Light on the cell cycle of the non-photosynthetic bacterium Ramlibacter tataouinensis

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.

In Vitro and in Silico Evidence of Phosphatase Diversity in the Biomineralizing Bacterium Ramlibacter tataouinensis

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.

P2TF: a comprehensive resource for analysis of prokaryotic transcription factors

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/.

Amlodipine in ischaemic left ventricular dysfunction with mild to moderate heart failure

OBJECTIVE

In this study, we evaluated the effectiveness of amlodipine in patients with severe ischaemic left ventricular dysfunction (LVD) and mild to moderate heart failure, but not current angina, assessing the effects of the drug on symptoms, left ventricular function and exercise capacity.

PATIENTS AND METHODS

We studied 36 patients with ischaemic LVD (radionuclide ejection fraction <40%, left ventricular end-diastolic dimension >60mm) and mild to moderate heart failure (NYHA class II or III) without angina treated with ACE inhibitors (36 of 36), digitalis (34 of 36) and diuretics (30 of 36). Among the 36 recruited patients, 33 fulfilled the study protocol, including 2 weeks of run-in (standard therapy), 8 weeks of treatment (standard therapy + amlodipine 5mg once daily) and 2 weeks of washout (standard therapy). Symptoms graded on a 10-point scale (heart failure score; a higher score representing improvement in symptoms), radionuclide left ventricular ejection fraction (rLVEF), echocardiographic left ventricular end-diastolic dimension (LVEDD), peak aerobic capacity (VO(2max)), exercise time (ET) and total work load (TWL) were measured after run-in, treatment and washout periods. All patients underwent coronary angiography and (201)Thallium (Tl) myocardial scintigraphy.

RESULTS

With respect to baseline and washout, after amlodipine treatment the HF score improved (6.6 +/- 1.3 after amlodipine vs 5.9 +/- 1 at baseline and 5.9 +/- 1.1 at washout; p < 0.02), rLVEF increased (33.12 +/- 9.02% vs 29.74 +/- 7.72% and 30.02 +/- 7.39%, respectively; p < 0.001), and VO(2max) (14.35 +/- 4.05 ml/kg/min vs 12.68 +/- 3.21 ml/kg/min and 12.62 +/- 3.59 ml/kg/min, respectively; p < 0.003), ET (440 +/- 169 sec vs 395 +/- 158 sec and 402 +/- 162 sec, respectively; p < 0.02) and TWL (2183.2 +/- 439 kpm vs 1615.5 +/- 427 kpm and 1708.8 +/- 437 kpm, respectively; p < 0.01) were also increased. The increase in VO(2max) was related to systolic blood pressure at rest and at the peak of exercise, and to the presence of viable and/or ischaemic myocardium at (201)Tl myocardial scintigraphy.

CONCLUSION

Amlodipine, in addition to standard therapy (including in all cases an ACE inhibitor), reduced symptoms and improved exercise capacity and ventricular function in patients with mild to moderate heart failure due to myocardial ischaemia. Thus, amlodipine is useful in patients with ischaemic LVD and heart failure without angina. The improvement in exercise capacity was greater in patients with scintigraphic evidence of viable and/or ischaemic myocardium and higher blood pressure. However, our study presented some limitations (i.e. an open study with few patients), and only generated a hypothesis that could lead to a wider, multicentre, cooperative trial. Treatment of patients with chronic ischaemic left ventricular dysfunction (LVD) with heart failure symptoms but without angina is a difficult clinical problem. Despite the fact that surgical myocardial revascularisation may improve survival, most patients are not good candidates for surgery. Thus, 'polypharmacy' remains the principal option for these individuals. ACE inhibitors have become a cornerstone in the treatment of all forms of LVD, and have been demonstrated to improve functional class and survival. Nitrates, digitalis and diuretics are also commonly used for their effects on symptoms. Despite there being no evidence that calcium antagonists are useful for the treatment of heart failure or impaired ventricular function after myocardial infarction, these drugs are still prescribed to many patients with ischaemic LVD. However, it is possible that the concomitant administration of ACE inhibitors could reduce the reflex neurohumoral activity caused by some calcium antagonists, while preserving some of the beneficial properties of these agents. Among other calcium antagonists, amlodipine does not adversely affect the clinical status of patients. Some studies have shown that it reduces symptoms, improves exercise tolerance and does not result in neurohormonal stimulation. Moreover, amlodipine appears to have a mortality benefit in patients with dilated cardiomyopathy but not in patients with underlying coronary disease where it appears to have a 'neutral' effect. Thus, it is not clear whether amlodipine is useful in patients with ischaemic LVD, particularly in patients with silent coronary artery disease. In this study, we evaluated the effectiveness of amlodipine, in addition to standard therapy, in patients with ischaemic LVD and mild to moderate heart failure, assessing the effects of the drug on symptoms, LV function and exercise capacity.

The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment

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.

Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing bacteria isolated from subdesert soil in Tunisia

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.

The NADP-reducing hydrogenase from Desulfovibrio fructosovorans: functional interaction between the C-terminal region of HndA and the N-terminal region of HndD subunits

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.

Construction and physiological studies of hydrogenase depleted mutants of Desulfovibrio fructosovorans

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.

Evidence for a fourth hydrogenase in Desulfovibrio fructosovorans

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.