Pld6 phospholipase D family member 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pld6provided by MGI
Official Full Name: phospholipase D family member 6provided by MGI
Primary source: MGI:MGI:2687283
See related: Ensembl:ENSMUSG00000043648 AllianceGenome:MGI:2687283
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Zuc; Gm10; mZuc; mitoPLD; 4933433K01Rik
Summary: Enables identical protein binding activity. Involved in germ cell development; meiotic cell cycle; and piRNA processing. Located in mitochondrial outer membrane. Orthologous to human PLD6 (phospholipase D family member 6). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in testis adult (RPKM 34.0), stomach adult (RPKM 4.9) and 3 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 B1.3; 11 37.79 cM

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (59674719..59678483, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (59783893..59787657, complement)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

pre-piRNAs are generated by parallel Zucchini-dependent and -independent mechanisms; cleavage by Zucchini occurs at previously unrecognized consensus motifs on pre-pre-piRNAs, requires the RNA helicase Armitage, and is accompanied by 2'-O-methylation of pre-piRNAs
Title: Zucchini consensus motifs determine the mechanism of pre-piRNA production.
PLD6 is a surface marker of undifferentiated spermatogonia in testes.
Title: Phospholipase D Family Member 6 Is a Surface Marker for Enrichment of Undifferentiated Spermatogonia in Prepubertal Boars.
MIWI (or PIWIL1) depletion had a smaller effect. In oocytes lacking PLD6 (or ZUCCHINI or MITOPLD), a mitochondrial nuclease/phospholipase involved in piRNA biogenesis in male germ cells, the piRNA level was decreased to 50% compared to wild-type.
Title: Roles of MIWI, MILI and PLD6 in small RNA regulation in mouse growing oocytes.
Drp1 binds a mitochondrial enzyme that produces phosphatidic acid, MitoPLD, and regulates mitochondrial division.
Title: Coincident Phosphatidic Acid Interaction Restrains Drp1 in Mitochondrial Division.
The Dnmt3l mutation greatly reduced DNA methylation levels at most retrotransposons, but its impact on their RNA abundance was limited in prospermatogonia. In Pld6 mutant germ cells, although only a few retrotransposons exhibited reduced DNA methylation, many showed increased expression at the RNA level.
Title: Switching of dominant retrotransposon silencing strategies from posttranscriptional to transcriptional mechanisms during male germ-cell development in mice.
Propose that MIGA proteins promote mitochondrial fusion by regulating mitochondrial phospholipid metabolism via MitoPLD.
Title: Mitoguardin Regulates Mitochondrial Fusion through MitoPLD and Is Required for Neuronal Homeostasis.
crystal structure of mZuc at 1.75 A resolution indicates greater architectural similarity to phospholipase-D family nucleases than to phospholipases; data suggest that the Zucchini proteins act in primary piRNA biogenesis as nucleases, perhaps generating the 5' ends of primary piRNAs.
Title: The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis.
MitoPLD performs a critical function in a pathway that creates a specialized form of RNAi required by developing spermatocytes to suppress transposon mobilization during meiosis.
Title: Roles for the lipid-signaling enzyme MitoPLD in mitochondrial dynamics, piRNA biogenesis, and spermatogenesis.
Data suggest that mitochondrial-surface phosphatidic acid generated by MitoPLD/Zuc recruits or activates nuage components critical for piRNA production.
Title: piRNA-associated germline nuage formation and spermatogenesis require MitoPLD profusogenic mitochondrial-surface lipid signaling.
Results indicate a conserved role for MITOPLD/Zuc in the piRNA pathway and link mitochondrial membrane metabolism/signaling to small RNA biogenesis.
Title: MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW213769 (e-PCR)
- UniSTS:208686

NoName (e-PCR)
- UniSTS:491993

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA endonuclease activity, producing 5'-phosphomonoesters	IBA Inferred from Biological aspect of Ancestor more info
enables cardiolipin hydrolase activity	ISO Inferred from Sequence Orthology more info
enables cardiolipin hydrolase activity	ISS Inferred from Sequence or Structural Similarity more info
enables endonuclease activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables phospholipase D activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in P granule organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lipid catabolic process	IEA Inferred from Electronic Annotation more info
involved_in meiotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrial fusion	ISO Inferred from Sequence Orthology more info
involved_in mitochondrial fusion	ISS Inferred from Sequence or Structural Similarity more info
involved_in piRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in piRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of mitochondrial fusion	ISO Inferred from Sequence Orthology more info
involved_in spermatid development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in mitochondrial outer membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial outer membrane	ISO Inferred from Sequence Orthology more info
located_in mitochondrial outer membrane	TAS Traceable Author Statement more info
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in nuclear membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: mitochondrial cardiolipin hydrolase

Names: choline phosphatase 6; mitochondrial phospholipase; novel Phospholipase D Active site motif-containing protein; phosphatidylcholine-hydrolyzing phospholipase D6; phospholipase D6; protein zucchini homolog

NP_001277212.1

EC 3.1.4.4

NP_898962.2

EC 3.1.4.4

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.

mRNA and Protein(s)

NM_001290283.1 → NP_001277212.1 mitochondrial cardiolipin hydrolase isoform a

See identical proteins and their annotated locations for NP_001277212.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).

Source sequence(s)

AL596204, AW554531, BC119245

Consensus CDS

CCDS70199.1

UniProtKB/Swiss-Prot

B7ZN71, Q3UTA3, Q5SWZ9, Q8BVM0

Related

ENSMUSP00000115503.2, ENSMUST00000125307.2

Conserved Domains (2) summary

cd09171
Location:92 → 203

PLDc_vPLD6_like; Catalytic domain of vertebrate phospholipase D6 and similar proteins

pfam13091
Location:93 → 203

PLDc_2; PLD-like domain
NM_183139.2 → NP_898962.2 mitochondrial cardiolipin hydrolase isoform b

See identical proteins and their annotated locations for NP_898962.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AL596204, AW554531, BC119245

UniProtKB/Swiss-Prot

Q5SWZ9

Related

ENSMUST00000051493.8

Conserved Domains (1) summary

cl15239
Location:92 → 138

PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

RNA

NR_110894.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) contains an alternate 5' terminal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AL596204, AW554531, CK137362