PITRM1

Pitrilysin metallopeptidase 1 also known as presequence protease, mitochondrial (PreP) and metalloprotease 1 (MTP-1) is an enzyme that in humans is encoded by the PITRM1 gene.[5][6][7] It is also sometimes called metalloprotease 1 (MP1).PreP facilitates proteostasis by utilizing an ~13300-A(3) catalytic chamber to degrade toxic peptides, including mitochondrial presequences and β-amyloid.[8] Deficiency of PreP is found associated with Alzheimer’s disease. Reduced levels of PreP via RNAi mediated knockdown have been shown to lead to defective maturation of the protein Frataxin.[9]

PITRM1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 4L3T, 4NGE, 4RPU
Identifiers
Aliases	PITRM1, MP1, PreP, pitrilysin metallopeptidase 1
External IDs	OMIM: 618211 MGI: 1916867 HomoloGene: 5742 GeneCards: PITRM1
Gene location (Human) Chr. Chromosome 10 (human)[1] Band 10p15.2 Start 3,137,728 bp[1] End 3,172,841 bp[1]
Gene location (Mouse) Chr. Chromosome 13 (mouse)[2] Band 13|13 A1 Start 6,548,149 bp[2] End 6,580,515 bp[2]
RNA expression pattern More reference expression data
Gene ontology Molecular function • peptidase activity • GO:0010577 enzyme activator activity • catalytic activity • hydrolase activity • metal ion binding • metallopeptidase activity • metalloendopeptidase activity • zinc ion binding Cellular component • mitochondrion • mitochondrial matrix Biological process • GO:0048554 positive regulation of catalytic activity • protein targeting to mitochondrion • proteolysis • protein processing Sources:Amigo / QuickGO
Orthologs
Species	Human	Mouse
Entrez	10531	69617
Ensembl	ENSG00000107959	ENSMUSG00000021193
UniProt	Q5JRX3	Q8K411
RefSeq (mRNA)	NM_001242307 NM_001242309 NM_014889 NM_014968 NM_001347725 NM_001347726 NM_001347727 NM_001347728 NM_001347729 NM_001347730	NM_145131 NM_001360106
RefSeq (protein)	NP_001229236 NP_001229238 NP_001334654 NP_001334655 NP_001334656 NP_001334657 NP_001334658 NP_001334659 NP_055704	NP_660113 NP_001347035
Location (UCSC)	Chr 10: 3.14 – 3.17 Mb	Chr 13: 6.55 – 6.58 Mb
PubMed search	[3]	[4]
Wikidata
View/Edit Human View/Edit Mouse

Structure

Gene

The PITRM1 gene is located at chromosome 10q15.2, consisting of 28 exons.

Protein

PreP is a 117 kDa M16C enzyme that is widely expressed in human tissues.[10] PreP is composed of PreP-N (aa 33-509) and PreP-C (aa 576-1037) domains, which are connected by an extended helical hairpin (aa 510-575). Its structure demonstrates that substrate selection by size-exclusion is a conserved mechanism in M16C proteases.[8]

Function

PreP is an Zn²⁺-dependent and ATP-independent metalloprotease, it doesn’t select substrates on the basis of post-translational modifications or embedded degradation tags.[11][12][13] Instead, it uses a negatively charged catalytic chamber to engulf substrates peptides of up to ~65 residues while excluding larger, folded proteins.[14][15] It primarily localizes to the mitochondrial matrix, and cuts a range of peptides into recyclable fragments.[16][17] The substrates of PreP are vital to proteostasis, as they can insert to mitochondrial membranes, disrupting electrical potential and uncoupling respiration.[18][19] Thus deletion of PRTRM1 leads to a delayed growth phenotype.[20][21] Notabley, PreP degrades several functionally relevant Aβ species, the aggregates of which are toxic to the neuron and play a key role in AD pathogenesis.[22][14][23]

Clinical significance

PreP is the Aβ-degrading protease in mitochondria. Immune-depletion of PreP in brain mitochondria prevents degradation of mitochondrial Aβ, and PreP activity is found diminished in AD patients.[8] It has been reported that the loss of PreP activity is due to methionine oxidation and this study provides a rational basis for therapeutic intervention in conditions characterized by excessive oxidation of PreP.[24] A recent study also suggests that PreP regulates islet amyloid polypeptide in beta cells.[25] Two siblings carrying a homozygous PITRM1 missense mutation (c.548G>A, p.Arg183Gln) were reported to be associated with an autosomal recessive, slowly progressive syndrome. Clinical features include mental retardation, spinocerebellar ataxia, cognitive decline and psychosis.[26] A mouse model hemizygous for PITRM1 displayed progressive ataxia which was suggested to be linked to brain degenerative lesions, including accumulation of Aβ‐positive amyloid deposits. Recently, two brothers from a consanguineous family presenting with childhood-onset recessive cerebellar pathology were shown to carry a homozygous mutation in PITRM1 (c.2795C>T, p.T931M). This mutation resulted in 95% reduction in PITRM1 protein.[27] PITRM1 knockdown was shown to lead to reduced levels of mature Frataxin protein,[28] a protein that when deficient causes Friedreich's ataxia, and may be implicated in pathology in patients carrying PITRM1 mutations.

Interactions

PITRM1 has been shown to interact with the following proteins: CCL22, CGB2, DDX41, DEFB104A, HDHD3, MRPL12, NDUFV2, PRDX6, PRKCSH, RARS2, RIF1, SUCLG2, TEKT3, TERF2, and VAPB.[29]

Model organisms

Model organisms have been used in the study of PITRM1 function. A conditional knockout mouse line called Pitrm1^{tm1a(KOMP)Wtsi} was generated at the Wellcome Trust Sanger Institute.[30] Male and female animals underwent a standardized phenotypic screen[31] to determine the effects of deletion.[32][33][34][35] Additional screens performed: - In-depth immunological phenotyping[36]

Pitrm1 knockout mouse phenotype

Characteristic	Phenotype
All data available at.[31][36]
Peripheral blood leukocytes 6 Weeks	Normal
Haematology 6 Weeks	Abnormal
Insulin	Normal
Homozygous viability at P14	Abnormal
Recessive lethal study	Abnormal
Body weight	Normal
Neurological assessment	Normal
Grip strength	Normal
Dysmorphology	Normal
Indirect calorimetry	Normal
Glucose tolerance test	Normal
Auditory brainstem response	Normal
DEXA	Normal
Radiography	Normal
Eye morphology	Normal
Clinical chemistry	Normal
Haematology 16 Weeks	Normal
Peripheral blood leukocytes 16 Weeks	Normal
Heart weight	Normal
Salmonella infection	Normal
Cytotoxic T Cell Function	Normal
Spleen Immunophenotyping	Normal
Mesenteric Lymph Node Immunophenotyping	Normal
Bone Marrow Immunophenotyping	Normal
Epidermal Immune Composition	Normal
Trichuris Challenge	Normal

References

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7. "Entrez Gene: PITRM1 pitrilysin metallopeptidase 1".
8. King JV, Liang WG, Scherpelz KP, Schilling AB, Meredith SC, Tang WJ (July 2014). "Molecular basis of substrate recognition and degradation by human presequence protease". Structure. 22 (7): 996–1007. doi:10.1016/j.str.2014.05.003. PMC 4128088. PMID 24931469.
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12. Ravid T, Hochstrasser M (September 2008). "Diversity of degradation signals in the ubiquitin-proteasome system". Nature Reviews. Molecular Cell Biology. 9 (9): 679–90. doi:10.1038/nrm2468. PMC 2606094. PMID 18698327.
13. Sauer RT, Baker TA (2011). "AAA+ proteases: ATP-fueled machines of protein destruction". Annual Review of Biochemistry. 80: 587–612. doi:10.1146/annurev-biochem-060408-172623. PMID 21469952.
14. Falkevall A, Alikhani N, Bhushan S, Pavlov PF, Busch K, Johnson KA, Eneqvist T, Tjernberg L, Ankarcrona M, Glaser E (September 2006). "Degradation of the amyloid beta-protein by the novel mitochondrial peptidasome, PreP". The Journal of Biological Chemistry. 281 (39): 29096–104. doi:10.1074/jbc.M602532200. PMID 16849325.
15. Johnson KA, Bhushan S, Ståhl A, Hallberg BM, Frohn A, Glaser E, Eneqvist T (May 2006). "The closed structure of presequence protease PreP forms a unique 10,000 Angstroms3 chamber for proteolysis". The EMBO Journal. 25 (9): 1977–86. doi:10.1038/sj.emboj.7601080. PMC 1456932. PMID 16601675.
16. Alikhani N, Berglund AK, Engmann T, Spånning E, Vögtle FN, Pavlov P, Meisinger C, Langer T, Glaser E (July 2011). "Targeting capacity and conservation of PreP homologues localization in mitochondria of different species". Journal of Molecular Biology. 410 (3): 400–10. doi:10.1016/j.jmb.2011.05.009. PMID 21621546.
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20. Kambacheld M, Augustin S, Tatsuta T, Müller S, Langer T (May 2005). "Role of the novel metallopeptidase Mop112 and saccharolysin for the complete degradation of proteins residing in different subcompartments of mitochondria". The Journal of Biological Chemistry. 280 (20): 20132–9. doi:10.1074/jbc.M500398200. PMID 15772085.
21. Nilsson Cederholm S, Bäckman HG, Pesaresi P, Leister D, Glaser E (November 2009). "Deletion of an organellar peptidasome PreP affects early development in Arabidopsis thaliana". Plant Molecular Biology. 71 (4–5): 497–508. doi:10.1007/s11103-009-9534-6. PMID 19701724.
22. Alikhani N, Guo L, Yan S, Du H, Pinho CM, Chen JX, Glaser E, Yan SS (2011). "Decreased proteolytic activity of the mitochondrial amyloid-β degrading enzyme, PreP peptidasome, in Alzheimer's disease brain mitochondria". Journal of Alzheimer's Disease. 27 (1): 75–87. doi:10.3233/JAD-2011-101716. hdl:1808/17858. PMC 3381900. PMID 21750375.
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26. Brunetti D, Torsvik J, Dallabona C, Teixeira P, Sztromwasser P, Fernandez-Vizarra E, et al. (March 2016). "Defective PITRM1 mitochondrial peptidase is associated with Aβ amyloidotic neurodegeneration". EMBO Molecular Medicine. 8 (3): 176–90. doi:10.15252/emmm.201505894. PMC 4772954. PMID 26697887.
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Further reading

• Schaeffer HJ, Catling AD, Eblen ST, Collier LS, Krauss A, Weber MJ (September 1998). "MP1: a MEK binding partner that enhances enzymatic activation of the MAP kinase cascade". Science. 281 (5383): 1668–71. doi:10.1126/science.281.5383.1668. PMID 9733512.
• Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S (October 1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library". Gene. 200 (1–2): 149–56. doi:10.1016/S0378-1119(97)00411-3. PMID 9373149.
• Maruyama K, Sugano S (January 1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene. 138 (1–2): 171–4. doi:10.1016/0378-1119(94)90802-8. PMID 8125298.