
Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
Backgrounds/aims: Transmembrane 4 L six family member 1 (TM4SF1) is highly expressed in and contributes to the progression of various malignancies. However, how it modulates hepatocellular carcinoma (HCC) progression and senescence remains to be elucidated.
Methods: TM4SF1 expression in HCC samples was evaluated using immunohistochemistry and flow cytometry.
Oncol Res
December 2024
Department of Rehabilitation, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530000, China.
Background: Transmembrane emp24 trafficking protein 3 (TMED3) is associated with the development of several tumors; however, whether TMED3 regulates the progression of prostate cancer remains unclear.
Materials And Methods: Short hairpin RNA was performed to repress TMED3 in prostate cancer cells (DU145 cells) and in a prostate cancer mice model to determine its function in prostate cancer and .
Results: In the present study, we found that TMED3 was highly expressed in prostate cancer cells.
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