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1.
Annu Rev Genet ; 53: 347-372, 2019 12 03.
Artículo en Inglés | MEDLINE | ID: mdl-31505133

RESUMEN

The rule of Mendelian inheritance is remarkably robust, but deviations from the equal transmission of alternative alleles at a locus [a.k.a. transmission ratio distortion (TRD)] are also commonly observed in genetic mapping populations. Such TRD reveals locus-specific selection acting at some point between the diploid heterozygous parents and progeny genotyping and therefore can provide novel insight into otherwise-hidden genetic and evolutionary processes. Most of the classic selfish genetic elements were discovered through their biasing of transmission, but many unselfish evolutionary and developmental processes can also generate TRD. In this review, we describe methodologies for detecting TRD in mapping populations, detail the arenas and genetic interactions that shape TRD during plant and animal reproduction, and summarize patterns of TRD from across the genetic mapping literature. Finally, we point to new experimental approaches that can accelerate both detection of TRD and characterization of the underlying genetic mechanisms.


Asunto(s)
Genética de Población/métodos , Patrón de Herencia , Plantas/genética , Espermatozoides/fisiología , Animales , Quimera , Mapeo Cromosómico , Femenino , Células Germinativas/fisiología , Heterocigoto , Depresión Endogámica , Masculino , Meiosis , Polen/genética , Autoincompatibilidad en las Plantas con Flores/genética , Razón de Masculinidad , Vertebrados/genética , Cigoto
2.
Mol Biol Evol ; 35(7): 1744-1756, 2018 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-29669130

RESUMEN

Selenium (Se), a sparse element on earth, is an essential micronutrient in the vertebrate diet and its intake depends on its content in soils and waters worldwide. Selenium is required due to its function in selenoproteins, which contain selenocysteine (Sec), the 21st amino acid in the genetic code, as one of their constituent residues. Selenocysteine is analogous to the amino acid cysteine (Cys), which uses the abounding element sulfur instead. Despite the irregular distribution of Se worldwide, its distinct biochemical properties have made the substitution of Sec for Cys rare in vertebrate proteins. Still, vertebrates inhabited environments with different amounts of Se and may have distinctly adapted to it. To address this question, we compared the evolutionary forces acting on the coding sequences of selenoprotein genes and genes that regulate Se between vertebrate clades and between the Se-dependent genes and their paralogs with Cys. We find that the strength of natural selection in genes that use or regulate Se is distinct between land vertebrates and teleost fishes and more variable than in the Cys paralogs, particularly in genes involved in the preferential supply of Se to some organs and the tissue-specific expression of selenoproteins. This is compatible with vertebrates adapting to Se scarcity in land and its abundance in waters. In agreement, teleost fishes duplicated and subfunctionalized or neofunctionalized selenoprotein genes and maintained their capacity for Se transport in the body, which declined (under neutrality) for millions of years in terrestrial vertebrates. Dietary Se has thus distinctly shaped vertebrate evolution.


Asunto(s)
Organismos Acuáticos/genética , Selección Genética , Selenoproteínas/genética , Vertebrados/genética , Animales , Duplicación de Gen , Selenio/metabolismo , Selenoproteínas/metabolismo
3.
Mol Immunol ; 87: 141-151, 2017 07.
Artículo en Inglés | MEDLINE | ID: mdl-28441623

RESUMEN

C-type lectins (CTLs) are involved in the innate immune defense of vertebrates and invertebrates against invading pathogens. This study cloned and characterized a novel C-type lectin (MnCTL) of the oriental river prawn, Macrobrachium nipponense. The cloned MnCTL cDNA encompasses an open reading frame of 774 nucleotides and encodes polypeptides of 257 residues. The deduced MnCTL protein contains a single carbohydrate recognition domain (CRD) with an EPN (Glu-Pro-Asn) motif in calcium-binding site 2. Phylogenetic analysis indicated that MnCTL has a closer evolutionary relationship with vertebrate lectins than with invertebrate lectins. Tissue expression analysis showed that high levels of MnCTL are ubiquitously distributed in the gills and stomach of M. nipponense. Quantitative real-time RT-PCR (qRT-PCR) analysis showed that MnCTL expression was up-regulated by bacteria or white spot syndrome virus (WSSV) challenge. Knock-down of the MnCTL gene in WSSV-challenged prawns significantly decreased MnALF1 and MnALF2 transcript levels. The recombinant MnCRD (rMnCRD) agglutinated both Gram-positive (Staphylococcus aureus) and Gram-negative bacteria (Vibrio parahaemolyticus) in the presence of calcium. Furthermore, rMnCRD could bind to all the tested bacteria with different activities. The sugar-binding assay showed that rMnCRD was able to bind lipopolysaccharide and peptidoglycan in a concentration-dependent manner. In addition, rMnCRD could accelerate bacterial clearance. On the contrary, MnCTL silencing by dsRNA interference could weaken the bacterial clearance ability. All these findings implicated MnCTL were involved in the antiviral and antibacterial innate immunity of M. nipponense.


Asunto(s)
Lectinas Tipo C/genética , Lectinas Tipo C/metabolismo , Palaemonidae/genética , Palaemonidae/metabolismo , Vertebrados/genética , Vertebrados/metabolismo , Secuencia de Aminoácidos , Animales , Proteínas de Artrópodos/genética , Proteínas de Artrópodos/metabolismo , Secuencia de Bases , Sitios de Unión , Evolución Biológica , Clonación Molecular/métodos , ADN Complementario/genética , Inmunidad Innata/genética , Lipopolisacáridos/genética , Lipopolisacáridos/metabolismo , Peptidoglicano/genética , Filogenia , Alineación de Secuencia , Staphylococcus aureus/genética , Staphylococcus aureus/metabolismo , Vibrio parahaemolyticus/genética , Vibrio parahaemolyticus/metabolismo , Virus del Síndrome de la Mancha Blanca 1/genética , Virus del Síndrome de la Mancha Blanca 1/metabolismo
4.
BMC Evol Biol ; 15: 22, 2015 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-25879701

RESUMEN

BACKGROUND: The A Disintegrin-like and Metalloproteinase domain with Thrombospondin-1 motifs (ADAMTS) enzymes comprise 19 mammalian zinc-dependent metalloproteinases (metzincins) with homologues in a wide range of invertebrates. ADAMTS enzymes have a broad range of functions in development and diseases due to their extracellular matrix remodelling activity. Here, we report a detailed characterisation of their evolutionary conservation across vertebrates. RESULTS: Using bioinformatics complemented with de novo sequencing, gene sequences for ADAMTS enzymes were obtained from a variety of organisms. Detailed evolutionary analyses revealed a high level of conservation across vertebrates with evidence of ADAMTS gene expansion during two rounds of whole genome duplication (WGD) in vertebrates, while tandem duplication events and gene loss were also apparent. However, the additional round of teleost-specific WGD did not have a significant effect on ADAMTS gene family members suggesting their conserved roles have remained constant in teleost fish. Quantitative reverse-transcriptase polymerase chain reaction analysis revealed dynamic expression of adamts genes throughout zebrafish embryonic development reflecting the key conserved roles they play in vertebrate embryogenesis. Notably, several adamts mRNAs were maternally expressed with a dramatic increase in mRNA levels coinciding with zygotic expression and organogenesis. Broad adamts mRNA expression was also demonstrated in several adult organs indicating potential roles in adult homeostasis. CONCLUSIONS: Our data highlight the evolution of the ADAMTS gene family through duplication processes across metazoans supplemented by a burst of amplification through vertebrate WGD events. It also strongly posits the zebrafish as a potential model species to further elucidate the function of ADAMTS enzymes during vertebrate development.


Asunto(s)
Evolución Molecular , Metaloendopeptidasas/química , Metaloendopeptidasas/genética , Proteínas de Pez Cebra/química , Proteínas de Pez Cebra/genética , Pez Cebra/genética , Proteínas ADAM/química , Proteínas ADAM/genética , Proteínas ADAM/metabolismo , Animales , Duplicación de Gen , Regulación del Desarrollo de la Expresión Génica , Genoma , Metaloendopeptidasas/metabolismo , Filogenia , Estructura Terciaria de Proteína , Vertebrados/genética , Pez Cebra/embriología , Proteínas de Pez Cebra/metabolismo
5.
BMC Biol ; 12: 13, 2014 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-24528677

RESUMEN

BACKGROUND: The habenula and the thalamus are two critical nodes in the forebrain circuitry and they connect the midbrain and the cerebral cortex in vertebrates. The habenula is derived from the epithalamus and rests dorsally to the thalamus. Both epithalamus and thalamus arise from a single diencephalon segment called prosomere (p)2. Shh is expressed in the ventral midline of the neural tube and in the mid-diencephalic organizer (MDO) at the zona limitans intrathalamica between thalamus and prethalamus. Acting as a morphogen, Shh plays an important role in regulating cell proliferation and survival in the diencephalon and thalamic patterning. The molecular regulation of the MDO Shh expression and the potential role of Shh in development of the habenula remain largely unclear. RESULTS: We show that deleting paired-box and homeobox-containing gene Pax6 results in precocious and expanded expression of Shh in the prospective MDO in fish and mice, whereas gain-of-function of pax6 inhibits MDO shh expression in fish. Using gene expression and genetic fate mapping, we have characterized the expression of molecular markers that demarcate the progenitors and precursors of habenular neurons. We show that the thalamic domain is shifted dorsally and the epithalamus is missing in the alar plate of p2 in the Pax6 mutant mouse. Conversely, the epithalamus is expanded ventrally at the expense of the thalamus in mouse embryos with reduced Shh activity. Significantly, attenuating Shh signaling largely rescues the patterning of p2 and restores the epithalamus in Pax6 mouse mutants, suggesting that Shh acts downstream of Pax6 in controlling the formation of the habenula. Similar to that found in the mouse, we show that pax6 controls the formation of the epithalamus mostly via the regulation of MDO shh expression in zebrafish. CONCLUSIONS: Our findings demonstrate that Pax6 has an evolutionarily conserved function in establishing the temporospatial expression of Shh in the MDO in vertebrates. Furthermore, Shh mediates Pax6 function in regulating the partition of the p2 domain into the epithalamus and thalamus.


Asunto(s)
Proteínas del Ojo/metabolismo , Regulación del Desarrollo de la Expresión Génica , Habénula/embriología , Habénula/metabolismo , Proteínas Hedgehog/genética , Proteínas de Homeodominio/metabolismo , Factores de Transcripción Paired Box/metabolismo , Proteínas Represoras/metabolismo , Vertebrados/embriología , Proteínas de Pez Cebra/genética , Animales , Biomarcadores/metabolismo , Tipificación del Cuerpo/genética , Embrión de Mamíferos/citología , Embrión de Mamíferos/metabolismo , Embrión no Mamífero/citología , Embrión no Mamífero/metabolismo , Habénula/citología , Proteínas Hedgehog/metabolismo , Ratones , Organizadores Embrionarios/citología , Organizadores Embrionarios/embriología , Factor de Transcripción PAX6 , Unión Proteica , Transducción de Señal/genética , Células Madre/citología , Células Madre/metabolismo , Tálamo/citología , Tálamo/embriología , Factores de Transcripción/metabolismo , Vertebrados/genética , Pez Cebra/embriología , Pez Cebra/metabolismo , Proteínas de Pez Cebra/metabolismo
6.
Front Neuroendocrinol ; 34(2): 65-87, 2013 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-23088995

RESUMEN

Neurons synthesizing melanin-concentrating hormone (MCH) are described in the posterior hypothalamus of all vertebrates investigated so far. However, their anatomy is very different according to species: they are small and periventricular in lampreys, cartilaginous fishes or anurans, large and neuroendocrine in bony fishes, or distributed over large regions of the lateral hypothalamus in many mammals. An analysis of their comparative anatomy alongside recent data about the development of the forebrain, suggests that although very different, MCH neurons of the caudal hypothalamus are homologous. We further hypothesize that their divergent anatomy is linked to divergence in the forebrain - in particular telencephalic evolution.


Asunto(s)
Hormonas Hipotalámicas/biosíntesis , Hipotálamo/anatomía & histología , Melaninas/biosíntesis , Neuronas/citología , Hormonas Hipofisarias/biosíntesis , Vertebrados/anatomía & histología , Animales , Evolución Biológica , Encéfalo/anatomía & histología , Peces/anatomía & histología , Humanos , Hipotálamo/fisiología , Lampreas/anatomía & histología , Mamíferos/anatomía & histología , Neuronas/fisiología , Vertebrados/genética
7.
PLoS One ; 7(3): e33066, 2012.
Artículo en Inglés | MEDLINE | ID: mdl-22479358

RESUMEN

BACKGROUND: Selenium is an essential trace element in mammals due to its presence in proteins in the form of selenocysteine (Sec). Human genome codes for 25 Sec-containing protein genes, and mouse and rat genomes for 24. METHODOLOGY/PRINCIPAL FINDINGS: We characterized the selenoproteomes of 44 sequenced vertebrates by applying gene prediction and phylogenetic reconstruction methods, supplemented with the analyses of gene structures, alternative splicing isoforms, untranslated regions, SECIS elements, and pseudogenes. In total, we detected 45 selenoprotein subfamilies. 28 of them were found in mammals, and 41 in bony fishes. We define the ancestral vertebrate (28 proteins) and mammalian (25 proteins) selenoproteomes, and describe how they evolved along lineages through gene duplication (20 events), gene loss (10 events) and replacement of Sec with cysteine (12 events). We show that an intronless selenophosphate synthetase 2 gene evolved in early mammals and replaced functionally the original multiexon gene in placental mammals, whereas both genes remain in marsupials. Mammalian thioredoxin reductase 1 and thioredoxin-glutathione reductase evolved from an ancestral glutaredoxin-domain containing enzyme, still present in fish. Selenoprotein V and GPx6 evolved specifically in placental mammals from duplications of SelW and GPx3, respectively, and GPx6 lost Sec several times independently. Bony fishes were characterized by duplications of several selenoprotein families (GPx1, GPx3, GPx4, Dio3, MsrB1, SelJ, SelO, SelT, SelU1, and SelW2). Finally, we report identification of new isoforms for several selenoproteins and describe unusually conserved selenoprotein pseudogenes. CONCLUSIONS/SIGNIFICANCE: This analysis represents the first comprehensive survey of the vertebrate and mammal selenoproteomes, and depicts their evolution along lineages. It also provides a wealth of information on these selenoproteins and their forms.


Asunto(s)
Mamíferos/metabolismo , Proteoma/metabolismo , Selenoproteínas/metabolismo , Vertebrados/metabolismo , Empalme Alternativo , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Evolución Molecular , Duplicación de Gen , Humanos , Mamíferos/genética , Datos de Secuencia Molecular , Mutación , Filogenia , Isoformas de Proteínas/clasificación , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Proteoma/clasificación , Proteoma/genética , Proteómica , Seudogenes/genética , Selenoproteínas/clasificación , Selenoproteínas/genética , Homología de Secuencia de Aminoácido , Homología de Secuencia de Ácido Nucleico , Vertebrados/genética
8.
Mol Phylogenet Evol ; 61(2): 300-7, 2011 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-21742044

RESUMEN

As a resource for vertebrate phylogenetics, we developed 75 new protein-coding genes using a combination of expressed sequence tags (ESTs) available in Genbank, and targeted amplification of complementary DNA (cDNA). In addition, we performed three additional analyses in order to assess the utility of our approach. First, we profiled the phylogenetic informativeness of these new markers using the online program PhyDesign. Next, we compared the utility of four different data-types used in phylogenetics: nucleotides (NUCL), amino acids (AA), 1st and 2nd codon positions only (N12), and modified sequences to account for codon degeneracy (DEGEN1; Regier et al., 2010). Lastly, we use these new markers to construct a vertebrate phylogeny and address the uncertain relationship between higher-level mammal groups: monotremes, marsupials, and placentals. Our results show that phylogenetic informativeness of the 75 new markers varies, both in the amount of phylogenetic signal and optimal timescale. When comparing the four data-types, we find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL. Our phylogenetic inference supports the Theria hypothesis of mammalian relationships, with marsupials and placentals being sister groups.


Asunto(s)
Evolución Molecular , Genómica/métodos , Filogenia , Vertebrados/genética , Aminoácidos/análisis , Animales , Codón/análisis , ADN Complementario/genética , Etiquetas de Secuencia Expresada , Marcadores Genéticos , Marsupiales/clasificación , Marsupiales/genética , Monotremata/clasificación , Monotremata/genética , Nucleótidos/análisis , Proteínas/genética , Vertebrados/clasificación
9.
BMC Genomics ; 11: 634, 2010 Nov 16.
Artículo en Inglés | MEDLINE | ID: mdl-21080938

RESUMEN

BACKGROUND: Alvinella pompejana is a representative of Annelids, a key phylum for evo-devo studies that is still poorly studied at the sequence level. A. pompejana inhabits deep-sea hydrothermal vents and is currently known as one of the most thermotolerant Eukaryotes in marine environments, withstanding the largest known chemical and thermal ranges (from 5 to 105°C). This tube-dwelling worm forms dense colonies on the surface of hydrothermal chimneys and can withstand long periods of hypo/anoxia and long phases of exposure to hydrogen sulphides. A. pompejana specifically inhabits chimney walls of hydrothermal vents on the East Pacific Rise. To survive, Alvinella has developed numerous adaptations at the physiological and molecular levels, such as an increase in the thermostability of proteins and protein complexes. It represents an outstanding model organism for studying adaptation to harsh physicochemical conditions and for isolating stable macromolecules resistant to high temperatures. RESULTS: We have constructed four full length enriched cDNA libraries to investigate the biology and evolution of this intriguing animal. Analysis of more than 75,000 high quality reads led to the identification of 15,858 transcripts and 9,221 putative protein sequences. Our annotation reveals a good coverage of most animal pathways and networks with a prevalence of transcripts involved in oxidative stress resistance, detoxification, anti-bacterial defence, and heat shock protection. Alvinella proteins seem to show a slow evolutionary rate and a higher similarity with proteins from Vertebrates compared to proteins from Arthropods or Nematodes. Their composition shows enrichment in positively charged amino acids that might contribute to their thermostability. The gene content of Alvinella reveals that an important pool of genes previously considered to be specific to Deuterostomes were in fact already present in the last common ancestor of the Bilaterian animals, but have been secondarily lost in model invertebrates. This pool is enriched in glycoproteins that play a key role in intercellular communication, hormonal regulation and immunity. CONCLUSIONS: Our study starts to unravel the gene content and sequence evolution of a deep-sea annelid, revealing key features in eukaryote adaptation to extreme environmental conditions and highlighting the proximity of Annelids and Vertebrates.


Asunto(s)
ADN Complementario/genética , Evolución Molecular , Filogenia , Poliquetos/genética , Adaptación Fisiológica/efectos de los fármacos , Adaptación Fisiológica/genética , Aminoácidos/genética , Animales , Composición de Base/genética , Teorema de Bayes , Bases de Datos Genéticas , Etiquetas de Secuencia Expresada , Regulación de la Expresión Génica , Biblioteca de Genes , Internet , Metales Pesados/toxicidad , Anotación de Secuencia Molecular , Datos de Secuencia Molecular , Estrés Oxidativo/efectos de los fármacos , Estrés Oxidativo/genética , Poliquetos/efectos de los fármacos , Estructura Terciaria de Proteína , Ribosomas/genética , Temperatura , Vertebrados/genética
10.
Integr Comp Biol ; 50(1): 53-62, 2010 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-21558187

RESUMEN

The cephalochordate, amphioxus, is phylogenetically placed at the most primitive position in the chordate clade. Despite many studies on the endocrine system of amphioxus, definitive evidence has not been reported for the presence an endocrine system comparable to the pituitary-gonadal axis, which is important in the regulation of reproduction in vertebrates. Recent genome analyses in the amphioxus, Branchiostoma floridae, showed that it does not have any pituitary hormone genes except the thyrostimulin gene. Thyrostimulin is a heterodimeric glycoprotein hormone consisting of α and ß subunits, and is present in various organs of vertebrates. Analyses of a phylogenetic tree and a synteny suggest that amphioxus' thyrostimulin is an ancestral type of the glycoprotein hormones in chordates. In addition, genes for sex steroidogenic enzymes belonging to the CYP family were found in the genome sequences. The conversion pathway of sex steroids from cholesterol to estrogen, androgen, and major sex steroids was also identified in the gonads of amphioxus in vitro. Furthermore, we demonstrated the expression of genes encoding thyrostimulin and sex steroidogenic enzymes by an in situ hybridization technique. Here, we discuss the evolution of hormones and reproductive functions in the neuroendocrine control system of chordates.


Asunto(s)
Cordados no Vertebrados/fisiología , Sistema Endocrino/fisiología , Evolución Molecular , Hipotálamo/fisiología , Vertebrados/fisiología , Secuencia de Aminoácidos , Animales , Cordados no Vertebrados/genética , Perfilación de la Expresión Génica , Glicoproteínas/química , Glicoproteínas/genética , Hipotálamo/metabolismo , Datos de Secuencia Molecular , Filogenia , Fisiología Comparada , Reproducción , Alineación de Secuencia , Sintenía , Vasotocina/genética , Vasotocina/metabolismo , Vertebrados/genética
12.
Mol Genet Metab ; 95(1-2): 81-95, 2008.
Artículo en Inglés | MEDLINE | ID: mdl-18675571

RESUMEN

Ablation of the murine Slc5a3 gene results in severe myo-inositol (Ins) deficiency and congenital central apnea due to abnormal respiratory rhythmogenesis. The lethal knockout phenotype may be rescued by supplementing the maternal drinking water with 1% Ins. In order to test the hypothesis that Ins deficiency leads to inositide deficiencies, which are corrected by prenatal treatment, we measured the effects of Ins rescue on Ins, phosphatidylinositol (PtdIns) and myo-inositol polyphosphate levels in brains of E18.5 knockout fetuses. As the Slc5a3 gene structure is unique in the sodium/solute cotransporter (SLC5) family, and exon 1 is shared with the mitochondrial ribosomal protein subunit 6 (Mrps6) gene, we also sought to determine whether expression of its cognate Mrps6 gene is abnormal in knockout fetuses. The mean level of Ins was increased by 92% in brains of rescued Slc5a3 knockout fetuses (0.48 versus 0.25 nmol/mg), but was still greatly reduced in comparison to wildtype (6.97 nmol/mg). The PtdIns, InsP(5) and InsP(6) levels were normal without treatment. Mrps6 gene expression was unaffected in the E18.5 knockout fetuses. This enigmatic model is not associated with neonatal PtdIns deficiency and rescue of the phenotype may be accomplished without restoration of Ins. The biochemical mechanism that both uniformly leads to death and allows for Ins rescue remains unknown. In conclusion, in neonatal brain tissue, Mrps6 gene expression may not be contingent on function of its embedded Slc5a3 gene, while inositide deficiency may not be the mechanism of lethal apnea in null Slc5a3 mice.


Asunto(s)
Apnea/metabolismo , Encéfalo/metabolismo , Expresión Génica , Inositol/metabolismo , Proteínas Mitocondriales/metabolismo , Fosfatidilinositoles/metabolismo , Proteínas Ribosómicas/metabolismo , Simportadores/deficiencia , Secuencia de Aminoácidos , Animales , Apnea/embriología , Apnea/genética , Apnea/patología , Encéfalo/embriología , Encéfalo/patología , Humanos , Ratones , Ratones Noqueados , Proteínas Mitocondriales/química , Proteínas Mitocondriales/genética , Datos de Secuencia Molecular , Fenotipo , Filogenia , Proteínas Ribosómicas/química , Proteínas Ribosómicas/genética , Alineación de Secuencia , Médula Espinal , Simportadores/química , Simportadores/genética , Vertebrados/clasificación , Vertebrados/genética
13.
Artículo en Inglés | MEDLINE | ID: mdl-18442940

RESUMEN

Identification and characterization of a bovine cDNA and the corresponding gene coding for a novel protein structurally related to Zar1, therefore called Zar1-like, are here reported for the first time. Structure of Zar1-like is similar to Zar1 gene, nevertheless they are located on distinct chromosomes. We demonstrated that the new gene as well as its genomic context are conserved along the whole vertebrate lineage. Analysis of the deduced protein primary structure showed a high conservation, among vertebrates, of the C-terminal region, where the putative presence of both zinc finger motifs and classical nuclear localization signals is also shared with Zar1. Bovine Zar1-like and the only two other available mRNA leader sequences (human and chicken) exhibit a number of upstream AUGs, suggesting that they are likely to be regulated at translational level. Expression patterns of the cattle transcripts show that Zar1-like is absent in early stages of embryo development, whereas Zar1 is expressed in matured oocytes and in in vitro produced pre-implantation embryos. In adult tissues Zar1-like transcript expression appears to be less restricted than Zar1, nevertheless, at least in bovine, both mRNAs are co-expressed in gonads, raising the question of a possible functional link.


Asunto(s)
Bovinos/genética , Proteínas del Huevo/genética , Secuencia de Aminoácidos , Animales , Clonación Molecular , Secuencia Conservada , ADN Complementario/química , Proteínas del Huevo/química , Proteínas del Huevo/metabolismo , Humanos , Datos de Secuencia Molecular , ARN Mensajero/metabolismo , Homología de Secuencia de Aminoácido , Vertebrados/genética
14.
FASEB J ; 22(2): 569-78, 2008 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-17898086

RESUMEN

In bacteria, functionally related gene products are often encoded by a common transcript. Such polycistronic transcripts are rare in eukaryotes. Here we isolated several clones from human cDNA libraries, which rescued the respiratory-deficient phenotype of a yeast mitochondrial 3-hydroxyacyl thioester dehydratase 2 (htd2) mutant strain. All complementing cDNAs were derived from the RPP14 transcript previously described to encode the RPP14 subunit of the human ribonuclease P (RNase P) complex. We identified a second, 3' open reading frame (ORF) on the RPP14 transcript encoding a protein showing similarity to known dehydratases and hydratase 2 enzymes. The protein was localized in mitochondria, and the recombinant enzyme exhibited (3R)-specific hydratase 2 activity. Based on our results, we named the protein human 3-hydroxyacyl-thioester dehydratase 2 (HsHTD2), which is involved in mitochondrial fatty acid synthesis. The bicistronic arrangement of RPP14 and HsHTD2, as well as the general exon structure of the gene, is conserved in vertebrates from fish to humans, indicating a genetic link conserved for 400 million years between RNA processing and mitochondrial fatty acid synthesis.


Asunto(s)
Ácidos Grasos/biosíntesis , Mitocondrias/genética , Mitocondrias/metabolismo , ARN/genética , Vertebrados/genética , Vertebrados/metabolismo , Secuencia de Aminoácidos , Animales , Secuencia Conservada , ADN Complementario/genética , Regulación Enzimológica de la Expresión Génica , Genoma/genética , Humanos , Hidroliasas/química , Hidroliasas/genética , Hidroliasas/aislamiento & purificación , Hidroliasas/metabolismo , Proteínas Mitocondriales , Datos de Secuencia Molecular , Mutación/genética , Sistemas de Lectura Abierta/genética , Filogenia , Ribonucleasa P/genética , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Alineación de Secuencia , Transcripción Genética/genética
15.
Nucleic Acids Res ; 35(10): 3442-52, 2007.
Artículo en Inglés | MEDLINE | ID: mdl-17478514

RESUMEN

YY1 is a DNA-binding transcription factor found in both vertebrates and invertebrates. Database searches identified 62 YY1 related sequences from all the available genome sequences ranging from flying insects to human. These sequences are characterized by high levels of sequence conservation, ranging from 66% to 100% similarity, in the zinc finger DNA-binding domain of the predicted proteins. Phylogenetic analyses uncovered duplication events of YY1 in several different lineages, including flies, fish and mammals. Retroposition is responsible for generating one duplicate in flies, PHOL from PHO, and two duplicates in placental mammals, YY2 and Reduced Expression 1 (REX1) from YY1. DNA-binding motif studies have demonstrated that YY2 still binds to the same consensus sequence as YY1 but with much lower affinity. In contrast, REX1 binds to DNA motifs divergent from YY1, but the binding motifs of REX1 and YY1 share some similarity at their core regions (5'-CCAT-3'). This suggests that the two duplicates, YY2 and REX1, although generated through similar retroposition events have undergone different selection schemes to adapt to new roles in placental mammals. Overall, the conservation of YY2 and REX1 in all placental mammals predicts that each duplicate has co-evolved with some unique features of eutherian mammals.


Asunto(s)
Proteínas de Unión al ADN/química , Evolución Molecular , Retroelementos , Factor de Transcripción YY1/química , Factor de Transcripción YY1/genética , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Animales , Proteínas de Unión al ADN/genética , Dípteros/genética , Ensayo de Cambio de Movilidad Electroforética , Duplicación de Gen , Genómica , Humanos , Invertebrados/genética , Factores de Transcripción de Tipo Kruppel/química , Mamíferos/genética , Datos de Secuencia Molecular , Homología de Secuencia de Aminoácido , Factores de Transcripción/química , Vertebrados/genética , Factor de Transcripción YY1/clasificación
16.
PLoS One ; 2(2): e189, 2007 Feb 07.
Artículo en Inglés | MEDLINE | ID: mdl-17285143

RESUMEN

The PDZ and LIM domain-containing protein family is encoded by a diverse group of genes whose phylogeny has currently not been analyzed. In mammals, ten genes are found that encode both a PDZ- and one or several LIM-domains. These genes are: ALP, RIL, Elfin (CLP36), Mystique, Enigma (LMP-1), Enigma homologue (ENH), ZASP (Cypher, Oracle), LMO7 and the two LIM domain kinases (LIMK1 and LIMK2). As conventional alignment and phylogenetic procedures of full-length sequences fell short of elucidating the evolutionary history of these genes, we started to analyze the PDZ and LIM domain sequences themselves. Using information from most sequenced eukaryotic lineages, our phylogenetic analysis is based on full-length cDNA-, EST-derived- and genomic- PDZ and LIM domain sequences of over 25 species, ranging from yeast to humans. Plant and protozoan homologs were not found. Our phylogenetic analysis identifies a number of domain duplication and rearrangement events, and shows a single convergent event during evolution of the PDZ/LIM family. Further, we describe the separation of the ALP and Enigma subfamilies in lower vertebrates and identify a novel consensus motif, which we call 'ALP-like motif' (AM). This motif is highly-conserved between ALP subfamily proteins of diverse organisms. We used here a combinatorial approach to define the relation of the PDZ and LIM domain encoding genes and to reconstruct their phylogeny. This analysis allowed us to classify the PDZ/LIM family and to suggest a meaningful model for the molecular evolution of the diverse gene architectures found in this multi-domain family.


Asunto(s)
Secuencias de Aminoácidos/genética , Secuencia de Consenso/genética , Evolución Molecular , Familia de Multigenes/genética , Dominios PDZ/genética , Dominios y Motivos de Interacción de Proteínas/genética , Dedos de Zinc/genética , Animales , Mapeo Cromosómico , ADN Complementario/genética , Exones/genética , Hongos/genética , Humanos , Intrones/genética , Invertebrados/genética , Filogenia , Plantas/genética , Alineación de Secuencia , Homología de Secuencia de Ácido Nucleico , Especificidad de la Especie , Vertebrados/genética
17.
Gene ; 377: 46-55, 2006 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-16781089

RESUMEN

Angiotensin-converting enzyme 2 (ACE2), a newly identified member in the renin-angiotensin system (RAS), acts as a negative regulator of ACE. It is mainly expressed in cardiac blood vessels and the tubular epithelia of kidneys and abnormal expression has been implicated in diabetes, hypertension and heart failure. The mechanism and physiological function of this zinc metallopeptidase in mammals are not yet fully understood. Non-mammalian vertebrate models offer attractive and simple alternatives that could facilitate the exploration of ACE2 function. In this paper we report the in silico analysis of Ace2 genes from the Gallus (chicken), Xenopus (frog), Fugu and Tetraodon (pufferfish) genome assembly databases, and from the Danio (zebrafish) cDNA library. Exon ambiguities of Danio and Xenopus Ace2s were resolved by RT-PCR and 3'RACE. Analyses of the exon-intron structures, alignment, phylogeny and hydrophilicity plots, together with the conserved synteny among these vertebrates, support the orthologous relationship between mammalian and non-mammalian ACE2s. The putative promoters of Ace2 from human, Tetraodon and Xenopus tropicalis drove the expression of enhanced green fluorescent protein (EGFP) specifically in the heart tissue of transgenic Xenopus thus making it a suitable model for future functional genomic studies. Additionally, the search for conserved cis-elements resulted in the discovery of WGATAR motifs in all the putative Ace2 promoters from 7 different animals, suggesting a possible role of GATA family transcriptional factors in regulating the expression of Ace2.


Asunto(s)
Peptidil-Dipeptidasa A/genética , Vertebrados/genética , Enzima Convertidora de Angiotensina 2 , Animales , Animales Modificados Genéticamente , Secuencia de Bases , Pollos/genética , Mapeo Cromosómico , ADN Complementario/genética , Exones , Proteínas Fluorescentes Verdes/genética , Humanos , Intrones , Datos de Secuencia Molecular , Peptidil-Dipeptidasa A/química , Filogenia , Regiones Promotoras Genéticas , Proteínas Recombinantes/genética , Takifugu/genética , Tetraodontiformes/genética , Xenopus/genética , Pez Cebra/genética
18.
Cytogenet Genome Res ; 110(1-4): 575-88, 2005.
Artículo en Inglés | MEDLINE | ID: mdl-16093711

RESUMEN

DIRS-1 is a retroelement from the slime mold Dictyostelium discoideum. Until recently only two related retrotransposons had been described: PAT from the nematode Panagrellus redivivus and Prt1 from the zygomycete fungus Phycomyces blakesleeanus. Analyses of the reverse transcriptase sequences encoded by these three elements suggested that they were closely related to each other and more distantly related to the Ty3/gypsy Long Terminal Repeat (LTR) retroelements. They have several unusual structural features that distinguish them from typical LTR elements. For instance, they each encode a tyrosine recombinase (YR), but not a DDE-type integrase or an aspartic protease. Although the DIRS-1-related elements are bordered by terminal repeats these differ from typical LTRs in a number of ways. In DIRS-1, for example, the terminal repeats are inverted (complementary), non-identical in sequence, and the outer edges of the terminal sequences are repeated (adjacent to each other) in the internal region. PAT has so-called "split" direct repeats in which the unrelated terminal sequences appear as direct repeats adjacent to each other in the internal region. The only repetition displayed by Prt1 is the presence of short inverted terminal repeats, but the sequenced copy of this element is believed to be a truncated version of an element with a structure resembling DIRS-1. The unusual structure of the terminal repeats of the DIRS1-like elements appears to be related to their replication via free circular intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. In recognition of these important distinctions it is proposed that the retrotransposons that encode tyrosine recombinases be called the tyrosine recombinase (or YR) retrotransposons. Recently a large number of additional YR retrotransposons have been described, including elements from fungi (zygomycetes and basidiomycetes), plants (green algae) and a wide range of animals including nematodes, insects, sea urchins, fish and amphibia, while remnants of elements related to DIRS-1 occur in the human genome. The complete set of YR retrotransposons can be divided into two major groups, the DIRS elements and the Ngaro elements, the two groups forming distinct clades on phylogenetic trees based on alignments of RT/RH and recombinase sequences, and also having some structural distinctions. A third group of transposable elements, which we call Cryptons, also carry tyrosine recombinases. These elements do not encode a reverse transcriptase and so are believed to be DNA transposons not retrotransposons. They have been detected in several pathogenic fungi, including the basidiomycete Cryptococcus neoformans, and the ascomycetes Coccidioides posadasii and Histoplasma capsulatum. Sequence comparisons suggest that the Crypton YRs are related to those of the YR retrotransposons. We suggest that the YR retrotransposons arose from the combination of a Crypton-like YR DNA transposon and the RT/RH encoding sequence of a retrotransposon.


Asunto(s)
Recombinasas/genética , Retroelementos , Secuencia de Aminoácidos , Animales , Invertebrados/genética , Datos de Secuencia Molecular , Filogenia , ADN Polimerasa Dirigida por ARN/genética , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Vertebrados/genética
19.
Trends Genet ; 20(8): 359-66, 2004 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-15262408

RESUMEN

One of the great challenges in biology is to understand how particular complex morphological and physiological characters originated in specific evolutionary lineages. In this article, we address the origin of the vertebrate hypothalamic-pituitary-peripheral gland (H-P-PG) endocrine system, a complex network of specialized tissues, ligands and receptors. Analysis of metazoan nucleotide and protein sequences reveals a patchwork pattern of H-P-PG gene conservation between vertebrates and closely related invertebrates (ascidians). This is consistent with a model of how the vertebrate H-P-PG endocrine system could have emerged in relatively few steps by gene family expansion and by regulatory and structural modifications to genes that are present in a chordate ancestor. Some of these changes might have resulted in new connections between metabolic or signaling pathways, such as the bridging of 'synthesis islands' to form an efficient system for steroid hormone synthesis.


Asunto(s)
Evolución Biológica , Sistema Endocrino/metabolismo , Invertebrados/genética , Filogenia , Vertebrados/genética , Animales , Antozoos/genética , Artrópodos/genética , Ciona intestinalis/genética , Secuencia Conservada/genética , Hipotálamo/metabolismo , Modelos Genéticos , Adenohipófisis/metabolismo , Homología de Secuencia
20.
Gene ; 290(1-2): 141-51, 2002 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-12062809

RESUMEN

A novel human gene has been identified by in-depth bioinformatics analysis of chromosome 21 segment 40/105 (21q21.1), with no coding region predicted in any previous analysis. Brain-derived DNA complementary to RNA (cDNA) sequencing predicts a 154-amino acid product with no similarity to any known protein. The gene has been named cysteine and tyrosine-rich protein 1 gene (symbol cysteine and tyrosine-rich 1, CYYR1). The CYYR1 messenger RNA was found by Northern blot analysis in a broad range of tissues (two transcripts of 3.4 and 2.2 kb). The gene consists of four exons and spans about 107 kb, including a very large intron of 85.8 kb. Analysis of expressed sequence tags shows high CYYR1 expression in cells belonging to the amine precursor uptake and decarboxylation system. We also cloned the cDNA of the murine ortholog Cyyr1, which was mapped by a radiation hybrid panel on chromosome 16 within the region corresponding to that containing the respective human homolog on chromosome 21. Sequence and phylogenetic analysis led to identification of several genes encoding CYYR1 homologous proteins. The most prominent feature identified in the protein family is a central, unique cysteine and tyrosine-rich domain, which is strongly conserved from lower vertebrates (fishes) to humans but is absent in bacteria and invertebrates.


Asunto(s)
Cromosomas Humanos Par 21/genética , Proteínas/genética , Vertebrados/genética , Secuencia de Aminoácidos , Animales , Northern Blotting , ADN Complementario/química , ADN Complementario/genética , Bases de Datos de Ácidos Nucleicos , Evolución Molecular , Etiquetas de Secuencia Expresada , Femenino , Expresión Génica , Humanos , Proteínas de la Membrana , Ratones , Datos de Secuencia Molecular , Filogenia , ARN Mensajero/genética , ARN Mensajero/metabolismo , Mapeo de Híbrido por Radiación , Alineación de Secuencia , Análisis de Secuencia de ADN , Homología de Secuencia de Aminoácido
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