Osmoprotectants in Halomonas elongata: high-affinity betaine transport system and choline-betaine pathway

Osmotic Contribution of Synthesized Betaine by Choline Dehydrogenase Using In Vivo and In Vitro Models of Post-traumatic Syringomyelia

Introduction

Syringomyelia (SM) is a debilitating spinal cord disorder in which a cyst, or syrinx, forms in the spinal cord parenchyma due to congenital and acquired causes. Over time syrinxes expand and elongate, which leads to compressing the neural tissues and a mild to severe range of symptoms. In prior omics studies, significant upregulation of betaine and its synthesis enzyme choline dehydrogenase (CHDH) were reported during syrinx formation/expansion in SM injured spinal cords, but the role of betaine regulation in SM etiology remains unclear. Considering betaine's known osmoprotectant role in biological systems, along with antioxidant and methyl donor activities, this study aimed to better understand osmotic contributions of synthesized betaine by CHDH in response to SM injuries in the spinal cord.

Methods

A post-traumatic SM (PTSM) rat model and in vitro cellular models using rat astrocytes and HepG2 liver cells were utilized to investigate the role of betaine synthesis by CHDH. Additionally, the osmotic contributions of betaine were evaluated using a combination of experimental as well as simulation approaches.

Results

In the PTSM injured spinal cord CHDH expression was observed in cells surrounding syrinxes. We next found that rat astrocytes and HepG2 cells were capable of synthesizing betaine via CHDH under osmotic stress in vitro to maintain osmoregulation. Finally, our experimental and simulation approaches showed that betaine was capable of directly increasing meaningful osmotic pressure.

Conclusions

The findings from this study demonstrate new evidence that CHDH activity in the spinal cord provides locally synthesized betaine for osmoregulation in SM pathophysiology.

Supplementary Information

The online version of this article contains supplementary material available 10.1007/s12195-022-00749-5.

Comparative Genomic Analysis of Labrenzia aggregata (Alphaproteobacteria) Strains Isolated From the Mariana Trench: Insights Into the Metabolic Potentials and Biogeochemical Functions

Hadal zones are marine environments deeper than 6,000 m, most of which comprise oceanic trenches. Microbes thriving at such depth experience high hydrostatic pressure and low temperature. The genomic potentials of these microbes to such extreme environments are largely unknown. Here, we compare five complete genomes of bacterial strains belonging to Labrenzia aggregata (Alphaproteobacteria), including four from the Mariana Trench at depths up to 9,600 m and one reference from surface seawater of the East China Sea, to uncover the genomic potentials of this species. Genomic investigation suggests all the five strains of L. aggregata as participants in nitrogen and sulfur cycles, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), thiosulfate oxidation, and dimethylsulfoniopropionate (DMSP) biosynthesis and degradation. Further comparisons show that, among the five strains, 85% gene functions are similar with 96.7% of them encoded on the chromosomes, whereas the numbers of functional specific genes related to osmoregulation, antibiotic resistance, viral infection, and secondary metabolite biosynthesis are majorly contributed by the differential plasmids. A following analysis suggests the plasmidic gene numbers increase along with isolation depth and most plasmids are dissimilar among the five strains. These findings provide a better understanding of genomic potentials in the same species throughout a deep-sea water column and address the importance of externally originated plasmidic genes putatively shaped by deep-sea environment.

Molecular insights into the urea-choline-O-sulfate interactions in aqueous solution

Urea and choline-O-sulfate (COS) are both osmolytes, but have opposite effects on protein structure. Urea has been well-known for years to destabilize protein structure. Though COS has been revealed as an osmoprotective molecule against urea induced denaturation of proteins, the mechanism of this compensation is still unexplored. This study focuses on a theoretical investigation of the interdependent behavior of urea and COS in a mixture, to explore how urea becomes a weaker denaturing agent in the presence of COS. In this study, we have considered every possible interaction among the solute (urea and COS) and solvent (water) both at room temperature and high temperature, employing two different force field parameters i.e., CHARMM General Force Field parameters (CGenFF) and General AMBER Force Field (GAFF) parameters through classical molecular dynamics simulation studies. Different techniques have been used to analyze the average interactions between COS and urea as well as their solvation properties, which show that in the presence of COS, urea becomes a less effective denaturant than when alone. The water-water interaction shows that the mixed osmolyte solution of urea and COS strengthens the water hydrogen bonding network. The enhanced solvation of urea and COS in the urea-COS mixture and their mutual interactions, results in the exclusion of free urea as well as COS from the solution. This synergistic behavior of urea and COS could be the major reason behind COS counteracting urea's denaturation of proteins.

Osmoregulatory Role of Betaine and Betaine/γ-Aminobutyric Acid Transporter 1 in Post-Traumatic Syringomyelia

Syringomyelia (SM) is primarily characterized by the formation of a fluid-filled cyst that forms in the parenchyma of the spinal cord following injury or other pathology. Recent omics studies in animal models have identified dysregulation of solute carriers, channels, transporters, and small molecules associated with osmolyte regulation during syrinx formation/expansion in the spinal cord. However, their connections to syringomyelia etiology are poorly understood. In this study, the biological functions of the potent osmolyte betaine and its associated solute carrier betaine/γ-aminobutyric acid (GABA) transporter 1 (BGT1) were studied in SM. First, a rat post-traumatic SM model was used to demonstrate that the BGT1 was primarily expressed in astrocytes in the vicinity of syrinxes. In an in vitro system, we found that astrocytes uptake betaine through BGT1 to regulate cell size under hypertonic conditions. Treatment with BGT1 inhibitors, especially NNC 05-2090, demonstrated midhigh micromolar range potency in vitro that reversed the osmoprotective effects of betaine. Finally, the specificity of these BGT1 inhibitors in the CNS was demonstrated in vivo, suggesting feasibility for targeting betaine transport in SM. In summary, these data provide an enhanced understanding of the role of betaine and its associated solute carrier BGT1 in cell osmoregulation and implicates the active role of betaine and BGT1 in syringomyelia progression.

The diversity of unique 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid coding common genes and Universal stress protein in Ectoine TRAP cluster (UspA) in 32 Halomonas species

OBJECTIVES

To decipher the diversity of unique ectoine-coding housekeeping genes in the genus Halomonas.

RESULTS

In Halomonas, 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid has a crucial role as a stress-tolerant chaperone, a compatible solute, a cell membrane stabilizer, and a reduction in cell damage under stressful conditions. Apart from the current 16S rRNA biomarker, it serves as a blueprint for identifying Halomonas species. Halomonas elongata 1H9 was found to have 11 ectoine-coding genes. The presence of a superfamily of conserved ectoine-coding among members of the genus Halomonas was discovered after genome annotations of 93 Halomonas spp. As a result of the inclusion of 11 single copy ectoine coding genes in 32 Halomonas spp., genome-wide evaluations of ectoine coding genes indicate that 32 Halomonas spp. have a very strong association with H. elongata 1H9, which has been proven evidence-based approach to elucidate phylogenetic relatedness of ectoine-coding child taxa in the genus Halomonas. Total 32 Halomonas species have a single copy number of 11 distinct ectoine-coding genes that help Halomonas spp., produce ectoine under stressful conditions. Furthermore, the existence of the Universal stress protein (UspA) gene suggests that Halomonas species developed directly from primitive bacteria, highlighting its role during the progression of microbial evolution.

Arsenocholine-O-sulfate: A novel compound as major arsenic species in the parasitic mushroom Tolypocladium ophioglossoides

The As concentrations, along with 34 other elements, and the As speciation were investigated in wild-grown samples of the parasitic mushroom Tolypocladium ophioglossoides with inductively coupled plasma mass spectrometry (ICPMS) and high performance liquid chromatography coupled to ICPMS. The As concentrations were 0.070-3.44 mg kg^-1 dry mass. More remarkable was the As speciation, where up to 56% of the extracted As were found to be an unknown As species, which was marginally retained under anion- and also cation-exchange conditions. After testing several different chromatographic settings, the compound was finally isolated and identified as 2-(sulfoxyethyl) trimethylarsonium ion (in short: arsenocholine-O-sulfate) with high resolution mass spectrometry. The compound was synthesized and further quantified in all investigated samples via ion-pair chromatography coupled to ICPMS. In addition to the high abundance of arsenocholine-O-sulfate in T. ophioglossoides, small amounts of this As species were also detected in one sample of the host mushroom, Elaphomyces asperulus. In a sample of another parasitic mushroom, Ophiocordyceps sinensis, arsenocholine-O-sulfate could not be detected, but the main species was another unknown compound that was oxidized to inorganic As(V) with hydrogen peroxide. This is the first discovery of arsenocholine-O-sulfate in nature. It is possible that it is present in many other organisms, at least in low concentrations, and just has not been detected there yet because of its unusual chromatographic behavior. The existence of arsenocholine-O-sulfate brings up questions again about the biotransformation pathways of As in the environment and the specific behavior of fungi.

Affinity tag effect on the salt rejection potential of Halomonas elongata aquaporin incorporated in thin film nanocomposite membrane

In this study, effect of affinity tags, Histidine (His) and Glutathione-S-Transferase (GST), on the activity of halophilic aquaporin was analyzed. The gene coding for H. elongata aquaporin was cloned into pET28a vector and expressed in E. coli BL21 successfully. Stopped flow light scattering measurements showed that His-tagged aquaporin is functional. The difference in the filtration parameters caused by affinity tags were determined by using thin film composite nano-filtration (NFC) membranes prepared with the aquaporins. At 100 mM salt concentration, water permeability (L/m².h) and the % salt rejection of NFC membranes produced with the His-tagged aquaporin was found to be higher than that of the membrane with GST-tagged aquaporin. Salt rejection of His-tagged aquaporin-membrane was found to be 53% with a lower solute permeability value (B). Use of short affinity tag (His tag) for cloning resulted in higher solute rejection ability of TFC membranes prepared with H. elongata aquaporins.

Betaine accumulation suppresses the de-novo synthesis of ectoine at a low osmotic concentration in Halomonas sp SBS 10, a bacterium with broad salinity tolerance

The study aims to find out osmoadaptive mechanism used to overcome the salinity stress by Halomonas sp SBS 10 isolated from the saltern crystallizer ponds of the Sambhar Salt Lake and its taxonomic position using neighbor-joining algorithm. The strain SBS 10 was tested for accumulation of two major compatable solutes betaine and ectoine and was observed that osmoprotection in the strain SBS 10 is achieved by the accumulation of betaine or by the de-novo synthesis of betaine or ectoine. Amount of endogenous content of the betaine and ectoine per milligram of cell biomass was estimated to be 581 µg, 587 µg, 588 µg, 617 µg, and 761 µg for betaine and 1.52 µg, 2.74 µg, 3.14 µg, 3.50 µg, and 52.67 µg for ectoine, when exposed to 5, 10, 15, 20 and 25% of NaCl concentration. Results obtained from HPLC analysis showed that the betaine accumulation suppresses the de-novo synthesis of ectoine partially at low NaCl concentration in the growth medium. However, at a high NaCl concentration, the ectoine concentration increases abruptly as compared to the betaine. This indicates that the ectoine accumulation is transcriptionally up-regulated by the salinity stress. Phylogenetic analysis based on the neighbor-joining algorithm included the strain SBS 10 in the genus Halomonas of the family Halomonadaceae belonging to the class Gammaproteobacteria. Most closely related type strain was found to be Halomonas gudaonensis SL014B-69^T (98.2% similarity). Ultrastructure characteristics showed the strain to be non-spore forming rod, 0.3-0.4 × 0.75-1.65 μm in size and motile with the help of peritrichous flagella.

Betaine accumulation suppresses the de-novo synthesis of ectoine at a low osmotic concentration in Halomonas sp SBS 10, a bacterium with broad salinity tolerance

The study aims to find out osmoadaptive mechanism used to overcome the salinity stress by Halomonas sp SBS 10 isolated from the saltern crystallizer ponds of the Sambhar Salt Lake and its taxonomic position using neighbor-joining algorithm. The strain SBS 10 was tested for accumulation of two major compatable solutes betaine and ectoine and was observed that osmoprotection in the strain SBS 10 is achieved by the accumulation of betaine or by the de-novo synthesis of betaine or ectoine. Amount of endogenous content of the betaine and ectoine per milligram of cell biomass was estimated to be 581 µg, 587 µg, 588 µg, 617 µg, and 761 µg for betaine and 1.52 µg, 2.74 µg, 3.14 µg, 3.50 µg, and 52.67 µg for ectoine, when exposed to 5, 10, 15, 20 and 25% of NaCl concentration. Results obtained from HPLC analysis showed that the betaine accumulation suppresses the de-novo synthesis of ectoine partially at low NaCl concentration in the growth medium. However, at a high NaCl concentration, the ectoine concentration increases abruptly as compared to the betaine. This indicates that the ectoine accumulation is transcriptionally up-regulated by the salinity stress. Phylogenetic analysis based on the neighbor-joining algorithm included the strain SBS 10 in the genus Halomonas of the family Halomonadaceae belonging to the class Gammaproteobacteria. Most closely related type strain was found to be Halomonas gudaonensis SL014B-69^T (98.2% similarity). Ultrastructure characteristics showed the strain to be non-spore forming rod, 0.3-0.4 × 0.75-1.65 μm in size and motile with the help of peritrichous flagella.

Characterization of a Glycyl-Specific TET Aminopeptidase Complex from Pyrococcus horikoshii

The TET peptidases are large self-compartmentalized complexes that form dodecameric particles. These metallopeptidases, members of the M42 family, are widely distributed in prokaryotes. Three different versions of TET complexes, with different substrate specificities, were found to coexist in the cytosol of the hyperthermophilic archaeon Pyrococcus horikoshii In the present work, we identified a novel type of TET complex that we named PhTET4. The recombinant PhTET4 enzyme was found to self-assemble as a tetrahedral edifice similar to other TET complexes. We determined PhTET4 substrate specificity using a broad range of monoacyl chromogenic and fluorogenic compounds. High-performance liquid chromatographic peptide degradation assays were also performed. These experiments demonstrated that PhTET4 is a strict glycyl aminopeptidase, devoid of amidolytic activity toward other types of amino acids. The catalytic efficiency of PhTET4 was studied under various conditions. The protein was found to be a hyperthermophilic alkaline aminopeptidase. Interestingly, unlike other peptidases from the same family, it was activated only by nickel ions.IMPORTANCE We describe here the first known peptidase displaying exclusive activity toward N-terminal glycine residues. This work indicates a specific role for intracellular glycyl peptidases in deep sea hyperthermophilic archaeal metabolism. These observations also provide critical evidence for the use of these archaeal extremozymes for biotechnological applications.

Quantitative RNA-seq Analysis Unveils Osmotic and Thermal Adaptation Mechanisms Relevant for Ectoine Production in Chromohalobacter salexigens

Quantitative RNA sequencing (RNA-seq) and the complementary phenotypic assays were implemented to investigate the transcriptional responses of Chromohalobacter salexigens to osmotic and heat stress. These conditions trigger the synthesis of ectoine and hydroxyectoine, two compatible solutes of biotechnological interest. Our findings revealed that both stresses make a significant impact on C. salexigens global physiology. Apart from compatible solute metabolism, the most relevant adaptation mechanisms were related to “oxidative- and protein-folding- stress responses,” “modulation of respiratory chain and related components,” and “ion homeostasis.” A general salt-dependent induction of genes related to the metabolism of ectoines, as well as repression of ectoine degradation genes by temperature, was observed. Different oxidative stress response mechanisms, secondary or primary, were induced at low and high salinity, respectively, and repressed by temperature. A higher sensitivity to H₂O₂ was observed at high salinity, regardless of temperature. Low salinity induced genes involved in “protein-folding-stress response,” suggesting disturbance of protein homeostasis. Transcriptional shift of genes encoding three types of respiratory NADH dehydrogenases, ATP synthase, quinone pool, Na⁺/H⁺ antiporters, and sodium-solute symporters, was observed depending on salinity and temperature, suggesting modulation of the components of the respiratory chain and additional systems involved in the generation of H⁺ and/or Na⁺ gradients. Remarkably, the Na⁺ intracellular content remained constant regardless of salinity and temperature. Disturbance of Na⁺- and H⁺-gradients with specific ionophores suggested that both gradients influence ectoine production, but with differences depending on the solute, salinity, and temperature conditions. Flagellum genes were strongly induced by salinity, and further induced by temperature. However, salt-induced cell motility was reduced at high temperature, possibly caused by an alteration of Na⁺ permeability by temperature, as dependence of motility on Na⁺-gradient was observed. The transcriptional induction of genes related to the synthesis and transport of siderophores correlated with a higher siderophore production and intracellular iron content only at low salinity. An excess of iron increased hydroxyectoine accumulation by 20% at high salinity. Conversely, it reduced the intracellular content of ectoines by 50% at high salinity plus high temperature. These findings support the relevance of iron homeostasis for osmoadaptation, thermoadaptation and accumulation of ectoines, in C. salexigens.

Understanding the interplay of carbon and nitrogen supply for ectoines production and metabolic overflow in high density cultures of Chromohalobacter salexigens

Background

The halophilic bacterium Chromohalobacter salexigens has been proposed as promising cell factory for the production of the compatible solutes ectoine and hydroxyectoine. This bacterium has evolved metabolic adaptations to efficiently grow under high salt concentrations by accumulating ectoines as compatible solutes. However, metabolic overflow, which is a major drawback for the efficient conversion of biological feedstocks, occurs as a result of metabolic unbalances during growth and ectoines production. Optimal production of ectoines is conditioned by the interplay of carbon and nitrogen metabolisms. In this work, we set out to determine how nitrogen supply affects the production of ectoines.

Results

Chromohalobacter salexigens was challenged to grow in media with unbalanced carbon/nitrogen ratio. In C. salexigens, overflow metabolism and ectoines production are a function of medium composition. At low ammonium conditions, the growth rate decreased importantly, up to 80%. Shifts in overflow metabolism were observed when changing the C/N ratio in the culture medium. ¹³C-NMR analysis of ectoines labelling revealed a high metabolic rigidity, with almost constant flux ratios in all conditions assayed. Unbalanced C/N ratio led to pyruvate accumulation, especially upon N-limitation. Analysis of an ect⁻ mutant demonstrated the link between metabolic overflow and ectoine biosynthesis. Under non ectoine synthesizing conditions, glucose uptake and metabolic overflow decreased importantly. Finally, in fed-batch cultures, biomass yield was affected by the feeding scheme chosen. High growth (up to 42.4 g L⁻¹) and volumetric ectoine yields (up to 4.21 g L⁻¹) were obtained by minimizing metabolite overflow and nutrient accumulation in high density cultures in a low nitrogen fed-batch culture. Moreover, the yield coefficient calculated for the transformation of glucose into biomass was 30% higher in fed-batch than in the batch culture, demonstrating that the metabolic efficiency of C. salexigens can be improved by careful design of culture feeding schemes.

Conclusions

Metabolic shifts observed at low ammonium concentrations were explained by a shift in the energy required for nitrogen assimilation. Carbon-limited fed-batch cultures with reduced ammonium supply were the best conditions for cultivation of C. salexigens, supporting high density growth and maintaining high ectoines production.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0643-7) contains supplementary material, which is available to authorized users.

Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments

The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.

Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade

Choline is ubiquitous in marine eukaryotes and appears to be widely distributed in surface marine waters; however, its metabolism by marine bacteria is poorly understood. Here, using comparative genomics and molecular genetic approaches, we reveal that the capacity for choline catabolism is widespread in marine heterotrophs of the marine Roseobacter clade (MRC). Using the model bacterium Ruegeria pomeroyi, we confirm that the betA, betB and betC genes, encoding choline dehydrogenase, betaine aldehyde dehydrogenase and choline sulfatase, respectively, are involved in choline metabolism. The betT gene, encoding an organic solute transporter, was essential for the rapid uptake of choline but not glycine betaine (GBT). Growth of choline and GBT as a sole carbon source resulted in the re‐mineralization of these nitrogen‐rich compounds into ammonium. Oxidation of the methyl groups from choline requires formyltetrahydrofolate synthetase encoded by fhs in R. pomeroyi, deletion of which resulted in incomplete degradation of GBT. We demonstrate that this was due to an imbalance in the supply of reducing equivalents required for choline catabolism, which can be alleviated by the addition of formate. Together, our results demonstrate that choline metabolism is ubiquitous in the MRC and reveal the role of Fhs in methyl group oxidation in R. pomeroyi.

Glutamine synthetase 2 is not essential for biosynthesis of compatible solutes in Halobacillus halophilus

Halobacillus halophilus, a moderately halophilic bacterium isolated from salt marshes, produces various compatible solutes to cope with osmotic stress. Glutamate and glutamine are dominant compatible solutes at mild salinities. Glutamine synthetase activity in cell suspensions of Halobacillus halophilus wild type was shown to be salt dependent and chloride modulated. A possible candidate to catalyze glutamine synthesis is glutamine synthetase A2, whose transcription is stimulated by chloride. To address the role of GlnA2 in the biosynthesis of the osmolytes glutamate and glutamine, a deletion mutant (ΔglnA2) was generated and characterized in detail. We compared the pool of compatible solutes and performed transcriptional analyses of the principal genes controlling the solute production in the wild type strain and the deletion mutant. These measurements did not confirm the hypothesized role of GlnA2 in the osmolyte production. Most likely the presence of another, yet to be identified enzyme has the main contribution in the measured activity in crude extracts and probably determines the total chloride-modulated profile. The role of GlnA2 remains to be elucidated.

Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics

A metagenome was obtained by pyrosequencing the total prokaryotic DNA from the water of a pond with intermediate salinity (13% salts) from a saltern located in Santa Pola, Spain. We analyzed and compared the phylogenomic and metabolic diversity of this saltern pond with respect to other two metagenomes obtained previously from the same saltern (ponds with 19% and 37% salts, respectively) and two reference metagenomes from marine and coastal lagoon habitats. A large microbial diversity, representing seven major higher taxa (Euryarchaeota, Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia and Betaproteobacteria), was found. However, most sequences (57%) were not assigned to any previously described genus. Principal component analysis of tetranucleotide frequencies of assembled contigs showed the presence of new groups of Euryarchaeota, different from those previously described but related to Haloquadratum walsbyi and other members of the Halobacteriaceae. Besides, some new Gammaproteobacteria, several closely related to the recently isolated bacterium 'Spiribacter salinus' were observed. Metabolically, the nitrogen and carbon cycles appear to be very simplified in this extreme habitat. Light is extensively used as energy source by bacteriorhodopsins and other rhodopsins. Microorganisms known to use the 'salt-in' strategy are probably able to combine the accumulation of potassium ions and of compatible solutes.

Microbial diversity and the presence of algae in halite endolithic communities are correlated to atmospheric moisture in the hyper-arid zone of the Atacama Desert

The Atacama Desert is one of the oldest and driest deserts in the world, and its hyper-arid core is described as 'the most barren region imaginable'. We used a combination of high-throughput sequencing and microscopy methods to characterize the endolithic microbial assemblages of halite pinnacles (salt rocks) collected in several hyper-arid areas of the desert. We found communities dominated by archaea that relied on a single phylotype of Halothece cyanobacteria for primary production. A few other phylotypes of salt-adapted bacteria and archaea, including Salinibacter, Halorhabdus, and Halococcus were major components of the halite communities, indicating specific adaptations to the unique halite environments. Multivariate statistical analyses of diversity metrics clearly separated the halite communities from that of the surrounding soil in the Yungay area. These analyses also revealed distribution patterns of halite communities correlated with atmospheric moisture. Microbial endolithic communities from halites exposed to coastal fogs and high relative humidity were more diverse; their archaeal and bacterial assemblages were accompanied by a novel algae related to oceanic picoplankton of the Mamiellales. In contrast, we did not find any algae in the Yungay pinnacles, suggesting that the environmental conditions in this habitat might be too extreme for eukaryotic photosynthetic life.

Proteogenomic insights into salt tolerance by a halotolerant alpha-proteobacterium isolated from an Andean saline spring

Tistlia consotensis is a halotolerant Rhodospirillaceae that was isolated from a saline spring located in the Colombian Andes with a salt concentration close to seawater (4.5%w/vol). We cultivated this microorganism in three NaCl concentrations, i.e. optimal (0.5%), without (0.0%) and high (4.0%) salt concentration, and analyzed its cellular proteome. For assigning tandem mass spectrometry data, we first sequenced its genome and constructed a six reading frame ORF database from the draft sequence. We annotated only the genes whose products (872) were detected. We compared the quantitative proteome data sets recorded for the three different growth conditions. At low salinity general stress proteins (chaperons, proteases and proteins associated with oxidative stress protection), were detected in higher amounts, probably linked to difficulties for proper protein folding and metabolism. Proteogenomics and comparative genomics pointed at the CrgA transcriptional regulator as a key-factor for the proteome remodeling upon low osmolarity. In hyper-osmotic condition, T. consotensis produced in larger amounts proteins involved in the sensing of changes in salt concentration, as well as a wide panel of transport systems for the transport of organic compatible solutes such as glutamate. We have described here a straightforward procedure in making a new environmental isolate quickly amenable to proteomics.

BIOLOGICAL SIGNIFICANCE

The bacterium Tistlia consotensis was isolated from a saline spring in the Colombian Andes and represents an interesting environmental model to be compared with extremophiles or other moderate organisms. To explore the halotolerance molecular mechanisms of the bacterium T. consotensis, we developed an innovative proteogenomic strategy consisting of i) genome sequencing, ii) quick annotation of the genes whose products were detected by mass spectrometry, and iii) comparative proteomics of cells grown in three salt conditions. We highlighted in this manuscript how efficient such an approach can be compared to time-consuming genome annotation when pointing at the key proteins of a given biological question. We documented a large number of proteins found produced in greater amounts when cells are cultivated in either hypo-osmotic or hyper-osmotic conditions. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

Role of central metabolism in the osmoadaptation of the halophilic bacterium Chromohalobacter salexigens

Bacterial osmoadaptation involves the cytoplasmic accumulation of compatible solutes to counteract extracellular osmolarity. The halophilic and highly halotolerant bacterium Chromohalobacter salexigens is able to grow up to 3 m NaCl in a minimal medium due to the de novo synthesis of ectoines. This is an osmoregulated pathway that burdens central metabolic routes by quantitatively drawing off TCA cycle intermediaries. Consequently, metabolism in C. salexigens has adapted to support this biosynthetic route. Metabolism of C. salexigens is more efficient at high salinity than at low salinity, as reflected by lower glucose consumption, lower metabolite overflow, and higher biomass yield. At low salinity, by-products (mainly gluconate, pyruvate, and acetate) accumulate extracellularly. Using [1-(13)C]-, [2-(13)C]-, [6-(13)C]-, and [U-(13)C6]glucose as carbon sources, we were able to determine the main central metabolic pathways involved in ectoines biosynthesis from glucose. C. salexigens uses the Entner-Doudoroff pathway rather than the standard glycolytic pathway for glucose catabolism, and anaplerotic activity is high to replenish the TCA cycle with the intermediaries withdrawn for ectoines biosynthesis. Metabolic flux ratios at low and high salinity were similar, revealing a certain metabolic rigidity, probably due to its specialization to support high biosynthetic fluxes and partially explaining why metabolic yields are so highly affected by salinity. This work represents an important contribution to the elucidation of specific metabolic adaptations in compatible solute-accumulating halophilic bacteria.

Temperature- and salinity-decoupled overproduction of hydroxyectoine by Chromohalobacter salexigens

Hydroxyectoine overproduction by the natural producer Chromohalobacter salexigens is presented in this study. Genetically engineered strains were constructed that at low salinity coexpressed, in a vector derived from a native plasmid, the ectoine (ectABC) and hydroxyectoine (ectD) genes under the control of the ectA promoter, in a temperature-independent manner. Hydroxyectoine production was further improved by increasing the copies of ectD and using a C. salexigens genetic background unable to synthesize ectoines.

Diverse microhabitats experienced by Halomonas variabilis on salt-secreting leaves

The leaf surfaces of the salt-excreting tree Tamarix aphylla harbor a wide diversity of halophilic microorganisms, including Halomonas sp., but little is known of the factors that shape community composition in this extreme habitat. We isolated a strain of Halomonas variabilis from the leaf surface of T. aphylla and used it to determine the heterogeneity of salt concentrations experienced by bacteria in this environment. This halophilic strain was transformed with a proU::gfp reporter gene fusion, the fluorescence of which was responsive to NaCl concentrations up to 200 g liter(-1). These bioreporting cells were applied to T. aphylla leaves and were subsequently recovered from dew droplets adhering to the leaf surface. Although cells from within a given dew droplet exhibited similar green fluorescent protein fluorescence, the fluorescence intensity varied between droplets and was correlated with the salt concentration measured in each drop. Growth of H. variabilis was observed in all droplets, regardless of the salt concentration. However, cells found in desiccated microniches between dew drops were low in abundance and generally dead. Other bacteria recovered from T. aphylla displayed higher desiccation tolerance than H. variabilis, both in culture and on inoculated plants, despite having lower osmotic tolerance. Thus, the Tamarix leaf surface can be described as a salty desert with occasional oases where water droplets form under humid conditions. While halotolerant bacteria such as Halomonas grow in high concentrations of salt in such wet microniches, other organisms are better suited to survive desiccation in sites that are not wetted.

Trends in the codon usage patterns of Chromohalobacter salexigens genes

Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for growth. In order to reveal the factors influencing architecture of protein coding genes in C. salexigens, pattern of synonymous codon usage bias has been investigated. Overall codon usage analysis of the microorganism revealed that C and G ending codons are predominantly used in all the genes which are indicative of mutational bias. Multivariate statistical analysis showed that the genes are separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. Both NC plot and correspondence analysis on Relative Synonymous Codon Usage (RSCU) indicates that the variation in codon usage among the genes may be due to mutational bias at the DNA level and natural selection acting at the level of mRNA translation. Gene length and the hydrophobicity of the encoded protein also influence the codon usage variation of genes to some extent. A comparison of the relative synonymous codon usage between 10% each of highly and lowly expressed genes determines 23 optimal codons, which are statistically over represented in the former group of genes and may provide useful information for salt-stressed gene prediction and gene-transformation. Furthermore, genes for regulatory functions; mobile and extrachromosomal element functions; and cell envelope are observed to be highly expressed. The study could provide insight into the gene expression response of halophilic bacteria and facilitate establishment of effective strategies to develop salt-tolerant crops of agronomic value.

Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels

This paper presents the characterization of the microbial community responsible for the in-situ bioremediation of hexachlorocyclohexane (HCH). Microbial community structure and function was analyzed using 16S rRNA amplicon and shotgun metagenomic sequencing methods for three sets of soil samples. The three samples were collected from a HCH-dumpsite (450 mg HCH/g soil) and comprised of a HCH/soil ratio of 0.45, 0.0007, and 0.00003, respectively. Certain bacterial; (Chromohalobacter, Marinimicrobium, Idiomarina, Salinosphaera, Halomonas, Sphingopyxis, Novosphingobium, Sphingomonas and Pseudomonas), archaeal; (Halobacterium, Haloarcula and Halorhabdus) and fungal (Fusarium) genera were found to be more abundant in the soil sample from the HCH-dumpsite. Consistent with the phylogenetic shift, the dumpsite also exhibited a relatively higher abundance of genes coding for chemotaxis/motility, chloroaromatic and HCH degradation (lin genes). Reassembly of a draft pangenome of Chromohalobacter salaxigenes sp. (∼8X coverage) and 3 plasmids (pISP3, pISP4 and pLB1; 13X coverage) containing lin genes/clusters also provides an evidence for the horizontal transfer of HCH catabolism genes.

Role of trehalose in salinity and temperature tolerance in the model halophilic bacterium Chromohalobacter salexigens

The disaccharide trehalose is considered as a universal stress molecule, protecting cells and biomolecules from injuries imposed by high osmolarity, heat, oxidation, desiccation and freezing. Chromohalobacter salexigens is a halophilic and extremely halotolerant γ-proteobacterium of the family Halomonadaceae. In this work, we have investigated the role of trehalose as a protectant against salinity, temperature and desiccation in C. salexigens. A mutant deficient in the trehalose-6-phosphate synthase gene (otsA::Ω) was not affected in its salt or heat tolerance, but double mutants ectoine- and trehalose-deficient, or hydroxyectoine-reduced and trehalose-deficient, displayed an osmo- and thermosensitive phenotype, respectively. This suggests a role of trehalose as a secondary solute involved in osmo- (at least at low salinity) and thermoprotection of C. salexigens. Interestingly, trehalose synthesis was osmoregulated at the transcriptional level, and thermoregulated at the post-transcriptional level, suggesting that C. salexigens cells need to be pre-conditioned by osmotic stress, in order to be able to quickly synthesize trehalose in response to heat stress. C. salexigens was more sensitive to desiccation than E. coli and desiccation tolerance was slightly improved when cells were grown at high temperature. Under these conditions, single mutants affected in the synthesis of trehalose or hydroxyectoine were more sensitive to desiccation than the wild-type strain. However, given the low survival rates of the wild type, the involvement of trehalose and hydroxyectoine in C. salexigens response to desiccation could not be firmly established.

Inhibitory effects of choline-O-sulfate on amyloid formation of human islet amyloid polypeptide

Choline-O-sulfate (2-(trimethylammonio)ethyl sulfate, COS) is a naturally occurring osmolyte that is synthesized by plants, lichens, algae, fungi, and several bacterial species. We examined the inhibitory effects of COS on amyloid formation of the human islet amyloid polypeptide (hIAPP or amylin) using a thioflavin T (ThT) fluorescence assay, circular dichroism spectroscopy and transmission electron microscopy. The results showed that COS suppresses a conformational change of hIAPP from a random coil to a β-sheet structure, resulting in the inhibition of amyloid formation. Comparisons with various structural analogs including carnitine, acetylcholine and non-detergent sulfobetaines (NDSBs) using the ThT fluorescence assay showed that COS is the most effective inhibitor of hIAPP amyloid formation, suggesting that the sulfate group, which is unique to COS, significantly contributes to the inhibition.

Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11(T))

Chromohalobacter salexigens is one of nine currently known species of the genus Chromohalobacter in the family Halomonadaceae. It is the most halotolerant of the so-called 'moderately halophilic bacteria' currently known and, due to its strong euryhaline phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens strain 1H11(T) and Halomonas elongata are the first and the second members of the family Halomonadaceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004.

Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043

BACKGROUND

Chromohalobacter salexigens (formerly Halomonas elongata DSM 3043) is a halophilic extremophile with a very broad salinity range and is used as a model organism to elucidate prokaryotic osmoadaptation due to its strong euryhaline phenotype.

RESULTS

C. salexigens DSM 3043's metabolism was reconstructed based on genomic, biochemical and physiological information via a non-automated but iterative process. This manually-curated reconstruction accounts for 584 genes, 1386 reactions, and 1411 metabolites. By using flux balance analysis, the model was extensively validated against literature data on the C. salexigens phenotypic features, the transport and use of different substrates for growth as well as against experimental observations on the uptake and accumulation of industrially important organic osmolytes, ectoine, betaine, and its precursor choline, which play important roles in the adaptive response to osmotic stress.

CONCLUSIONS

This work presents the first comprehensive genome-scale metabolic model of a halophilic bacterium. Being a useful guide for identification and filling of knowledge gaps, the reconstructed metabolic network iOA584 will accelerate the research on halophilic bacteria towards application of systems biology approaches and design of metabolic engineering strategies.

Studies of dimethylglycine oxidase isoenzymes in Arthrobacter globiformis cells

Glycine betaine (GB) could be used by Arthrobacter globiformis cells as a sole carbon source. The cells took up this molecule in the low as well as in the high salinity medium. Addition of GB to the mineral medium with high salt concentration revealed that GB was also used as an osmoprotectant. Dimethylglycine oxidase (DMGO) was involved in the catabolism of GB. Two genes for DMGO were detected in a cloned 26267 bp fragment of A. globiformis DNA. The genes involved in the tetrahydrofolate-dependent assimilation of methyl groups were located nearby the two of DMGO genes. Both cloned A. globiformis DMGO were active. The activity of DMGO was detected in A. globiformis cells and it depended on the addition of GB and the salinity of the medium. Reverse transcription-PCR demonstrated that the addition of GB influenced the transcription of dmg genes.

Involvement of EupR, a response regulator of the NarL/FixJ family, in the control of the uptake of the compatible solutes ectoines by the halophilic bacterium Chromohalobacter salexigens

BACKGROUND

Osmosensing and associated signal transduction pathways have not yet been described in obligately halophilic bacteria. Chromohalobacter salexigens is a halophilic bacterium with a broad range of salt tolerance. In response to osmotic stress, it synthesizes and accumulates large amounts of the compatible solutes ectoine and hydroxyectoine. In a previous work, we showed that ectoines can be also accumulated upon transport from the external medium, and that they can be used as carbon sources at optimal, but not at low salinity. This was related to an insufficient ectoine(s) transport under these conditions.

RESULTS

A C. salexigens Tn1732-induced mutant (CHR95) showed a delayed growth with glucose at low and optimal salinities, could not grow at high salinity, and was able to use ectoines as carbon sources at low salinity. CHR95 was affected in the transport and/or metabolism of glucose, and showed a deregulated ectoine uptake at any salinity, but it was not affected in ectoine metabolism. Transposon insertion in CHR95 caused deletion of three genes, Csal0865-Csal0867: acs, encoding an acetyl-CoA synthase, mntR, encoding a transcriptional regulator of the DtxR/MntR family, and eupR, encoding a putative two-component response regulator with a LuxR_C-like DNA-binding helix-turn-helix domain. A single mntR mutant was sensitive to manganese, suggesting that mntR encodes a manganese-dependent transcriptional regulator. Deletion of eupR led to salt-sensitivity and enabled the mutant strain to use ectoines as carbon source at low salinity. Domain analysis included EupR as a member of the NarL/FixJ family of two component response regulators. Finally, the protein encoded by Csal869, located three genes downstream of eupR was suggested to be the cognate histidine kinase of EupR. This protein was predicted to be a hybrid histidine kinase with one transmembrane and one cytoplasmic sensor domain.

CONCLUSIONS

This work represents the first example of the involvement of a two-component response regulator in the osmoadaptation of a true halophilic bacterium. Our results pave the way to the elucidation of the signal transduction pathway involved in the control of ectoine transport in C. salexigens.

Interplay between iron homeostasis and the osmotic stress response in the halophilic bacterium Chromohalobacter salexigens

In this study, the connection between iron homeostasis and the osmostress response in the halophile Chromohalobacter salexigens was investigated. A decrease in the requirement for both iron and histidine and a lower level of siderophore synthesis were observed at high salinity, and these findings were correlated with a lower protein content in salt-stressed cells. A six-gene operon (cfuABC-fur-hisI-orf6 operon) located downstream of the ectABC ectoine synthesis genes was characterized. A fur strain (in which the ferric iron uptake regulator Fur was affected) had the Mn resistance phenotype typical of fur mutants, was deregulated for siderophore production, and displayed delayed growth under iron limitation conditions, indicating that fur encodes a functional iron regulator. hisI was essential for histidine synthesis, which in turn was necessary for siderophore production. Fur boxes were found in the promoters of the cfuABC-fur-hisI-orf6 and ectABC operons, suggesting that Fur directly interacts with DNA in these regions. Fur mediated the osmoregulated inhibition of cfuABC-fur-hisI-orf6 operon expression by iron and functioned as a positive regulator of the ectABC genes under high-salinity conditions, linking the salt stress response with iron homeostasis. Excess iron led to a higher cytoplasmic hydroxyectoine content, suggesting that hydroxyectoine protects against the oxidative stress caused by iron better than ectoine. This study provides the first evidence of involvement of the iron homeostasis regulator Fur as part of the complex circuit that controls the response to osmotic stress in halophilic bacteria.

Unravelling the adaptation responses to osmotic and temperature stress in Chromohalobacter salexigens, a bacterium with broad salinity tolerance

Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for growth. Osmoprotection is achieved by the accumulation of compatible solutes either by transport (betaine, choline) or synthesis (mainly ectoine and hydroxyectoine). Ectoines can play additional roles as nutrients and, in the case of hydroxyectoine, in thermotolerance. A supplementary solute, trehalose, not present in cells grown at 37°C, is accumulated at higher temperatures, suggesting its involvement in the response to heat stress. Trehalose is also accumulated at 37°C in ectoine-deficient mutants, indicating that ectoines suppress trehalose synthesis in the wild-type strain. The genes for ectoine (ectABC) and hydroxyectoine (ectD, ectE) production are arranged in three different clusters within the C. salexigens chromosome. In order to cope with changing environment, C. salexigens regulates its cytoplasmic pool of ectoines by a number of mechanisms that we have started to elucidate. This is a highly complex process because (i) hydroxyectoine can be synthesized by other enzymes different to EctD (ii) ectoines can be catabolized to serve as nutrients, (iii) the involvement of several transcriptional regulators (σ^S, σ³², Fur, EctR) and hence different signal transduction pathways, and (iv) the existence of post-trancriptional control mechanisms. In this review we summarize our present knowledge on the physiology and genetics of the processes allowing C. salexigens to cope with osmotic stress and high temperature, with emphasis on the transcriptional regulation.

The molecular basis of salt adaptation in Methanosarcina mazei Gö1

The study on the molecular basis of salt adaptation and its regulation in archaea is still in its infancy, but genomics and functional genome analyses combined with classical biochemistry shed light on the processes conferring salt adaptation in the methanogenic archaeon Methanosarcina mazei Gö1. In this article, we will review discoveries made within the last years that will culminate in the description of the overall cellular response of M. mazei Gö1 to elevated salinities. This response includes accumulation of solutes and export of Na+ as well as potential uptake/export of K+ but also a restructuring of the cell surface.

Pseudomonas syringae BetT is a low-affinity choline transporter that is responsible for superior osmoprotection by choline over glycine betaine

The plant pathogen Pseudomonas syringae derives better osmoprotection from choline than from glycine betaine, unlike most bacteria that have been characterized. In this report, we identified a betaine/carnitine/choline family transporter (BCCT) in P. syringae pv. tomato strain DC3000 that mediates the transport of choline and acetylcholine. This transporter has a particularly low affinity (K(m) of 876 microM) and high capacity (V(max) of 80 nmol/min/mg of protein) for choline transport relative to other known BCCTs. Although BetT activity increased in response to hyperosmolarity, BetT mediated significant uptake under low-osmolarity conditions, suggesting a role in transport for both osmoprotection and catabolism. Growth studies with mutants deficient in BetT and other choline transporters demonstrated that BetT was responsible for the superior osmoprotection conferred to P. syringae by choline over glycine betaine when these compounds were provided at high concentrations (>100 microM). These results suggest that P. syringae has evolved to survive in relatively choline-rich habitats, a prediction that is supported by the common association of P. syringae with plants and the widespread production of choline, but genus- and species-specific production of glycine betaine, by plants. Among the three putative BCCT family transporters in Pseudomonas aeruginosa and six in Pseudomonas putida, different transporters were predicted to function based on similarity to Escherichia coli BetT than to P. syringae BetT. Functional P. putida and P. aeruginosa transporters were identified, and their possession of a long C-terminal tail suggested an osmoregulatory function for this tail; this function was confirmed for P. syringae BetT using deletion derivatives.

Identification of salt-inducible peptide with putative kinase activity in halophilic bacterium Virgibacillus halodenitrificans

Strain XII, a moderately halophilic bacterium, expressed a peptide in response to saline media. This peptide was designated as salt-inducible factor (Sif-A). The purpose of this study is to describe Sif-A, which might be involved in the osmoresistance mechanism of strain XII. The complete sequence of sif-A was determined using PCR. sif-A codes for a polypeptide of 20.518 kDa. The polypeptide has a putative signal peptide of 27 amino acids (2.667 kDa) preceding the mature protein (17.869 kDa). Motif analysis of the deduced amino acid sequence indicated that there is a p-loop NTPase domain on the C-terminal of the peptide, which might correlate with its function. The sequence of the 16S rRNA gene was analyzed phylogenetically to classify strain XII. This organism was found to have the closest association with Virgibacillus halodenitrificans, which was proven by its phenotypic characteristics.

Uncoupling of choline-O-sulphate utilization from osmoprotection in Pseudomonas putida

The genomic context of the recognized bet genes for choline-O-sulphate (COS) utilization in Pseudomonas putida KT2440 is such that betC (choline sulphatase) lies adjacent to an ATP-binding cassette transporter and a LysR type regulator, but well away from betBA, encoding enzymes for transformation of choline into glycine betaine. The consequences of such genetic layout of the functions for COS metabolism have been examined with a suite of genetic and biochemical approaches. An early clue of the utilities of the betencoded products was exposed by the phenotypes of a betC deletion. This mutant still accumulated intact COS but failed to use this compound as carbon or nitrogen source. Furthermore, betC expression was downregulated at high salt concentrations, showing that the principal role of this gene lied in COS metabolism, not in osmoprotection. In contrast, the betBA genes were required for choline transformation into the highly effective compatible solute glycine betaine (and the concomitant endurance to high salt) and also for its utilization as carbon or nitrogen source. Thus, unlike in the cases of Bacillus subtilis and Sinorhizobium meliloti, betC is unrelated to osmoprotection in Pseudomonas putida while the betBA genes are required for both betaine synthesis and tolerance to high osmotic pressure.

Osmoprotection of Salmonella enterica serovar Typhimurium by Nγ-acetyldiaminobutyrate, the precursor of the compatible solute ectoine

N(gamma)-acetyl-2,4-diaminobutyrate (NADA), the precursor of the compatible solute ectoine, was shown to function as an osmoprotectant for the non-halophilic bacterium Salmonella enterica serovar Typhimurium. The addition of NADA-containing extracts of an ectoine synthase mutant of the broad salt-growing halophile Chromohalobacter salexigens DSM 3043(T) could alleviate the inhibitory effects of high salinity in S. enterica, which lacks the ectoine biosynthetic pathway. NADA, purified from extracts of the mutant, protected S. enterica against salinity stress. This osmoprotective effect was slightly lower than that of ectoine, but more potent than that of hydroxyectoine. Accumulation of purified NADA by S. enterica was demonstrated by (13)C-NMR spectroscopy and HPLC analysis. In addition, it was shown that NADA was taken up by S. enterica via the ProP and ProU transport systems, which are known to transport glycine betaine and proline. This finding provides evidence that these permeases can recognize a diaminoacid that carries an unsubstituted alpha-amino group. This is the first time that NADA has been connected with osmoprotective functions in non-halophilic bacteria.

The ectD gene, which is involved in the synthesis of the compatible solute hydroxyectoine, is essential for thermoprotection of the halophilic bacterium Chromohalobacter salexigens

The halophilic bacterium Chromohalobacter salexigens synthesizes and accumulates compatible solutes in response to salt and temperature stress. (13)C-nuclear magnetic resonance analysis of cells grown in minimal medium at the limiting temperature of 45 degrees C revealed the presence of hydroxyectoine, ectoine, glutamate, trehalose (not present in cells grown at 37 degrees C), and the ectoine precursor, Ngamma-acetyldiaminobutyric acid. High-performance liquid chromatography analyses showed that the levels of ectoine and hydroxyectoine were maximal during the stationary phase of growth. Accumulation of hydroxyectoine was up-regulated by salinity and temperature, whereas accumulation of ectoine was up-regulated by salinity and down-regulated by temperature. The ectD gene, which is involved in the conversion of ectoine to hydroxyectoine, was isolated as part of a DNA region that also contains a gene whose product belongs to the AraC-XylS family of transcriptional activators. Orthologs of ectD were found within the sequenced genomes of members of the proteobacteria, firmicutes, and actinobacteria, and their products were grouped into the ectoine hydroxylase subfamily, which was shown to belong to the superfamily of Fe(II)- and 2-oxoglutarate-dependent oxygenases. Analysis of the ectoine and hydroxyectoine contents of an ectABC ectD mutant strain fed with 1 mM ectoine or hydroxyectoine demonstrated that ectD is required for the main ectoine hydroxylase activity in C. salexigens. Although in minimal medium at 37 degrees C the wild-type strain grew with 0.5 to 3.0 M NaCl, with optimal growth at 1.5 M NaCl, at 45 degrees C it could not cope with the lowest (0.75 M NaCl) or the highest (3.0 M NaCl) salinity, and it grew optimally at 2.5 M NaCl. The ectD mutation caused a growth defect at 45 degrees C in minimal medium with 1.5 to 2.5 M NaCl, but it did not affect growth at 37 degrees C at any salinity tested. With 2.5 M NaCl, the ectD mutant synthesized 38% (at 37 degrees C) and 15% (at 45 degrees C) of the hydroxyectoine produced by the wild-type strain. All of these data reveal that hydroxyectoine synthesis mediated by the ectD gene is thermoregulated and essential for thermoprotection of C. salexigens.

Ectoines as compatible solutes and carbon and energy sources for the halophilic bacterium Chromohalobacter salexigens

AIMS

To investigate the catabolism of ectoine and hydroxyectoine, which are the major compatible solutes synthesized by Chromohalobacter salexigens.

METHODS AND RESULTS

Growth curves performed in M63 minimal medium with low (0.75 mol l(-1) NaCl), optimal (1.5 mol l(-1) NaCl) or high (2.5 mol l(-1) NaCl) salinity revealed that betaine and ectoines were used as substrate for growth at optimal and high salt. Ectoine transport was maximal at optimal salinity, and showed 3- and 1.5-fold lower values at low and high salinity respectively. The salt-sensitive ectA mutant CHR62 showed an ectoine transport rate 6.8-fold higher than that of the wild type. Incubation of C. salexigens in a mixture of glucose and ectoine resulted in a biphasic growth pattern. However, CO(2) production due to ectoine catabolism was lower, but not completely abolished, in the presence of glucose. When used as the sole carbon source, glycine betaine effectively inhibited ectoine and hydroxyectoine synthesis at any salinity.

CONCLUSIONS

The catabolic pathways for ectoine and hydroxyectoine in C. salexigens operate at optimal and high (although less efficiently) salinity. Endogenous ectoine(s) may repress its own transport. Ectoine utilization was only partially repressed by glucose. Betaine, when used as carbon source, suppresses synthesis of ectoines even under high osmolarity conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is a previous step to the subsequent isolation and manipulation of the catabolic genes, so as to generate strains with enhanced production of ectoine and hydroxyectoine.

Identification and characterization of salt-inducible polypeptide in Paenibacillus sp., a moderately halophilic bacterium

In response to salt, Paenibacillus sp. strain XII expresses a 21.4 kDa polypeptide. N-terminal sequencing and sequence homology analysis indicate homology between the N-terminal sequence of the polypeptide and a segment of the N-terminus of the spore coat associated protein CotN of Oceanobacillus iheyensis, an extremely halotolerant bacteria of the deep-sea.

Contribution of chemical changes in membrane lipids to the osmoadaptation of the halophilic bacterium Chromohalobacter salexigens

The long-term response of the broad-salt growing halophile Chromohalobacter salexigens DSM 3043T to salt stress has been investigated with respect to adaptive changes in membrane lipid composition. This study included the wild-type and three salt-sensitive, ectoine-deficient strains: CHR62 (ectA::Tn1732, unable to grow above 0.75 M NaCl), CHR63 (ectC::Tn1732, unable to grow above 1.5 M NaCl), and CHR64, which was able to grow in minimal medium M63 up to 2.5 M NaCl, but its growth was slower than the wild-type strain at salinities above 1.5 M NaCl. This mutant accumulated ectoine and hydroxyectoine as major compatible solutes, but also the ectoine precursor, N-gamma-acetyldiaminobutyric acid, and was found to be affected in the ectoine synthase gene ectC. The main phospholipids of the wild-type strain were phosphatidylethanolamine, phosphatidylglycerol (PG), and cardiolipin (CL). Major fatty acids were detected as 16:0, 18:1, and 16:1, including significant amounts of cyc-19:0, and cyc-17:0. CL and cyclopropane fatty acids (CFA) levels were elevated when the wild-type strain was grown at high salinity (2.5 M NaCl). Membranes of the most salt-sensitive trains CHR62 and CHR63, but not of the less salt-sensitive strain CHR64, contained lower levels of CL. The proportion of cyc-19:0 in CHR64 was three-fold (at 2.0M NaCl) and 2.5-fold (at 2.5 M NaCl) lower than that of the wild type, suggesting that this mutant has a limited capacity to incorporate CFA into phospholipids at high salt. The addition of 1 mM ectoine to cultures of the wild-type strain increased the ratio PG/CL from 1.8 to 3.3 at 0.75 M NaCl, and from 1 to 6.5 at 2.5 M NaCl, and led to a slight decrease in CFA content. Addition of 1 mM ectoine to the mutants restored the steady-state levels of CL and CFA found in the wild-type strain supplemented with ectoine. These findings suggest that exogenous ectoine might attenuate the osmostress response involving changes in membrane lipids.

How to be moderately halophilic with broad salt tolerance: clues from the genome of Chromohalobacter salexigens

We analyzed the amino acid composition of different categories of proteins of the moderately halophilic bacterium Chromohalobacter salexigens, as deduced from its genome sequence. Comparison with non-halophilic representatives of the gamma-Proteobacteria (Escherichia coli, Pseudomonas aeruginosa, Vibrio cholerae) shows only a slight excess of acidic residues in the cytoplasmic proteins, and no significant differences were found in the acidity of membrane-bound proteins. In contrast, a very pronounced difference in mean pI value was observed for the periplasmic binding proteins of the ABC transport systems of C. salexigens and the non-halophiles E. coli and P. aeruginosa. V. cholerae, which is adapted to life in brackish water, showed intermediate values. The findings suggest that there is a major difference between the proteins of the moderate halophile C. salexigens and non-halophilic bacteria in their periplasmic proteins, exemplified by the substrate binding proteins of transport systems. The highly acidic nature of these proteins may enable them to function at high salt concentrations. The evolution of highly salt-tolerant prokaryotes may have depended on an increase in acidity of the proteins located external to the cytoplasmic membrane, enabling effective transport of nutrients into the cell.