RESUMEN
BACKGROUND: The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. RESULTS: The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. CONCLUSIONS: The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.
RESUMEN
UNLABELLED: Bacterial genomes encode numerous homologs of Cas9, the effector protein of the type II CRISPR-Cas systems. The homology region includes the arginine-rich helix and the HNH nuclease domain that is inserted into the RuvC-like nuclease domain. These genes, however, are not linked to cas genes or CRISPR. Here, we show that Cas9 homologs represent a distinct group of nonautonomous transposons, which we denote ISC (insertion sequences Cas9-like). We identify many diverse families of full-length ISC transposons and demonstrate that their terminal sequences (particularly 3' termini) are similar to those of IS605 superfamily transposons that are mobilized by the Y1 tyrosine transposase encoded by the TnpA gene and often also encode the TnpB protein containing the RuvC-like endonuclease domain. The terminal regions of the ISC and IS605 transposons contain palindromic structures that are likely recognized by the Y1 transposase. The transposons from these two groups are inserted either exactly in the middle or upstream of specific 4-bp target sites, without target site duplication. We also identify autonomous ISC transposons that encode TnpA-like Y1 transposases. Thus, the nonautonomous ISC transposons could be mobilized in trans either by Y1 transposases of other, autonomous ISC transposons or by Y1 transposases of the more abundant IS605 transposons. These findings imply an evolutionary scenario in which the ISC transposons evolved from IS605 family transposons, possibly via insertion of a mobile group II intron encoding the HNH domain, and Cas9 subsequently evolved via immobilization of an ISC transposon. IMPORTANCE: Cas9 endonucleases, the effectors of type II CRISPR-Cas systems, represent the new generation of genome-engineering tools. Here, we describe in detail a novel family of transposable elements that encode the likely ancestors of Cas9 and outline the evolutionary scenario connecting different varieties of these transposons and Cas9.
Asunto(s)
Proteínas Arqueales/metabolismo , Proteínas Bacterianas/metabolismo , Elementos Transponibles de ADN/fisiología , Endonucleasas/metabolismo , Mutagénesis Insercional/fisiología , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Proteínas Arqueales/genética , Proteínas Bacterianas/genética , Secuencia de Bases , Sistemas CRISPR-Cas , Elementos Transponibles de ADN/genética , Endonucleasas/genética , Regulación de la Expresión Génica Arqueal/fisiología , Regulación Bacteriana de la Expresión Génica/fisiología , Datos de Secuencia Molecular , Mutagénesis Insercional/genética , FilogeniaRESUMEN
The RAG1 and RAG2 proteins are essential subunits of the V(D)J recombinase that is required for the generation of the enormous variability of antibodies and T-cell receptors in jawed vertebrates. It was demonstrated previously that the 600-aa catalytic core of RAG1 evolved from the transposase of the Transib superfamily transposons. However, although homologs of RAG1 and RAG2 genes are adjacent in the purple sea urchin genome, a transposon encoding both proteins so far has not been reported. Here we describe such transposons in the genomes of green sea urchin, a starfish and an oyster. Comparison of the domain architectures of the RAG1 homologs in these transposons, denoted TransibSU, and other Transib superfamily transposases provides for reconstruction of the structure of the hypothetical TransibVDJ transposon that gave rise to the VDJ recombinases at the onset of vertebrate evolution some 500 million years ago.
Asunto(s)
Elementos Transponibles de ADN/genética , Proteínas de Unión al ADN/genética , Evolución Molecular , Proteínas de Homeodominio/genética , Animales , Genoma , Ostreidae/genética , Filogenia , Recombinación Genética , Erizos de Mar/genética , Estrellas de Mar/genética , Transposasas/genéticaRESUMEN
Search of metagenomics sequence databases for homologs of virophage capsid proteins resulted in the discovery of a new family of virophages in the sheep rumen metagenome. The genomes of the rumen virophages (RVP) encode a typical virophage major capsid protein, ATPase and protease combined with a Polinton-type, protein primed family B DNA polymerase. The RVP genomes appear to be linear molecules, with terminal inverted repeats. Thus, the RVP seem to represent virophage-Polinton hybrids that are likely capable of formation of infectious virions. Virion proteins of mimiviruses were detected in the same metagenomes as the RVP suggesting that the virophages of the new family parasitize on giant viruses that infect protist inhabitants of the rumen.
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Bacteriófagos/clasificación , Metagenoma , Rumen/virología , Adenosina Trifosfatasas/metabolismo , Animales , Bacteriófagos/fisiología , Cápside/metabolismo , ADN de Cadena Simple/genética , ADN Viral/genética , Genoma , Genoma Viral , Sistemas de Lectura Abierta , Péptido Hidrolasas/metabolismo , Filogenia , Ovinos/virologíaRESUMEN
The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.
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Ctenóforos/genética , Evolución Molecular , Genoma/genética , Sistema Nervioso , Animales , Ctenóforos/clasificación , Ctenóforos/inmunología , Ctenóforos/fisiología , Genes del Desarrollo , Genes Homeobox , Mesodermo/metabolismo , Metabolómica , MicroARNs , Datos de Secuencia Molecular , Músculos/fisiología , Sistema Nervioso/metabolismo , Neuronas/metabolismo , Neurotransmisores , Filogenia , Transcriptoma/genéticaRESUMEN
Autonomous non-long terminal repeat (non-LTR) retrotransposons and their repetitive remnants are ubiquitous components of mammalian genomes. Recently, we identified non-LTR retrotransposon families, Ingi-1_AAl and Ingi-1_EE, in two hedgehog genomes. Here we rename them to Vingi-1_AAl and Vingi-1_EE and report a new clade "Vingi," which is a sister clade of Ingi that lacks the ribonuclease H domain. In the European hedgehog genome, there are 11 non-autonomous families of elements derived from Vingi-1_EE by internal deletions. No retrotransposons related to Vingi elements were found in any of the remaining 33 mammalian genomes nearly completely sequenced to date, but we identified several new families of Vingi and Ingi retrotransposons outside mammals. Our data suggest the horizontal transfer of Vingi elements to hedgehog, although the vertical transfer cannot be ruled out. The compact structure and trans-mobilization of nonautonomous derivatives of Vingi can make them useful for in vivo retrotransposition assay system.
Asunto(s)
Erizos/genética , Retroelementos/genética , Secuencias Repetidas Terminales , Animales , Secuencia de Bases , Evolución Molecular , Genoma , Humanos , Datos de Secuencia Molecular , FilogeniaRESUMEN
BACKGROUND: In eukaryotes, long terminal repeat (LTR) retrotransposons such as Copia, BEL and Gypsy integrate their DNA copies into the host genome using a particular type of DDE transposase called integrase (INT). The Gypsy INT-like transposase is also conserved in the Polinton/Maverick self-synthesizing DNA transposons and in the 'cut and paste' DNA transposons known as TDD-4 and TDD-5. Moreover, it is known that INT is similar to bacterial transposases that belong to the IS3, IS481, IS30 and IS630 families. It has been suggested that LTR retrotransposons evolved from a non-LTR retrotransposon fused with a DNA transposon in early eukaryotes. In this paper we analyze a diverse superfamily of eukaryotic cut and paste DNA transposons coding for INT-like transposase and discuss their evolutionary relationship to LTR retrotransposons. RESULTS: A new diverse eukaryotic superfamily of DNA transposons, named Ginger (for 'Gypsy INteGrasE Related') DNA transposons is defined and analyzed. Analogously to the IS3 and IS481 bacterial transposons, the Ginger termini resemble those of the Gypsy LTR retrotransposons. Currently, Ginger transposons can be divided into two distinct groups named Ginger1 and Ginger2/Tdd. Elements from the Ginger1 group are characterized by approximately 40 to 270 base pair (bp) terminal inverted repeats (TIRs), and are flanked by CCGG-specific or CCGT-specific target site duplication (TSD) sequences. The Ginger1-encoded transposases contain an approximate 400 amino acid N-terminal portion sharing high amino acid identity to the entire Gypsy-encoded integrases, including the YPYY motif, zinc finger, DDE domain, and, importantly, the GPY/F motif, a hallmark of Gypsy and endogenous retrovirus (ERV) integrases. Ginger1 transposases also contain additional C-terminal domains: ovarian tumor (OTU)-like protease domain or Ulp1 protease domain. In vertebrate genomes, at least two host genes, which were previously thought to be derived from the Gypsy integrases, apparently have evolved from the Ginger1 transposase genes. We also introduce a second Ginger group, designated Ginger2/Tdd, which includes the previously reported DNA transposon TDD-4. CONCLUSIONS: The Ginger superfamily represents eukaryotic DNA transposons closely related to LTR retrotransposons. Ginger elements provide new insights into the evolution of transposable elements and certain transposable element (TE)-derived genes.
RESUMEN
Rapidly growing number of sequenced genomes requires fast and accurate computational tools for analysis of different transposable elements (TEs). In this paper we focus on a rapid and reliable procedure for classification of autonomous non-LTR retrotransposons based on alignment and clustering of their reverse transcriptase (RT) domains. Typically, the RT domain protein sequences encoded by different non-LTR retrotransposons are similar to each other in terms of significant BLASTP E-values. Therefore, they can be easily detected by the routine BLASTP searches of genomic DNA sequences coding for proteins similar to the RT domains of known non-LTR retrotransposons. However, detailed classification of non-LTR retrotransposons, i.e. their assignment to specific clades, is a slow and complex procedure that is not formalized or integrated as a standard set of computational methods and data. Here we describe a tool (RTclass1) designed for the fast and accurate automated assignment of novel non-LTR retrotransposons to known or novel clades using phylogenetic analysis of the RT domain protein sequences. RTclass1 classifies a particular non-LTR retrotransposon based on its RT domain in less than 10 min on a standard desktop computer and achieves 99.5% accuracy. RT1class1 works either as a stand-alone program installed locally or as a web-server that can be accessed distantly by uploading sequence data through the internet (http://www.girinst.org/RTphylogeny/RTclass1).
Asunto(s)
Clasificación/métodos , Filogenia , ADN Polimerasa Dirigida por ARN/genética , Retroelementos , Algoritmos , Secuencia de Aminoácidos , Modelos Genéticos , Estructura Terciaria de Proteína/genética , ADN Polimerasa Dirigida por ARN/química , Reproducibilidad de los Resultados , Retroelementos/genética , Análisis de Secuencia de ADN/métodos , Secuencias Repetidas Terminales/genéticaRESUMEN
Despite their enormous diversity and abundance, all currently known eukaryotic DNA transposons belong to only 15 superfamilies. Here, we report two new superfamilies of DNA transposons, named Sola and Zator. Sola transposons encode DDD-transposases (transposase, TPase) and are flanked by 4-bp target site duplications (TSD). Elements from the Sola superfamily are distributed in a variety of species including bacteria, protists, plants, and metazoans. They can be divided into three distinct groups of elements named Sola1, Sola2, and Sola3. The elements from each group have extremely low sequence identity to each other, different termini, and different target site preferences. However, all three groups belong to a single superfamily based on significant PSI-Blast identities between their TPases. The DDD TPase sequences encoded by Sola transposons are not similar to any known TPases. The second superfamily named Zator is characterized by 3-bp TSD. The Zator superfamily is relatively rare in eukaryotic species, and it evolved from a bacterial transposon encoding a TPase belonging to the "transposase 36" family (Pfam07592). These transposons are named TP36 elements (abbreviated from transposase 36).
Asunto(s)
Elementos Transponibles de ADN/genética , Células Eucariotas/metabolismo , Hydra/genética , Secuencia de Aminoácidos , Animales , Bacterias/enzimología , Secuencia de Bases , Biocatálisis , Genoma/genética , Datos de Secuencia Molecular , Mutagénesis Insercional , Filogenia , Alineación de Secuencia , Homología de Secuencia de Ácido Nucleico , Transposasas/químicaRESUMEN
Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.
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Cordados/genética , Evolución Molecular , Genoma/genética , Animales , Cordados/clasificación , Secuencia Conservada , Elementos Transponibles de ADN/genética , Duplicación de Gen , Genes/genética , Ligamiento Genético , Humanos , Intrones/genética , Cariotipificación , Familia de Multigenes , Filogenia , Polimorfismo Genético/genética , Proteínas/genética , Sintenía , Factores de Tiempo , Vertebrados/clasificación , Vertebrados/genéticaRESUMEN
Ancient, inactive copies of transposable elements of the PIF/Harbinger superfamily have been described in vertebrates. We reconstructed components of the Harbinger3_DR transposon in zebrafish, including a transposase and a second, transposon-encoded protein that has a Myb-like trihelix domain. The reconstructed Harbinger transposon shows efficient cut-and-paste transposition in human cells and preferentially inserts into a 15-bp consensus target sequence. The Myb-like protein is required for transposition and physically interacts with the N-terminal region of the transposase via its C-terminal domain. The Myb-like protein enables transposition in part by promoting nuclear import of the transposase, by directly binding to subterminal regions of the transposon, and by recruiting the transposase to the transposon ends. We investigated the functions of two transposon-derived human proteins: HARBI1, a domesticated transposase-derived protein, and NAIF1, which contains a trihelix motif similar to that described in the Myb-like protein. Physical interaction, subcellular localization, and DNA-binding activities of HARBI1 and NAIF1 suggest strong functional homologies between the Harbinger3_DR system and their related, host-encoded counterparts. The Harbinger transposon will serve as a useful experimental system for transposon biology and for investigating the enzymatic functions of domesticated, transposon-derived cellular genes.
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Proteínas Reguladoras de la Apoptosis/genética , Elementos Transponibles de ADN/genética , Proteínas Nucleares/genética , Homología de Secuencia de Aminoácido , Transposasas/genética , Transporte Activo de Núcleo Celular , Secuencia de Aminoácidos , Animales , Proteínas Reguladoras de la Apoptosis/química , Emparejamiento Base , Secuencia de Bases , Núcleo Celular/metabolismo , Secuencia de Consenso , Células HeLa , Humanos , Datos de Secuencia Molecular , Mutagénesis Insercional , Proteínas Nucleares/química , Unión Proteica , Transporte de Proteínas , Proteínas Proto-Oncogénicas c-myb/metabolismo , Secuencias Repetitivas de Ácidos Nucleicos/genética , Fracciones Subcelulares , Transposasas/química , Pez CebraRESUMEN
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
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Proteínas Algáceas/genética , Proteínas Algáceas/fisiología , Evolución Biológica , Chlamydomonas reinhardtii/genética , Genoma , Animales , Chlamydomonas reinhardtii/fisiología , Cloroplastos/metabolismo , Biología Computacional , ADN de Algas/genética , Flagelos/metabolismo , Genes , Genómica , Proteínas de Transporte de Membrana/genética , Proteínas de Transporte de Membrana/fisiología , Datos de Secuencia Molecular , Familia de Multigenes , Fotosíntesis/genética , Filogenia , Plantas/genética , Proteoma , Análisis de Secuencia de ADNRESUMEN
Rolling-circle eukaryotic transposons, known as Helitron transposons, were first discovered in plants (Arabidopsis thaliana and Oryza sativa) and in the nematode Caenorhabditis elegans. To date, Helitrons have been identified in a diverse range of species, from protists to mammals. They represent a major class of eukaryotic transposons and are fundamentally different from classical transposons in terms of their structure and mechanism of transposition. Helitrons seem to have a major role in the evolution of host genomes. They frequently capture diverse host genes, some of which can evolve into novel host genes or become essential for helitron transposition.
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Elementos Transponibles de ADN , Evolución Molecular , Animales , Células Eucariotas , Duplicación de Gen , Variación Genética , Genoma , Humanos , Modelos Biológicos , Modelos GenéticosRESUMEN
Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.
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Evolución Biológica , Genoma , Anémonas de Mar/genética , Animales , Adhesión Celular , Evolución Molecular , Genes , Ligamiento Genético , Genoma Humano , Genómica , Humanos , Intrones , Redes y Vías Metabólicas , Familia de Multigenes , Músculos/fisiología , Fenómenos Fisiológicos del Sistema Nervioso , Filogenia , Anémonas de Mar/metabolismo , Análisis de Secuencia de ADN , Transducción de Señal , SinteníaRESUMEN
Eukaryotic genomes contain vast amounts of repetitive DNA derived from transposable elements (TEs). Large-scale sequencing of these genomes has produced an unprecedented wealth of information about the origin, diversity, and genomic impact of what was once thought to be "junk DNA." This has also led to the identification of two new classes of DNA transposons, Helitrons and Polintons, as well as several new superfamilies and thousands of new families. TEs are evolutionary precursors of many genes, including RAG1, which plays a role in the vertebrate immune system. They are also the driving force in the evolution of epigenetic regulation and have a long-term impact on genomic stability and evolution. Remnants of TEs appear to be overrepresented in transcription regulatory modules and other regions conserved among distantly related species, which may have implications for our understanding of their impact on speciation.
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Evolución Molecular , Genoma/fisiología , Secuencias Repetitivas de Ácidos Nucleicos/genética , Secuencias Repetitivas de Ácidos Nucleicos/fisiología , Animales , Secuencia Conservada/fisiología , Elementos Transponibles de ADN/genética , Elementos Transponibles de ADN/fisiología , Genes/fisiología , Especiación Genética , Humanos , Secuencias Repetidas Terminales/genética , Secuencias Repetidas Terminales/fisiologíaRESUMEN
Eukaryotes contain numerous transposable or mobile elements capable of parasite-like proliferation in the host genome. All known transposable elements in eukaryotes belong to two types: retrotransposons and DNA transposons. Here we report a previously uncharacterized class of DNA transposons called Polintons that populate genomes of protists, fungi, and animals, including entamoeba, soybean rust, hydra, sea anemone, nematodes, fruit flies, beetle, sea urchin, sea squirt, fish, lizard, frog, and chicken. Polintons from all these species are characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. In addition, Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Analogously to known transposable elements, Polintons exist as autonomous and nonautonomous elements. Our data suggest that Polintons have evolved from a linear plasmid that acquired a retroviral integrase at least 1 billion years ago. According to the model of Polinton transposition proposed here, a Polinton DNA molecule excised from the genome serves as a template for extrachromosomal synthesis of its double-stranded DNA copy by the Polinton-encoded DNA polymerase and is inserted back into genome by its integrase.
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Elementos Transponibles de ADN , Evolución Molecular , Hongos/genética , Genoma/genética , Urocordados/genética , Vertebrados/genética , Adenosina Trifosfatasas/clasificación , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/metabolismo , Animales , Secuencia de Bases , Cisteína Endopeptidasas/clasificación , Cisteína Endopeptidasas/genética , Cisteína Endopeptidasas/metabolismo , ADN Polimerasa beta/clasificación , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Hongos/enzimología , Datos de Secuencia Molecular , Filogenia , Urocordados/enzimología , Vertebrados/metabolismoRESUMEN
The V(D)J recombination reaction in jawed vertebrates is catalyzed by the RAG1 and RAG2 proteins, which are believed to have emerged approximately 500 million years ago from transposon-encoded proteins. Yet no transposase sequence similar to RAG1 or RAG2 has been found. Here we show that the approximately 600-amino acid "core" region of RAG1 required for its catalytic activity is significantly similar to the transposase encoded by DNA transposons that belong to the Transib superfamily. This superfamily was discovered recently based on computational analysis of the fruit fly and African malaria mosquito genomes. Transib transposons also are present in the genomes of sea urchin, yellow fever mosquito, silkworm, dog hookworm, hydra, and soybean rust. We demonstrate that recombination signal sequences (RSSs) were derived from terminal inverted repeats of an ancient Transib transposon. Furthermore, the critical DDE catalytic triad of RAG1 is shared with the Transib transposase as part of conserved motifs. We also studied several divergent proteins encoded by the sea urchin and lancelet genomes that are 25%-30% identical to the RAG1 N-terminal domain and the RAG1 core. Our results provide the first direct evidence linking RAG1 and RSSs to a specific superfamily of DNA transposons and indicate that the V(D)J machinery evolved from transposons. We propose that only the RAG1 core was derived from the Transib transposase, whereas the N-terminal domain was assembled from separate proteins of unknown function that may still be active in sea urchin, lancelet, hydra, and starlet sea anemone. We also suggest that the RAG2 protein was not encoded by ancient Transib transposons but emerged in jawed vertebrates as a counterpart of RAG1 necessary for the V(D)J recombination reaction.
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Anemone/genética , Elementos Transponibles de ADN/genética , Genes RAG-1 , Genoma , Hydra/genética , Recombinación Genética , Erizos de Mar/genética , VDJ Recombinasas/metabolismo , Aedes/genética , Animales , Drosophila/genética , Proteínas de Homeodominio/genética , HumanosRESUMEN
The type I restriction-modification (hsd) systems of 73 Campylobacter jejuni strains were characterized according to their DNA and amino acid sequences, and/or gene organization. A number of new genes were identified which are not present in the sequenced strain NCTC 11168. The closely related organism Helicobacter pylori has three type I systems; however, no evidence was found that C. jejuni strains contain multiple type I systems, although hsd loci are present in at least two different chromosomal locations. Also, unlike H. pylori, intervening ORFs are present, in some strains, between hsdR and hsdS and between hsdS and hsdM. No definitive function can be ascribed to these ORFs, designated here as rloA-H (R-linked ORF) and mloA-B (M-linked ORF). Based on parsimony analysis of amino acid sequences to assess character relatedness, the C. jejuni type I R-M systems are assigned to one of three families: 'IAB', 'IC' or 'IF'. This study confirms that HsdM proteins within a family are highly conserved but share little homology with HsdM proteins from other families. The 'IC' hsd loci are >99 % identical at the nucleotide level, as are the 'IF' hsd loci. Additionally, whereas the nucleotide sequences of the 'IAB' hsdR and hsdM genes show a high degree of similarity, the nucleotide sequences of the 'IAB' hsdS and rlo genes vary considerably. This diversity suggests that recombination between 'IAB' hsd loci would lead not only to new hsdS alleles but also to the exchange of rlo genes; five C. jejuni hsd loci are presumably the result of such recombination. The importance of these findings with regard to the evolution of C. jejuni type I R-M systems is discussed.
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Campylobacter jejuni/enzimología , Desoxirribonucleasas de Localización Especificada Tipo I/genética , Variación Genética , Animales , Proteínas Bacterianas/genética , Campylobacter jejuni/genética , Enzimas de Restricción-Modificación del ADN/genética , Proteínas de Escherichia coli/genética , Humanos , Datos de Secuencia Molecular , Filogenia , Análisis de Secuencia de ADNRESUMEN
Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.