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RPL10A (ribosomal protein L10a)

Written2020-12Irmak Gürcüoğlu, A. Elif Erson-Bensan
Department of Biological Sciences, Middle East Technical University, Ankara, Turkey, irmak.gurcuoglu@metu.edu.tr; erson@metu.edu.tr

Abstract 60S Ribosomal Protein L10A (RPL10A) gene maps to Chromosome 6, plus strand. RPL10A has 6 exons and 5 introns. RPL10A protein has only one domain called the universal ribosomal protein uL1 family. RPL10A protein functions at the E site of 80S monosomes or polysomes.

Keywords 60S Ribosomal Protein L10A, RPL10A, Ribosome, Polysome, Translation, Development

(Note : for Links provided by Atlas : click)

Identity

Alias (NCBI)NEDD6
CSA19
L10A
HGNC (Hugo) RPL10A
HGNC Alias symbCsa-19
L10A
HGNC Previous nameNEDD6
LocusID (NCBI) 4736
Atlas_Id 46376
Location 6p21.31  [Link to chromosome band 6p21]
Location_base_pair Starts at 35468401 and ends at 35470780 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping RPL10A.png]
Local_order From telomere to centromere : MKRN6P, FANCE, RPL10A, MIR7111, LOC110121220, TEAD3, TULP1
 
  Local order of RPL10A together with neighboring upstream and downstream genes on chromosome 6. Arrows indicate the direction of transcription and arrow length indicates approximate gene sizes.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

DNA/RNA

Note RPL10A gene consists of 6 exons and 5 introns. The gene maps to 6p21.31 and is 2,38 kb long (NCBI Reference Sequence: NC_000006.12 (35468401..35470781). Highlighted in red is the protein coding sequence from exons 1-6 (Figure 2).
 
  RPL10A gene has 6 exons and 5 introns. Numbers indicate the exons. Red exons show protein coding regions while blue indicates untranslated regions of exons.
Description RPL10A gene is 2,38 kb long and is on the positive strand.
Transcription Full length isoform is 718 bp long (NM_007104). 4 exons totally contribute, 1st and 6th exons partially contribute to the open reading frame (ORF). RPL10A has an other predicted transcript of 974 bp (XM_017010900.1).
Pseudogene There are 13 pseudogenes of RPL10A. RPL10AP1, RPL10AP2, RPL10AP3, RPL10AP4, RPL10AP5, RPL10AP6, RPL10AP7, RPL10AP8, RPL10AP9, RPL10AP10, RPL10AP11, RPL10AP12, RPL10AP13

Protein

Note RPL10A gene encodes a 217 amino acid protein. The protein is a member of the universal ribosomal protein uL1 family and has a molecular weight of 24,831 Da.
 
  RPL10A has one functional domain. Numbers above the bars indicate amino acids.
Description RPL10A has one domain called the Ribosomal_L1 superfamily domain. There are 13 conserved mRNA/rRNA interface residues on this domain (NCBI Conserved Domains).
Expression RPL10A protein is expressed in all tissues but highest expression is in female organs, digestive tract, gastrointestinal tract, pancreas, kidney, muscle, skin and lymphoid tissues (The Human Protein Atlas, 2020).
Function Ribosomal Protein L10A is required for joining the 60S and 40S ribosomal subunits into the functional 80S ribosome (Turtoi, Brown, Oskamp, & Schneeweiss, 2008). RPL10A protein is common and detected across all eukaryotic groups. The number and sequence of amino acids are highly conserved among animals, fungi, plants, and protists (Campo, Casano, & Barreno, 2013).
RPL10A is found on the exit tunnel of 80S ribosomes and preferentially provides the translation of specific subsets of mRNAs by binding to Internal Ribosome Entry Sites (IRES) on the mRNAs. These specific mRNAs belong to several functional groups, including extracellular matrix (ECM) organization and glycosphingolipid metabolic processes RPL10A enhances expression of genes promoting growth Insulin Like Growth Factor2 ( IGF2), Pleiotrophin ( PTN), Early Growth Response 1 ( EGR1), and cancer metastasis genes such as PKN3 (Protein Kinase N3) (Shi, et al., 2017).
RPL10A expression is detected in somatic, gonadal, and primordial germ cells. Rpl10a has an unclear extra-ribosomal function related to ovary development during post-migratory proliferation of primordial germ cells in Oncorhynchusmykis (rainbow trout) and Fenneropenaeus merguiensis (banana shrimp) (Makkapan, Yoshizaki, Tashiro, & Chotigeat, 2014 ; Wonglapsuwan, Miyazaki, Loongyai, & Chotigeat, 2009).
Rpl10A is an important factor in the development of zebrafish. Rpl10a knockout (KO) zebrafish embryos showed morphological abnormalities, including short body lengths, bent tails, smaller yolk extensions, reduction in pigmentation and smaller eyes. Rpl10a deficient zebrafish died by 3-7 days after fertilization (Palasin, et al., 2019).
RAC-alpha serine/threonine-protein kinase (Akt) and Forkhead box protein O (FOXO) proteins are highly phosphosphorylated in RPL10A over-expressed fruit fly mutants. As a result, insulin receptor ( INSR) which affects cell proliferation is overexpressed in these mutants (Chaichanit, Wonglapsuwan, & Chotigeat, 2018).
Arabidopsis thaliana Rpl10A is involved in defense response to geminivirus and begomovirus infections. NSP-Interacting Kinase 1 (NIK1) oligomerization phosphorylates Rpl10A, providing its translocation into the nucleus (Carvalho, et al., 2008).
Use of RPL10A in Translational Ribosomal Affinity Purification Assays
RPL10A protein is a critical protein in ribosome related pull down assays. eGFP or HA tagged phusion protein of RPL10A is used in the "Ribosome Profiling" and "Translational Ribosomal Affinity Purification (TRAP)" assays followed by RNA-seq, microarray, and RT-qPCR experiments.
Rpl10a pulldown of ribosome associated RNAs has been reported in plant systems such as A. thaliana, Zea Mays, and Oryza sative to study impact of stress conditions, development and metabolism (Sablok, Powell, & Kazan, 2017).
Cell adhesion molecule L1CAM knockdown in BrM3 brain metastatic derivative of the H2030 KRAS-mutant human lung adenocarcinoma cell line1(H2030 BrM) was used to investigate L1CAM-related signaling pathway elements. RPL10A pull down with TRAP method indicated the translation profile of downstream genes of L1CAM-related pathways that have a role in proliferation, motility, and adhesion to reveal the role of L1CAM in metastasis (Er et al., 2018).
RPL10A pull down in TRAP assay is also used in studies of nervous system tissues. mRNA translation of striatonigral and striatopallidal medium spiny neurons (MSNs) upon pharmacological perturbation of dopaminergic signaling was investigated in adult mice that were treated acutely or chronically with cocaine or saline. TRAP method revealed changes in translation profiles of thousands of genes of striatonigral and striatopallidal MSNs in treated mice. Translational profiling with TRAP methodology enables studies of the molecular biology of specific cell types, cell lines, and in even the most heterogeneous cell populated tissues such as central nervous system (Heiman et al., 2008).
Homology Human Ribosomal Protein L10A has homologs in chimpanzee (Pan troglodytes), Rhesus macaque (Macaca mullatta), wolf (Canis lupus), Taurine cattle (Bos taurus), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), frog (Xenopus tropicalis), fruit fly (Drosophila melanogaster), mosquitoes (Anapheles gambiae), nematode (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae), kluyveromyces yeast (Kluyveromyces lactis), mold (Eremothecium gossypii), fission yeast (Schizosaccharomyces pombe), rice blast fungus (Magnaporthe grisea), red bread mold (Neurospora crassa), Arabidopsis (Arabidopsis thaliana). RPL10A gene orthologs have been reported for more than 300 organisms.

Mutations

Note RPL10A mutations in various cancers is not very common according to the cBioPortal database.

Implicated in

  
Entity Ovarian serous cystadenocarcinoma
Note 6% of patients showed truncating mutation or amplification (TCGA, Firehose Legacy).
  
  
Entity Pancreatic cancer
Note 5% of 109 patients showed amplification or deep deletion (UTSW, Nat Commun 2015).
  
  
Entity Uterine Carcinosarcoma
Note 5% of 56 patients showed amplification (TCGA, Firehose Legacy).
  
  
Entity Breast Cancer
Note RPL10A was proposed as a breast cancer hub gene along with other ribosomal proteins in a bioinformatics study (Fang & Zhang, 2018). In breast cancers, only 1% of 2173 patients showed genomic amplification (METABRIC, Nature 2012 & Nat Commun 2016). In addition, 0.7% of 1352 patients showed truncating mutations, amplification, or deep deletion in breast invasive carcinoma TCGA PanCan 2018, Broad 2012, Sanger, BCCRC 2012).
  
  
Entity Leukemia
Note RPL10A mutations were detected in 8% of pediatric T-cell acute lymphoblastic leukemia patients (Bastide & David, 2018).
  

Bibliography

The ribosome , ( slow ) beating heart of cancer ( stem ) cell
Bastide, A., & David, A.
Oncogenesis 2018, 7(4): 34.
PMID 29674660
 
Evolutionary implications of intron-exon distribution and the properties and sequences of the RPL10A gene in eukaryotes
Campo, E. M., Casano, L. M., & Barreno, E.
Molecular Phylogenetics and Evolution 2013, 66(3), 857-867
 
Regulated Nuclear Trafficking of rpL10A Mediated by NIK1 Represents a Defense Strategy of Plant Cells against Virus
Carvalho, C. M., Santos, A. A., Pires, S. R., Rocha, C. S., Saraiva, D. I., Machado, J. P. B., Fontes, E. P. B.
PLoS Pathogens 2008, 4(12):e1000247.
PMID 19112492
 
Ribosomal protein L10A and signaling pathway
Chaichanit, N., Wonglapsuwan, M., & Chotigeat, W
Gene 2018, 674, 170-177
PMID 29953919
 
Pericyte-like spreading by disseminated cancer cells activates YAP and MRTF for metastatic colonization
Er, E. E., Valiente, M., Ganesh, K., Zou, Y., Agrawal, S., Schachner, M., Massagué, J.
Nature Cell Biology (2018), 20, 966-978
PMID 30038252
 
Identification of breast cancer hub genes and analysis of prognostic values using integrated bioinformatics analysis
Fang, E., & Zhang, X
Cancer Biomarkers 2018, 21(2), 373-381
PMID 29081411
 
A translational profiling approach for the molecular characterization of CNS cell types
Heiman, M., Schaefer, A., Gong, S., Peterson, J. D., Day, M., Ramsey, K. E., Heintz, N.
Cell 2008, 135(4), 738-748
PMID 19013281
 
Expression profile of ribosomal protein L10a throughout gonadal development in rainbow trout (Oncorhynchus mykiss)
Makkapan, W., Yoshizaki, G., Tashiro, M., & Chotigeat, W.
Fish Physiol Biochem. 2014 Aug;40(4):1069-81.
PMID 24385218
 
Abnormal development of zebrafish after knockout and knockdown of ribosomal protein L10a
Palasin, K., Uechi, T., Yoshihama, M., Srisowanna, N., Choijookhuu, N., Hishikawa, Y., Chotigeat, W.
Scientific Reports 2019, 9(1):18130.
PMID 31792295
 
Emerging Roles and Landscape of Translating mRNAs in Plants
Sablok, G., Powell, J., & Kazan K.
Frontiers in Plant Science 2017, 8(9): 1443.
PMID 28919899
 
Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide
Shi, Z., Fujii, K., Kovary, K. M., Genuth, N. R., Röst, H. L., Teruel, M. N., & Barna, M.
Molecular Cell 2017, 67(1)
PMID 28625553
 
Early gene expression in human lymphocytes after gamma-irradiation-a genetic pattern with potential for biodosimetry
Turtoi, A., Brown, I., Oskamp, D., & Schneeweiss, F. H. A.
International Journal of Radiation Biology 2008, 84(5), 375-387
 
Characterization and Biological Activity of the Ribosomal Protein L10a of the White Shrimp: Fenneropenaeus merguiensis De Man During Vitellogenesis
Wonglapsuwan, M., Miyazaki, T., Loongyai, W., & Chotigeat, W.
Marine Biotechnology 2009, 12(2), 230-240
PMID 19697087
 

Citation

This paper should be referenced as such :
Gürcüoğlu I, Erson-Bensan AE.
RPL10A (ribosomal protein L10a);
Atlas Genet Cytogenet Oncol Haematol. in press


External links

 

Nomenclature
HGNC (Hugo)RPL10A   10299
Cards
AtlasRPL10AID46376ch6p21
Entrez_Gene (NCBI)RPL10A    ribosomal protein L10a
AliasesCSA19; Csa-19; L10A; NEDD6
GeneCards (Weizmann)RPL10A
Ensembl hg19 (Hinxton)ENSG00000198755 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000198755 [Gene_View]  ENSG00000198755 [Sequence]  chr6:35468401-35470780 [Contig_View]  RPL10A [Vega]
ICGC DataPortalENSG00000198755
TCGA cBioPortalRPL10A
AceView (NCBI)RPL10A
Genatlas (Paris)RPL10A
SOURCE (Princeton)RPL10A
Genetics Home Reference (NIH)RPL10A
Genomic and cartography
GoldenPath hg38 (UCSC)RPL10A  -     chr6:35468401-35470780 +  6p21.31   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)RPL10A  -     6p21.31   [Description]    (hg19-Feb_2009)
GoldenPathRPL10A - 6p21.31 [CytoView hg19]  RPL10A - 6p21.31 [CytoView hg38]
ImmunoBaseENSG00000198755
Genome Data Viewer NCBIRPL10A [Mapview hg19]  
OMIM615660   
Gene and transcription
Genbank (Entrez)AB082926 AF086557 AK092386 AK313181 BC006791
RefSeq transcript (Entrez)NM_007104
Consensus coding sequences : CCDS (NCBI)RPL10A
Gene ExpressionRPL10A [ NCBI-GEO ]   RPL10A [ EBI - ARRAY_EXPRESS ]   RPL10A [ SEEK ]   RPL10A [ MEM ]
Gene Expression Viewer (FireBrowse)RPL10A [ Firebrowse - Broad ]
GenevisibleExpression of RPL10A in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)4736
GTEX Portal (Tissue expression)RPL10A
Human Protein AtlasENSG00000198755-RPL10A [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP62906   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP62906  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP62906
PhosPhoSitePlusP62906
Domaine pattern : Prosite (Expaxy)RIBOSOMAL_L1 (PS01199)   
Domains : Interpro (EBI)Ribosomal_L1    Ribosomal_L1-like    Ribosomal_L1/biogenesis    Ribosomal_L1_3-a/b-sand    Ribosomal_L1_CS   
Domain families : Pfam (Sanger)Ribosomal_L1 (PF00687)   
Domain families : Pfam (NCBI)pfam00687   
Conserved Domain (NCBI)RPL10A
PDB (RSDB)4UG0    4V6X    5AJ0    5LKS    5T2C    6EK0    6IP5    6LQM    6LSR    6LU8    6OLG    6QZP    6Y6X    6Z6L    6Z6M    6Z6N    6ZM7    6ZME    6ZMI    6ZMO   
PDB Europe4UG0    4V6X    5AJ0    5LKS    5T2C    6EK0    6IP5    6LQM    6LSR    6LU8    6OLG    6QZP    6Y6X    6Z6L    6Z6M    6Z6N    6ZM7    6ZME    6ZMI    6ZMO   
PDB (PDBSum)4UG0    4V6X    5AJ0    5LKS    5T2C    6EK0    6IP5    6LQM    6LSR    6LU8    6OLG    6QZP    6Y6X    6Z6L    6Z6M    6Z6N    6ZM7    6ZME    6ZMI    6ZMO   
PDB (IMB)4UG0    4V6X    5AJ0    5LKS    5T2C    6EK0    6IP5    6LQM    6LSR    6LU8    6OLG    6QZP    6Y6X    6Z6L    6Z6M    6Z6N    6ZM7    6ZME    6ZMI    6ZMO   
Structural Biology KnowledgeBase4UG0    4V6X    5AJ0    5LKS    5T2C    6EK0    6IP5    6LQM    6LSR    6LU8    6OLG    6QZP    6Y6X    6Z6L    6Z6M    6Z6N    6ZM7    6ZME    6ZMI    6ZMO   
SCOP (Structural Classification of Proteins)4UG0    4V6X    5AJ0    5LKS    5T2C    6EK0    6IP5    6LQM    6LSR    6LU8    6OLG    6QZP    6Y6X    6Z6L    6Z6M    6Z6N    6ZM7    6ZME    6ZMI    6ZMO   
CATH (Classification of proteins structures)4UG0    4V6X    5AJ0    5LKS    5T2C    6EK0    6IP5    6LQM    6LSR    6LU8    6OLG    6QZP    6Y6X    6Z6L    6Z6M    6Z6N    6ZM7    6ZME    6ZMI    6ZMO   
SuperfamilyP62906
AlphaFold pdb e-kbP62906   
Human Protein Atlas [tissue]ENSG00000198755-RPL10A [tissue]
HPRD10199
Protein Interaction databases
DIP (DOE-UCLA)P62906
IntAct (EBI)P62906
Complex Portal (EBI)P62906 CPX-5183 60S cytosolic large ribosomal subunit
BioGRIDRPL10A
STRING (EMBL)RPL10A
ZODIACRPL10A
Ontologies - Pathways
QuickGOP62906
Ontology : AmiGOnuclear-transcribed mRNA catabolic process, nonsense-mediated decay  maturation of LSU-rRNA  cytoplasmic translation  cytoplasmic translation  RNA binding  RNA binding  structural constituent of ribosome  structural constituent of ribosome  protein binding  nucleus  cytosol  focal adhesion  rRNA processing  translation  translational initiation  SRP-dependent cotranslational protein targeting to membrane  postsynaptic density  membrane  viral transcription  cytosolic large ribosomal subunit  cytosolic large ribosomal subunit  cytosolic large ribosomal subunit  cytosolic ribosome  polysomal ribosome  response to ethanol  extracellular exosome  
Ontology : EGO-EBInuclear-transcribed mRNA catabolic process, nonsense-mediated decay  maturation of LSU-rRNA  cytoplasmic translation  cytoplasmic translation  RNA binding  RNA binding  structural constituent of ribosome  structural constituent of ribosome  protein binding  nucleus  cytosol  focal adhesion  rRNA processing  translation  translational initiation  SRP-dependent cotranslational protein targeting to membrane  postsynaptic density  membrane  viral transcription  cytosolic large ribosomal subunit  cytosolic large ribosomal subunit  cytosolic large ribosomal subunit  cytosolic ribosome  polysomal ribosome  response to ethanol  extracellular exosome  
Pathways : KEGGRibosome   
REACTOMEP62906 [protein]
REACTOME PathwaysR-HSA-975957 [pathway]   
NDEx NetworkRPL10A
Atlas of Cancer Signalling NetworkRPL10A
Wikipedia pathwaysRPL10A
Orthology - Evolution
OrthoDB4736
GeneTree (enSembl)ENSG00000198755
Phylogenetic Trees/Animal Genes : TreeFamRPL10A
Homologs : HomoloGeneRPL10A
Homology/Alignments : Family Browser (UCSC)RPL10A
Gene fusions - Rearrangements
Fusion Cancer (Beijing)RPL10A [6p21.31]  -  FAM166B [9p13.3]  [FUSC001062]
Fusion : QuiverRPL10A
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerRPL10A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RPL10A
dbVarRPL10A
ClinVarRPL10A
MonarchRPL10A
1000_GenomesRPL10A 
Exome Variant ServerRPL10A
GNOMAD BrowserENSG00000198755
Varsome BrowserRPL10A
ACMGRPL10A variants
VarityP62906
Genomic Variants (DGV)RPL10A [DGVbeta]
DECIPHERRPL10A [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisRPL10A 
Mutations
ICGC Data PortalRPL10A 
TCGA Data PortalRPL10A 
Broad Tumor PortalRPL10A
OASIS PortalRPL10A [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRPL10A  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DRPL10A
Mutations and Diseases : HGMDRPL10A
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaRPL10A
DgiDB (Drug Gene Interaction Database)RPL10A
DoCM (Curated mutations)RPL10A
CIViC (Clinical Interpretations of Variants in Cancer)RPL10A
NCG (London)RPL10A
Cancer3DRPL10A
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM615660   
Orphanet
DisGeNETRPL10A
MedgenRPL10A
Genetic Testing Registry RPL10A
NextProtP62906 [Medical]
GENETestsRPL10A
Target ValidationRPL10A
Huge Navigator RPL10A [HugePedia]
ClinGenRPL10A
Clinical trials, drugs, therapy
MyCancerGenomeRPL10A
Protein Interactions : CTDRPL10A
Pharm GKB GenePA34661
PharosP62906
Clinical trialRPL10A
Miscellaneous
canSAR (ICR)RPL10A
HarmonizomeRPL10A
DataMed IndexRPL10A
Probes
Litterature
PubMed144 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXRPL10A
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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