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Opazo JC, Vandewege MW, Hoffmann FG, Zavala K, Meléndez C, Luchsinger C, Cavieres VA, Vargas-Chacoff L, Morera FJ, Burgos PV, Tapia-Rojas C, Mardones GA. How Many Sirtuin Genes Are Out There? Evolution of Sirtuin Genes in Vertebrates With a Description of a New Family Member. Mol Biol Evol 2023; 40:6993039. [PMID: 36656997 PMCID: PMC9897032 DOI: 10.1093/molbev/msad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural studies to allow a deeper and more precise interpretation of their results in an evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our results show a well-resolved phylogeny that represents an improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin gene family member (SIRT3.2) that was apparently lost in the last common ancestor of amniotes but retained in all other groups of jawed vertebrates. According to our experimental analyses, elephant shark SIRT3.2 protein is located in mitochondria, the overexpression of which leads to an increase in cellular levels of ATP. Moreover, in vitro analysis demonstrated that it has deacetylase activity being modulated in a similar way to mammalian SIRT3. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.
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Affiliation(s)
| | - Michael W Vandewege
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Catalina Meléndez
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Charlotte Luchsinger
- Department of Physiology, School of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Viviana A Cavieres
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Luis Vargas-Chacoff
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile,Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, Universidad Austral de Chile, Valdivia, Chile
| | - Francisco J Morera
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Applied Biochemistry Laboratory, Facultad de Ciencias Veterinarias, Instituto de Farmacología y Morfofisiología, Universidad Austral de Chile, Valdivia, Chile
| | - Patricia V Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile
| | - Cheril Tapia-Rojas
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
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2
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The gastric proton pump in gobiid and mudskipper fishes. Evidence of stomach loss? Comp Biochem Physiol A Mol Integr Physiol 2022; 274:111300. [PMID: 36031062 DOI: 10.1016/j.cbpa.2022.111300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/20/2022] [Accepted: 08/21/2022] [Indexed: 01/01/2023]
Abstract
Stomach loss has occurred independently multiple times during gnathostome evolution with notable frequency within the Teleostei. Significantly, this loss of acid-peptic digestion has been found to correlate with the secondary genomic loss of the gastric proton pump subunits (atp4a, atp4b) and pepsinogens/pepsins (pga, pgc). Gastric glands produce gastric juice containing the acid and pepsin and thus their presence is a hallmark feature of a digestive system capable of acid-peptic digestion. However, in gobiid fishes although oesogaster and gastric glands have been identified histologically, their functional significance has been questioned. In the present study we address whether the gastric proton pump is present and expressed in gastric glands of the goby Neogobius species (Gobiidae) and in members of the family Oxudercidae, a group of amphibious gobiid fishes commonly known as mudskippers (genera: Periophthalmus, Boleophthalmus, Periophthalmodon and Scartelaos). We confirmed the presence of gastric glands and have immunohistochemically localized gastric proton pump expression to these glands in Neogobius fluviatilis and Periophthalmus novemradiatus, Periophthalmus barbarus and Boleophthalmus boddarti. Genome analysis in Neogobius melanostomus, Periophthalmus magnuspinnatus, Scartelaos histophorus, Boleophthalmus pectinirostris, and Periophthalmodon schlosseri revealed the presence of both atp4a and atp4b subunit orthologues in all species in a conserved genomic loci organization. Moreover, it was possible to deduce that the complete open reading frame and the key functional amino acid residues are present. The conserved expression of the gastric proton pump provides clear evidence of the potential for gastric acid secretion indicating that acid digestion is retained in these gobiid fishes and not lost.
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3
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Moffatt K, Rossi M, Park E, Svendsen JC, Wilson JM. Inhibition of gastric acid secretion with omeprazole affects fish specific dynamic action and growth rate: Implications for the development of phenotypic stomach loss. Front Physiol 2022; 13:966447. [PMID: 36237533 PMCID: PMC9552000 DOI: 10.3389/fphys.2022.966447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
An acid-secreting stomach provides many selective advantages to fish and other vertebrates; however, phenotypic stomach loss has occurred independently multiple times and is linked to loss of expression of both the gastric proton pump and the protease pepsin. Reasons underpinning stomach loss remain uncertain. Understanding the importance of gastric acid-secretion to the metabolic costs of digestion and growth will provide information about the metabolic expense of acid-production and performance. In this study, omeprazole, a well characterized gastric proton pump inhibitor, was used to simulate the agastric phenotype by significantly inhibiting gastric acidification in Nile tilapia. The effects on post-prandial metabolic rate and growth were assessed using intermittent flow respirometry and growth trials, respectively. Omeprazole reduced the duration (34.4%) and magnitude (34.5%) of the specific dynamic action and specific growth rate (21.3%) suggesting a decrease in digestion and assimilation of the meal. Gastric pH was measured in control and omeprazole treated fish to confirm that gastric acid secretion was inhibited for up to 12 h post-treatment (p < 0.05). Gastric evacuation measurements confirm a more rapid emptying of the stomach in omeprazole treated fish. These findings reinforce the importance of stomach acidification in digestion and growth and present a novel way of determining costs of gastric digestion.
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Affiliation(s)
| | - Mark Rossi
- Wilfrid Laurier University, Waterloo, Canada
| | - Edward Park
- Wilfrid Laurier University, Waterloo, Canada
| | - Jon Christian Svendsen
- Technical University of Denmark, National Institute of Aquatic Resources, Lyngby, Denmark
| | - Jonathan M. Wilson
- Wilfrid Laurier University, Waterloo, Canada
- CIIMAR University of Porto, Matosinhos, Portugal
- *Correspondence: Jonathan M. Wilson,
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4
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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: 12] [Impact Index Per Article: 2.4] [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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5
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Gonçalves O, Freitas R, Ferreira P, Araújo M, Zhang G, Mazan S, Cohn MJ, Castro LFC, Wilson JM. Molecular ontogeny of the stomach in the catshark Scyliorhinus canicula. Sci Rep 2019; 9:586. [PMID: 30679499 PMCID: PMC6346038 DOI: 10.1038/s41598-018-36413-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 11/21/2018] [Indexed: 01/27/2023] Open
Abstract
The origin of extracellular digestion in metazoans was accompanied by structural and physiological alterations of the gut. These adaptations culminated in the differentiation of a novel digestive structure in jawed vertebrates, the stomach. Specific endoderm/mesenchyme signalling is required for stomach differentiation, involving the growth and transcription factors: 1) Shh and Bmp4, required for stomach outgrowth; 2) Barx1, Sfrps and Sox2, required for gastric epithelium development and 3) Cdx1 and Cdx2, involved in intestinal versus gastric identity. Thus, modulation of endoderm/mesenchyme signalling emerges as a plausible mechanism linked to the origin of the stomach. In order to gain insight into the ancient mechanisms capable of generating this structure in jawed vertebrates, we characterised the development of the gut in the catshark Scyliorhinus canicula. As chondrichthyans, these animals retained plesiomorphic features of jawed vertebrates, including a well-differentiated stomach. We identified a clear molecular regionalization of their embryonic gut, characterised by the expression of barx1 and sox2 in the prospective stomach region and expression of cdx1 and cdx2 in the prospective intestine. Furthermore, we show that gastric gland development occurs close to hatching, accompanied by the onset of gastric proton pump activity. Our findings favour a scenario in which the developmental mechanisms involved in the origin of the stomach were present in the common ancestor of chondrichthyans and osteichthyans.
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Affiliation(s)
- Odete Gonçalves
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Univ. Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), Univ. Porto, Porto, Portugal
| | - Renata Freitas
- I3S- Institute for Innovation and Health Research, Univ. Porto, Porto, Portugal. .,IBMC- Institute for Molecular and Cell Biology, Univ. Porto, Porto, Portugal.
| | - Patrícia Ferreira
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Univ. Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), Univ. Porto, Porto, Portugal
| | - Mafalda Araújo
- I3S- Institute for Innovation and Health Research, Univ. Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Univ. Porto, Porto, Portugal
| | - GuangJun Zhang
- Department of Comparative Pathobiology, Purdue Univ., Lafayette, USA.,Purdue Institute for Integrative Neuroscience, Purdue Univ., Lafayette, USA.,Purdue Univ. Center for Cancer, Purdue Univ., Lafayette, USA.,Purdue Institute for Inflammation, Immunology and Infectious Diseases, Purdue Univ., Lafayette, USA
| | - Sylvie Mazan
- CNRS, Sorbonne Universités, UPMC Univ. Paris, Observatoire Océanologique, Banyuls, France
| | - Martin J Cohn
- Howard Hughes Medical Institute, UF Genetics Institute, Univ. Florida, Florida, USA.,Department of Biology, UF Genetics Institute, Univ. Florida, Florida, USA.,Department of Molecular Genetics and Microbiology, UF Genetics Institute, Univ. Florida, Florida, USA
| | - L Filipe C Castro
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Univ. Porto, Porto, Portugal. .,Department of Biology, Faculty of Sciences, Univ. Porto, Porto, Portugal.
| | - Jonathan M Wilson
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Univ. Porto, Porto, Portugal. .,Department of Biology, Wilfrid Laurier Univ., Waterloo, Canada.
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6
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Li X, Zhang C, Gong T, Ni X, Li J, Zhan D, Liu M, Song L, Ding C, Xu J, Zhen B, Wang Y, Qin J. A time-resolved multi-omic atlas of the developing mouse stomach. Nat Commun 2018; 9:4910. [PMID: 30464175 PMCID: PMC6249217 DOI: 10.1038/s41467-018-07463-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023] Open
Abstract
The mammalian stomach is structurally highly diverse and its organ functionality critically depends on a normal embryonic development. Although there have been several studies on the morphological changes during stomach development, a system-wide analysis of the underlying molecular changes is lacking. Here, we present a comprehensive, temporal proteome and transcriptome atlas of the mouse stomach at multiple developmental stages. Quantitative analysis of 12,108 gene products allows identifying three distinct phases based on changes in proteins and RNAs and the gain of stomach functions on a longitudinal time scale. The transcriptome indicates functionally important isoforms relevant to development and identifies several functionally unannotated novel splicing junction transcripts that we validate at the peptide level. Importantly, many proteins differentially expressed in stomach development are also significantly overexpressed in diffuse-type gastric cancer. Overall, our study provides a resource to understand stomach development and its connection to gastric cancer tumorigenesis.
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Affiliation(s)
- Xianju Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Chunchao Zhang
- Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tongqing Gong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Xiaotian Ni
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China.,Department of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jin'e Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Dongdong Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China.,Department of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Jianming Xu
- Department of Gastrointestinal Oncology, Affiliated Hospital Cancer Center, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Bei Zhen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China. .,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China. .,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
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7
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Lopes-Marques M, Ruivo R, Fonseca E, Teixeira A, Castro LFC. Unusual loss of chymosin in mammalian lineages parallels neo-natal immune transfer strategies. Mol Phylogenet Evol 2017; 116:78-86. [DOI: 10.1016/j.ympev.2017.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 08/07/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022]
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8
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Ennulat D, Lynch KM, Kimbrough CL, Mirabile RC, Rehm S. Evaluation of Pepsinogen I as a Biomarker of Drug-induced Gastric Mucosal Injury in Cynomolgus Monkeys. Toxicol Pathol 2016; 45:296-301. [PMID: 28007014 DOI: 10.1177/0192623316678696] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Gastric mucosal injury is frequently observed in nonclinical studies of nonhuman primates. Because microscopic evaluation of stomach is generally a terminal procedure, our objective was to determine whether serum pepsinogen I (PG I) could serve as a noninvasive biomarker for detection of gastric mucosal injury in monkey. Serum PG I was measured using a commercial human immunoassay in cynomolgus monkeys ( n = 166) prior to dosing and/or terminally in 11 studies of up to 1 month duration. Mean ( SD) PG I values (ug/L) for monkeys with ( n = 59) and without ( n = 100) gastric mucosal degeneration were 101 (215) and 28 (12.6), respectively. For monkeys with baseline and terminal PG I data, mean ( SD) fold change (ratio of terminal to baseline PG I) for monkeys with ( n = 57) and without ( n = 76) glandular degeneration were 4.1 (11.3) and 1 (0.28). Receiver operating characteristic area under the curve (AUC) data demonstrated moderate diagnostic accuracy for serum PG I for glandular degeneration, AUC ( SE) 0.789 (0.04), with improved diagnostic accuracy as a fold change of baseline, AUC ( SE) 0.816 (0.04), consistent with the large interindividual but low intraindividual variability of serum PG I values in control monkeys. These data demonstrate that serum PG I is a useful biomarker of drug-induced gastric mucosal injury in the cynomolgus monkey.
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Affiliation(s)
- Daniela Ennulat
- 1 GlaxoSmithKline, Safety Assessment, King of Prussia, Pennsylvania, USA
| | - Karen M Lynch
- 1 GlaxoSmithKline, Safety Assessment, King of Prussia, Pennsylvania, USA
| | - Carie L Kimbrough
- 2 GlaxoSmithKline, Statistical Sciences, Research Triangle Park, North Carolina, USA.,3 PAREXEL International, Durham, North Carolina, USA
| | - Rosanna C Mirabile
- 1 GlaxoSmithKline, Safety Assessment, King of Prussia, Pennsylvania, USA
| | - Sabine Rehm
- 1 GlaxoSmithKline, Safety Assessment, King of Prussia, Pennsylvania, USA
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9
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The Gastric Phenotype in the Cypriniform Loaches: A Case of Reinvention? PLoS One 2016; 11:e0163696. [PMID: 27783698 PMCID: PMC5082673 DOI: 10.1371/journal.pone.0163696] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/13/2016] [Indexed: 12/15/2022] Open
Abstract
The stomach, which is characterized by acid peptic digestion in vertebrates, has been lost secondarily multiple times in the evolution of the teleost fishes. The Cypriniformes are largely seen as an agastric order; however, within the superfamily Cobitoidea, the closely related sister groups Nemacheilidae and Balitoridae have been identified as gastric families. The presence of these most recently diverged gastric families in an otherwise agastric clade indicates that either multiple (>2–3) loss events occurred with the Cyprinidae, Catostomidae and Cobitidae, or that gastric reinvention arose in a recent ancestor of the Nemacheilidae/Balitoridae sister clade. In the present study, the foregut regions of Cobitidae, Nemacheilidae/Balitoridae and the ancestral Botiidae family members were examined for the presence of gastric glands and gastric proton pump (Atp4a) α subunit expression by histology and immunohistochemistry respectively. Atp4a gene expression was assessed by reverse transcriptase-polymerase chain reaction (RT-PCR). Gastric glands expressing apical H+/K+-ATPase α subunit and isolated partial sequences of atp4a, identified using degenerate primers showing clear orthology to other vertebrate atp4a sequences, were detected in representative species from Nemacheilidae/ Balitoridae and Botiidae, but not Cobitidae (Misgurnus anguillicaudatus). In summary, we provide evidence for an uninterrupted gastric evolutionary lineage in the Cobitoidea, making it highly improbable that the stomach was reinvented in the Nemacheilidae/Balitoridae clade consistent with Dollo’s principle. These results also indicate that the gastric trait may be present elsewhere in the Cobitoidea.
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10
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German DP, Foti DM, Heras J, Amerkhanian H, Lockwood BL. Elevated Gene Copy Number Does Not Always Explain Elevated Amylase Activities in Fishes. Physiol Biochem Zool 2016; 89:277-93. [PMID: 27327179 DOI: 10.1086/687288] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Amylase activity variation in the guts of several model organisms appears to be explained by amylase gene copy number variation. We tested the hypothesis that amylase gene copy number is always elevated in animals with high amylolytic activity. We therefore sequenced the amylase genes and examined amylase gene copy number in prickleback fishes (family Stichaeidae) with different diets including two species of convergently evolved herbivores with the elevated amylase activity phenotype. We found elevated amylase gene copy number (six haploid copies) with sequence variation among copies in one herbivore (Cebidichthys violaceus) and modest gene copy number (two to three haploid copies) with little sequence variation in the remaining taxa, which included herbivores, omnivores, and a carnivore. Few functional differences in amylase biochemistry were observed, and previous investigations showed similar digestibility among the convergently evolved herbivores with differing amylase genetics. Hence, the phenotype of elevated amylase activity can be achieved by different mechanisms (i.e., elevated expression of fewer genes, increased gene copy number, or expression of more efficient amylase proteins) with similar results. Phylogenetic and comparative genomic analyses of available fish amylase genes show mostly lineage-specific duplication events leading to gene copy number variation, although a whole-genome duplication event or chromosomal translocation may have produced multiple amylase copies in the Ostariophysi, again showing multiple routes to the same result.
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11
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Nagasawa T, Sano K, Kawaguchi M, Kobayashi KI, Yasumasu S, Inokuchi T. Purification and molecular cloning of aspartic proteinases from the stomach of adult Japanese fire belly newts, Cynops pyrrhogaster. J Biochem 2016; 159:449-60. [PMID: 26711235 PMCID: PMC4885938 DOI: 10.1093/jb/mvv128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/06/2015] [Indexed: 11/12/2022] Open
Abstract
Six aspartic proteinase precursors, a pro-cathepsin E (ProCatE) and five pepsinogens (Pgs), were purified from the stomach of adult newts (Cynops pyrrhogaster). On sodium dodecylsulfate-polyacrylamide gel electrophoresis, the molecular weights of the Pgs and active enzymes were 37-38 kDa and 31-34 kDa, respectively. The purified ProCatE was a dimer whose subunits were connected by a disulphide bond. cDNA cloning by polymerase chain reaction and subsequent phylogenetic analysis revealed that three of the purified Pgs were classified as PgA and the remaining two were classified as PgBC belonging to C-type Pg. Our results suggest that PgBC is one of the major constituents of acid protease in the urodele stomach. We hypothesize that PgBC is an amphibian-specific Pg that diverged during its evolutional lineage. PgBC was purified and characterized for the first time. The purified urodele pepsin A was completely inhibited by equal molar units of pepstatin A. Conversely, the urodele pepsin BC had low sensitivity to pepstatin A. In acidic condition, the activation rates of newt pepsin A and BC were similar to those of mammalian pepsin A and C1, respectively. Our results suggest that the enzymological characters that distinguish A- and C-type pepsins appear to be conserved in mammals and amphibians.
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Affiliation(s)
- Tatsuki Nagasawa
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554
| | - Kaori Sano
- Department of Chemistry, Faculty of Science, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295; and
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554
| | - Ken-Ichiro Kobayashi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554
| | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554
| | - Tomofumi Inokuchi
- Department of Biology, Faculty of Education, Utsunomiya University, 350 Mine, Utsunomiya, Tochigi 321-8505, Japan
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Marques CL, Fernández I, Viegas MN, Cox CJ, Martel P, Rosa J, Cancela ML, Laizé V. Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives. Cell Mol Life Sci 2016; 73:841-57. [PMID: 26341094 PMCID: PMC11108344 DOI: 10.1007/s00018-015-2024-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 07/27/2015] [Accepted: 08/14/2015] [Indexed: 11/24/2022]
Abstract
BMP2, BMP4 and BMP16 form a subfamily of bone morphogenetic proteins acting as pleiotropic growth factors during development and as bone inducers during osteogenesis. BMP16 is the most recent member of this subfamily and basic data regarding protein structure and function, and spatio-temporal gene expression is still scarce. In this work, insights on BMP16 were provided through the comparative analysis of structural and functional data for zebrafish BMP2a, BMP2b, BMP4 and BMP16 genes and proteins, determined from three-dimensional models, patterns of gene expression during development and in adult tissues, regulation by retinoic acid and capacity to activate BMP-signaling pathway. Structures of Bmp2a, Bmp2b, Bmp4 and Bmp16 were found to be remarkably similar; with residues involved in receptor binding being highly conserved. All proteins could activate the BMP-signaling pathway, suggesting that they share a common function. On the contrary, stage- and tissue-specific expression of bmp2, bmp4 and bmp16 suggested the genes might be differentially regulated (e.g. different transcription factors, enhancers and/or regulatory modules) but also that they are involved in distinct physiological processes, although with the same function. Retinoic acid, a morphogen known to interact with BMP-signaling during bone formation, was shown to down-regulate the expression of bmp2, bmp4 and bmp16, although to different extents. Taxonomic and phylogenetic analyses indicated that bmp16 diverged before bmp2 and bmp4, is not restricted to teleost fish lineage as previously reported, and that it probably arose from a whole genomic duplication event that occurred early in vertebrate evolution and disappeared in various tetrapod lineages through independent events.
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Affiliation(s)
- Cátia L Marques
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- PhD Program in Biomedical Sciences, University of Algarve, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal
| | - Ignacio Fernández
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Michael N Viegas
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Cymon J Cox
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Paulo Martel
- Centre for Molecular and Structural Biomedicine (CBME/IBB-LA), University of Algarve, Faro, Portugal
| | - Joana Rosa
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- PhD Program in Biomedical Sciences, University of Algarve, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal
| | - M Leonor Cancela
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal
| | - Vincent Laizé
- Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal.
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Structure, molecular evolution, and hydrolytic specificities of largemouth bass pepsins. Comp Biochem Physiol B Biochem Mol Biol 2016; 192:49-59. [DOI: 10.1016/j.cbpb.2015.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 11/16/2015] [Accepted: 11/20/2015] [Indexed: 01/27/2023]
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Revuelta MV, van Kan JAL, Kay J, Ten Have A. Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes. Genome Biol Evol 2015; 6:1480-94. [PMID: 24869856 PMCID: PMC4079213 DOI: 10.1093/gbe/evu110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The A1 family of eukaryotic aspartic proteinases (APs) forms one of the 16 AP families. Although one of the best characterized families, the recent increase in genome sequence data has revealed many fungal AP homologs with novel sequence characteristics. This study was performed to explore the fungal AP sequence space and to obtain an in-depth understanding of fungal AP evolution. Using a comprehensive phylogeny of approximately 700 AP sequences from the complete proteomes of 87 fungi and 20 nonfungal eukaryotes, 11 major clades of APs were defined of which clade I largely corresponds to the A1A subfamily of pepsin-archetype APs. Clade II largely corresponds to the A1B subfamily of nepenthesin-archetype APs. Remarkably, the nine other clades contain only fungal APs, thus indicating that fungal APs have undergone a large sequence diversification. The topology of the tree indicates that fungal APs have been subject to both “birth and death” evolution and “functional redundancy and diversification.” This is substantiated by coclustering of certain functional sequence characteristics. A meta-analysis toward the identification of Cluster Determining Positions (CDPs) was performed in order to investigate the structural and biochemical basis for diversification. Seven CDPs contribute to the secondary structure of the enzyme. Three other CDPs are found in the vicinity of the substrate binding cleft. Tree topology, the large sequence variation among fungal APs, and the apparent functional diversification suggest that an amendment to update the current A1 AP classification based on a comprehensive phylogenetic clustering might contribute to refinement of the classification in the MEROPS peptidase database.
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Affiliation(s)
- María V Revuelta
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - John Kay
- School of Biosciences, Cardiff University, United Kingdom
| | - Arjen Ten Have
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
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Castro LFC, Gonçalves O, Mazan S, Tay BH, Venkatesh B, Wilson JM. Recurrent gene loss correlates with the evolution of stomach phenotypes in gnathostome history. Proc Biol Sci 2013; 281:20132669. [PMID: 24307675 DOI: 10.1098/rspb.2013.2669] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The stomach, a hallmark of gnathostome evolution, represents a unique anatomical innovation characterized by the presence of acid- and pepsin-secreting glands. However, the occurrence of these glands in gnathostome species is not universal; in the nineteenth century the French zoologist Cuvier first noted that some teleosts lacked a stomach. Strikingly, Holocephali (chimaeras), dipnoids (lungfish) and monotremes (egg-laying mammals) also lack acid secretion and a gastric cellular phenotype. Here, we test the hypothesis that loss of the gastric phenotype is correlated with the loss of key gastric genes. We investigated species from all the main gnathostome lineages and show the specific contribution of gene loss to the widespread distribution of the agastric condition. We establish that the stomach loss correlates with the persistent and complete absence of the gastric function gene kit--H(+)/K(+)-ATPase (Atp4A and Atp4B) and pepsinogens (Pga, Pgc, Cym)--in the analysed species. We also find that in gastric species the pepsinogen gene complement varies significantly (e.g. two to four in teleosts and tens in some mammals) with multiple events of pseudogenization identified in various lineages. We propose that relaxation of purifying selection in pepsinogen genes and possibly proton pump genes in response to dietary changes led to the numerous independent events of stomach loss in gnathostome history. Significantly, the absence of the gastric genes predicts that reinvention of the stomach in agastric lineages would be highly improbable, in line with Dollo's principle.
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Affiliation(s)
- L Filipe C Castro
- CIMAR Associate Laboratory, Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, , Porto, Portugal, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, , Porto, Portugal, Development and Evolution of Vertebrates, CNRS-UPMC-UMR 7150, , Station Biologique, Roscoff, France, Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, , A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
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Geahlen JH, Lapid C, Thorell K, Nikolskiy I, Huh WJ, Oates EL, Lennerz JKM, Tian X, Weis VG, Khurana SS, Lundin SB, Templeton AR, Mills JC. Evolution of the human gastrokine locus and confounding factors regarding the pseudogenicity of GKN3. Physiol Genomics 2013; 45:667-83. [PMID: 23715263 DOI: 10.1152/physiolgenomics.00169.2012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In a screen for genes expressed specifically in gastric mucous neck cells, we identified GKN3, the recently discovered third member of the gastrokine family. We present confirmatory mouse data and novel porcine data showing that mouse GKN3 expression is confined to mucous cells of the corpus neck and antrum base and is prominently expressed in metaplastic lesions. GKN3 was proposed originally to be expressed in some human populations and a pseudogene in others. To investigate that hypothesis, we studied human GKN3 evolution in the context of its paralogous genomic neighbors, GKN1 and GKN2. Haplotype analysis revealed that GKN3 mimics GKN2 in patterns of exonic SNP allocation, whereas GKN1 appeared to be more stringently selected. GKN3 showed signatures of both directional selection and population based selective sweeps in humans. One such selective sweep includes SNP rs10187256, originally identified as an ancestral tryptophan to premature STOP codon mutation. The derived (nonancestral) allele went to fixation in Asia. We show that another SNP, rs75578132, identified 5 bp downstream of rs10187256, exhibits a second selective sweep in almost all Europeans, some Latinos, and some Africans, possibly resulting from a reintroduction of European genes during African colonization. Finally, we identify a mutation that would destroy the splice donor site in the putative exon3-intron3 boundary, which occurs in all human genomes examined to date. Our results highlight a stomach-specific human genetic locus, which has undergone various selective sweeps across European, Asian, and African populations and thus reflects geographic and ethnic patterns in genome evolution.
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Affiliation(s)
- Jessica H Geahlen
- Division of Gastroenterology, Department of Medicine, School of Medicine, Washington University, St. Louis, Missouri 63110, USA
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Inokuchi T, Ikuzawa M, Yamazaki S, Watanabe Y, Shiota K, Katoh T, Kobayashi KI. Molecular cloning of pepsinogens A and C from adult newt (Cynops pyrrhogaster) stomach. Comp Biochem Physiol B Biochem Mol Biol 2013; 165:226-35. [PMID: 23701991 DOI: 10.1016/j.cbpb.2013.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 04/30/2013] [Accepted: 05/13/2013] [Indexed: 11/24/2022]
Abstract
The full-length cDNAs of three pepsinogens (Pgs) were cloned from the stomach of newt, Cynops pyrrhogaster, and nucleotide sequences of the full-length cDNAs were determined. Molecular phylogenetic analysis showed that two Pgs, named PgC1 and PgC2, belong to the pepsinogen C group, and one Pg, named PgA, belongs to the pepsinogen A group. The sequences contain an open reading frame (ORF) encoding 385 amino acid residues for PgC1, 383 amino acid residues for PgC2 and 377 amino acid residues for PgA. In addition, all of the three amino acid sequences conserve some unique characteristics such as six cysteine residues and putative active site two aspartic acid residues. All of the pepsinogen mRNAs were detected in the stomach by RT-PCR but not in other organs. Although a slight difference at the time of the start of expression was seen among the three pepsinogen genes, all of them were expressed in the larval stage after hatching. This is the first report on cloning of pepsinogens from urodele stomach.
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Affiliation(s)
- Tomofumi Inokuchi
- Department of Biology, Faculty of Education, Utsunomiya University, 350 Mine, Utsunomiya, Tochigi, 321-8505, Japan.
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Chi L, Xu S, Xiao Z, Lin F, Ma D, Zhao C, Xiao Y, Liu Q, Li J. Pepsinogen A and C genes in turbot (Scophthalmus maximus): Characterization and expression in early development. Comp Biochem Physiol B Biochem Mol Biol 2013; 165:58-65. [DOI: 10.1016/j.cbpb.2013.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 02/26/2013] [Accepted: 03/05/2013] [Indexed: 02/02/2023]
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