Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
A human gene encoding a protein homologous to ribosomal protein L39 is normally expressed in the testis and derepressed in multiple cancer cells
Introduction
Comprehensive studies of biopolymers in a cell or tissue type are rapidly growing [1], [2]. These studies include genomics (DNA analysis), transcriptomics (mRNA analysis), and proteomics (protein analysis). Complete genome sequence and high throughput technologies such as DNA microarray [3] provide massive amounts of data, which require new approaches to bioinformatics for analysis. Even using these innovative methodologies, it is a challenging task to completely understand the expression, structure, and function of all biopolymers in the cell. To circumvent this difficulty, technologies and informatics can be focused on a particular organelle or functional protein complex, allowing useful amounts of information to be obtained rapidly [4]. This approach has been applied to the nuclear pore complex and spliceosome [2]. The term “ribosomics” has been proposed for the study of human cytoplasmic ribosome and its components at the DNA, RNA, protein, and protein complex levels [5]. Recent progress in ribosomics includes systematic analysis of rRNA, ribosomal proteins, and ribosomal subunits in apoptosis [6], [7], [8], and production of antibodies against 28 ribosomal proteins and their application to cancer cells [5], [7].
In the course of further studies in ribosomics involving analysis of ribosomal protein genes, we have found a human gene that encodes a protein (L39-2) highly homologous to ribosomal protein L39, a component of the large subunit of the human ribosome [9]. In the present study, we describe the locus, structure, and expression of this gene and its relevance to the biological activities of the ribosome.
Section snippets
cDNAs
The I.M.A.G.E. consortium clone of L39-2 cDNA (Genbank accession no. AA460213) was identified by NCBI BLAST search of a human EST database and obtained from Incyte Genomics (St. Louis, MO). After sequence confirmation, the cDNA was subcloned into pCMV-Tag 2B (Stratagene, La Jolla, CA) to express an N-terminally FLAG-tagged protein. The cDNA of human ribosomal protein L39 [10] was amplified from a human fetal brain cDNA library by polymerase chain reaction (PCR) and subcloned into pCMV-Tag 2B as
A gene located on chromosome 3 encodes a protein that resembles ribosomal protein L39
BLAST search of the human genome database with the coding region of human ribosomal protein L39 cDNA [10] revealed that all autosomal and X chromosomes have DNA fragments homologous to the L39 sequence. Apart from the true gene, named RPL39 located on the long arm of the X chromosome [11], most of these DNA fragments did not appear to be functional genes because they harbored a translational signal disrupted by nonsense mutations or frameshifts, and no candidate message transcribed from the
Discussion
The mapping and structure of many ribosomal protein genes from humans and other metazoans were reported long before the completion of genome sequencing. One general belief was that each ribosomal protein has one functional gene and many pseudogenes in the genome [12]. However, a recent report has revealed two functional genes for rat ribosomal protein S27 (S27-1 and S27-2 [17]). This observation, together with our finding of the L39-2 gene, suggests that there are exceptions to this rule, and
Acknowledgements
We thank Mrs. Kumiko Matsuo and Setsuko Kobayashi for their excellent technical and secretarial assistance. This work was supported by a grant-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan and “Kenkyu-Shoureihi” (Research Facilitation Grant) from RIKEN (to D.N.) and by a National Institutes of Health Grant R01 GM55147 (to T.S.) and in part by a grant from the Organized Research Combination System of the Science and Technology
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Proteostasis regulated by testis-specific ribosomal protein RPL39L maintains mouse spermatogenesis
2021, iScienceCitation Excerpt :However, we previously found that the expression of Rpl39l is highly enriched in spermatogonial stem cells (SSCs) (Yang et al., 2013), in line with recent single cell RNA sequencing analyses showing the expression of Rpl39l in undifferentiated SSCs (Green et al., 2018; Tan et al., 2020). Although expression of Rpl39l was also found in embryonic stem cells and several cancerous cells (Nadano et al., 2002; Wong et al., 2014), its roles during spermatogenesis remains to be determined. Several studies in yeast and cancerous cells have suggested that RPL39 potentially interacts with nascent polypeptide chain, Ubc, and RNA editor (ADAR) (Dave et al., 2014; Zhang et al., 2013).
Deletion of ribosomal paralogs Rpl39 and Rpl39l compromises cell proliferation via protein synthesis and mitochondrial activity
2021, International Journal of Biochemistry and Cell BiologyCitation Excerpt :How various RP paralogs participate in the regulation of spermatogenesis and what their functional relationships are remain to be fully understood. Unexpectedly, Rpl39l, in addition to selectively express in male gonad, has aberrant activation in many carcinomas and cancer cell lines, accompanied by the expression of Rpl39, suggesting that both RPL39 and RPL39L contribute to the heterogeneity of ribosomes in these cells (Nadano et al., 2002; Uechi et al., 2002; Wong et al., 2014). RPL39 and RPL39L are both 51-amino acid long and only differ in 3 amino acids.
Identification and expression of an autosomal paralogue of ribosomal protein S4, X-linked, in mice: Potential involvement of testis-specific ribosomal proteins in translation and spermatogenesis
2013, GeneCitation Excerpt :Transfection was performed by lipofection with HilyMax (Wako Pure Chemical Industries, Osaka, Japan) in accordance with the manufacturer's instructions. For microscopy, cells on coverslips were fixed with 2% paraformaldehyde, permeabilized with 0.1% Triton X-100, treated with propidium iodide for nuclear staining or with appropriate antibodies and observed using a Zeiss LSM5 Pascal confocal laser microscope (Nadano et al., 2002; Sugihara et al., 2010). Mouse testis was fixed in phosphate-buffered saline including 4% paraformaldehyde for 3 h at 4 °C, immersed in the same buffer including 20% sucrose overnight, placed in Tissue-Tek OCT compound (Sakura Finetek, Tokyo, Japan) and then frozen at − 80 °C.
Cloning and overexpression of ribosomal protein L39 gene from deltamethrin-resistant Culex pipiens pallens
2007, Experimental ParasitologyRPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function
2023, Nature CommunicationsSpecialized Ribosomes in Health and Disease
2023, International Journal of Molecular Sciences
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Present address: Department of Molecular and Cell Genetics, School of Life Science, Faculty of Medicine, Tottori University, Tottori, Japan.