Miiuy croaker hepcidin gene and comparative analyses reveal evidence for positive selection
Hepcidin antimicrobial peptide (HAMP) is a small cysteine-rich peptide and a key molecule of the innate immune system against bacterial infections. Molecular cloning and genomic characterization of HAMP gene in the miiuy croaker (Miichthys miiuy) were reported in this study. The miiuy croaker HAMP w...
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| description | Hepcidin antimicrobial peptide (HAMP) is a small cysteine-rich peptide and a key molecule of the innate immune system against bacterial infections. Molecular cloning and genomic characterization of HAMP gene in the miiuy croaker (Miichthys miiuy) were reported in this study. The miiuy croaker HAMP was predicted to encode a prepropeptide of 99 amino acids, a tentative RX(K/R)R cleavage motif and eight characteristic cysteine residues were also identified. The gene organization is also similar to corresponding genes in mammals and fish consisting of three exons and two introns. Sequence polymorphism analysis showed that only two different sequences were identified and encoded two proteins in six individuals. As reported for most other species, the expression level was highest in liver and an up-regulation of transcription was seen in spleen, intestine and kidney examined at 24 h after injection of pathogenic bacteria, Vibrio anguillarum, the expression pattern implied that miiuy croaker HAMP is an important component of the first line defense against invading pathogens. In addition, we report on the underlying mechanism that maintains sequences diversity among fish and mammalian species, respectively. A series of site-model tests implemented in the CODEML program revealed that moderate positive Darwinian selection is likely to cause the molecular evolution in the fish HAMP2 genes and it also showed that the fish HAMP1 genes and HAMP2 genes under different selection pressures. |
| doi_str_mv | 10.1371/journal.pone.0035449 |
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King</contributor><creatorcontrib>Xu, Tianjun ; Sun, Yuena ; Shi, Ge ; Wang, Rixin ; Jordan, I. King</creatorcontrib><description>Hepcidin antimicrobial peptide (HAMP) is a small cysteine-rich peptide and a key molecule of the innate immune system against bacterial infections. Molecular cloning and genomic characterization of HAMP gene in the miiuy croaker (Miichthys miiuy) were reported in this study. The miiuy croaker HAMP was predicted to encode a prepropeptide of 99 amino acids, a tentative RX(K/R)R cleavage motif and eight characteristic cysteine residues were also identified. The gene organization is also similar to corresponding genes in mammals and fish consisting of three exons and two introns. Sequence polymorphism analysis showed that only two different sequences were identified and encoded two proteins in six individuals. As reported for most other species, the expression level was highest in liver and an up-regulation of transcription was seen in spleen, intestine and kidney examined at 24 h after injection of pathogenic bacteria, Vibrio anguillarum, the expression pattern implied that miiuy croaker HAMP is an important component of the first line defense against invading pathogens. In addition, we report on the underlying mechanism that maintains sequences diversity among fish and mammalian species, respectively. A series of site-model tests implemented in the CODEML program revealed that moderate positive Darwinian selection is likely to cause the molecular evolution in the fish HAMP2 genes and it also showed that the fish HAMP1 genes and HAMP2 genes under different selection pressures.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0035449</identifier><identifier>PMID: 22511989</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amino Acid Sequence ; Amino acids ; Analysis ; Animals ; Antimicrobial agents ; Antimicrobial Cationic Peptides - genetics ; Antimicrobial Cationic Peptides - metabolism ; Antimicrobial Cationic Peptides - physiology ; Bacteria ; Bacterial infections ; Base Sequence ; Biodiversity ; Biological evolution ; Biology ; Cloning ; Cloning, Molecular ; Cysteine ; Cystine ; Engineering ; Evolution ; Evolution, Molecular ; Evolutionary genetics ; Exons ; Fish ; Fish Proteins - genetics ; Fish Proteins - metabolism ; Fish Proteins - physiology ; Gene expression ; Gene regulation ; Genes ; Genetic aspects ; Genetic polymorphisms ; Health aspects ; Hepcidin ; Hepcidins ; Immune system ; Infection ; Innate immunity ; Intestine ; Introns ; Laboratories ; Liver ; Mammals ; Miichthys miiuy ; Model testing ; Molecular biology ; Molecular evolution ; Natural selection ; Paralichthys olivaceus ; Peptides ; Perciformes - genetics ; Phylogenetics ; Phylogeny ; Polymorphism ; Polymorphism, Genetic ; Positive selection ; Proteins ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, Protein ; Sequences ; Shellfish ; Species diversity ; Spleen ; Transcription ; Vibrio anguillarum ; Water-borne diseases ; Waterborne diseases</subject><ispartof>PloS one, 2012-04, Vol.7 (4), p.e35449-e35449</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Xu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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King</contributor><creatorcontrib>Xu, Tianjun</creatorcontrib><creatorcontrib>Sun, Yuena</creatorcontrib><creatorcontrib>Shi, Ge</creatorcontrib><creatorcontrib>Wang, Rixin</creatorcontrib><title>Miiuy croaker hepcidin gene and comparative analyses reveal evidence for positive selection</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Hepcidin antimicrobial peptide (HAMP) is a small cysteine-rich peptide and a key molecule of the innate immune system against bacterial infections. Molecular cloning and genomic characterization of HAMP gene in the miiuy croaker (Miichthys miiuy) were reported in this study. The miiuy croaker HAMP was predicted to encode a prepropeptide of 99 amino acids, a tentative RX(K/R)R cleavage motif and eight characteristic cysteine residues were also identified. The gene organization is also similar to corresponding genes in mammals and fish consisting of three exons and two introns. Sequence polymorphism analysis showed that only two different sequences were identified and encoded two proteins in six individuals. As reported for most other species, the expression level was highest in liver and an up-regulation of transcription was seen in spleen, intestine and kidney examined at 24 h after injection of pathogenic bacteria, Vibrio anguillarum, the expression pattern implied that miiuy croaker HAMP is an important component of the first line defense against invading pathogens. In addition, we report on the underlying mechanism that maintains sequences diversity among fish and mammalian species, respectively. A series of site-model tests implemented in the CODEML program revealed that moderate positive Darwinian selection is likely to cause the molecular evolution in the fish HAMP2 genes and it also showed that the fish HAMP1 genes and HAMP2 genes under different selection pressures.</description><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Animals</subject><subject>Antimicrobial agents</subject><subject>Antimicrobial Cationic Peptides - genetics</subject><subject>Antimicrobial Cationic Peptides - metabolism</subject><subject>Antimicrobial Cationic Peptides - physiology</subject><subject>Bacteria</subject><subject>Bacterial infections</subject><subject>Base Sequence</subject><subject>Biodiversity</subject><subject>Biological evolution</subject><subject>Biology</subject><subject>Cloning</subject><subject>Cloning, Molecular</subject><subject>Cysteine</subject><subject>Cystine</subject><subject>Engineering</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Evolutionary genetics</subject><subject>Exons</subject><subject>Fish</subject><subject>Fish Proteins - genetics</subject><subject>Fish Proteins - metabolism</subject><subject>Fish Proteins - physiology</subject><subject>Gene expression</subject><subject>Gene regulation</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic polymorphisms</subject><subject>Health aspects</subject><subject>Hepcidin</subject><subject>Hepcidins</subject><subject>Immune system</subject><subject>Infection</subject><subject>Innate immunity</subject><subject>Intestine</subject><subject>Introns</subject><subject>Laboratories</subject><subject>Liver</subject><subject>Mammals</subject><subject>Miichthys miiuy</subject><subject>Model testing</subject><subject>Molecular biology</subject><subject>Molecular evolution</subject><subject>Natural selection</subject><subject>Paralichthys olivaceus</subject><subject>Peptides</subject><subject>Perciformes - genetics</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Polymorphism</subject><subject>Polymorphism, Genetic</subject><subject>Positive selection</subject><subject>Proteins</subject><subject>Selection, Genetic</subject><subject>Sequence Alignment</subject><subject>Sequence Analysis, Protein</subject><subject>Sequences</subject><subject>Shellfish</subject><subject>Species diversity</subject><subject>Spleen</subject><subject>Transcription</subject><subject>Vibrio anguillarum</subject><subject>Water-borne diseases</subject><subject>Waterborne 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croaker hepcidin gene and comparative analyses reveal evidence for positive selection</title><author>Xu, Tianjun ; Sun, Yuena ; Shi, Ge ; Wang, Rixin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-316321132bd6826ca8f9b8c488afe1e0cbad1a2fecc040a46536dd861cf79dcc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Amino Acid Sequence</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Animals</topic><topic>Antimicrobial agents</topic><topic>Antimicrobial Cationic Peptides - genetics</topic><topic>Antimicrobial Cationic Peptides - metabolism</topic><topic>Antimicrobial Cationic Peptides - physiology</topic><topic>Bacteria</topic><topic>Bacterial infections</topic><topic>Base Sequence</topic><topic>Biodiversity</topic><topic>Biological evolution</topic><topic>Biology</topic><topic>Cloning</topic><topic>Cloning, Molecular</topic><topic>Cysteine</topic><topic>Cystine</topic><topic>Engineering</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Evolutionary genetics</topic><topic>Exons</topic><topic>Fish</topic><topic>Fish Proteins - genetics</topic><topic>Fish Proteins - metabolism</topic><topic>Fish Proteins - physiology</topic><topic>Gene expression</topic><topic>Gene regulation</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic polymorphisms</topic><topic>Health aspects</topic><topic>Hepcidin</topic><topic>Hepcidins</topic><topic>Immune system</topic><topic>Infection</topic><topic>Innate immunity</topic><topic>Intestine</topic><topic>Introns</topic><topic>Laboratories</topic><topic>Liver</topic><topic>Mammals</topic><topic>Miichthys miiuy</topic><topic>Model testing</topic><topic>Molecular biology</topic><topic>Molecular evolution</topic><topic>Natural selection</topic><topic>Paralichthys olivaceus</topic><topic>Peptides</topic><topic>Perciformes - 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King</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Miiuy croaker hepcidin gene and comparative analyses reveal evidence for positive selection</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2012-04-12</date><risdate>2012</risdate><volume>7</volume><issue>4</issue><spage>e35449</spage><epage>e35449</epage><pages>e35449-e35449</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Hepcidin antimicrobial peptide (HAMP) is a small cysteine-rich peptide and a key molecule of the innate immune system against bacterial infections. Molecular cloning and genomic characterization of HAMP gene in the miiuy croaker (Miichthys miiuy) were reported in this study. The miiuy croaker HAMP was predicted to encode a prepropeptide of 99 amino acids, a tentative RX(K/R)R cleavage motif and eight characteristic cysteine residues were also identified. The gene organization is also similar to corresponding genes in mammals and fish consisting of three exons and two introns. Sequence polymorphism analysis showed that only two different sequences were identified and encoded two proteins in six individuals. As reported for most other species, the expression level was highest in liver and an up-regulation of transcription was seen in spleen, intestine and kidney examined at 24 h after injection of pathogenic bacteria, Vibrio anguillarum, the expression pattern implied that miiuy croaker HAMP is an important component of the first line defense against invading pathogens. In addition, we report on the underlying mechanism that maintains sequences diversity among fish and mammalian species, respectively. A series of site-model tests implemented in the CODEML program revealed that moderate positive Darwinian selection is likely to cause the molecular evolution in the fish HAMP2 genes and it also showed that the fish HAMP1 genes and HAMP2 genes under different selection pressures.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22511989</pmid><doi>10.1371/journal.pone.0035449</doi><tpages>e35449</tpages><oa>free_for_read</oa></addata></record> |
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| issn | 1932-6203 1932-6203 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Amino Acid Sequence Amino acids Analysis Animals Antimicrobial agents Antimicrobial Cationic Peptides - genetics Antimicrobial Cationic Peptides - metabolism Antimicrobial Cationic Peptides - physiology Bacteria Bacterial infections Base Sequence Biodiversity Biological evolution Biology Cloning Cloning, Molecular Cysteine Cystine Engineering Evolution Evolution, Molecular Evolutionary genetics Exons Fish Fish Proteins - genetics Fish Proteins - metabolism Fish Proteins - physiology Gene expression Gene regulation Genes Genetic aspects Genetic polymorphisms Health aspects Hepcidin Hepcidins Immune system Infection Innate immunity Intestine Introns Laboratories Liver Mammals Miichthys miiuy Model testing Molecular biology Molecular evolution Natural selection Paralichthys olivaceus Peptides Perciformes - genetics Phylogenetics Phylogeny Polymorphism Polymorphism, Genetic Positive selection Proteins Selection, Genetic Sequence Alignment Sequence Analysis, Protein Sequences Shellfish Species diversity Spleen Transcription Vibrio anguillarum Water-borne diseases Waterborne diseases |
| title | Miiuy croaker hepcidin gene and comparative analyses reveal evidence for positive selection |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-20T04%3A43%3A42IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Miiuy%20croaker%20hepcidin%20gene%20and%20comparative%20analyses%20reveal%20evidence%20for%20positive%20selection&rft.jtitle=PloS%20one&rft.au=Xu,%20Tianjun&rft.date=2012-04-12&rft.volume=7&rft.issue=4&rft.spage=e35449&rft.epage=e35449&rft.pages=e35449-e35449&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0035449&rft_dat=%3Cgale_plos_%3EA477130678%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1324447696&rft_id=info:pmid/22511989&rft_galeid=A477130678&rft_doaj_id=oai_doaj_org_article_f9afc3788f734dedb06f1a77076f1c28&rfr_iscdi=true |