RPL10A (ribosomal protein L10a)

2020-12-01   Irmak Gürcüoğlu , A. Elif Erson-Bensan 

Department of Biological Sciences, Middle East Technical University, Ankara, Turkey, irmak.gurcuoglu@metu.edu.tr; erson@metu.edu.tr

Identity

HGNC
LOCATION
6p21.31
IMAGE
Atlas Image
LEGEND
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.
LOCUSID
ALIAS
CSA19,Csa-19,L10A,NEDD6
FUSION GENES

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.

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).
Atlas Image
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

Proteins

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.
Atlas Image
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 name
Ovarian serous cystadenocarcinoma
Note
6% of patients showed truncating mutation or amplification (TCGA, Firehose Legacy).
Entity name
Pancreatic cancer
Note
5% of 109 patients showed amplification or deep deletion (UTSW, Nat Commun 2015).
Entity name
Uterine Carcinosarcoma
Note
5% of 56 patients showed amplification (TCGA, Firehose Legacy).
Entity name
Leukemia
Note
RPL10A mutations were detected in 8% of pediatric T-cell acute lymphoblastic leukemia patients (Bastide & David, 2018).

Bibliography

Pubmed IDLast YearTitleAuthors
296746602018The ribosome, (slow) beating heart of cancer (stem) cell.Bastide A et al
232013952013Evolutionary implications of intron-exon distribution and the properties and sequences of the RPL10A gene in eukaryotes.Del Campo EM et al
191124922008Regulated nuclear trafficking of rpL10A mediated by NIK1 represents a defense strategy of plant cells against virus.Carvalho CM et al
299539192018Ribosomal protein L10A and signaling pathway.Chaichanit N et al
300382522018Pericyte-like spreading by disseminated cancer cells activates YAP and MRTF for metastatic colonization.Er EE et al
290814112017Identification of breast cancer hub genes and analysis of prognostic values using integrated bioinformatics analysis.Fang E et al
190132812008A translational profiling approach for the molecular characterization of CNS cell types.Heiman M et al
243852182014Expression profile of ribosomal protein L10a throughout gonadal development in rainbow trout (Oncorhynchus mykiss).Makkapan W et al
317922952019Abnormal development of zebrafish after knockout and knockdown of ribosomal protein L10a.Palasin K et al
289198992017Emerging Roles and Landscape of Translating mRNAs in Plants.Sablok G et al
286255532017Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide.Shi Z et al
184640672008Early gene expression in human lymphocytes after gamma-irradiation-a genetic pattern with potential for biodosimetry.Turtoi A et al
196970872010Characterization and biological activity of the ribosomal protein L10a of the white shrimp: Fenneropenaeus merguiensis De Man during vitellogenesis.Wonglapsuwan M et al

Other Information

Locus ID:

NCBI: 4736
MIM: 615660
HGNC: 10299
Ensembl: ENSG00000198755

Variants:

dbSNP: 4736
ClinVar: 4736
TCGA: ENSG00000198755
COSMIC: RPL10A

RNA/Proteins

Gene IDTranscript IDUniprot
ENSG00000198755ENST00000322203P62906

Expression (GTEx)

0
500
1000
1500
2000
2500
3000

Pathways

PathwaySourceExternal ID
RibosomeKEGGko03010
RibosomeKEGGhsa03010
Ribosome, eukaryotesKEGGhsa_M00177
Ribosome, eukaryotesKEGGM00177
Metabolism of proteinsREACTOMER-HSA-392499
TranslationREACTOMER-HSA-72766
Eukaryotic Translation InitiationREACTOMER-HSA-72613
Cap-dependent Translation InitiationREACTOMER-HSA-72737
Formation of a pool of free 40S subunitsREACTOMER-HSA-72689
GTP hydrolysis and joining of the 60S ribosomal subunitREACTOMER-HSA-72706
L13a-mediated translational silencing of Ceruloplasmin expressionREACTOMER-HSA-156827
SRP-dependent cotranslational protein targeting to membraneREACTOMER-HSA-1799339
Eukaryotic Translation ElongationREACTOMER-HSA-156842
Peptide chain elongationREACTOMER-HSA-156902
Eukaryotic Translation TerminationREACTOMER-HSA-72764
DiseaseREACTOMER-HSA-1643685
Infectious diseaseREACTOMER-HSA-5663205
Influenza InfectionREACTOMER-HSA-168254
Influenza Life CycleREACTOMER-HSA-168255
Influenza Viral RNA Transcription and ReplicationREACTOMER-HSA-168273
Viral mRNA TranslationREACTOMER-HSA-192823
Gene ExpressionREACTOMER-HSA-74160
Nonsense-Mediated Decay (NMD)REACTOMER-HSA-927802
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)REACTOMER-HSA-975957
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)REACTOMER-HSA-975956
MetabolismREACTOMER-HSA-1430728
Metabolism of amino acids and derivativesREACTOMER-HSA-71291
Selenoamino acid metabolismREACTOMER-HSA-2408522
Selenocysteine synthesisREACTOMER-HSA-2408557
rRNA processingREACTOMER-HSA-72312
Major pathway of rRNA processing in the nucleolus and cytosolREACTOMER-HSA-6791226
rRNA processing in the nucleus and cytosolREACTOMER-HSA-8868773

Protein levels (Protein atlas)

Not detected
Low
Medium
High

References

Pubmed IDYearTitleCitations
208776242010Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.17
126945812003Identification of ribosomal proteins S2 and L10a as tumor antigens recognized by HLA-A26-restricted CTL.4

Citation

Irmak Gürcüoğlu ; A. Elif Erson-Bensan

RPL10A (ribosomal protein L10a)

Atlas Genet Cytogenet Oncol Haematol. 2020-12-01

Online version: http://atlasgeneticsoncology.org/gene/46376/rpl10a