RESUMEN

Ramlibacter tataouinensis TTB310, a non-photosynthetic betaproteobacterium isolated from a semi-arid region of southern Tunisia, forms both rods and cysts. Cysts are resistant to desiccation and divide when water and nutrients are available. Rods are motile and capable of dissemination. Due to the strong correlation between sunlight and desiccation, light is probably an important external signal for anticipating desiccating conditions. Six genes encoding potential light sensors were identified in strain TTB310. Two genes encode for bacteriophytochromes, while the four remaining genes encode for putative blue light receptors. We determined the spectral and photochemical properties of the two recombinant bacteriophytochromes RtBphP1 and RtBphP2. In both cases, they act as sensitive red light detectors. Cyst divisions and a complete cyst-rod-cyst cycle are the main processes in darkness, whereas rod divisions predominate in red or far-red light. Mutant phenotypes caused by the inactivation of genes encoding bacteriophytochromes or heme oxygenase clearly show that both bacteriophytochromes are involved in regulating the rod-rod division. This process could favor rapid rod divisions at sunrise, after dew formation but before the progressive onset of desiccation. Our study provides the first evidence of a light-based strategy evolved in a non-photosynthetic bacterium to exploit scarse water in a desert environment.

Asunto(s)

Ciclo Celular/efectos de la radiación , Comamonadaceae/fisiología , Comamonadaceae/efectos de la radiación , Metabolismo Energético/efectos de la radiación , Luz , Oscuridad , Hemo Oxigenasa (Desciclizante)/metabolismo , Mutación , Fenotipo , Análisis Espectral

RESUMEN

Microbial phosphatase activity can trigger the precipitation of metal-phosphate minerals, a process called phosphatogenesis with global geochemical and environmental implications. An increasing diversity of phosphatases expressed by diverse microorganisms has been evidenced in various environments. However, it is challenging to link the functional properties of genomic repertoires of phosphatases with the phosphatogenesis capabilities of microorganisms. Here, we studied the betaproteobacterium Ramlibacter tataouinensis (Rta), known to biomineralize Ca-phosphates in the environment and the laboratory. We investigated the functional repertoire of this biomineralization process at the cell, genome and molecular level. Based on a mineralization assay, Rta is shown to hydrolyse the phosphoester bonds of a wide range of organic P molecules. Accordingly, its genome has an unusually high diversity of phosphatases: five genes belonging to two non-homologous families, phoD and phoX, were detected. These genes showed diverse predicted cis-regulatory elements. Moreover, they encoded proteins with diverse structural properties according to molecular models. Heterologously expressed PhoD and PhoX in Escherichia coli had different profiles of substrate hydrolysis. As evidenced for Rta cells, recombinant E. coli cells induced the precipitation of Ca-phosphate mineral phases, identified as poorly crystalline hydroxyapatite. The phosphatase genomic repertoire of Rta (containing phosphatases of both the PhoD and PhoX families) was previously evidenced as prevalent in marine oligotrophic environments. Interestingly, the Tataouine sand from which Rta was isolated showed similar P-depleted, but Ca-rich conditions. Overall, the diversity of phosphatases in Rta allows the hydrolysis of a broad range of organic P substrates and therefore the release of orthophosphates (inorganic phosphate) under diverse trophic conditions. Since the release of orthophosphates is key to the achievement of high saturation levels with respect to hydroxyapatite and the induction of phosphatogenesis, Rta appears as a particularly efficient driver of this process as shown experimentally.

RESUMEN

BACKGROUND: Transcription factors (TFs) are DNA-binding proteins that regulate gene expression by activating or repressing transcription. Some have housekeeping roles, while others regulate the expression of specific genes in response to environmental change. The majority of TFs are multi-domain proteins, and they can be divided into families according to their domain organisation. There is a need for user-friendly, rigorous and consistent databases to allow researchers to overcome the inherent variability in annotation between genome sequences. DESCRIPTION: P2TF (Predicted Prokaryotic Transcription Factors) is an integrated and comprehensive database relating to transcription factor proteins. The current version of the database contains 372,877 TFs from 1,987 completely sequenced prokaryotic genomes and 43 metagenomes. The database provides annotation, classification and visualisation of TF genes and their genetic context, providing researchers with a one-stop shop in which to investigate TFs. The P2TF database analyses TFs in both predicted proteomes and reconstituted ORFeomes, recovering approximately 3% more TF proteins than just screening predicted proteomes. Users are able to search the database with sequence or domain architecture queries, and resulting hits can be aligned to investigate evolutionary relationships and conservation of residues. To increase utility, all searches can be filtered by taxonomy, TF genes can be added to the P2TF cart, and gene lists can be exported for external analysis in a variety of formats. CONCLUSIONS: P2TF is an open resource for biologists, allowing exploration of all TFs within prokaryotic genomes and metagenomes. The database enables a variety of analyses, and results are presented for user exploration as an interactive web interface, which provides different ways to access and download the data. The database is freely available at http://www.p2tf.org/.

Asunto(s)

Bases de Datos de Proteínas , Metagenoma , Anotación de Secuencia Molecular , Células Procariotas/metabolismo , Programas Informáticos , Factores de Transcripción/genética , Evolución Biológica , Regulación de la Expresión Génica , Internet , Sistemas de Lectura Abierta , Filogenia , Estructura Terciaria de Proteína , Factores de Transcripción/metabolismo

RESUMEN

Ramlibacter tataouinensis TTB310(T) (strain TTB310), a betaproteobacterium isolated from a semi-arid region of South Tunisia (Tataouine), is characterized by the presence of both spherical and rod-shaped cells in pure culture. Cell division of strain TTB310 occurs by the binary fission of spherical "cyst-like" cells ("cyst-cyst" division). The rod-shaped cells formed at the periphery of a colony (consisting mainly of cysts) are highly motile and colonize a new environment, where they form a new colony by reversion to cyst-like cells. This unique cell cycle of strain TTB310, with desiccation tolerant cyst-like cells capable of division and desiccation sensitive motile rods capable of dissemination, appears to be a novel adaptation for life in a hot and dry desert environment. In order to gain insights into strain TTB310's underlying genetic repertoire and possible mechanisms responsible for its unusual lifestyle, the genome of strain TTB310 was completely sequenced and subsequently annotated. The complete genome consists of a single circular chromosome of 4,070,194 bp with an average G+C content of 70.0%, the highest among the Betaproteobacteria sequenced to date, with total of 3,899 predicted coding sequences covering 92% of the genome. We found that strain TTB310 has developed a highly complex network of two-component systems, which may utilize responses to light and perhaps a rudimentary circadian hourglass to anticipate water availability at the dew time in the middle/end of the desert winter nights and thus direct the growth window to cyclic water availability times. Other interesting features of the strain TTB310 genome that appear to be important for desiccation tolerance, including intermediary metabolism compounds such as trehalose or polyhydroxyalkanoate, and signal transduction pathways, are presented and discussed.

Asunto(s)

Adaptación Fisiológica/genética , División Celular/genética , Comamonadaceae/citología , Comamonadaceae/fisiología , Clima Desértico , Genoma Bacteriano , Genómica , Adaptación Fisiológica/efectos de la radiación , Metabolismo de los Hidratos de Carbono/genética , Metabolismo de los Hidratos de Carbono/efectos de la radiación , División Celular/efectos de la radiación , Membrana Celular/metabolismo , Membrana Celular/efectos de la radiación , Movimiento Celular/genética , Movimiento Celular/efectos de la radiación , Forma de la Célula/genética , Forma de la Célula/efectos de la radiación , Ritmo Circadiano/genética , Ritmo Circadiano/efectos de la radiación , Comamonadaceae/enzimología , Comamonadaceae/genética , Reparación del ADN/genética , Reparación del ADN/efectos de la radiación , ADN Bacteriano/genética , Espacio Extracelular/genética , Espacio Extracelular/metabolismo , Espacio Extracelular/efectos de la radiación , Ácidos Grasos/metabolismo , Hidrólisis/efectos de la radiación , Luz , Fluidez de la Membrana/genética , Fluidez de la Membrana/efectos de la radiación , Lípidos de la Membrana/metabolismo , Presión Osmótica/efectos de la radiación , Estrés Oxidativo/genética , Estrés Oxidativo/efectos de la radiación , Polisacáridos Bacterianos/biosíntesis , Polisacáridos Bacterianos/metabolismo , Transporte de Proteínas/genética , Transporte de Proteínas/efectos de la radiación , Análisis de Secuencia de ADN , Transducción de Señal/genética , Transducción de Señal/efectos de la radiación , Trehalosa/biosíntesis , Trehalosa/metabolismo

RESUMEN

Ramlibacter gen. nov. is proposed for two aerobic, chemo-organotrophic, cyst-producing soil bacterial strains. These bacteria are Gram-negative, non-flagellated rods or cysts, isolated from subdesert soil in Tataouine, Tunisia. Phylogenetic analyses of the rrs sequences of the two strains showed that they do not constitute a robust clade at the genus level with any previously described bacteria and that they are a deep branch of a clade also grouping the genera Acidovorax and Hydrogenophaga within the beta-Proteobacteria. They belong to two different species, as verified by DNA-DNA hybridization (23.5% reassociation). The type species of the genus is Ramlibacter tataouinensis sp. nov., with the type strain TTB310T (=DSM 14655T =ATCC BAA-407T =LMG 21543T). The second species is Ramlibacter henchirensis sp. nov., with the type strain TMB834T (=DSM 14656T =ATCC BAA-408T =LMG 21542T). The G + C contents of R. tataouinensis and R. henchirensis are 69.6 and 66.6 mol%, respectively.

Asunto(s)

Betaproteobacteria/clasificación , Microbiología del Suelo , Betaproteobacteria/genética , Betaproteobacteria/aislamiento & purificación , Betaproteobacteria/metabolismo , ADN Bacteriano/química , ADN Bacteriano/genética , Ácidos Grasos/análisis , Microscopía de Contraste de Fase , Datos de Secuencia Molecular , Hibridación de Ácido Nucleico , Filogenia , Túnez

RESUMEN

The hndABCD operon from Desulfovibrio fructosovorans encodes an uncommon heterotetrameric NADP-reducing iron hydrogenase. The presence of a [2Fe-2S] cluster likely located in the C-terminal region of the HndA subunit has already been revealed. We have cloned and expressed the truncated hndA gene in Escherichia coli to isolate the structural [2Fe-2S] module. Optical and EPR spectra are found identical to that of the native HndA subunit and the midpoint redox potential (-385 mV) is similar to that of the native protein (-395 mV). These results clearly demonstrate that the C-terminal region of HndA is a structurally independent [2Fe2S] ferredoxin-like domain. In the same way, the N-terminal domain of the HndD subunit was overproduced in E. coli and characterized. The presence of a [2Fe-2S] cluster was evidenced by optical spectroscopy. The midpoint redox potential (-380 mV) of this domain was found very close to that of the truncated HndA subunit but the EPR properties were significantly different. The various EPR properties allowed us to observe an electron exchange between the two [2Fe-2S] ferredoxin-like domains of the HndA and HndD subunits. Moreover, domain-domain interactions, observed by far-western experiments, indicate that these subunits are direct partners in the native complex.

Asunto(s)

Desulfovibrio/enzimología , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Espectroscopía de Resonancia por Spin del Electrón , Genes Bacterianos , Datos de Secuencia Molecular , Operón , Oxidación-Reducción , Oxidorreductasas/química , Subunidades de Proteína/genética , Subunidades de Proteína/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alineación de Secuencia

RESUMEN

Desulfovibrio fructosovorans possesses two periplasmic hydrogenases (a nickel-iron and an iron hydrogenase) and a cytoplasmic NADP-dependent hydrogenase. The hydAB genes encoding the periplasmic iron hydrogenase were replaced, in the wild-type strain as well as in single mutants depleted of one of the other two hydrogenases, by the acc1 gene encoding resistance to gentamycin. Molecular characterization and remaining activity measurements of the resulting single and double mutants were performed. All mutated strains exhibited similar growth when H(2) was the electron donor but they grew differently on fructose, lactate or pyruvate as electron donors. Our results indicate that the loss of one enzyme might be compensated by another even though hydrogenases have different localization in the cells.

Asunto(s)

Desulfovibrio/enzimología , Desulfovibrio/crecimiento & desarrollo , Eliminación de Gen , Hidrogenasas/metabolismo , Proteínas Bacterianas , Medios de Cultivo , Desulfovibrio/genética , Deuterio , Electroporación , Hidrogenasas/genética , Proteínas Hierro-Azufre/genética , Proteínas Hierro-Azufre/metabolismo , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Protones , Sulfatos/metabolismo , Transformación Bacteriana

RESUMEN

A strain devoid of the three hydrogenases characterized for Desulfovibrio fructosovorans was constructed using marker exchange mutagenesis. As expected, the H(2)-dependent methyl viologen reduction activity of the strain was null, but physiological studies showed no striking differences between the mutated and wild-type strains. The H(+)-D(2) exchange activity measured in the mutated strain indicates the presence of a fourth hydrogenase in D. fructosovorans.

Asunto(s)

Desulfovibrio/enzimología , Hidrogenasas/aislamiento & purificación , Proteínas Bacterianas , Desulfovibrio/genética , Deuterio , Hidrogenasas/genética , Proteínas Hierro-Azufre/genética , Mutagénesis , Oxidorreductasas/genética , Paraquat/metabolismo