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Wang K, Tian S, Galindo-González J, Dávalos LM, Zhang Y, Zhao H. Molecular adaptation and convergent evolution of frugivory in Old World and neotropical fruit bats. Mol Ecol 2020; 29:4366-4381. [PMID: 32633855 DOI: 10.1111/mec.15542] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/22/2020] [Accepted: 06/30/2020] [Indexed: 12/21/2022]
Abstract
Although cases of independent adaptation to the same dietary niche have been documented in mammalian ecology, the molecular correlates of such shifts are seldom known. Here, we used genomewide analyses of molecular evolution to examine two lineages of bats that, from an insectivorous ancestor, have both independently evolved obligate frugivory: the Old World family Pteropodidae and the neotropical subfamily Stenodermatinae. New genome assemblies from two neotropical fruit bats (Artibeus jamaicensis and Sturnira hondurensis) provide a framework for comparisons with Old World fruit bats. Comparative genomics of 10 bat species encompassing dietary diversity across the phylogeny revealed convergent molecular signatures of frugivory in both multigene family evolution and single-copy genes. Evidence for convergent molecular adaptations associated with frugivorous diets includes the composition of three subfamilies of olfactory receptor genes, losses of three bitter taste receptor genes, losses of two digestive enzyme genes and convergent amino acid substitutions in several metabolic genes. By identifying suites of adaptations associated with the convergent evolution of frugivory, our analyses both reveal the extent of molecular mechanisms under selection in dietary shifts and will facilitate future studies of molecular ecology in mammals.
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Affiliation(s)
- Kai Wang
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.,The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan, China
| | - Shilin Tian
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.,Novogene Bioinformatics Institute, Beijing, China
| | - Jorge Galindo-González
- Biotechnology and Applied Ecology Institute (INBIOTECA), Universidad Veracruzana, Xalapa,Veracruz, Mexico
| | - Liliana M Dávalos
- Department of Ecology and Evolution and Center for Inter-Disciplinary Environmental Research, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Yuzhi Zhang
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.,College of Science, Tibet University, Lhasa, China
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2
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Chen YH, Zhao H. Evolution of digestive enzymes and dietary diversification in birds. PeerJ 2019; 7:e6840. [PMID: 31086749 PMCID: PMC6487185 DOI: 10.7717/peerj.6840] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/24/2019] [Indexed: 11/20/2022] Open
Abstract
As the most species-rich class of tetrapod vertebrates, Aves possesses diverse feeding habits, with multiple origins of insectivory, carnivory, frugivory, nectarivory, granivory and omnivory. Since digestive enzymes mediate and limit energy and nutrient uptake, we hypothesized that genes encoding digestive enzymes have undergone adaptive evolution in birds. To test this general hypothesis, we identified 16 digestive enzyme genes (including seven carbohydrase genes (hepatic amy, pancreatic amy, salivary amy, agl, g6pc, gaa and gck), three lipase genes (cyp7a1, lipf and pnlip), two protease genes (ctrc and pgc), two lysozyme genes (lyz and lyg) and two chitinase genes (chia and chit1)) from the available genomes of 48 bird species. Among these 16 genes, three (salivary amy, lipf and chit1) were not found in all 48 avian genomes, which was further supported by our synteny analysis. Of the remaining 13 genes, eight were single-copy and five (chia, gaa, lyz, lyg and pgc) were multi-copy. Moreover, the multi-copy genes gaa, lyg and pgc were predicted to exhibit functional divergence among copies. Positively selected sites were detected in all of the analyzed digestive enzyme genes, except agl, g6pc, gaa and gck, suggesting that different diets may have favored differences in catalytic capacities of these enzymes. Furthermore, the analysis also revealed that the pancreatic amylase gene and one of the lipase genes (cyp7a1) have higher ω (the ratio of nonsynonymous to the synonymous substitution rates) values in species consuming a larger amount of seeds and meat, respectively, indicating an intense selection. In addition, the gck carbohydrase gene in species consuming a smaller amount of seeds, fruits or nectar, and a lipase gene (pnlip) in species consuming less meat were found to be under relaxed selection. Thus, gene loss, gene duplication, functional divergence, positive selection and relaxed selection have collectively shaped the evolution of digestive enzymes in birds, and the evolutionary flexibility of these enzymes may have facilitated their dietary diversification.
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Affiliation(s)
- Yan-Hong Chen
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huabin Zhao
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
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3
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Mamat O, Fukumura Y, Saito T, Takahashi M, Mitomi H, Sai JK, Kawasaki S, Yao T. Fundic gland differentiation of oncocytic/pancreatobiliary subtypes of pancreatic intraductal papillary mucinous neoplasm. Histopathology 2016; 69:570-81. [DOI: 10.1111/his.12967] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 03/12/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Osman Mamat
- Department of Human Pathology; School of Medicine; Juntendo University; Tokyo Japan
| | - Yuki Fukumura
- Department of Human Pathology; School of Medicine; Juntendo University; Tokyo Japan
| | - Tsuyoshi Saito
- Department of Human Pathology; School of Medicine; Juntendo University; Tokyo Japan
| | - Michiko Takahashi
- Department of Human Pathology; School of Medicine; Juntendo University; Tokyo Japan
| | - Hiroyuki Mitomi
- Department of Human Pathology; School of Medicine; Juntendo University; Tokyo Japan
- Department of Pathology; Japan Labour Health and Welfare Organization; Kanto Rosai Hospital; Kawasaki Japan
| | - Jin Kan Sai
- Department of Gastroenterology; Juntendo University; Tokyo Japan
| | - Seiji Kawasaki
- Department of Hepatobiliary Pancreatic Surgery; School of Medicine; Juntendo University; Tokyo Japan
| | - Takashi Yao
- Department of Human Pathology; School of Medicine; Juntendo University; Tokyo Japan
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4
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Szecsi PB. The aspartic proteases. Scandinavian Journal of Clinical and Laboratory Investigation 2011. [DOI: 10.1080/00365519209104650] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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5
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Taggart RT. Genetic variation of human aspartic proteinases. Scandinavian Journal of Clinical and Laboratory Investigation 2011. [DOI: 10.1080/00365519209104659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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Takahashi K. Gene structures of pepsinogens A and C. Scandinavian Journal of Clinical and Laboratory Investigation 2011. [DOI: 10.1080/00365519209104658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Hassan MI, Toor A, Ahmad F. Progastriscin: structure, function, and its role in tumor progression. J Mol Cell Biol 2010; 2:118-27. [PMID: 20231168 DOI: 10.1093/jmcb/mjq001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Progastricsin (PGC) is a major seminal plasma protein having aspartyl proteinases-like activity and showing close sequence similarity to pepsins. PGC is also present as zymogen in gastric mucosa. In this article, we have reviewed all important features of PGC. Furthermore, we have compared all features of PGC with those of different aspartyl proteinases. The complete amino acid sequence of PGC reveals that it is composed of 374 residues (gastricsin moiety of 331 residues and the activation segment of 43 residues). The gene of human PGC is located at single locus on chromosome 6, whereas the human pepsinogen genetic locus is polymorphic and codes for at least three distinct polypeptide sequences on chromosome 11. The major useful function of PGC includes production of pro-antimicrobial substance in seminal plasma. The crystal structure of human PGC is known, which shows that it is quite similar to that of porcine pepsinogen. The tertiary structure of PGC is comprised of commonly bilobal structure with a large active-site cleft between the lobes. Two aspartate residues in the center of the cleft, namely Asp32 and Asp215, function as catalytic residues. The sequence and structural features of PGC indicate that it is diverged from its pepsinogen ancestor in the early phase of the evolution of gastric aspartyl proteinases. Our detailed review of PGC structure, function and activation mechanism will also be of interest to cancer biologists as well as gastroenterologists.
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Affiliation(s)
- Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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8
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He Z, O'Reilly RC, Mehta D. Gastric pepsin in middle ear fluid of children with otitis media: clinical implications. Curr Allergy Asthma Rep 2008; 8:513-8. [PMID: 18940143 DOI: 10.1007/s11882-008-0094-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gastroesophageal reflux and extraesophageal reflux have been postulated to be involved in the pathogenesis of otitis media. This is supported by recent studies revealing the presence of gastric pepsin in the middle ear space of children with otitis media but not in control patients without otitis media. Reflux's role in otitis media appears to be most pronounced in younger children and those with purulent effusions.
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Affiliation(s)
- Zhaoping He
- Division of Pediatric Otolaryngology, Alfred I. duPont Hospital for Children, Wilmington, DE 19899, USA
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9
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Feng S, Li W, Lin H. Characterization and expression of the pepsinogen C gene and determination of pepsin-like enzyme activity from orange-spotted grouper (Epinephelus coioides). Comp Biochem Physiol B Biochem Mol Biol 2008; 149:275-84. [DOI: 10.1016/j.cbpb.2007.09.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 09/21/2007] [Accepted: 09/21/2007] [Indexed: 10/22/2022]
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10
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Hynek R, Vankova H, Tesarova M, Kas J. DEGREE OF PHOSPHORYLATION OF PEPSINOGEN IN GASTRIC CANCER. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-100106949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Radovan Hynek
- a Department of Biochemistry and Microbiology , Institute of Chemical Technology , Technická 5, Prague 6, 166 28, Czech Republic
| | - Hana Vankova
- b Department of Pathological Physiology, 1st Faculty of Medicine , Charles University , U Nemocnice 5, Prague 2, 128 53, Czech Republic
| | - Marketa Tesarova
- a Department of Biochemistry and Microbiology , Institute of Chemical Technology , Technická 5, Prague 6, 166 28, Czech Republic
| | - Jan Kas
- a Department of Biochemistry and Microbiology , Institute of Chemical Technology , Technická 5, Prague 6, 166 28, Czech Republic
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11
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Narita Y, Oda SI, Kageyama T. Rodent monophyly deduced from the unique gastric proteinase constitution and molecular phylogenetic analyses using pepsinogen-C cDNA sequences. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2006; 1:273-82. [PMID: 20483259 DOI: 10.1016/j.cbd.2006.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 04/16/2006] [Accepted: 04/18/2006] [Indexed: 10/24/2022]
Abstract
Pepsinogens are zymogens of pepsins, the gastric digestive proteinases. Although pepsinogen A is predominant in most mammalian species hitherto known, pepsinogen C is expressed exclusively and the lack of pepsinogen A is evidenced in the rat and guinea pig. Furthermore, in these two rodents, considerable amount of procathepsin E is also expressed in gastric mucosa although it is almost undetectable in other mammals. In this paper, in order to clarify whether such unique gastric proteinase constitution is common among rodents, we carried out purification and characterization of gastric proteinases, and molecular cloning of pepsinogen-C cDNAs from several rodent species including the degu and coypu. Pepsinogen C and procathepsin E were isolated but pepsinogen A was undetectable in the rodents, leading to the conclusion that that rodents commonly share the unique gastric proteinase constitution. This feature could be treated as a new "molecular synapomorphy", supporting strongly monophyly of the order Rodentia. From the molecular phylogenetic analyses of pepsinogen-C cDNA sequences, monophyly of the order Rodentia was also supported by the analyses with high statistic reliabilities.
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Affiliation(s)
- Yuichi Narita
- Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
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Narita Y, Oda SI, Moriyama A, Kageyama T. Primary structure, unique enzymatic properties, and molecular evolution of pepsinogen B and pepsin B. Arch Biochem Biophys 2002; 404:177-85. [PMID: 12147255 DOI: 10.1016/s0003-9861(02)00209-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Purification of pepsinogen B from dog stomach was achieved. Activation of pepsinogen B to pepsin B is likely to proceed through a one-step pathway although the rate is very slow. Pepsin B hydrolyzes various peptides including beta-endorphin, insulin B chain, dynorphin A, and neurokinin A, with high specificity for the cleavage of the Phe-X bonds. The stability of pepsin B in alkaline pH is noteworthy, presumably due to its less acidic character. The complete primary structure of pepsinogen B was clarified for the first time through the molecular cloning of the respective cDNA. Molecular evolutional analyses show that pepsinogen B is not included in other known pepsinogen groups and constitutes an independent cluster in the consensus tree. Pepsinogen B might be a sister group of pepsinogen C and the divergence of these two zymogens seems to be the latest event of pepsinogen evolution.
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Affiliation(s)
- Yuichi Narita
- Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan.
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13
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Narita Y, Oda S, Takenaka O, Kageyama T. Phylogenetic position of Eulipotyphla inferred from the cDNA sequences of pepsinogens A and C. Mol Phylogenet Evol 2001; 21:32-42. [PMID: 11603935 DOI: 10.1006/mpev.2001.0996] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although to date the phylogenetic position of the provisional order Eulipotyphla has been assessed by various molecular markers, it has not been conclusively clarified due to low statistical supporting values and inconsistent results. To clarify the phylogenetic position of Eulipotyphla, we cloned cDNAs for pepsinogens A and C from five mammalian species belonging to four different orders and determined their nucleotide sequences. Molecular phylogenetic analysis based on the 1st and 2nd codon positions of the protein-coding region of cDNA sequences strongly supported the close relationship between Eulipotyphla and Chiroptera. Carnivora was found to be a sister group to these two orders. The monophyly of the order Rodentia and that of the cohort Glires (Rodentia and Lagomorpha) was also shown by the present phylogenetic trees of pepsinogens.
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Affiliation(s)
- Y Narita
- Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
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14
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Kim HS, Yoon H, Minn I, Park CB, Lee WT, Zasloff M, Kim SC. Pepsin-mediated processing of the cytoplasmic histone H2A to strong antimicrobial peptide buforin I. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 165:3268-74. [PMID: 10975843 DOI: 10.4049/jimmunol.165.6.3268] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The intestinal epithelium forms a first line of innate host defense by secretion of proteins with antimicrobial activity against microbial infection. Despite the extensive studies on the antimicrobial host defense in many gastrointestinal tracts, little is known about the antimicrobial defense system of the stomach. The potent antimicrobial peptide buforin I, consisting of 39 aa, was isolated recently from the stomach tissue of an Asian toad, Bufo bufo gargarizans. In this study we examined the mechanism of buforin I production in toad stomach tissue. Buforin I is produced by the action of pepsin isozymes, named pepsin Ca and Cb, cleaving the Tyr39-Ala40 bond of histone H2A. Immunohistochemical analysis revealed that buforin I is present extracellularly on the mucosal surface, and unacetylated histone H2A, a precursor of buforin I, is localized in the cytoplasm of gastric gland cells. Furthermore, Western blot analysis showed that buforin I is also present in the gastric fluids, and immunoelectron microscopy detected localization of the unacetylated histone H2A in the cytoplasmic granules of gastric gland cells. The distinct subcellular distribution of the unacetylated histone H2A and the detection of the unacetylated buforin I both on the mucosal surface and in the lumen suggest that buforin I is produced from the cytoplasmic unacetylated histone H2A secreted into the gastric lumen and subsequently processed by pepsins. Our results indicate that buforin I along with pepsins in the vertebrate stomach may contribute to the innate host defense of the stomach against invading microorganisms.
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Affiliation(s)
- H S Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Taejon, Korea
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15
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Xin H, Stephans JC, Duan X, Harrowe G, Kim E, Grieshammer U, Kingsley C, Giese K. Identification of a novel aspartic-like protease differentially expressed in human breast cancer cell lines. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1501:125-37. [PMID: 10838186 DOI: 10.1016/s0925-4439(00)00014-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Four different human breast cancer cell lines were examined to search for genes associated with tumor growth and metastasis. Each of these cell lines, MDA-MB-453, MCF-7, MDA-MB-231 and MDA-MB-435, displays different phenotypic characteristics ranging from poorly to highly tumorigenic and metastatic. The differences in gene expression profiles of these cell lines generated by differential display technique should allow one to identify candidates as putative oncogenes or tumor/metastasis suppressor genes. A novel cDNA expressed in the highly tumorigenic and metastatic cell line, MDA-MB-435, was identified and isolated by this approach. The function for this gene, designated ALP56 (aspartic-like protease 56 kDa), in tumor progression is suggested by the homology of the encoded protein to aspartic proteases, such as cathepsin D. The amino acid residues in two catalytic domains of this family are highly conserved in those domains of ALP56. Northern hybridization indicated that the expression of ALP56 is associated with growth and metastasis of MDA-MB-435 tumors in immunodeficient mice. In situ hybridization of biopsies from breast cancer and colon cancer patients indicated that ALP56 is upregulated in human primary tumors and liver metastasis. These results suggest that this novel gene correlates with human tumor progression.
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Affiliation(s)
- H Xin
- Chiron Corporation, 4560 Horton Street, Emeryville, CA 94608, USA
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16
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Kageyama T, Ichinose M, Tsukada-Kato S, Omata M, Narita Y, Moriyama A, Yonezawa S. Molecular cloning of neonate/infant-specific pepsinogens from rat stomach mucosa and their expressional change during development. Biochem Biophys Res Commun 2000; 267:806-12. [PMID: 10673373 DOI: 10.1006/bbrc.1999.2047] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To clarify the nature of rat neonate/infant-specific pepsinogens, we carried out their purification and molecular cloning. Prochymosin was found to be the major neonatal pepsinogen. The general proteolytic activity of its active form, chymosin, was, however, lower than those of pepsins A and C which are predominant in adult animals. Molecular cloning of rat prochymosin cDNA was achieved along with cDNA for another neonate-specific pepsinogen, pepsinogen F, although determination of pepsinogen F in neonatal gastric mucosa was unsuccessful, presumably due to its lack of proteolytic activity or different proteolytic specificity. Northern blot analysis confirmed that genes for prochymosin and pepsinogen F are expressed only at neonatal/infant stages and the switching of gene expression to that of pepsinogen C occurred at late infant stages. A phylogenetic tree based on nucleotide sequences showed clearly that pepsinogens fall into four major groups, namely prochymosin and pepsinogen F of the neonate/infant and pepsinogens A and C of adult animals. Although, to date, prochymosin and pepsinogen F were believed to be expressed in only a limited number of mammals, the present results suggest that they might be expressed at the neonatal/infant stage in a variety of mammals.
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Affiliation(s)
- T Kageyama
- Center for Human Evolutionary Modeling Research, Primate Research Institute, Kyoto University, Inuyama, 484-8506, Japan.
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17
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Khan AR, Khazanovich-Bernstein N, Bergmann EM, James MN. Structural aspects of activation pathways of aspartic protease zymogens and viral 3C protease precursors. Proc Natl Acad Sci U S A 1999; 96:10968-75. [PMID: 10500110 PMCID: PMC34228 DOI: 10.1073/pnas.96.20.10968] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The three-dimensional structures of the inactive protein precursors (zymogens) of the serine, cysteine, aspartic, and metalloprotease classes of proteolytic enzymes are known. Comparisons of these structures with those of the mature, active proteases reveal that, in general, the preformed, active conformations of the residues involved in catalysis are rendered sterically inaccessible to substrates by the residues of the zymogens' N-terminal extensions or prosegments. The prosegments interact in nonsubstrate-like fashions with the residues of the active sites in most of the cases. The gastric aspartic proteases have a well-characterized zymogen conversion pathway. Structures of human progastricsin, the inactive intermediate 2, and active human pepsin are known and have been used to define the conversion pathway. The structure of the zymogen precursor of plasmepsin II, the malarial aspartic protease, shows a new twist on the mode of inactivation used by the gastric zymogens. The prosegment of proplasmepsin disrupts the active conformation of the two catalytic aspartic acid residues by inducing a major reorientation of the two domains of the mature protease. The picornaviral 2A and 3C proteases have a chymotrypsin-like tertiary structure but with a cysteine nucleophile. These enzymes cleave themselves from the viral polyprotein in cis (intramolecular cleavage) and carry out trans cleavages of other scissile peptides important for the virus life cycle. Although the structure of the precursor viral polyprotein is unknown, it probably resembles the organization of the proenzymes of the bacterial serine proteases, subtilisin, and alpha-lytic protease. Cleavage of the prosegment is known to occur in cis for these precursor molecules.
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Affiliation(s)
- A R Khan
- Medical Research Council Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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18
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Sakamoto N, Saiga H, Yasugi S. Analysis of temporal expression pattern and cis-regulatory sequences of chicken pepsinogen A and C. Biochem Biophys Res Commun 1998; 250:420-4. [PMID: 9753645 DOI: 10.1006/bbrc.1998.9290] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three groups of pepsinogens exist in vertebrates, namely, pepsinogen A, pepsinogen C, and prochymosin, which are produced at different developmental stages. In the chicken, prochymosin is expressed only in the embryonic stage, while pepsinogens A and C are secreted from adult chicken proventricular (glandular stomach) mucosa. In order to understand the mechanism of transcriptional regulation of these genes, we have cloned the genes encoding chicken pepsinogens A and C and analyzed the sequences possibly involved in their regulation. 5'-Upstream sequences of both genes contain putative binding motifs for transcription factors such as GATA, Sox, and HNF-3 beta, which are expressed in the chicken gut epithelium. Moreover, we found seven putative binding motifs for human MZF-1 in intron 8 of pepsinogen A gene. These transcription factors may act as regulators of expression of chicken pepsinogen genes.
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Affiliation(s)
- N Sakamoto
- Department of Biology, Faculty of Science, Tokyo Metropolitan University, Japan.
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19
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López-Otín C, Diamandis EP. Breast and prostate cancer: an analysis of common epidemiological, genetic, and biochemical features. Endocr Rev 1998; 19:365-96. [PMID: 9715372 DOI: 10.1210/edrv.19.4.0337] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- C López-Otín
- Departamento de Bioquímica, Facultad de Medicina, Universidad de Oviedo, Spain
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20
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Khan AR, James MN. Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes. Protein Sci 1998; 7:815-36. [PMID: 9568890 PMCID: PMC2143990 DOI: 10.1002/pro.5560070401] [Citation(s) in RCA: 342] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Proteolytic enzymes are synthesized as inactive precursors, or "zymogens," to prevent unwanted protein degradation, and to enable spatial and temporal regulation of proteolytic activity. Upon sorting or appropriate compartmentalization, zymogen conversion to the active enzyme typically involves limited proteolysis and removal of an "activation segment." The sizes of activation segments range from dipeptide units to independently folding domains comprising more than 100 residues. A common form of the activation segment is an N-terminal extension of the mature enzyme, or "prosegment," that sterically blocks the active site, and thereby prevents binding of substrates. In addition to their inhibitory role, prosegments are frequently important for the folding, stability, and/or intracellular sorting of the zymogen. The mechanisms of conversion to active enzymes are diverse in nature, ranging from enzymatic or nonenzymatic cofactors that trigger activation, to a simple change in pH that results in conversion by an autocatalytic mechanism. Recent X-ray crystallographic studies of zymogens and comparisons with their active counterparts have identified the structural changes that accompany conversion. This review will focus upon the structural basis for inhibition by activation segments, as well as the molecular events that lead to the conversion of zymogens to active enzymes.
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Affiliation(s)
- A R Khan
- Department of Biochemistry, University of Alberta, Edmonton, Canada
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Khan AR, Cherney MM, Tarasova NI, James MN. Structural characterization of activation 'intermediate 2' on the pathway to human gastricsin. NATURE STRUCTURAL BIOLOGY 1997; 4:1010-5. [PMID: 9406551 DOI: 10.1038/nsb1297-1010] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The crystal structure of an activation intermediate of human gastricsin has been determined at 2.4 A resolution. The human digestive enzyme gastricsin (pepsin C) is an aspartic proteinase that is synthesized as the inactive precursor (zymogen) progastricsin (pepsinogen C or hPGC). In the zymogen, a positively-charged N-terminal prosegment of 43 residues (Ala 1p-Leu 43p; the suffix 'p' refers to the prosegment) sterically prevents the approach of a substrate to the active site. Zymogen conversion occurs in an autocatalytic and stepwise fashion at low pH through the formation of intermediates. The structure of the non-covalent complex of a partially-cleaved peptide of the prosegment (Ala 1p-Phe 26p) with mature gastricsin (Ser 1-Ala 329) suggests an activation pathway that may be common to all gastric aspartic proteinases.
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Affiliation(s)
- A R Khan
- Department of Biochemistry, University of Alberta, Edmonton, Canada
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22
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Fast detection of phosphorylation of human pepsinogen A, human pepsinogen C and swine pepsinogen using a combination of reversed-phase high-performance liquid chromatography and capillary zone electrophoresis for peptide mapping. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0378-4347(96)00293-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Balbín M, López-Otín C. Hormonal regulation of the human pepsinogen C gene in breast cancer cells. Identification of a cis-acting element mediating its induction by androgens, glucocorticoids, and progesterone. J Biol Chem 1996; 271:15175-81. [PMID: 8663058 DOI: 10.1074/jbc.271.25.15175] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Pepsinogen C is an aspartic proteinase mainly involved in the digestion of proteins in the stomach, which is also synthesized by certain human breast tumors. To examine the possibility that extragastric production of this proteolytic enzyme could be mediated by hormonal factors, we have analyzed pepsinogen C gene expression in human breast cancer cells subjected to different hormonal treatments. Northern blot analyses revealed the expression of pepsinogen C gene by T-47D breast cancer cells after induction with dihydrotestosterone, dexamethasone, and progesterone but not with estradiol, retinoic acid, or ethanol. Reverse transcription-polymerase chain reaction analysis in a series of breast cancer cell lines confirmed the amplification of pepsinogen C mRNA after induction with dihydrotestosterone, in those cells expressing the androgen receptor mRNA. The promoter region of the pepsinogen C gene was functionally characterized by transient expression of a vector containing the promoter region cloned in front of the chloramphenicol acetyltransferase (CAT) reporter gene. CAT activity in T-47D cells was stimulated in the presence of dihydrotestosterone, dexamethasone, and progesterone but not by estradiol. By further deletion mapping of the pepsinogen C promoter, a minimal region (AGAACTattTGTTCC) was identified as being responsible for glucocorticoid-, androgen-, and progesterone-regulated gene expression.
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Affiliation(s)
- M Balbín
- Departamento de Biología Funcional, Universidad de Oviedo, 33006 Oviedo, Spain
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24
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Roberts NB, Peek K, Keen JN, Taylor WH. Five human gastric aspartic proteinases: N-terminal amino acid sequences and amino acid composition. Int J Biochem Cell Biol 1995; 27:133-7. [PMID: 7767781 DOI: 10.1016/1357-2725(94)00085-p] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Human pepsin A consists of 4 or more isoenzymes (designated 1, 3a, 3b and 3c) one of which, pepsin 1, contains up to 50% carbohydrate moieties. The amino-acid composition and N-terminal sequence of pepsin 1 and the other isoforms have been determined and compared with data obtained for pepsin 3b and gastricsin (pepsin C or pepsin 5). Pepsins were isolated from penta-gastrin stimulated gastric juice using repetitive chromatography on DEAE-cellulose, or high performance ion-exchange chromatography. Sequencing was performed using automated solid-phase Edman degradation with a microsequence facility. The amino-acid compositions were similar for pepsins 1, 3a, b and c and the N-terminal sequences of pepsins 1, 3a and c, reported for the first time, were shown to be identical with that for pepsin 3b (the main component of pepsin A) although residue 28 was unassigned in pepsin 1. Residue 30 in all four isoenzymes is valine and we cannot confirm reports of major pepsins with leucine in this position. For gastricsin the sequence differed from the pepsin isoenzymes and in position 24 we find pro rather than ala as was first described. These observations suggest that pepsin 1 is identical to 3b or a mixture of 3a, 3b and 3c but not gastricsin. This data supports the hypotheses that the four pepsin isoenzymes are products of the same gene(s) but have undergone varying levels of post translational modification.
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Affiliation(s)
- N B Roberts
- Department of Clinical Chemistry, Royal Liverpool University Hospital, U.K
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25
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Affiliation(s)
- P B Szecsi
- Department of Clinical Chemistry, Malmö General Hospital, Lunds University, Sweden
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26
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James M, Moore S, Sielecki A, Chernaia M, Tarasova N. The molecular structure of human progastricsin and its comparison with that of porcine pepsinogen. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1995; 362:11-8. [PMID: 8540308 DOI: 10.1007/978-1-4615-1871-6_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- M James
- Medical Research Council of Canada, Department of Biochemistry, University of Alberta, Edmonton, Canada
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27
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Konishi J, Azuma T, Kohli Y, Fujiki N. Genetic heterogeneity of combined gastric and duodenal ulcers detected by pepsinogen C gene polymorphism. J Gastroenterol Hepatol 1994; 9:334-9. [PMID: 7948814 DOI: 10.1111/j.1440-1746.1994.tb01251.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
It has been reported recently that there was genetic heterogeneity in gastric ulcer disease depending upon the location of the ulcer, and that there was a significant association between the restriction fragment length polymorphism (RFLP) for pepsinogen C (PGC) gene and gastric body ulcer. In the present study, the association of the RFLP for PGC gene with combined gastric and duodenal ulcers was investigated to analyse genetic factors in its aetiology. Eighty unrelated controls and 47 patients with combined gastric and duodenal ulcers were studied. The allele frequencies of the large (3.6 kilobase EcoRI fragment) and the small fragment (3.5 kilobase EcoRI fragment) were, respectively 80.6 and 19.4% in controls, 60.0 and 40.0% in patients with combined gastric body and duodenal ulcers, 69.0 and 31.0% in patients with combined gastric angular and duodenal ulcers, and 81.8 and 18.2% in patients with combined gastric antral and duodenal ulcers. The allele frequency of the small fragment was significantly higher in patients with combined gastric body and duodenal ulcers than in controls. The genotypes that possessed the small fragment were significantly more frequent in patients with combined gastric body and duodenal ulcers (66.7%) than in controls (33.8%) and combined gastric antral and duodenal ulcers (27.3%). These results suggest that there is genetic heterogeneity in combined gastric and duodenal ulcers depending upon the location of gastric ulcer, and that combined gastric body and duodenal ulcers are associated with the small fragment allele of the PGC RFLP in the same way as solitary gastric body ulcers.
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Affiliation(s)
- J Konishi
- Second Department of Internal Medicine, Fukui Medical School, Japan
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28
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29
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Bowcock AM, Azuma T, Barnes RI, Wu SH, Bell GI, Taggart RT. Detection of a polymorphism within the pepsinogen C gene with PCR: construction of a linkage map around PGC from 6p11-6p21.3. Genomics 1992; 14:398-402. [PMID: 1427855 DOI: 10.1016/s0888-7543(05)80232-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An insertion/deletion polymorphism between exons 7 and 8 of the pepsinogen C gene (PGC), previously detectable with Southern analysis, was formatted for detection with PCR. Alleles were rapidly typed by UV irradiation of ethidium bromide-stained agarose gels. Whereas Southern analysis revealed two alleles, the smaller fragments generated with PCR allowed the resolution of three alleles that were previously scored as a single allele and increased the heterozygosity of the system from 0.20 to 0.53. After a set of reference families was genotyped with the PCR-based polymorphism, a linkage map around the PGC gene on chromosome 6 was constructed. This included the HLA cluster and the highly informative D6S223 locus. PGC lies 22 cM proximal to HLA-DPB and between D6S5 and D6S4 at distances of 4.5 and 13.1 cM, respectively.
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Affiliation(s)
- A M Bowcock
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas 75235
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30
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Foltmann B, Drøhse HB, Nielsen PK, James MN. Separation of porcine pepsinogen A and progastricsin. Sequencing of the first 73 amino acid residues in progastricsin. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1121:75-82. [PMID: 1599954 DOI: 10.1016/0167-4838(92)90339-f] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Porcine pepsinogen A (EC 3.4.23.1) and progastricsin (EC 3.4.23.3) have been separated by chromatography on DEAE-cellulose followed by chromatography on DEAE-Sepharose. Agar gel electrophoresis at pH 6.0 showed the presence of three components of pepsinogen A and two of progastricsin. During activation at pH 2 a segment of 43 amino acid residues (the prosegment peptide) is cleaved from the N-terminus of progastricsin. The sequence of this was determined; in addition, the first 30 residues of gastricsin were sequenced. The sequence of the first 73 amino acid residues of progastricsin shows an overall identity with progastricsins from man, monkey and rat of 67%. The overall identity with other zymogens for gastric proteinases is 27%. The highly conserved Lys36p (pig pepsinogen A numbering) is changed to Arg in porcine progastricsin.
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Affiliation(s)
- B Foltmann
- Institute of Biochemical Genetics, University of Copenhagen, Denmark
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31
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Bank RA, Eriksson AW, Pals G. High-performance liquid chromatography: purification and chromatographic behaviour of molecular variants of pepsinogen A from human urine. JOURNAL OF CHROMATOGRAPHY 1991; 571:47-59. [PMID: 1810967 DOI: 10.1016/0378-4347(91)80433-d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
By combining conventional DEAE chromatography with high-performance liquid chromatography on Sephacryl S-200 HR and Mono-Q columns, we have been able to isolate and fractionate human pepsinogen A (PGA) isozymogens from large amounts of urine. This method of fractionation is simple and allows one to obtain pepsinogen in a native non-denatured conformation. The isozymogens are homogeneous by electrophoretic and chromatographic criteria; this was confirmed by N-terminal amino acid sequencing. Purified PGA-3 and PGA-5 can be converted into an additional, more anionic, isoform on incubation at 37 degrees C. This isoform exists not only in vitro but also in vivo. The net negative charge of the PGA isozymogens is in the order PGA-5 less than deamidated PGA-5 less than PGA-3 less than deamidated PGA-3. Surprisingly, the elution order on the Mono-Q column was PGA-5/PGA-3/deamidated PGA-5/deamidated PGA-3. We have performed molecular modelling on PGA to investigate this phenomenon in terms of surface charge (not net charge) of the proteins. The model provides evidence that (1) only a fraction of the protein surface interacts with the support and (2) regions of localized charge at the protein surface may allow portions of the external surface to dominate chromatographic behaviour, resulting in a steering of the proteins with respect to the oppositely charged matrix. Pepsinogens may serve as model proteins for elucidating some of the variables that determine the chromatographic behaviour of proteins on ion-exchange columns.
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Affiliation(s)
- R A Bank
- Institute of Human Genetics, Faculty of Medicine, Vrije Universiteit, Amsterdam, Netherlands
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32
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Kageyama T, Tanabe K, Koiwai O. Development-dependent expression of isozymogens of monkey pepsinogens and structural differences between them. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 202:205-15. [PMID: 1935977 DOI: 10.1111/j.1432-1033.1991.tb16364.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The developmental changes in the expression of monkey pepsinogens and structural differences between the polypeptides were investigated. Monkey pepsinogens included five different components, namely, pepsinogens A-(1-4) and progastricsin. Their respective relative levels and specific activities changed significantly during development. The sequential expression of genes for type-A pepsinogens was particularly noteworthy. Pepsinogen A-3 was the major zymogen at the newborn stage, accounting for nearly half of the total pepsinogens at this stage. Pepsinogen A-2 became predominant at the 4-month stage, and pepsinogen A-1 predominated at the juvenile and adult stages. Enzymatic properties of pepsinogens A-1, A-2 and A-3 were similar but not identical to those of pepsinogen A-4 and progastricsin, in particular with respect to the activation processes. Each pepsin digested various protein substrates but some differences in specificity were evident. cDNA clones for five pepsinogens were isolated, and the nucleotide sequences were determined. Each cDNA contained leader, pro, and pepsin regions that encoded 15, 47, and 326 amino acid residues, respectively, with the exception of the cDNA for progastricsin in which the pro and pepsin regions encoded 43 and 329 amino acid residues, respectively. Type-A pepsinogens exhibited a high degree of similarity, with over 96% of bases in the nucleotide sequences of the protein-coding regions being identical. Northern analysis revealed that the level of expression of genes for type-A pepsinogens and for progastricsin was significant at the fetal stage and increased with development.
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Affiliation(s)
- T Kageyama
- Department of Biochemistry, Primate Research Institute, Kyoto University, Japan
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33
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Birch NP, Loh YP. Homology cloning of aspartic proteases from an endocrine cell line using the polymerase chain reaction. Biochem Biophys Res Commun 1991; 177:920-6. [PMID: 2059219 DOI: 10.1016/0006-291x(91)90626-i] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Oligonucleotides directed towards the active site regions of aspartic proteases were used as primers for the polymerase chain reaction to identify a unique sequence (asppcr1) from the AtT-20 anterior pituitary corticotrope cell line. Asppcr1 showed the greatest similarity (85% identity) to human cathepsin E [(1989) J. Biol. Chem. 264, 16748-16753]. Northern blot analysis of AtT-20 RNA revealed a single 1.9 kB message. Nuclease protection experiments indicated that asppcr1 mRNA was present in pancreas, spleen, testis and liver at low levels and undetectable in heart and brain. This contrasted with the lysosomal aspartic protease, cathepsin D whose mRNA showed a broader tissue distribution. The restricted message distribution of asppcr1 supports a more specific role for this aspartic protease in aspect(s) of cellular physiology.
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Affiliation(s)
- N P Birch
- Section on Cellular Neurobiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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34
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Taggart RT, Azuma T, Wu S, Bell GI, Bowcock AM. A highly informative polymorphism of the pepsinogen C gene detected by polymerase chain reaction. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1991; 306:95-9. [PMID: 1812765 DOI: 10.1007/978-1-4684-6012-4_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- R T Taggart
- Department of Molecular Biology and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201
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35
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Wnuk W, Loizeau E. Separation and characterization of human pepsinogens and pepsins by high-resolution discontinuous electrophoresis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1991; 306:91-4. [PMID: 1812764 DOI: 10.1007/978-1-4684-6012-4_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- W Wnuk
- Division of Gastroenterology, University Hospital of Geneva, Switzerland
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36
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Structure and development of rabbit pepsinogens. Stage-specific zymogens, nucleotide sequences of cDNAs, molecular evolution, and gene expression during development. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)44864-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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37
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