Deletion of PREPL, a Gene Encoding a Putative Serine Oligopeptidase, in Patients with Hypotonia-Cystinuria Syndrome Jaak Jaeken, Kevin Martens, Inge.

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Deletion of PREPL, a Gene Encoding a Putative Serine Oligopeptidase, in Patients with Hypotonia-Cystinuria Syndrome Jaak Jaeken, Kevin Martens, Inge François, François Eyskens, Claudine Lecointre, Rita Derua, Sandra Meulemans, Jerry W. Slootstra, Etienne Waelkens, Francis de Zegher, John W.M. Creemers, Gert Matthijs The American Journal of Human Genetics Volume 78, Issue 1, Pages 38-51 (January 2006) DOI: 10.1086/498852 Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 1 Clinical presentation of HCS. A, Patient 5-I during childhood (top) and adulthood (bottom). B, Growth curve of patient 3-I, illustrating the excellent response to growth hormone treatment. Vertical arrow indicates the age at which the treatment was started. The American Journal of Human Genetics 2006 78, 38-51DOI: (10.1086/498852) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 2 Genetics of HCS. A, Deletions present in the HCS families. All deletions disrupt the coding sequences of SLC3A1 and PREPL, located on chromosome 2p21. Sizes range from 23.8 kb to 75.5 kb. Sequences flanking the breakpoints are shown and are numbered in accordance with BAC clone 24i5. B, Junction fragments spanning the breakpoint. C, Haplotype analysis for deletion A, B, and C alleles. Dashed lines indicate the breakpoint. Conserved alleles are shaded in gray. For deletion B, the conserved subhaplotypes proximal to the breakpoint are shaded in light gray and dark gray. Families 5 (deletion B/deletion B) and 6 (deletion A/deletion B) are excluded because parents were not available. p= Paternal haplotype; m= maternal haplotype. The American Journal of Human Genetics 2006 78, 38-51DOI: (10.1086/498852) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 3 Expression analysis of PREPL. A, Genomic organization of PREPL. B, In silico analysis of the 5′ UTR revealed two transcriptional start sites. The first transcription start is present in isoforms PREPL3 and PREPL5, and the second is present in the remaining isoforms. Isoforms PREPL1–4 use the start codon in exon 2, generating a 638-aa protein. PREPL5–7 isoforms contain an additional start site in exon 1B, generating a 727-aa protein. C, Human multiple-tissue northern blot shows a broad tissue distribution of a 5.1-kb transcript, with highest expression in brain, kidney, and skeletal muscle. Tissue specific transcripts are present in brain (∼4.1 kb) and kidney (∼2.8 kb) tissue. The American Journal of Human Genetics 2006 78, 38-51DOI: (10.1086/498852) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 4 The PREPL homologues. A, Amino acid identity of different PREPLS orthologues and amino acid similarity of different PREPLS homologues. The light-gray and dark-gray bars represent the identity (left panel) or similarity (right panel) percentages of the complete sequence and catalytic domain, respectively. An asterisk indicates an incomplete amino acid sequence present in the database. B, Schematic representation of the domain structure of the PREPL isoforms. Identity/similarity percentages of the different domains with PREP and OpdB are shown. The American Journal of Human Genetics 2006 78, 38-51DOI: (10.1086/498852) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 5 Multiple sequence alignments of the PREPL variants with PREP and OpdB. Predicted secondary structure elements of PREPL are shown above the sequence, whereas the PREP secondary structure elements (based on Fulop et al. 1998) are shown below the sequence. Identical residues between PREPL and one homologue are shaded in light gray, whereas completely conserved residues are shaded in dark gray. Catalytic triad residues are indicated by an asterisk, whereas important residues of the S1 binding pocket are boxed. The American Journal of Human Genetics 2006 78, 38-51DOI: (10.1086/498852) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 6 Functional analysis of PREPL. A, Immunofluorescence analysis of PREPLS and PREPLL in CHO cells. Both isoforms show similar cytoplasmic staining, and similar results were obtained for PREPLS when the FLAG epitope was linked to the carboxyterminus instead of to the aminoterminus. B, Enzymatic activity of immunopurified, recombinant proteins was determined using FP-biotin and was visualized with streptavidin-HRP. Expression of recombinant proteins was confirmed with biotinylated anti-FLAG M2 antibody. C, Wild-type PREPLS (lane 2) and mutant His607Ala (lane 6) show reactivity with FP-biotin. In contrast, mutations of the predicted catalytic residues (lanes 3, 4, and 5) ablated activity. D, Full-length PREPLA–B, OpdB, and PREP are all FP-biotin reactive. Reactivity was abolished in the truncated constructs of OpdB and PREP (lanes 4 and 6) but not in truncated PREPL (lane 2), confirming the fundamental difference in domain structure. ΔPREPL = truncated construct of PREPL (aa 342–638), ΔOpdB = truncated construct of OpdB (aa 405–687), and ΔPREP = truncated construct of PREP (aa 428–710). The American Journal of Human Genetics 2006 78, 38-51DOI: (10.1086/498852) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure A1 Multiple sequence alignment of the 5′ UTR splice variants. The two alternative ATG-start codons are shaded. The aligment is stopped at the end of exon 2. The American Journal of Human Genetics 2006 78, 38-51DOI: (10.1086/498852) Copyright © 2006 The American Society of Human Genetics Terms and Conditions