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Amino Acids: The Forum for Amino Acid, Peptide and Protein Research (v.35, #4)
Proline metabolism in health and disease
by Chien-an A. Hu; James M. Phang; David Valle (pp. 651-652).
Functional genomics and SNP analysis of human genes encoding proline metabolic enzymes by Chien-an A. Hu; D. Bart Williams; Siqin Zhaorigetu; Shadi Khalil; Guanghua Wan; David Valle (pp. 655-664).
Proline metabolism in mammals involves two other amino acids, glutamate and ornithine, and five enzymatic activities, Δ1-pyrroline-5-carboxylate (P5C) reductase (P5CR), proline oxidase, P5C dehydrogenase, P5C synthase and ornithine-δ-aminotransferase (OAT). With the exception of OAT, which catalyzes a reversible reaction, the other four enzymes are unidirectional, suggesting that proline metabolism is purpose-driven, tightly regulated, and compartmentalized. In addition, this tri-amino-acid system also links with three other pivotal metabolic systems, namely the TCA cycle, urea cycle, and pentose phosphate pathway. Abnormalities in proline metabolism are relevant in several diseases: six monogenic inborn errors involving metabolism and/or transport of proline and its immediate metabolites have been described. Recent advances in the Human Genome Project, in silico database mining techniques, and research in dissecting the molecular basis of proline metabolism prompted us to utilize functional genomic approaches to analyze human genes which encode proline metabolic enzymes in the context of gene structure, regulation of gene expression, mRNA variants, protein isoforms, and single nucleotide polymorphisms.
Keywords: Apoptosis; FASTSNP; Functional genomics; OAT; OH-POX; OMIM; P53; Δ1-Pyrroline-5-carboxylate (P5C); P5CDH; P5CR/PYCR; P5CS/PYCS; POX/PRODH; l-Proline; Promoter analysis; SNP
Human Δ1-pyrroline-5-carboxylate synthase: function and regulation by C.-A. A. Hu; S. Khalil; S. Zhaorigetu; Z. Liu; M. Tyler; G. Wan; D. Valle (pp. 665-672).
Mammalian Δ1-pyrroline-5-carboxylate synthase (P5CS) is a bifunctional ATP- and NAD(P)H-dependent mitochondrial enzyme that catalyzes the coupled phosphorylation and reduction-conversion of l-glutamate to P5C, a pivotal step in the biosynthesis of l-proline, l-ornithine and l-arginine. Previously, we reported cloning and characterization of two P5CS transcript variants generated by exon sliding that encode two protein isoforms differing only by a two amino acid-insert at the N-terminus of the γ-glutamyl kinase active site. The short form (P5CS.short) is highly expressed in the gut and is inhibited by ornithine. In contrast, the long form (P5CS.long) is expressed ubiquitously and is insensitive to ornithine. Interestingly, we found that all the established human cell lines we have studied expressed P5CS.long but not P5CS.short. In addition, expression of P5CS.long can be modulated by hormones: downregulation by hydrocortisone and dexamethasone and upregulation by estradiol, for example. Using a quantitative proteomic approach, we showed that P5CS.long is upregulated by p53 in p53-induced apoptosis in DLD-1 colorectal cancer cells. Functional genomic analysis confirmed that there are two p53-binding consensus sequences in the promoter region and in the intron 1 of the human P5CS gene. Interestingly, overexpression of P5CS by adenoviruses harboring P5CS.long or P5CS.short in various cell types has no effect on cell growth or survival. It would be of importance to further investigate the role of P5CS as a p53 downstream effector and how P5CS.short expression is regulated by hormones and factors of alternative splicing in cells isolated from model animals.
Keywords: Alternative splicing; Apoptosis; Exon sliding; Hormones; P53; l-Proline; Quantitative proteomics; Δ1-Pyrroline-5-carboxylate (P5C); P5C synthase (P5CS); Prostate cancer (PCa) cells
PRODH variants and risk for schizophrenia by Alecia Willis; Hans Uli Bender; Gary Steel; David Valle (pp. 673-679).
Schizophrenia is a common, devastating neuropsychiatric disorder whose etiology is largely unknown. Multiple studies in humans and in mouse and fly models suggest a role for proline and PRODH, the gene encoding the first enzyme in the pathway of proline catabolism, in contributing risk for schizophrenia. Other studies, however, reach contradictory conclusions. Here, we provide a critical review of the data in the context of what is known about proline metabolism and suggest studies for the future. Overall, there is considerable evidence supporting a role for certain loss of function PRODH variants conferring risk for schizophrenia in some individuals.
Keywords: Schizophrenia; Proline; PRODH ; Hyperprolinemia I; Hyperprolinemia II
The metabolism of proline, a stress substrate, modulates carcinogenic pathways by James M. Phang; Steven P. Donald; Jui Pandhare; Yongmin Liu (pp. 681-690).
The resurgence of interest in tumor metabolism has led investigators to emphasize the metabolism of proline as a “stress substrate” and to suggest this pathway as a potential anti-tumor target. Proline oxidase, a.k.a. proline dehydrogenase (POX/PRODH), catalyzes the first step in proline degradation and uses proline to generate ATP for survival or reactive oxygen species for programmed cell death. POX/PRODH is induced by p53 under genotoxic stress and initiates apoptosis by both mitochondrial and death receptor pathways. Furthermore, POX/PRODH is induced by PPARγ and its pharmacologic ligands, the thiazolidinediones. The anti-tumor effects of PPARγ may be critically dependent on POX/PRODH. In addition, it is upregulated by nutrient stress through the mTOR pathway to maintain ATP levels. We propose that proline is made available as a stress substrate by the degradation of collagen in the microenvironmental extracellular matrix by matrix metalloproteinases. In a manner analogous to autophagy, this proline-dependent process for bioenergetics from collagen in extracellular matrix can be designated “ecophagy”.
Keywords: Proline oxidase; Proline dehydrogenase; mTOR; PPARγ; Apoptosis; Bioenergetics
Proline metabolism in the conceptus: implications for fetal growth and development by G. Wu; F. W. Bazer; S. Datta; G. A. Johnson; P. Li; M. C. Satterfield; T. E. Spencer (pp. 691-702).
Although there are published studies of proline biochemistry and nutrition in cultured cells and postnatal animals, little is known about proline metabolism and function in the conceptus (embryo/fetus, associated placental membranes, and fetal fluids). Because of the invasive nature of biochemical research on placental and fetal growth, animal models are often used to test hypotheses of biological importance. Recent evidence from studies with pigs and sheep shows that proline is a major substrate for polyamine synthesis via proline oxidase, ornithine aminotransferase, and ornithine decarboxylase in placentae. Both porcine and ovine placentae have a high capacity for proline catabolism and polyamine production. In addition, allantoic and amniotic fluids contain enzymes to convert proline into ornithine, which is delivered through the circulation to placental tissues. There is exquisite metabolic coordination among integrated pathways that support highest rates of polyamine synthesis and concentrations in placentae during early gestation when placental growth is most rapid. Interestingly, reduced placental and fetal growth are associated with reductions in placental proline transport, proline oxidase activity, and concentrations of polyamines in gestating dams with either naturally occurring or malnutrition-induced growth retardation. Conversely, increasing proline availability in maternal plasma through nutritional or pharmacological modulation in pigs and sheep enhances concentrations of proline and polyamines in placentae and fetal fluids, as well as fetal growth. These novel findings suggest an important role for proline in conceptus metabolism, growth and development, as well as a potential treatment for intrauterine growth restriction, which is a significant problem in both human medicine and animal agriculture.
Keywords: Proline; Placenta; Fetus; Nutrition; Fetal growth
The importance of proline residues in the structure, stability and susceptibility to proteolytic degradation of collagens by Stephen M. Krane (pp. 703-710).
Collagens are among proteins that undergo several post-translational modifications, such as prolyl hydroxylation, that occur during elongation of the nascent chains in the endoplasmic reticulum. The major structural collagens, types I, II and III, have large, uninterrupted triple helices, comprising three polyproline II-like chains supercoiled around a common axis. The structure has a requirement for glycine, as every third residue, and is stabilized by the high content of proline and 4-hydroxyproline residues. Action of prolyl hydroxylases is critical. Spontaneous or targeted genetic defects in prolyl hydroxylases can be lethal or result in severe osteogenesis imperfecta. Prolines, as determinants of substrate specificity and susceptibility, also play a role in degradation of collagen by collagenolytic matrix metalloproteinases (MMPs). Targeted mutations in mice in the collagenase cleavage domain have profound effects on collagen turnover and the function of connective tissues. Prolines are thus critical determinants of collagen structure and function.
Keywords: Prolylhydroxylases; Collagen structure; Osteogenesis imperfecta; Collagenases; Matrix metalloproteinases
Direct linking of metabolism and gene expression in the proline utilization A protein from Escherichia coli by Yuzhen Zhou; Weidong Zhu; Padmanetra S. Bellur; Dustin Rewinkel; Donald F. Becker (pp. 711-718).
The control of gene expression by enzymes provides a direct pathway for cells to respond to fluctuations in metabolites and nutrients. One example is the proline utilization A (PutA) protein from Escherichia coli. PutA is a membrane-associated enzyme that catalyzes the oxidation of l-proline to glutamate using a flavin containing proline dehydrogenase domain and a NAD+ dependent Δ1-pyrroline-5-carboxylate dehydrogenase domain. In some Gram-negative bacteria such as E. coli, PutA is also endowed with a ribbon–helix–helix DNA-binding domain and acts as a transcriptional repressor of the proline utilization genes. PutA switches between transcriptional repressor and enzymatic functions in response to proline availability. Molecular insights into the redox-based mechanism of PutA functional switching from recent studies are reviewed. In addition, new results from cell-based transcription assays are presented which correlate PutA membrane localization with put gene expression levels. General membrane localization of PutA, however, is not sufficient to activate the put genes.
Keywords: PutA; Transcriptional regulation; Membrane-binding; Proline utilization; DNA-binding; Multifunctional enzyme
Structural biology of proline catabolism by John J. Tanner (pp. 719-730).
The proline catabolic enzymes proline dehydrogenase and Δ1-pyrroline-5-carboxylate dehydrogenase catalyze the 4-electron oxidation of proline to glutamate. These enzymes play important roles in cellular redox control, superoxide generation, apoptosis and cancer. In some bacteria, the two enzymes are fused into the bifunctional enzyme, proline utilization A. Here we review the three-dimensional structural information that is currently available for proline catabolic enzymes. Crystal structures have been determined for bacterial monofunctional proline dehydrogenase and Δ1-pyrroline-5-carboxylate dehydrogenase, as well as the proline dehydrogenase and DNA-binding domains of proline utilization A. Some of the functional insights provided by analyses of these structures are discussed, including substrate recognition, catalytic mechanism, biochemical basis of inherited proline catabolic disorders and DNA recognition by proline utilization A.
Keywords: Proline; Proline catabolism; Proline metabolism; Protein structure; X-ray crystallography; Proline dehydrogenase; P5C dehydrogenase; Proline utilization A; Ribbon–helix–helix
Prolidase-dependent regulation of collagen biosynthesis by A. Surazynski; W. Miltyk; J. Palka; J. M. Phang (pp. 731-738).
Prolidase [EC.3.4.13.9] is a cytosolic imidodipeptidase, which specifically splits imidodipeptides with C-terminal proline or hydroxyproline. The enzyme plays an important role in the recycling of proline from imidodipeptides (mostly derived from degradation products of collagen) for resynthesis of collagen and other proline-containing proteins. The enzyme activity is up-regulated by β1-integrin receptor stimulation. The increase in the enzyme activity is due to its phosphorylation on serine/threonine residues. Collagen is not only structural component of extracellular matrix. It has been recognized as a ligand for integrin receptors, which play an important role in signaling that regulate ion transport, lipid metabolism, kinase activation and gene expression. Therefore, changes in the quantity, structure and distribution of collagens in tissues may affect cell signaling, metabolism and function. Several line of evidence suggests that prolidase activity may be a step-limiting factor in the regulation of collagen biosynthesis. It has been shown in different physiologic and pathologic conditions. It is of great importance during wound healing, inflammation, aging, tissue fibrosis and possibly skeletal abnormalities seen in Osteogenesis Imperfecta. The mechanism of prolidase-dependent regulation of collagen biosynthesis was found at both transcriptional and post-transcriptional levels. In this study, we provide evidence for prolidase-dependent transcriptional regulation of collagen biosynthesis. The mechanism was found at the level of NF-kB, known inhibitor of type I collagen gene expression. Modulation of integrin-dependent signaling by stimulatory (i.e. thrombin) or inhibitory (i.e. echistatin) β1-integrin ligands or by nitric oxide donors (i.e. DETA/NO) affect prolidase at post-transcriptional level. All those factors may represent novel approach to pharmacotherapy of connective tissue disorders.
Keywords: Prolidase; Collagen metabolism; β1-integrin signaling
Human prolidase and prolidase deficiency: an overview on the characterization of the enzyme involved in proline recycling and on the effects of its mutations by A. Lupi; R. Tenni; A. Rossi; G. Cetta; A. Forlino (pp. 739-752).
Here we summarized what is known at the present about function, structure and effect of mutations in the human prolidase. Among the peptidases, prolidase is the only metalloenzyme that cleaves the iminodipeptides containing a proline or hydroxyproline residue at the C-terminal end. It is relevant in the latest stage of protein catabolism, particularly of those molecules rich in imino acids such as collagens, thus being involved in matrix remodelling. Beside its intracellular functions, prolidase has an antitoxic effect against some organophosphorus molecules, can be used in dietary industry as bitterness reducing agent and recently has been used as target enzyme for specific melanoma prodrug activation. Recombinant human prolidase was produced in prokaryotic and eukaryotic hosts with biochemical properties similar to the endogenous enzyme and represents a valid tool both to better understand the structure and biological function of the enzyme and to develop an enzyme replacement therapy for the prolidase deficiency (PD). Prolidase deficiency is a rare recessive disorder caused by mutations in the prolidase gene and characterized by severe skin lesions. Single amino acid substitutions, exon splicing, deletions and a duplication were described as causative for the disease and are mainly located at highly conserved amino acids in the sequence of prolidase from different species. The pathophysiology of PD is still poorly understood; we offer here a review of the molecular mechanisms so far hypothesized.
Keywords: Prolidase; Proline; Prolidase deficiency; Genotype–phenotype correlation
Proline accumulation in plants: a review by Nathalie Verbruggen; Christian Hermans (pp. 753-759).
Proline (Pro) accumulation is a common physiological response in many plants in response to a wide range of biotic and abiotic stresses. Controversy has surrounded the possible role(s) of proline accumulation. In this review, knowledge on the regulation of Pro metabolism during development and stress, results of genetic manipulation of Pro metabolism and current debate on Pro toxicity in plants are presented.
Keywords: Osmotic stress; Genetic engineering; Proline toxicity; P5CS; P5CR; P5CDH; PDH
Growth control via TOR kinase signaling, an intracellular sensor of amino acid and energy availability, with crosstalk potential to proline metabolism by Xin-Hua Liao; Amit Majithia; Xiuli Huang; Alan R. Kimmel (pp. 761-770).
The TOR (Target of Rapamycin) protein kinase pathway plays a central role in sensing and responding to nutrients, stress, and intracellular energy state. TOR complex 1 (TORC1) is comprised of TOR, Raptor, and Lst8 and its activity is sensitive to inhibition by the macrolide antibiotic rapamycin. TORC1 regulates protein synthesis, ribosome biogenesis, autophagy, and ultimately cell growth through the phosphorylation of S6 K, 4E-BP, and other substrates. As TORC1 activity is positively or negatively modulated in response to upstream regulators, cellular growth rate is, respectively, enhanced or suppressed. A separate multiprotein TOR complex, TORC2, is insensitive to direct inhibition by rapamycin and does not regulate growth patterns directly; TORC2 can, however, impact certain aspects of TORC1 signaling and cell survival. TOR signaling is an ancient pathway, conserved among the yeasts, Dictyostelium, C. elegans, Drosophila, mammals, and Arabidopsis. This review will focus on the regulation of TORC1 in mammalian cells in the context of amino acid sensing/regulation and intracellular ATP homeostasis, but will also include comparisons among other organisms.
Keywords: TORC1; Rapamycin; Raptor; FKBP12; S6 K; 4E-BP