LACTB is a mammalian active-site serine protein that has evolved from a bacterial penicillin-binding protein. Penicillin-binding proteins are involved in the metabolism of peptidoglycan, the major bacterial cell wall constituent, implying that LACTB has been endowed with novel biochemical properties during eukaryote evolution. Here we demonstrate that LACTB is localized in the mitochondrial intermembrane space, where it is polymerized into stable filaments with a length extending more than a hundred nanometers. We infer that LACTB, through polymerization, promotes intramitochondrial membrane organization and micro-compartmentalization. These findings have implications for our understanding of mitochondrial evolution and function. M itochondria descend from ancient Gram-negative bacteria that, through endosymbiosis, became permanent residents of eukaryotic cells (1-3). As a consequence, mitochondria and Gram-negative bacteria share several biochemical features, including DNA organization, core metabolism, and a doublemembrane architecture. In Gram-negative bacteria, but not in mitochondria, a mesh-like layer of peptidoglycan is deposited between the outer and inner membrane, offering protection against mechanical stress. Following endosymbiosis, the peptidoglycan layer lost its structural importance, and was subsequently eliminated from the early eukaryotic cell. Although eukaryotes lack peptidoglycan, proteins deriving from the penicillin-binding protein (PBP) family (4) are found in all major eukaryotic lineages, including vertebrates (5).The bacterial PBPs constitute a large family of serine proteases that is distinguished by 3 conserved amino acid motifs that contribute to the formation of the catalytic site. The -SXXKmotif contains the catalytic serine residue, which undergoes reversible acylation through substrate binding, whereas the -[SY]X[NT]-and the - [KH][ST]G-motifs contribute to substrate docking (4). PBPs catalyze the hydrolysis or transpeptidation of the terminal D-alanyl-D-alanine moiety in peptidoglycan stem peptides. The acceptor for the transpeptidation reaction is the -amino group of lysine or diaminopimelate in an adjacent stem peptide. Through these reactions, PBPs contribute to modulate the extent of peptidoglycan cross-linking during bacterial cell division and cell wall elongation (4).In contrast, the function of PBP homologues in eukaryotic organisms remains largely unexplored. Amino acid sequence analyses show that the 3 conserved amino acid motifs required for catalytic activity are conserved in all eukaryotic PBP homologues (5), suggesting that they can function as active-site serine enzymes. Within the metazoan division, nematodes harbor the largest number of PBP homologues (5), and in Caenorhabditis elegans the PBP homologue LACT-1 may be involved in pathogen recognition (6). LACTB is the only PBP homologue of mammals, and LACTB has been identified in all mammalian genomes sequenced to date (5,7,8). Recently, a causative link between LACTB and obesity was detected through gene coexp...

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SummaryThe in vivo niche and basic cellular properties of nephron progenitors are poorly described. Here we studied the cellular organization and function of the MAPK/ERK pathway in nephron progenitors. Live-imaging of ERK activity by a Förster resonance energy transfer biosensor revealed a dynamic activation pattern in progenitors, whereas differentiating precursors exhibited sustained activity. Genetic experiments demonstrate that MAPK/ERK activity controls the thickness, coherence, and integrity of the nephron progenitor niche. Molecularly, MAPK/ERK activity regulates niche organization and communication with extracellular matrix through PAX2 and ITGA8, and is needed for CITED1 expression denoting undifferentiated status. MAPK/ERK activation in nephron precursors propels differentiation by priming cells for distal and proximal fates induced by the Wnt and Notch pathways. Thus, our results demonstrate a mechanism through which MAPK/ERK activity controls both progenitor maintenance and differentiation by regulating a distinct set of targets, which maintain the biomechanical milieu of tissue-residing progenitors and prime precursors for nephrogenesis.

CLN1 disease (OMIM #256730) is an early childhood ceroid-lipofuscinosis associated with mutated CLN1, whose product Palmitoyl-Protein Thioesterase 1 (PPT1) is a lysosomal enzyme involved in the removal of palmitate residues from S-acylated proteins. In neurons, PPT1 expression is also linked to synaptic compartments. The aim of this study was to unravel molecular signatures connected to CLN1. We utilized SH-SY5Y neuroblastoma cells overexpressing wild type CLN1 (SH-p.wtCLN1) and five selected CLN1 patients’ mutations. The cellular distribution of wtPPT1 was consistent with regular processing of endogenous protein, partially detected inside Lysosomal Associated Membrane Protein 2 (LAMP2) positive vesicles, while the mutants displayed more diffuse cytoplasmic pattern. Transcriptomic profiling revealed 802 differentially expressed genes (DEGs) in SH-p.wtCLN1 (as compared to empty-vector transfected cells), whereas the number of DEGs detected in the two mutants (p.L222P and p.M57Nfs*45) was significantly lower. Bioinformatic scrutiny linked DEGs with neurite formation and neuronal transmission. Specifically, neuritogenesis and proliferation of neuronal processes were predicted to be hampered in the wtCLN1 overexpressing cell line, and these findings were corroborated by morphological investigations. Palmitoylation survey identified 113 palmitoylated protein-encoding genes in SH-p.wtCLN1, including 25 ones simultaneously assigned to axonal growth and synaptic compartments. A remarkable decrease in the expression of palmitoylated proteins, functionally related to axonal elongation (GAP43, CRMP1 and NEFM) and of the synaptic marker SNAP25, specifically in SH-p.wtCLN1 cells was confirmed by immunoblotting. Subsequent, bioinformatic network survey of DEGs assigned to the synaptic annotations linked 81 DEGs, including 23 ones encoding for palmitoylated proteins. Results obtained in this experimental setting outlined two affected functional modules (connected to the axonal and synaptic compartments), which can be associated with an altered gene dosage of wtCLN1. Moreover, these modules were interrelated with the pathological effects associated with loss of PPT1 function, similarly as observed in the Ppt1 knockout mice and patients with CLN1 disease.

Mutations in the CLN1 gene that encodes Palmitoyl protein thioesterase 1 (PPT1) or CLN1, cause Infantile NCL (INCL, MIM#256730). PPT1 removes long fatty acid chains such as palmitate from modified cysteine residues of proteins. The data shown here result from isolated protein complexes from PPT1-expressing SH-SY5Y stable cells that were subjected to single step affinity purification coupled to mass spectrometry (AP-MS). Prior to the MS analysis, we utilised a modified filter-aided sample preparation (FASP) protocol. Based on label free quantitative analysis of the data by SAINT, 23 PPT1 interacting partners (IP) were identified. A dense connectivity in PPT1 network was further revealed by functional coupling and extended network analyses, linking it to mitochondrial ATP synthesis coupled protein transport and thioester biosynthetic process. Moreover, the terms: inhibition of organismal death, movement disorders and concentration of lipid were predicted to be altered in the PPT1 network. Data presented here are related to Scifo et al. (J. Proteomics, 123 (2015) 42–53).