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YME1L1 YME1 like 1 ATPase [ Homo sapiens (human) ]

Gene ID: 10730, updated on 3-Nov-2024

Summary

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Official Symbol
YME1L1provided by HGNC
Official Full Name
YME1 like 1 ATPaseprovided by HGNC
Primary source
HGNC:HGNC:12843
See related
Ensembl:ENSG00000136758 MIM:607472; AllianceGenome:HGNC:12843
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FTSH; MEG4; PAMP; OPA11; YME1L
Summary
The protein encoded by this gene is the human ortholog of yeast mitochondrial AAA metalloprotease, Yme1p. It is localized in the mitochondria and can functionally complement a yme1 disruptant yeast strain. It is proposed that this gene plays a role in mitochondrial protein metabolism and could be involved in mitochondrial pathologies. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
Expression
Ubiquitous expression in thyroid (RPKM 32.8), testis (RPKM 26.7) and 25 other tissues See more
Orthologs
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Genomic context

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See YME1L1 in Genome Data Viewer
Location:
10p12.1
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (27110111..27154384, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (27140165..27184407, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (27399040..27443313, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11703 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11711 Neighboring gene family with sequence similarity 238 member C Neighboring gene ankyrin repeat domain containing 26 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3178 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11810 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:27361449-27361982 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3179 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2243 Neighboring gene RNA, U6 small nuclear 490, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3180 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:27444170-27444368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3181 Neighboring gene microtubule associated serine/threonine kinase like Neighboring gene RNA, U2 small nuclear 24, pseudogene Neighboring gene acyl-CoA binding domain containing 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Targeting the mitochondrial protein YME1L to inhibit osteosarcoma cell growth in vitro and in vivo. Sun X, et al. Cell Death Dis, 2024 May 20. PMID 38769124, Free PMC Article
  2. Stress-regulated translational attenuation adapts mitochondrial protein import through Tim17A degradation. Rainbolt TK, et al. Cell Metab, 2013 Dec 3. PMID 24315374, Free PMC Article
  3. YME1L degradation reduces mitochondrial proteolytic capacity during oxidative stress. Rainbolt TK, et al. EMBO Rep, 2015 Jan. PMID 25433032, Free PMC Article
  4. Regulation of mitochondrial plasticity by the i-AAA protease YME1L. Ohba Y, et al. Biol Chem, 2020 May 26. PMID 32087062
  5. Examination of the Role of Mg(2+) in the Mechanism of Nucleotide Binding to the Monomeric YME1L AAA+ Domain. Miller JM, et al. Biochemistry, 2020 Nov 17. PMID 33155794

See all (112) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Targeting the mitochondrial protein YME1L to inhibit osteosarcoma cell growth in vitro and in vivo.
    Title: Targeting the mitochondrial protein YME1L to inhibit osteosarcoma cell growth in vitro and in vivo.
  2. The mitochondrial protein YME1 Like 1 is important for non-small cell lung cancer cell growth.
    Title: The mitochondrial protein YME1 Like 1 is important for non-small cell lung cancer cell growth.
  3. Regulation of mitochondrial plasticity by the i-AAA protease YME1L.
    Title: Regulation of mitochondrial plasticity by the i-AAA protease YME1L.
  4. Examination of the Role of Mg(2+) in the Mechanism of Nucleotide Binding to the Monomeric YME1L AAA+ Domain.
    Title: Examination of the Role of Mg(2+) in the Mechanism of Nucleotide Binding to the Monomeric YME1L AAA+ Domain.
  5. identify the mTORC1-LIPIN1-YME1L axis as a post-translational regulator of mitochondrial proteostasis at the interface between metabolism and mitochondrial dynamics
    Title: Lipid signalling drives proteolytic rewiring of mitochondria by YME1L.
  6. in the absence of ROMO1, mitochondria lose the inner membrane YME1L protease, which participates in OPA1 processing and ROMO1 turnover. While ROMO1 is dispensable for general protein import along the presequence pathway, we show that it participates in the dynamics of TIM21 during respiratory chain biogenesis and is specifically required for import of YME1L.
    Title: ROMO1 is a constituent of the human presequence translocase required for YME1L protease import.
  7. Data show that engineered YME1L protease discriminates between degradation signals by amino acid composition, implying the use of sequence-specific signals in mitochondrial proteostasis.
    Title: Engineered AAA+ proteases reveal principles of proteolysis at the mitochondrial inner membrane.
  8. These results identify mutations in YME1L1 as a cause of a mitochondriopathy with optic nerve atrophy highlighting the importance of YME1L1 for mitochondrial functionality in humans.
    Title: Homozygous YME1L1 mutation causes mitochondriopathy with optic atrophy and mitochondrial network fragmentation.
  9. YME1L1 was identified as the first NUMT (nuclear mtDNA) suppressor gene in human and demonstrate that inactivation of YME1L1 induces migration of mtDNA to the nuclear genome.
    Title: Migration of mitochondrial DNA in the nuclear genome of colorectal adenocarcinoma.
  10. differential stress-induced degradation of YME1L and OMA1 as a mechanism for sensitively adapting mitochondrial inner membrane protease activity and function in response to distinct types of cellular insults.
    Title: Reciprocal Degradation of YME1L and OMA1 Adapts Mitochondrial Proteolytic Activity during Stress.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Optic atrophy 11
MedGen: C4310628 OMIM: 617302 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables ATP-dependent peptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ATP-dependent peptidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP-dependent peptidase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables metalloendopeptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cellular response to starvation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mitochondrial protein catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrial protein processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrion organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrion organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neuronal stem cell population maintenance ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of mitochondrial fusion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein hexamerization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein quality control for misfolded or incompletely synthesized proteins IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein quality control for misfolded or incompletely synthesized proteins IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of stem cell division ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in membrane HDA PubMed 
is_active_in mitochondrial inner membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrial inner membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial inner membrane TAS
Traceable Author Statement
more info
  
located_in mitochondrion HTP PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
ATP-dependent zinc metalloprotease YME1L1
Names
ATP-dependent metalloprotease FtsH1 homolog
YME1-like protein 1
meg-4
presenilin-associated metalloprotease

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_047122.1 RefSeqGene

    Range
    5895..50168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001253866.2 → NP_001240795.1  ATP-dependent zinc metalloprotease YME1L1 isoform 4

    See identical proteins and their annotated locations for NP_001240795.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AI042625, AJ132637, AK297973, AL162272
    Consensus CDS
    CCDS58072.1
    UniProtKB/TrEMBL
    A8K5H7
    Related
    ENSP00000398713.2, ENST00000427324.6
    Conserved Domains (1) summary
    TIGR01241
    Location:243 → 676
    FtsH_fam; ATP-dependent metalloprotease FtsH

  2. NM_014263.4 → NP_055078.1  ATP-dependent zinc metalloprotease YME1L1 isoform 3

    See identical proteins and their annotated locations for NP_055078.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an internal coding exon compared to transcript variant 1. However, it maintains the same reading frame, and encodes an isoform (3) that is missing a 57 aa segment compared to isoform 1.
    Source sequence(s)
    AI042625, AJ132637, AL162272
    Consensus CDS
    CCDS7151.1
    UniProtKB/TrEMBL
    A8K5H7
    Related
    ENSP00000365184.3, ENST00000376016.8
    Conserved Domains (1) summary
    cl27568
    Location:276 → 709
    TIP49; TIP49 C-terminus

  3. NM_139312.3 → NP_647473.1  ATP-dependent zinc metalloprotease YME1L1 isoform 1

    See identical proteins and their annotated locations for NP_647473.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AI042625, AJ132637, AL162272, DA395557, DA489399
    Consensus CDS
    CCDS7152.1
    UniProtKB/Swiss-Prot
    B4DNM1, D3DRV8, D3DRV9, Q5T8D9, Q96TA2, Q9H1Q0, Q9UMR9
    UniProtKB/TrEMBL
    Q96I63
    Related
    ENSP00000318480.3, ENST00000326799.7
    Conserved Domains (4) summary
    TIGR01241
    Location:333 → 766
    FtsH_fam; ATP-dependent metalloprotease FtsH
    pfam00004
    Location:375 → 506
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam01434
    Location:586 → 764
    Peptidase_M41; Peptidase family M41
    cl21455
    Location:331 → 395
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    27110111..27154384 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011519300.4 → XP_011517602.1  ATP-dependent zinc metalloprotease YME1L1 isoform X1

    UniProtKB/TrEMBL
    Q96I63
    Conserved Domains (4) summary
    TIGR01241
    Location:300 → 733
    FtsH_fam; ATP-dependent metalloprotease FtsH
    pfam00004
    Location:342 → 473
    AAA; ATPase family associated with various cellular activities (AAA)
    pfam01434
    Location:553 → 731
    Peptidase_M41; Peptidase family M41
    cl21455
    Location:298 → 362
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    27140165..27184407 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054364629.1 → XP_054220604.1  ATP-dependent zinc metalloprotease YME1L1 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_139313.1: Suppressed sequence

    Description
    NM_139313.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96TA2.2 GenPept UniProtKB/Swiss-Prot:Q96TA2

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