{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T07:52:09Z","timestamp":1777535529763,"version":"3.51.4"},"reference-count":91,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2016,1,29]],"date-time":"2016-01-29T00:00:00Z","timestamp":1454025600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0147977","type":"journal-article","created":{"date-parts":[[2016,1,29]],"date-time":"2016-01-29T13:49:02Z","timestamp":1454075342000},"page":"e0147977","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Characterization and Expression of the Lucina pectinata Oxygen and Sulfide Binding Hemoglobin Genes"],"prefix":"10.1371","volume":"11","author":[{"given":"Ingrid M.","family":"Montes-Rodr\u00edguez","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linda E.","family":"Rivera","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan","family":"L\u00f3pez-Garriga","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carmen L.","family":"Cadilla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2016,1,29]]},"reference":[{"key":"ref1","first-page":"16043","article-title":"Hemoglobins of the <italic>Lucina pectinata<\/italic>\/Bacteria Symbiosis. I. Molecular properties, kinetics and equilibria of reactions with ligands","volume":"265","author":"DW Kraus","year":"1990"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1144\/GSL.SP.2000.177.01.12","article-title":"Functional anatomy, chemosymbiosis and evolution of the Lucinidae","volume":"177","author":"JD Taylor","year":"2000","journal-title":"Geol Soc London, Spec Publ"},{"issue":"Pt 2","key":"ref3","first-page":"312","article-title":"The metabolic demands of endosymbiotic chemoautotrophic metabolism on host physiological capacities","volume":"214","author":"JJ Childress","year":"2010"},{"key":"ref4","first-page":"86","article-title":"Structure of the sulfide-reactive Hemoglobin from the clam <italic>Lucina pectinata<\/italic>","volume":"244","author":"M Rizzi","year":"1994"},{"key":"ref5","first-page":"100","article-title":"The kinetics of ligand binding to plant hemoglobins. Structural implications","volume":"264","author":"QH Gibson","year":"1989"},{"key":"ref6","first-page":"1","article-title":"Structural bases for sulfide recognition in <italic>Lucina pectinata<\/italic> hemoglobin I","volume":"258","author":"M Rizzi","year":"1996"},{"key":"ref7","first-page":"142","article-title":"The sulfide binding function of annelid hemoglobins: relic of an old biosystem?","volume":"99","author":"X Bailly","year":"2005"},{"key":"ref8","first-page":"311","article-title":"Orientation of the heme vinyl groups in the hydrogen sulfide-binding hemoglobin I from <italic>Lucina pectinata<\/italic>","volume":"4","author":"E Silfa","year":"1998"},{"key":"ref9","first-page":"569","article-title":"Nonvertebrate Hemoglobins: Functions and Molecular Adaptations","volume":"81","author":"RE Weber","year":"2001"},{"key":"ref10","first-page":"9414","article-title":"Structure and Ligand Selection of Hemoglobin II from <italic>Lucina pectinata<\/italic>","volume":"283","author":"JA Gavira","year":"2008"},{"key":"ref11","first-page":"16054","article-title":"Hemoglobins of the <italic>Lucina pectinata<\/italic>\/ Bacteria Symbiosis. II. An electron paramagnetic resonance and optical spectral study of the ferric proteins","volume":"265","author":"DW Kraus","year":"1990"},{"issue":"Pt 1","key":"ref12","first-page":"25","article-title":"Crystallization and diffraction patterns of the oxy and cyano forms of the <italic>Lucina pectinata<\/italic> haemoglobins complex","volume":"65","author":"CR Ruiz-Mart\u00ednez","year":"2009"},{"issue":"pt 3","key":"ref13","first-page":"196","article-title":"Capillary crystallization and molecular-replacement solution of haemoglobin II from the clam <italic>Lucina pectinata<\/italic>","volume":"62","author":"JA Gavira","year":"2006"},{"key":"ref14","first-page":"831","article-title":"The cDNA-derived amino acid sequence of hemoglobin I from <italic>Lucina pectinata<\/italic>","volume":"18","author":"FM Antommattei-P\u00e9rez","year":"1999"},{"key":"ref15","first-page":"683","article-title":"The cDNA-derived amino acid sequence of hemoglobin II from <italic>Lucina pectinata<\/italic>","volume":"22","author":"E Torres-Mercado","year":"2003"},{"key":"ref16","first-page":"122","article-title":"Characterization of the full length mRNA coding for <italic>Lucina pectinata<\/italic> HbIII revealed an alternative polyadenylation site","volume":"410","author":"L Rivera","year":"2008"},{"key":"ref17","first-page":"195","article-title":"Tyrosine B10 and heme-ligand interactions of <italic>Lucina pectinata<\/italic> hemoglobin II: control of heme reactivity","volume":"1747","author":"R Pietri","year":"2005"},{"key":"ref18","first-page":"334","article-title":"Hydrogen-bonding conformations of tyrosine B10 tailor the hemeprotein reactivity of ferryl species","volume":"11","author":"W De Jes\u00fas-Bonilla","year":"2006"},{"key":"ref19","first-page":"758","article-title":"Hemoglobin I from <italic>Lucina pectinata<\/italic>: a model for distal heme-ligand control","volume":"1764","author":"R Pietri","year":"2006"},{"key":"ref20","first-page":"156","article-title":"Single-Step Method of RNA Isolation by Acid Guanidinium Extraction","volume":"162","author":"P Chomczynski","year":"1987"},{"key":"ref21","first-page":"136","article-title":"A simple and loss-free method to remove TRIzol contaminations from minute RNA samples","volume":"387","author":"S Krebs","year":"2009"},{"key":"ref22"},{"key":"ref23","first-page":"4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"JD Thompson","year":"1994"},{"key":"ref24","first-page":"572","article-title":"Strategies for Multiple Sequence Alignment","volume":"32","author":"HB Nicholas","year":"2002"},{"key":"ref25","first-page":"1102","article-title":"The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences","volume":"28","author":"P Stothard","year":"2000"},{"key":"ref26","first-page":"437","article-title":"Exploring conservation of transcription factor binding sites with CONREAL","volume":"395","author":"E Berezikov","year":"2007"},{"key":"ref27","first-page":"28","article-title":"In Conference on Intelligent systems for Molecular Biology","author":"TL Bailey","year":"1994"},{"key":"ref28","first-page":"1","article-title":"JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles","volume":"42","author":"A Mathelier","year":"2014"},{"key":"ref29","first-page":"R24","article-title":"Quantifying similarity between motifs","volume":"8","author":"S Gupta","year":"2007"},{"key":"ref30","first-page":"622","article-title":"Estimating transcription factor bindability on DNA","volume":"15","author":"T Tsunoda","year":"1999"},{"key":"ref31","first-page":"403","article-title":"Basic Local Alignment Search Tool","volume":"215","author":"SF Altschul","year":"1990"},{"key":"ref32","first-page":"3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"SF Altschul","year":"1997"},{"key":"ref33","first-page":"W5","article-title":"NCBI BLAST: a better web interface","volume":"36","author":"M Johnson","year":"2008"},{"key":"ref34","first-page":"279","article-title":"JDotter: a Java interface to multiple dotplots generated by dotter","volume":"20","author":"R Brodie","year":"2004"},{"key":"ref35","article-title":"GeneDoc: Analysis and Visualization of Genetic Variation","volume":"14","author":"KB Nicholas","year":"1997","journal-title":"EMBNEW.NEWS"},{"key":"ref36","first-page":"D360","article-title":"The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants","volume":"32","author":"S Ouyang","year":"2004"},{"key":"ref37","first-page":"113","article-title":"Relative quantification of mRNA: comparison of methods currently used for real-time PCR data analysis","volume":"8","author":"\u0160 Ciko\u0161","year":"2007"},{"issue":"SUPPL. 2","key":"ref38","first-page":"447","article-title":"CONREAL web server: Identification and visualization of conserved transcription factor binding sites","volume":"33","author":"E Berezikov","year":"2005"},{"key":"ref39","first-page":"167","article-title":"The functional consequences of alternative promoter use in mammalian genomes","volume":"24","author":"R V. Davuluri","year":"2008"},{"key":"ref40","first-page":"475","article-title":"Miniature inverted-repeat transposable elements: discovery, distribution, and activity","volume":"56","author":"I Fattash","year":"2013"},{"key":"ref41","first-page":"2549","article-title":"Tandem repeat-containing MITEs in the clam <italic>Donax trunculus<\/italic>","volume":"5","author":"E \u0160atovi\u0107","year":"2013"},{"key":"ref42","first-page":"1005","article-title":"Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa","volume":"29","author":"C Lu","year":"2012"},{"key":"ref43","first-page":"321","article-title":"A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp. japonica","volume":"83","author":"N Oki","year":"2008"},{"key":"ref44","first-page":"225","article-title":"Detection and characterization of two novel hypervariable microsatellite repeat regions within intron 2 of the alpha-globin gene of the bivalve mollusc <italic>Anadara trapezia<\/italic>","volume":"183","author":"NT Nassif","year":"1996"},{"key":"ref45","first-page":"308","article-title":"Pearl, a novel family of putative transposable elements in bivalve mollusks","volume":"56","author":"PM Gaffney","year":"2003"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1098\/rstb.1958.0010","article-title":"On the Basic Form and Adaptations to Habitat in the Lucinacea (Eulamellibranchia)","volume":"241","author":"JA Allen","year":"1958","journal-title":"Philos Trans R Soc"},{"key":"ref47","first-page":"4144","article-title":"Respiration Strategies Utilized by the Gill Endosymbiont from the Host Lucinid Codakia orbicularis (Bivalvia: Lucinidae)","volume":"70","author":"MR Duplessis","year":"2004"},{"key":"ref48","first-page":"1","article-title":"In <italic>Disorders of Hemoglobins<\/italic>: <italic>Genetics<\/italic><italic>Pathophysiology<\/italic>, <italic>Clinical Management<\/italic>","author":"R Hardison","year":"2001"},{"key":"ref49","first-page":"11696","article-title":"Ascaris hemoglobin gene: plant-like structure reflects the ancestral globin gene","volume":"89","author":"DR Sherman","year":"1992"},{"issue":"August","key":"ref50","first-page":"6672","article-title":"Origin of a \u201cbridge\u201d intron in the gene for a two-domain globin","volume":"88","author":"Y Naito","year":"1991"},{"key":"ref51","first-page":"979","article-title":"Evolution of myoglobin","volume":"54","author":"T Suzuki","year":"1998"},{"key":"ref52","first-page":"13583","article-title":"Characterization of the Myoglobin and its Coding Gene of the Mollusc <italic>Biomphalaria glabrata<\/italic>*","volume":"273","author":"S Dewilde","year":"1998"},{"key":"ref53","first-page":"61","article-title":"A minor globin gene of the bivalve mollusc <italic>Anadara trapezia<\/italic>","volume":"1089","author":"DA Titchen","year":"1991"},{"key":"ref54","first-page":"1205","article-title":"The hemoglobin gene of the deep-sea clam <italic>Calyptogena soyoae<\/italic> has a novel intron in A-helix","volume":"32","author":"T Suzuki","year":"2000"},{"key":"ref55","unstructured":"Alternative splicing in <italic>C<\/italic>. <italic>elegans<\/italic>. [<ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.wormbook.org\" xlink:type=\"simple\">http:\/\/www.wormbook.org<\/ext-link>]"},{"key":"ref56","first-page":"119","article-title":"Regulation of gene expression by alternative untranslated regions","volume":"22","author":"TA Hughes","year":"2006"},{"key":"ref57","first-page":"453","article-title":"Regulation of gene expression by alternative promoters","volume":"10","author":"TA Ayoubi","year":"1996"},{"key":"ref58","first-page":"17349","article-title":"Structural determinants of BRCA1 translational regulation","volume":"277","author":"K Sobczak","year":"2002"},{"key":"ref59","first-page":"11487","article-title":"Repression of translation of human estrogen receptor \u03b1 by G-quadruplex formation","volume":"48","author":"GD Balkwill","year":"2009"},{"key":"ref60","first-page":"5509","article-title":"Developmental specificity of recruitment of TBP to the TATA box of the human \u03b3-globin gene","volume":"99","author":"Z-J Duan","year":"2002"},{"key":"ref61","first-page":"1099","article-title":"Hemoglobins from Bacteria to Man: Evolution of Different Patterns Of Gene Expression","volume":"1117","author":"R Hardison","year":"1998"},{"key":"ref62","first-page":"13","article-title":"Hydrogen sulfide-linked sulfhydration of NF-\u03baB mediates its antiapoptotic actions","author":"N Sen","year":"2012"},{"key":"ref63","first-page":"148","article-title":"Introns and gene expression: Cellular constraints, transcriptional regulation, and evolutionary consequences","volume":"37","author":"P Heyn","year":"2015"},{"key":"ref64","first-page":"4364","article-title":"Analysis of canonical and non-canonical splice sites in mammalian genomes","volume":"28","author":"M Burset","year":"2000"},{"key":"ref65","first-page":"855","article-title":"Evolution and consequences of transposable elements","volume":"3","author":"JF McDonald","year":"1993"},{"key":"ref66","first-page":"215","article-title":"The evolutionary dynamics of repetitive DNA in eukaryotes","author":"B Charlesworth","year":"1994"},{"key":"ref67","first-page":"2034","article-title":"Intervening Sequences in Paralogous Genes: A Comparative Genomic Approach to Study the Evolution of X Chromosome Introns","volume":"20","author":"B Cardazzo","year":"2003"},{"key":"ref68","first-page":"227","article-title":"Why repetitive DNA is essential to genome function","volume":"80","author":"JA Shapiro","year":"2005"},{"key":"ref69","first-page":"331","article-title":"DNA Transposons and the Evolution of Eukaryotic Genomes","volume":"41","author":"C Feschotte","year":"2007"},{"key":"ref70","first-page":"982","article-title":"Rice transposable elements: a survey of 73, 000 sequencetagged-connectors","volume":"10","author":"L Mao","year":"2000"},{"key":"ref71","first-page":"1160","article-title":"Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize","volume":"97","author":"Q Zhang","year":"2000"},{"key":"ref72","first-page":"17620","article-title":"Dramatic amplification of a rice transposable element during recent domestication","volume":"103","author":"K Naito","year":"2006"},{"issue":"May","key":"ref73","first-page":"1559","article-title":"A two-edged role for the transposable element <italic>Kiddo<\/italic> in the <italic>rice ubiquitin2<\/italic> promoter","volume":"17","author":"G Yang","year":"2005"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"127","DOI":"10.4161\/mge.20773","article-title":"Miniature inverted-repeat transposable elements (MITEs) in rice were originated and amplified predominantly after the divergence of Oryza and Brachypodium and contributed considerable diversity to the species","volume":"2","author":"J Chen","year":"2012","journal-title":"Mob Genet Elements"},{"key":"ref75","first-page":"83","article-title":"Sunken wood habitat for thiotrophic symbiosis in mangrove swamps","volume":"67","author":"MCZ Laurent","year":"2009"},{"key":"ref76","first-page":"112","article-title":"Heme Proteins in Sulfide-Oxidizing Bacteria\/Mollusc Symbioses","volume":"35","author":"DW Kraus","year":"1995"},{"key":"ref77","first-page":"3304","article-title":"Effects of long-term starvation on a host bivalve (Codakia orbicularis, Lucinidae) and its symbiont population","volume":"75","author":"A Caro","year":"2009"},{"key":"ref78","first-page":"33","article-title":"Elemental sulfur in the gills of three species of clams containing chemoautotrophic symbiotic bacteria: a possible inorganic energy storage compound","volume":"88","author":"RD Vetter","year":"1985"},{"key":"ref79","first-page":"163","article-title":"In situ localization of sulphur in the thioautotrophic symbiotic model Lucina pectinata (Gmelin, 1791) by cryo-EFTEM microanalysis","volume":"98","author":"J-P Lechaire","year":"2006"},{"key":"ref80","first-page":"1395","article-title":"C-to-U RNA editing: Mechanisms leading to genetic diversity","volume":"278","author":"V Blanc","year":"2003"},{"key":"ref81","first-page":"903","article-title":"C to U RNA editing mediated by APOBEC 1 requires RNA-binding protein RBM47","volume":"15","author":"N Fossat","year":"2014","journal-title":"C to U RNA editing mediated by APOBEC 1 requires RNA-binding protein RBM47"},{"key":"ref82","first-page":"1812","article-title":"The emerging role of RNA editing in plasticity","volume":"218","author":"JJC Rosenthal","year":"2015"},{"key":"ref83","first-page":"17754","article-title":"Extra double-stranded RNA binding domain (dsRBD) in a squid RNA editing enzyme confers resistance to high salt environment","volume":"287","author":"JP Palavicini","year":"2012"},{"key":"ref84","first-page":"201","article-title":"A large-scale analysis of mRNA polyadenylation of human and mouse genes","volume":"33","author":"B Tian","year":"2005"},{"key":"ref85","first-page":"1947","article-title":"Beyond the 3\u2019 end: experimental validation of extended transcript isoforms","volume":"35","author":"V Moucadel","year":"2007"},{"key":"ref86","first-page":"1952","article-title":"Notable diversity in hemoglobin expression patterns among species of the deep-sea clam, Calyptogena","volume":"60","author":"K Kawano","year":"2003"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1126\/science.226.4672.328","article-title":"Surprise finding with insect globin genes","volume":"226","author":"R Lewin","year":"1984","journal-title":"Science (80-)"},{"key":"ref88","first-page":"90","article-title":"Correlation of DNA exonic regions with protein structural units in haemoglobin","volume":"291","author":"M Go","year":"1981"},{"key":"ref89","first-page":"5675","article-title":"Commentary history hemoglobins: Plant, animal, protist, and bacteria","volume":"93","author":"RC Hardison","year":"1996"},{"key":"ref90","first-page":"759","article-title":"Organization of non-vertebrate globin genes","volume":"103","author":"SN Vinogradov","year":"1992"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/0014-5793(92)80915-4","article-title":"Unexpected intron location in non-vertebrate globin genes","volume":"312","author":"L Moens","year":"1992","journal-title":"Fed Eur Biochem Soc lett"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0147977","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,22]],"date-time":"2018-10-22T08:54:35Z","timestamp":1540198475000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0147977"}},"subtitle":[],"editor":[{"given":"John Travers","family":"Hancock","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,1,29]]},"references-count":91,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,1,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0147977","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,1,29]]}}}