Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA

<p>Abstract</p> <p>Background</p> <p>Archaea are prokaryotic organisms with simplified versions of eukaryotic transcription systems. Genes coding for the general transcription factors TBP and TFB are present in multiple copies in several Archaea, including <it>Halobacterium </it>sp. NRC-1. Multiple TBP and TFBs have been proposed to participate in transcription of genes via recognition and recruitment of RNA polymerase to different classes of promoters.</p> <p>Results</p> <p>We attempted to knock out all six TBP and seven TFB genes in <it>Halobacterium </it>sp. NRC-1 using the <it>ura</it>3-based gene deletion system. Knockouts were obtained for six out of thirteen genes, <it>tbp</it>CDF and <it>tfb</it>ACG, indicating that they are not essential for cell viability under standard conditions. Screening of a population of 1,000 candidate mutants showed that genes which did not yield mutants contained less that 0.1% knockouts, strongly suggesting that they are essential. The transcriptomes of two mutants, Δ<it>tbp</it>D and Δ<it>tfb</it>A, were compared to the parental strain and showed coordinate down regulation of many genes. Over 500 out of 2,677 total genes were regulated in the Δ<it>tbp</it>D and Δ<it>tfb</it>A mutants with 363 regulated in both, indicating that over 10% of genes in both strains require the action of both TbpD and TfbA for normal transcription. Culturing studies on the Δ<it>tbp</it>D and Δ<it>tfb</it>A mutant strains showed them to grow more slowly than the wild-type at an elevated temperature, 49°C, and they showed reduced viability at 56°C, suggesting TbpD and TfbA are involved in the heat shock response. Alignment of TBP and TFB protein sequences suggested the expansion of the TBP gene family, especially in <it>Halobacterium </it>sp. NRC-1, and TFB gene family in representatives of five different genera of haloarchaea in which genome sequences are available.</p> <p>Conclusion</p> <p>Six of thirteen TBP and TFB genes of <it>Halobacterium </it>sp. NRC-1 are non-essential under standard growth conditions. TbpD and TfbA coordinate the expression of over 10% of the genes in the NRC-1 genome. The Δ<it>tbp</it>D and Δ<it>tfb</it>A mutant strains are temperature sensitive, possibly as a result of down regulation of heat shock genes. Sequence alignments suggest the existence of several families of TBP and TFB transcription factors in <it>Halobacterium </it>which may function in transcription of different classes of genes.</p

A new Eocaiman (Alligatoridae, Crocodylia) from the Itaboraí Basin, Paleogene of Rio de Janeiro, Brazil

A new small species of Eocaiman is described on the basis of three anterior left mandibular rami and one isolated tooth. The specimens came from the middle-upper Paleocene Itabora ́ı Basin (Rio de Janeiro State, Brazil; Itaboraian South American Land Mammal Age). The new taxon differs from the other two Eocaiman species, such as its small size, likely participation of the splenial in the mandibular symphysis, a reduced angle between the longitudinal axis of the symphysis and the mandibular ramus, and enlarged ninth and tenth dentary teeth (in addition to the large first and fourth dentary teeth). The participation of the splenial in the mandibular symphysis is a unique character among caimanines (with the only possible exception being Tsoabichi greenriverensis). The new taxon provides new information on the taxonomic and anatomical diversity of the genus Eocaiman, a taxon of prime importance to understand the evolutionary origins of caimans given its position as the basalmost member of Caimaninae. Furthermore, the new taxon has a relatively small body size in comparison with other species of Eocaiman, a case paralleled by other Itaboraian reptilian groups (e.g. snakes), suggesting that this ecosystem provides critical data to test the relationship between reptilian body size and climate.Fil: Pinheiro, André E. P.. Universidade Federal do Rio de Janeiro. Departamento de Geologia. Laboratório de Macrofósseis; BrasilFil: Fortier, Daniel C.. Universidade Federal do Rio Grande do Sul; Brasil. Universidade Federal de Minas Gerais. Intituto de Geociências; BrasilFil: Pol, Diego. Museo Paleontológico Egidio Feruglio; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Campos, Diógenes A.. Museu de Ciências da Terra. Departamento Nacional de Produção Mineral; BrasilFil: Bergqvist, Lílian P.. Universidade Federal do Rio de Janeiro. Departamento de Geologia. Laboratório de Macrofósseis; Brasi