Inositol polyphosphate 5-phosphatase OCRL

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Oculocerebrorenal syndrome of Lowe

Lowe syndrome, formally called oculocerebrorenal syndrome, oculocerebrorenal syndrome of Lowe or OCRL, is an X-linked multisystemic disorder mainly affecting eyes, nervous system (both the central and the peripheral) and kidneys and it is caused by mutations in OCRL1 protein. The syndrome is rare, its prevalence is 1 in 500 000 in the general population (based on the observations of the American Lowe Syndrome Association and the Italian Association of Lowe syndrome). Almost all of the patients are male. The syndrome is believed to occur worldwide as there are documented cases in America, Europe, Australia, Japan and India.[1][2]

There is a rather wide range of different phenotypes in Lowe syndrome patients so the individual cases may vary significantly. Amongst the hallmarks of Lowe syndrome are dense congenital cataracts, some degree of intellectual impairment and usually severe mental retardation, severe growth retardation and generalized hypotonia, proximal renal tubular dysfunction of the renal Fanconi type, which slowly progresses towards renal failure/end-stage renal disease (ERSD) in adulthood.[1][2]

Renal tubular dysfunction is accompanied by low-molecular-weight (LMW) proteinuria in all patients. Aminoaciduria, phosphaturia, hypercalciuria, polyuria, bicarbonate, sodium and potassium wasting, renal tubular acidosis are often present as well. In affected patients impaired vision presists in spite of the catarcts being removed. Hypotonia may improve slightly with age, but normal state is never achieved. Hypotonia is connected with joint hypermobility which can result in joint dislocation. Nearly all patients suffer from osteopenia, some patients suffer from repeated bone fractures with poor healing and in about 50 % of patients scoliosis is present. Other frequent physical complications of Lowe syndrome are arthritis, dental malformations, bleeding disorder (platelet malfunction) and cryptorchidism (undescended testes). In some cases, cysts on the skin, in the mouth, kidneys and brain has been found.[1][2]

Up to 50% of patients suffer from certain kinds of seizures. Behavioral problems are usually present in Lowe syndrome patients. Those may include maladaptive behaviors, obsessive-compulsive behaviors, stubbornness, repetitive behavior (such as repetitive purposeless movements), tantrums and aggressive or self-abusive behavior.[1][2]

Some of the defects, such as congenital cataracts and hypotonia, are present at birth while others evolve later. The absence of deep tendon reflexes is often observed soon after birth as well which may point to hypotonia and together with cataracts it is the first diagnostic clue. LWM proteinuria is also detected soon after birth and it is the first symptom of tubular dysfunction that appears. LMW proteinuria is present in all patients. Usual life span of OCRL patients is not longer than 40 years. [1][2][3]

As for heterozygous females, most of them have lens opacities in post-pubertal age. Besides that, manifestations of the Lowe syndrome are usually not observed.[1]

Diagnosis and treatment

Lowe syndrome is inherited in an X-linked manner. About two-thirds of cases are transmitted by maternal carriers. Affected males are not known to reproduce. Female carriers show heterozygous female phenotype, which might indicate the need for genetic counseling. The remaining one third (approximately) is attributed to a de novo variants. There is a high risk (4,5%) of germline mosaicism in Lowe syndrome families. If OCRL pathogenic variant has been identified in a family member, prenatal genetic testing can be performed. Unfortunately, the severity of the disease can not be estimated.[1][2][3]

Treatment is only symptomatic. Patients usually require more than one medical specialist to manage various clinical problems.[1][2][3] Regular surveillance by specialists in many fields is also needed for a lifetime. [1][2]

OCRL1

Domains

The 901 amino acid long OCRL1 or Lowe oculocerebronal syndrome protein or Inositol polyphosphate 5-phosphatase OCRL is composed of multiple domains which enable it to interact with various partners. OCRL1 consists of an N-terminus pleckstrin homology (PH) domain without a basic patch required for phosphoinositide recognition and binding. On the other hand, it contains a loop outside of the domain fold that is involved in OCRL1 recruitment to endocytic clathrin-coated pits. [4]

PH domain is followed by one of the major conserved domains of OCRL1 which is a central 5-phosphatase (5P) domain, in which two characteristic motifs are present (WXGDXN(F/Y)R and P(A/S)W(C/T)DRIL separated by 60-75 amino acids (AAs)). These play an important role in both substrate binding and catalysis.[5] This domain has a Dnase I-like fold. [6]

Next is an ASPM-SPD-2-Hydin (ASH) domain composed of nine β-strands forming two layers and a small α-helix. The β-sheet structure is similar to the immunoglobulin G fold. ASH domain also includes a Rab-binding site which mediates the interaction of OCRL1 with Rab-GTPases. This interaction is crucial for targeting OCRL1 to the Golgi complex and endosomal membranes.[7]

At a region towards the C-terminus there is a catalytically inactive Rho-GAP-like domain. It shows homology to the Rho-GAP domain found in proteins that bind and stimulate the GTPase activity of the Rho family proteins. The two reasons why this domain has no GTPase stimulating activity are the replacement of the catalytic Arg by His and absence of a signle helix.[8] The ASH-RhoGAP module mediates the interactions of OCRL1 with proteins that promote specific targeting to various cellular compartments such as early endosomes, Golgi complex, lysosomes and primary cilium.[9] Since these two function as a single folding module, destabilization in one of them will affect the stability of the other. [8]

Function

The membrane lipids phosphatidylinositol can be phosphorylated at positions 3, 4 and 5 of the inositol ring, which generates eight possible species called phosphoinositides. OCRL1 is one of the phosphatases that removes phosphate groups from specific positions of the inositol ring because it selectively acts as a 5-phosphatase. Phosphatidylinositols together with proteins of the Rab family typically have their distinct subcellular localization and they are both an integral part of the recognition machinery of membrane compartments which regulates membrane trafficking between organelles. Rab GTPases regulate membrane trafficking through interactions with various effectors, one of them being the phosphatase OCRL1.[10]

OCRL1 shows multiple binding sites for clathrin coat components (clathrin heavy chain and AP2 clathrin adaptor) so it seems to have a role in clathrin-mediated endocytosis because it is recruited to clathrin‐coated pits at the later stages of the vesicular formation process.[11] The two motifs involved in clathrin binding are located in the PH and Rho-GAP-like domains.[8] The 8 AA insertion in the longer isoform A enhances the interaction with clathrins.[12]

OCRL1 phosphatase activity prevents ectopic accumulation of PtdIns(4,5)P2 (and possibly PtdIns(3,4,5)P3) on intracellular membrane. This helps maintaining phosphoinositide spatial segregation and homeostasis within the cell.[8]

OCRL1 has been also reported to localize to the basal body and the transition zone of the primary cilium. Therefore, it also participates in ciliogenesis by contributing to protein trafficking to this organelle in an Rab8/IPIP27-dependent manner.[13]


Mutations in OCRL1

Structure of partial 5P domain and ASH domain of OCRL1 (pink) interacting with Rab8a (light blue) complex with GNP, Mg+2 (purple) and sulfate (PDB code 3qbt).

Drag the structure with the mouse to rotate

Given the important functions of OCRL1 and the amount of its interaction partners it is not surprising that point mutations can cause a serious OCRL. Although, some mutations cause only a mild type of OCRL which is called Dent-2 disease.[14] This diseases is caused by different mutations in all domains of OCRL1 just like OCRL.[15][14][16] However, it is characterized merely by heterogeneous kidney malfunctions.[17] Even though certain continuum between the two diseases has been suggested it is unclear what causes the different symptoms of various mutations.[18] As to the OCRL1 mutations causing OCRL so far only two have been studied closely. It is the substitution of F by V at the position 668 (F668V) and the substitution of N by K at the position 591 (N591K).[10][14]

A full crystal structure of the OCRL1 is not known but there are in total 5 structures of different domains which add up together almost the entire protein (2kie, 2q2v, 3qbt, 3qis, 4cmi). What’s more, one crystal structure of partial 5P domain and ASH domain (AA 540-678) in interaction with Rab8a was solved (3qbt) and shows well the interaction surface of the proteins. There are two main interaction sites. The first is located in the hinge region (AA 555-559) between ASH domain and 5P domain which is represented by the single 5P domain alpha helix in the crystal structure of 3QBT. The second important binding site is located in the beta-strand 9 of the ASH domain (AA 664-670).[10] To see the most important AAs in the binding sites see and .

It is clear from the structure that F668 is important in the binding site #2 because it sits in the of the Rab8a protein created by the I41, G42 and F70. Its substitution by V is therefore a major one since V is smaller and less hydrophobic than F. The mutation then causes disruption of this interaction and reduces the binding ability of OCRL1 with Rab8a by almost 6 folds. Moreover, the mutation causes the protein to be mainly localized in cytoplasm which can significantly hinder its normal function which is connected with vesicular formation.[10]

The N591K mutation also causes significant reduction in binding of Rab8a protein but the reason for this is different than in the case of F668V mutation. This AA is not part of any binding site but it seems to be important in the maintenance of the correct features of the ASH domain which are essential for the Rab8a binding. The effect of this mutation was studied in silico and the study showed that the mutation caused the ASH domain to alter its flexibility and overall fold. Although the most significant change was observed in the AAs that surrounded the N591K mutation, the substitution caused subsequent changes in most parts of the protein which brought about decreases of prevalence of hydrogen bonds between Rab8a and OCRL1 which led to a lower stability of their interaction.[14]

Inositol polyphosphate 5-phosphatase 3D structures

3D structures of inositol polyphosphate 5-phosphatase OCRL

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Lewis RA, Nussbaum RL, Brewer ED. Lowe Syndrome PMID:20301653
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 Bokenkamp A, Ludwig M. The oculocerebrorenal syndrome of Lowe: an update. Pediatr Nephrol. 2016 Dec;31(12):2201-2212. doi: 10.1007/s00467-016-3343-3. Epub , 2016 Mar 24. PMID:27011217 doi:http://dx.doi.org/10.1007/s00467-016-3343-3
  3. ↑ 3.0 3.1 3.2 Kenworthy L, Charnas L. Evidence for a discrete behavioral phenotype in the oculocerebrorenal syndrome of Lowe. Am J Med Genet. 1995 Nov 20;59(3):283-90. doi: 10.1002/ajmg.1320590304. PMID:8599350 doi:http://dx.doi.org/10.1002/ajmg.1320590304
  4. ↑ Mao Y, Balkin DM, Zoncu R, Erdmann KS, Tomasini L, Hu F, Jin MM, Hodsdon ME, De Camilli P. A PH domain within OCRL bridges clathrin-mediated membrane trafficking to phosphoinositide metabolism. EMBO J. 2009 Jul 8;28(13):1831-42. Epub 2009 Jun 18. PMID:19536138 doi:10.1038/emboj.2009.155
  5. ↑ Lowe M. Structure and function of the Lowe syndrome protein OCRL1. Traffic. 2005 Sep;6(9):711-9. doi: 10.1111/j.1600-0854.2005.00311.x. PMID:16101675 doi:http://dx.doi.org/10.1111/j.1600-0854.2005.00311.x
  6. ↑ Pirruccello M, De Camilli P. Inositol 5-phosphatases: insights from the Lowe syndrome protein OCRL. Trends Biochem Sci. 2012 Apr;37(4):134-43. doi: 10.1016/j.tibs.2012.01.002. Epub , 2012 Feb 28. PMID:22381590 doi:http://dx.doi.org/10.1016/j.tibs.2012.01.002
  7. ↑ Perdomo-Ramirez A, Anton-Gamero M, Rizzo DS, Trindade A, Ramos-Trujillo E, Claverie-Martin F. Two new missense mutations in the protein interaction ASH domain of OCRL1 identified in patients with Lowe syndrome. Intractable Rare Dis Res. 2020 Nov;9(4):222-228. doi: 10.5582/irdr.2020.03092. PMID:33139981 doi:http://dx.doi.org/10.5582/irdr.2020.03092
  8. ↑ 8.0 8.1 8.2 8.3 Erdmann KS, Mao Y, McCrea HJ, Zoncu R, Lee S, Paradise S, Modregger J, Biemesderfer D, Toomre D, De Camilli P. A role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway. Dev Cell. 2007 Sep;13(3):377-90. PMID:17765681 doi:http://dx.doi.org/10.1016/j.devcel.2007.08.004
  9. ↑ De Matteis MA, Staiano L, Emma F, Devuyst O. The 5-phosphatase OCRL in Lowe syndrome and Dent disease 2. Nat Rev Nephrol. 2017 Aug;13(8):455-470. doi: 10.1038/nrneph.2017.83. Epub 2017, Jul 3. PMID:28669993 doi:http://dx.doi.org/10.1038/nrneph.2017.83
  10. ↑ 10.0 10.1 10.2 10.3 Hou X, Hagemann N, Schoebel S, Blankenfeldt W, Goody RS, Erdmann KS, Itzen A. A structural basis for Lowe syndrome caused by mutations in the Rab-binding domain of OCRL1. EMBO J. 2011 Mar 4. PMID:21378754 doi:10.1038/emboj.2011.60
  11. ↑ Sharma S, Skowronek A, Erdmann KS. The role of the Lowe syndrome protein OCRL in the endocytic pathway. Biol Chem. 2015 Dec;396(12):1293-300. doi: 10.1515/hsz-2015-0180. PMID:26351914 doi:http://dx.doi.org/10.1515/hsz-2015-0180
  12. ↑ Choudhury R, Noakes CJ, McKenzie E, Kox C, Lowe M. Differential clathrin binding and subcellular localization of OCRL1 splice isoforms. J Biol Chem. 2009 Apr 10;284(15):9965-73. doi: 10.1074/jbc.M807442200. Epub 2009 , Feb 11. PMID:19211563 doi:http://dx.doi.org/10.1074/jbc.M807442200
  13. ↑ Coon BG, Hernandez V, Madhivanan K, Mukherjee D, Hanna CB, Barinaga-Rementeria Ramirez I, Lowe M, Beales PL, Aguilar RC. The Lowe syndrome protein OCRL1 is involved in primary cilia assembly. Hum Mol Genet. 2012 Apr 15;21(8):1835-47. doi: 10.1093/hmg/ddr615. Epub 2012 Jan , 6. PMID:22228094 doi:10.1093/hmg/ddr615
  14. ↑ 14.0 14.1 14.2 14.3 Acosta-Tapia N, Galindo JF, Baldiris R. Insights into the Effect of Lowe Syndrome-Causing Mutation p.Asn591Lys of OCRL-1 through Protein-Protein Interaction Networks and Molecular Dynamics Simulations. J Chem Inf Model. 2020 Feb 24;60(2):1019-1027. doi: 10.1021/acs.jcim.9b01077., Epub 2020 Jan 30. PMID:31967472 doi:http://dx.doi.org/10.1021/acs.jcim.9b01077
  15. ↑ Ye Q, Shen Q, Rao J, Zhang A, Zheng B, Liu X, Shen Y, Chen Z, Wu Y, Hou L, Jian S, Wei M, Ma M, Sun S, Li Q, Dang X, Wang Y, Xu H, Mao J. Multicenter study of the clinical features and mutation gene spectrum of Chinese children with Dent disease. Clin Genet. 2020 Mar;97(3):407-417. doi: 10.1111/cge.13663. Epub 2020 Jan 13. PMID:31674016 doi:http://dx.doi.org/10.1111/cge.13663
  16. ↑ Pirruccello M, Swan LE, Folta-Stogniew E, De Camilli P. Recognition of the F&H motif by the Lowe syndrome protein OCRL. Nat Struct Mol Biol. 2011 Jun 12. doi: 10.1038/nsmb.2071. PMID:21666675 doi:10.1038/nsmb.2071
  17. ↑ Gianesello L, Del Prete D, Anglani F, Calo LA. Genetics and phenotypic heterogeneity of Dent disease: the dark side of the moon. Hum Genet. 2021 Mar;140(3):401-421. doi: 10.1007/s00439-020-02219-2. Epub 2020, Aug 29. PMID:32860533 doi:http://dx.doi.org/10.1007/s00439-020-02219-2
  18. ↑ Hichri H, Rendu J, Monnier N, Coutton C, Dorseuil O, Poussou RV, Baujat G, Blanchard A, Nobili F, Ranchin B, Remesy M, Salomon R, Satre V, Lunardi J. From Lowe syndrome to Dent disease: correlations between mutations of the OCRL1 gene and clinical and biochemical phenotypes. Hum Mutat. 2011 Apr;32(4):379-88. doi: 10.1002/humu.21391. Epub 2011 Mar 10. PMID:21031565 doi:10.1002/humu.21391

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