An extremely halophilic proteobacterium combines a highly acidic proteome with a low cytoplasmic potassium content

Localized Amino Acid Enrichment Analysis as a Tool for Understanding Protein Extremophilicity

Sequence conservation analyses offer us a powerful glimpse of natural selection at work. Standard tools for measuring sequence conservation report conservation as a function of a specific location in a multiple sequence alignment and have proven indispensable in identifying highly constrained features such as active site residues. The advent of large-scale genomic sequencing efforts allows researchers to expand this paradigm and investigate more nuanced relationships between sequence and function. Here, we present a simple tool (SWiLoDD: Sliding Window Localized Differentiation Detection) that allows researchers to analyze local, rather than site-specific, conservation using a sliding window approach. Our tool accepts multiple sequence alignments partitioned based on a biological differentiator and returns alignment position-based, localized differential enrichment metrics for amino acids of choice. We present two case studies of this analysis in action: local-but-diffuse glycine enrichments in the ATPase subunits of thermophilic and psychrophilic bacterial gyrase homologs, and ligand- and interface-specific amino acid enrichments in halophilic bacterial crotonyl-CoA carboxylases/reductases. Though we have described examples of extremophilic bacterial proteins in this study, our tool may be used to investigate any set of homologous sequences from which sub-groups can be meaningfully partitioned. Our results suggest that investigating differential localized conservation in partitioned MSAs will expand our understanding of how sequence conservation and protein function are connected.

A Native LH1-RC-HiPIP Supercomplex from an Extremophilic Phototroph

Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic purple phototrophic bacterium and has been widely used as a model for exploring the osmoadaptive and photosynthetic strategies employed by phototrophic extreme halophiles that enable them to thrive in hypersaline environments. Here we present the cryo-EM structures of (1) a unique native Hlr. halophila triple-complex formed from light-harvesting (LH1), the reaction center (RC), and high-potential iron-sulfur protein (HiPIP) at 2.44 Å resolution, and (2) a HiPIP-free LH1-RC complex at 2.64 Å resolution. Differing from the LH1 in the Hlr. halophila LH1-LH2 co-complex where LH1 encircles LH2, the RC-associated LH1 complex consists of 16 (rather than 18) αβ-subunits circularly surrounding the RC. These distinct forms of LH1 indicate that the number of subunits in a Hlr. halophila LH1 complex is flexible and its size is a function of the photocomplex it encircles. Like LH1 in the LH1-LH2 co-complex, the RC-associated LH1 complex also contained two forms of αβ-polypeptides and both dimeric and monomeric molecules of bacteriochlorophyll a. The majority of the isolated Hlr. halophila LH1-RC complexes contained the electron donor HiPIP bound to the surface of the RC cytochrome subunit near the heme-1 group. The bound HiPIP consisted of an N-terminal functional domain and a long C-terminal extension firmly attached to the cytochrome subunit. Despite overall highly negative surface-charge distributions for both the cytochrome subunit and HiPIP, the interface between the two proteins was relatively uncharged and neutral, forming a pathway for electron tunneling. The structure of the Hlr. halophila LH1-RC-HiPIP complex provides insights into the mechanism of light energy acquisition coupled with a long-distance electron donating process toward the charge separation site in a multi-extremophilic phototroph.

How sensitive are protein hydration shells to electrolyte concentration and protein composition?

Proteins of obligate halophilic organisms have an unusually high number of acidic amino acids, thought to enable them to function in multimolar KCl environments. Clarifying the molecular scale mechanisms by which this occurs is relevant for biotechnology, to enable enzymatic synthesis of economically important small molecules in salty environments and other environments with low water activity. Previous studies have suggested that acidic amino acids are necessary at high salt concentration to keep the proteins hydrated by competing with the ions in solution for available water (the "solvent-only" model). We use a combination of solvation shell spectroscopy and molecular dynamics simulations for in total 13 proteins, at high and low KCl concentration, to investigate this scenario. We show that the solvation shells of halophilic and mesophilic proteins of widely different amino acid compositions, net charges, sizes, and structure respond similarly, in terms of composition and of hydrogen bond network, to changes in KCl concentration. The results do not support the solvent-only model, and point to other mechanisms behind the acidity of halophilic proteins. Excess acidic amino acids may ensure protein solubility by the combined effects of having particularly favorable electrostatic interactions with the solvent, ensuring very short range protein-protein repulsion, and having smaller hydrophobic solvent accessible surface area than other charged amino acids. Also possible is that highly acidic proteins are well-tolerated-but not necessarily indispensable-in terms of stability and solubility.

Electrostatics introduce a trade-off between mesophilic stability and adaptation in halophilic proteins

Extremophile organisms have adapted to extreme physicochemical conditions. Halophilic organisms, in particular, survive at very high salt concentrations. To achieve this, they have engineered the surface of their proteins to increase the number of short, polar and acidic amino acids, while decreasing large, hydrophobic and basic residues. While these adaptations initially decrease protein stability in the absence of salt, they grant halophilic proteins remarkable stability in environments with extremely high salt concentrations, where non-adapted proteins unfold and aggregate. The molecular mechanisms by which halophilic proteins achieve this, however, are not yet clear. Here, we test the hypothesis that the halophilic amino acid composition destabilizes the surface of the protein, but in exchange improves the stability in the presence of salts. To do that, we have measured the folding thermodynamics of various protein variants with different degrees of halophilicity in the absence and presence of different salts, and at different pH values to tune the ionization state of the acidic amino acids. Our results show that halophilic amino acids decrease the stability of halophilic proteins under mesophilic conditions, but in exchange improve salt-induced stabilization and solubility. We also find that, in contrast to traditional assumptions, contributions arising from hydrophobic effect and preferential ion exclusion are more relevant for haloadaptation than electrostatics. Overall, our findings suggest a trade-off between folding thermodynamics and halophilic adaptation to optimize proteins for hypersaline environments.

The polyextremophile Natranaerobius thermophilus adopts a dual adaptive strategy to long-term salinity stress, simultaneously accumulating compatible solutes and K. Appl Environ Microbiol 2024;90:e0014524. [PMID: 38578096 PMCID: PMC11107154 DOI: 10.1128/aem.00145-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The bacterium Natranaerobius thermophilus is an extremely halophilic alkalithermophile that can thrive under conditions of high salinity (3.3-3.9 M Na+), alkaline pH (9.5), and elevated temperature (53°C). To understand the molecular mechanisms of salt adaptation in N. thermophilus, it is essential to investigate the protein, mRNA, and key metabolite levels on a molecular basis. Based on proteome profiling of N. thermophilus under 3.1, 3.7, and 4.3 M Na+ conditions compared to 2.5 M Na+ condition, we discovered that a hybrid strategy, combining the "compatible solute" and "salt-in" mechanisms, was utilized for osmotic adjustment dur ing the long-term salinity adaptation of N. thermophilus. The mRNA level of key proteins and the intracellular content of compatible solutes and K+ support this conclusion. Specifically, N. thermophilus employs the glycine betaine ABC transporters (Opu and ProU families), Na+/solute symporters (SSS family), and glutamate and proline synthesis pathways to adapt to high salinity. The intracellular content of compatible solutes, including glycine betaine, glutamate, and proline, increases with rising salinity levels in N. thermophilus. Additionally, the upregulation of Na+/ K+/ H+ transporters facilitates the maintenance of intracellular K+ concentration, ensuring cellular ion homeostasis under varying salinities. Furthermore, N. thermophilus exhibits cytoplasmic acidification in response to high Na+ concentrations. The median isoelectric points of the upregulated proteins decrease with increasing salinity. Amino acid metabolism, carbohydrate and energy metabolism, membrane transport, and bacterial chemotaxis activities contribute to the adaptability of N. thermophilus under high salt stress. This study provides new data that support further elucidating the complex adaptation mechanisms of N. thermophilus under multiple extremes.IMPORTANCEThis study represents the first report of simultaneous utilization of two salt adaptation mechanisms within the Clostridia class in response to long-term salinity stress.

Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation

Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme environmental conditions, it is possible to explore the genomic-proteomic compositional determinants of molecular mechanisms of adaptation developed by them in response to harsh environmental conditions. Using a wealth of currently available complete genomes/proteomes we were able to explore signatures of adaptation to three environmental factors, pH, salinity, and temperature, observing major trends in compositions of their nucleic acids and proteins. We derived predictors of thermostability, halophilic, and pH adaptations and complemented them by the principal components analysis. We observed a clear difference between thermophilic and salinity/pH adaptations, whereas latter invoke seemingly overlapping mechanisms. The genome-proteome compositional trade-off reveals an intricate balance between the work of base paring and base stacking in stabilization of coding DNA and r/tRNAs, and, at the same time, universal requirements for the stability and foldability of proteins regardless of the nucleotide biases. Nevertheless, we still found hidden fingerprints of ancient evolutionary connections between the nucleotide and amino acid compositions indicating their emergence, mutual evolution, and adjustment. The evolutionary perspective on the adaptation mechanisms is further studied here by means of the comparative analysis of genomic/proteomic traits of archaeal and bacterial species. The overall picture of genomic/proteomic signals of adaptation obtained here provides a foundation for future engineering and design of functional biomolecules resistant to harsh environments.

Pretty in pink? Complementary strategies for analysing pink biofilms on historical buildings

Salt-weathering is a deterioration mechanism affecting building materials that results from repetitive cycles of salt crystallisation-dissolution in the porous mineral network under changing environmental conditions, causing damage to surfaces. However, an additional biodeterioration phenomenon frequently associated with salt efflorescence is the appearance of coloured biofilms, comprising halotolerant/halophilic microorganisms, containing carotenoid pigments that cause pinkish patinas. In this work, two Austrian historical salt-weathered buildings showing pink biofilms, the St. Virgil's Chapel and the Charterhouse Mauerbach, were investigated. Substrate chemistry (salt concentration/composition) was analysed by ion chromatography and X-ray diffraction to correlate these parameters with the associated microorganisms. Microbiomes were analysed by sequencing full-length 16S rRNA amplicons using Nanopore technology. Data demonstrates that microbiomes are not only influenced by salt concentration, but also by its chemical composition. The chapel showed a high overall halite (NaCl) concentration, but the factor influencing the microbiome was the presence/absence of K+. The K+ areas showed a dominance of Aliifodinibius and Salinisphaera species, capable of tolerating high salt concentrations through the "salt-in" strategy by transporting K+ into cells. Conversely, areas without K+ showed a community shift towards Halomonas species, which favour the synthesis of compatible solutes for salt tolerance. In the charterhouse, the main salts were sulphates. In areas with low concentrations, Rubrobacter species dominated, while in areas with high concentrations, Haloechinothrix species did. Among archaea, Haloccoccus species were dominant in all samples, except at high sulphate concentrations, where Halalkalicoccus prevailed. Finally, the biological pigments visible in both buildings were analysed by Raman spectroscopy, showing the same spectra in all areas investigated, regardless of the building and the microbiomes, demonstrating the presence of carotenoids in the pink biofilms. Comprehensive information on the factors affecting the microbiome associated with salt-weathered buildings should provide the basis for selecting the most appropriate desalination treatment to remove both salt efflorescence and associated biofilms.

Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions

The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.

Prevalence and mechanism of synergistic carboxylate-cation-water interactions in halophilic proteins

The cytoplasmic proteins of some halophilic organisms remain stable and functional at multimolar concentrations of KCl, i.e., under conditions that most mesophilic proteins cannot withstand. Their stability arises from their unusual amino acid composition. The most dramatic difference between halophilic and mesophilic proteins is that the former are rich in acidic amino acids. It has been proposed that one of the evolutionary driving forces for this difference is the occurrence of synergistic interactions between multiple acidic amino acids at the surface of the protein, the potassium cations in solution, and water. We investigate this possibility with molecular dynamics simulations, using high-quality force fields for the protein-water, protein-ion, and ion-ion interactions. We create a rigorous thermodynamic definition of interactions between acidic amino acids on proteins that can be used to distinguish between synergistic, noninteracting and interfering interactions. Our results demonstrate that synergistic interactions between neighboring acidic amino acids in halophilic proteins are frequent at multimolar KCl concentration. Synergistic interactions have an electrostatic origin, and are associated with stronger water-to-carboxylate hydrogen bonds than for acidic amino acids without synergistic interactions. Synergistic interactions are not observed in minimal systems of carboxylates, indicating that the protein environment is critical for their emergence. Our results demonstrate that synergistic interactions are neither associated with rigid amino acid orientations nor with highly structured and slow moving water networks, as had been originally proposed. Moreover, synergistic interactions can also be found in unfolded protein conformations. However, because these conformations are only a small subset of the unfolded state ensemble, synergistic interactions should contribute to the net stabilization of the folded state.

Alternative CUG Codon Usage in the Halotolerant Yeast Debaryomyces hansenii: Gene Expression Profiles Provide New Insights into Ambiguous Translation

The halotolerant yeast Debaryomyces hansenii belongs to the CTG-Ser1 clade of fungal species that use the CUG codon to translate as leucine or serine. The ambiguous decoding of the CUG codon is relevant for expanding protein diversity, but little is known about the role of leucine–serine ambiguity in cellular adaptations to extreme environments. Here, we examine sequences and structures of tRNA_CAG from the CTG-Ser1 clade yeasts, finding that D. hansenii conserves the elements to translate ambiguously. Then, we show that D. hansenii has tolerance to conditions of salinity, acidity, alkalinity, and oxidative stress associated with phenotypic and ultrastructural changes. In these conditions, we found differential expression in both the logarithmic and stationary growth phases of tRNA^Ser, tRNA^Leu, tRNA_CAG, LeuRS, and SerRS genes that could be involved in the adaptive process of this yeast. Finally, we compare the proteomic isoelectric points and hydropathy profiles, detecting that the most important variations among the physicochemical characteristics of D. hansenii proteins are in their hydrophobic and hydrophilic interactions with the medium. We propose that the ambiguous translation, i.e., leucylation or serynation, on translation of the CUG-encoded residues, could be linked to adaptation processes in extreme environments.

Mapping Archaeal Diversity in Soda Lakes by Coupling 16S rRNA PCR-DGGE Analysis with Remote Sensing and GIS Technology

The haloarchaeal diversity of four hypersaline alkaline lakes from the Wadi El-Natrun depression (Northern Egypt) was investigated using culture-independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene phylotypes, which was combined with remote sensing and geographic information system (GIS) data to highlight the distribution pattern of the microbial diversity in water and sediment samples. The majority of archaeal sequences identified in all four lakes belonged to the phyla Euryarchaeota and Crenarchaeota. Sediment samples from Beida Lake and water samples from El-Hamra Lake showed the highest levels of archaeal diversity. Sequence similarities ≥ 95% were found between six of the acquired clones and uncultured Halorhabdus, Euryarchaeota, and archaeon clones. In addition, two clones shared a high level of sequence similarity (97%) with unclassified archaea, while other nine clones exhibited 96% to 99% sequence similarity with uncultured archaeon clones, and only one clone showed 97% identity with an uncultured Crenarchaeota. Likewise, 7 DGGE bands presented a sequence similarity of 90 to 98% to Halogranum sp., Halalkalicoccus tibetensis, Halalkalicoccus jeotgali, uncultured Halorubrum, Halobacteriaceae sp., or uncultured haloarchaeon. In conclusion, while the variety of alkaliphilic haloarchaea in the examined soda lakes was restricted, the possibility of uncovering novel species for biotechnological applications from these extreme habitats remains promising.

The Osmoprotectant Switch of Potassium to Compatible Solutes in an Extremely Halophilic Archaea Halorubrum kocurii 2020YC7

The main osmoadaptive mechanisms of extremely halophilic archaea include the “salt-in” strategy and the “compatible solutes” strategy. Here we report the osmoadaptive mechanism of an extremely halophilic archaea H. kocurii 2020YC7, isolated from a high salt environment sample. Genomic data revealed that strain 2020YC7 harbors genes trkA, trkH, kch for K⁺ uptake, kefB for K⁺ output, treS for trehalose production from polysaccharide, and betaine/carnitine/choline transporter family gene for glycine betaine uptake. Strain 2020YC7 could accumulate 8.17 to 28.67 μmol/mg protein K⁺ in a defined medium, with its content increasing along with the increasing salinity from 100 to 200 g/L. When exogenous glycine betaine was added, glycine betaine functioned as the primary osmotic solute between 200 and 250 g/L NaCl, which was accumulated up to 15.27 mg/mg protein in 2020YC7 cells. RT-qPCR results completely confirmed these results. Notably, the concentrations of intracellular trehalose decreased from 5.26 to 2.61 mg/mg protein as the NaCl increased from 50 to 250 g/L. In combination with this result, the transcript level of gene treS, which catalyzes the production of trehalose from polysaccharide, was significantly up-regulated at 50–100 g/L NaCl. Therefore, trehalose does not act as an osmotic solute at high NaCl concentrations (more than 100 g/L) but at relatively low NaCl concentrations (50–100 g/L). And we propose that the degradation of cell wall polysaccharide, as a source of trehalose in a low-salt environment, may be one of the reasons for the obligate halophilic characteristics of strain 2020YC7.

Salt- and pH-Dependent Thermal Stability of Photocomplexes from Extremophilic Bacteriochlorophyll b-Containing Halo-rhodospira Species

Halorhodospira (Hlr.) species are the most halophilic and alkaliphilic of all purple bacteria. Hlr. halochloris exhibits the lowest LH1 Q_y transition energy among phototrophic organisms and is the only known triply extremophilic anoxygenic phototroph, displaying a thermophilic, halophilic, and alkaliphilic phenotype. Recently, we reported that electrostatic charges are responsible for the unusual spectroscopic properties of the Hlr. halochloris LH1 complex. In the present work, we examined the effects of salt and pH on the spectroscopic properties and thermal stability of LH1-RCs from Hlr. halochloris compared with its mesophilic counterpart, Hlr. abdelmalekii. Experiments in which the photocomplexes were subjected to different levels of salt or variable pH revealed that the thermal stability of LH1-RCs from both species was largely retained in the presence of high salt concentrations and/or at alkaline pH but was markedly reduced by lowering the salt concentration and/or pH. Based on the amino acid sequences of LH1 polypeptides and their composition of acidic/basic residues and the Hofmeister series for cation/anion species, we discuss the importance of electrostatic charge in stabilizing the Hlr. halochloris LH1-RC complex to allow it to perform photosynthesis in its warm, hypersaline, and alkaline habitat.

Adaptation to Varying Salinity in Halomonas elongata: Much More Than Ectoine Accumulation

The halophilic γ-proteobacterium Halomonas elongata DSM 2581 ^T thrives at salt concentrations well above 10 % NaCl (1.7 M NaCl). A well-known osmoregulatory mechanism is the accumulation of the compatible solute ectoine within the cell in response to osmotic stress. While ectoine accumulation is central to osmoregulation and promotes resistance to high salinity in halophilic bacteria, ectoine has this effect only to a much lesser extent in non-halophiles. We carried out transcriptome analysis of H. elongata grown on two different carbon sources (acetate or glucose), and low (0.17 M NaCl), medium (1 M), and high salinity (2 M) to identify additional mechanisms for adaptation to high saline environments. To avoid a methodological bias, the transcripts were evaluated by applying two methods, DESeq2 and Transcripts Per Million (TPM). The differentially transcribed genes in response to the available carbon sources and salt stress were then compared to the transcriptome profile of Chromohalobacter salexigens, a closely related moderate halophilic bacterium. Transcriptome profiling supports the notion that glucose is degraded via the cytoplasmic Entner-Doudoroff pathway, whereas the Embden-Meyerhoff-Parnas pathway is employed for gluconeogenesis. The machinery of oxidative phosphorylation in H. elongata and C. salexigens differs greatly from that of non-halophilic organisms, and electron flow can occur from quinone to oxygen along four alternative routes. Two of these pathways via cytochrome bo' and cytochrome bd quinol oxidases seem to be upregulated in salt stressed cells. Among the most highly regulated genes in H. elongata and C. salexigens are those encoding chemotaxis and motility proteins, with genes for chemotaxis and flagellar assembly severely downregulated at low salt concentrations. We also compared transcripts at low and high-salt stress (low growth rate) with transcripts at optimal salt concentration and found that the majority of regulated genes were down-regulated in stressed cells, including many genes involved in carbohydrate metabolism, while ribosome synthesis was up-regulated, which is in contrast to what is known from non-halophiles at slow growth. Finally, comparing the acidity of the cytoplasmic proteomes of non-halophiles, extreme halophiles and moderate halophiles suggests adaptation to an increased cytoplasmic ion concentration of H. elongata. Taken together, these results lead us to propose a model for salt tolerance in H. elongata where ion accumulation plays a greater role in salt tolerance than previously assumed.

Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance

Net positive charge(s) on ribosomal proteins (r-proteins) have been reported to influence the assembly and folding of ribosomes. A high percentage of r-proteins from extremely halophilic archaea are known to be acidic or even negatively charged. Those proteins that remain positively charged are typically far less positively charged. Here, the analysis is extended to non-archaeal halophilic bacteria, eukaryotes, and halotolerant archaea. The net charges (pH 7.4) of the r-proteins that comprise the S10-spc operon/cluster from individual microbial and eukaryotic genomes were estimated and intercompared. It was observed that, as a general rule, the net charges of individual proteins remained mostly basic as the salt tolerance of the bacterial strains increased from 5 to 15%. The most striking exceptions were the extremely halophilic bacterial strains, Salinibacter ruber SD01, Acetohalobium arabaticum DSM 5501 and Selenihalanaerobacter shriftii ATCC BAA-73, which are reported to require a minimum of 18% to 21% salt for their growth. All three strains have higher numbers of acidic S10-spc cluster r-proteins than what is seen in the moderate halophiles or the halotolerant strains. Of the individual proteins, only uL2 never became acidic. uS14 and uL16 also seldom became acidic. The net negative charges on several of the S10-spc cluster r-proteins are a feature generally shared by all extremely halophilic archaea and bacteria. The S10-spc cluster r-proteins of halophilic fungi and algae (eukaryotes) were exceptions: these were positively charged despite the halophilicity of the organisms. IMPORTANCE The net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster show an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. In non-halophilic bacteria, the S10-spc cluster r-proteins are generally basic (positively charged), while the rest of the proteomes in these strains are generally acidic. On the other hand, the whole proteomes of the extremely halophilic strains are overall negatively charged, including the S10-spc cluster r-proteins. Given that the distribution of charged residues in the ribosome exit tunnel influences cotranslational folding, the contrasting charges observed in the S10-spc cluster r-proteins have potential implications for the rate of passage of these proteins through the ribosomal exit tunnel. Furthermore, the universal protein uL2, which lies in the oldest part of the ribosome, is always positively charged irrespective of the strain/organism it belongs to. This has implications for its role in the prebiotic context.

Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern

Anaerobic archaeal methanogens are key players in the global carbon cycle due to their role in the final stages of organic matter decomposition in anaerobic environments such as wetland sediments. Here we present the first draft metagenome-assembled genome (MAG) sequence of an unclassified Methanosarcinaceae methanogen phylogenetically placed adjacent to the Methanolobus and Methanomethylovorans genera that appears to be a distinct genus and species. The genome is derived from sediments of a hypersaline (97–148 ppt chloride) unrestored industrial saltern that has been observed to be a significant methane source. The source sediment is more saline than previous sources of Methanolobus and Methanomethylovorans. We propose a new genus name, Methanosalis, to house this genome, which we designate with the strain name SBSPR1A. The MAG was binned with CONCOCT and then improved via scaffold extension and reassembly. The genome contains pathways for methylotrophic methanogenesis from trimethylamine and dimethylamine, as well as genes for the synthesis and transport of compatible solutes. Some genes involved in acetoclastic and hydrogenotrophic methanogenesis are present, but those pathways appear incomplete in the genome. The MAG was more abundant in two former industrial salterns than in a nearby reference wetland and a restored wetland, both of which have much lower salinity levels, as well as significantly lower methane emissions than the salterns.

Proteins maintain hydration at high [KCl] concentration regardless of content in acidic amino acids

Proteins of halophilic organisms, which accumulate molar concentrations of KCl in their cytoplasm, have a much higher content in acidic amino acids than proteins of mesophilic organisms. It has been proposed that this excess is necessary to maintain proteins hydrated in an environment with low water activity, either via direct interactions between water and the carboxylate groups of acidic amino acids or via cooperative interactions between acidic amino acids and hydrated cations. Our simulation study of five halophilic proteins and five mesophilic counterparts does not support either possibility. The simulations use the AMBER ff14SB force field with newly optimized Lennard-Jones parameters for the interactions between carboxylate groups and potassium ions. We find that proteins with a larger fraction of acidic amino acids indeed have higher hydration levels, as measured by the concentration of water in their hydration shell and the number of water/protein hydrogen bonds. However, the hydration level of each protein is identical at low (b_KCl = 0.15 mol/kg) and high (b_KCl = 2 mol/kg) KCl concentrations; excess acidic amino acids are clearly not necessary to maintain proteins hydrated at high salt concentration. It has also been proposed that cooperative interactions between acidic amino acids in halophilic proteins and hydrated cations stabilize the folded protein structure and would lead to slower dynamics of the solvation shell. We find that the translational dynamics of the solvation shell is barely distinguishable between halophilic and mesophilic proteins; if such a cooperative effect exists, it does not have that entropic signature.

Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties

Extreme halophilic Archaea thrive in high salt, where, through proteomic adaptation, they cope with the strong osmolarity and extreme ionic conditions of their environment. In spite of wide fundamental interest, however, studies providing insights into this adaptation are scarce, because of practical difficulties inherent to the purification and characterization of halophilic enzymes. In this work, we describe the evolutionary history of malate dehydrogenases (MalDH) within Halobacteria (a class of the Euryarchaeota phylum). We resurrected nine ancestors along the inferred halobacterial MalDH phylogeny, including the Last Common Ancestral MalDH of Halobacteria (LCAHa) and compared their biochemical properties with those of five modern halobacterial MalDHs. We monitored the stability of these various MalDHs, their oligomeric states and enzymatic properties, as a function of concentration for different salts in the solvent. We found that a variety of evolutionary processes such as amino acid replacement, gene duplication, loss of MalDH gene and replacement owing to horizontal transfer resulted in significant differences in solubility, stability and catalytic properties between these enzymes in the three Halobacteriales, Haloferacales and Natrialbales orders since the LCAHa MalDH.We also showed how a stability trade-off might favor the emergence of new properties during adaptation to diverse environmental conditions. Altogether, our results suggest a new view of halophilic protein adaptation in Archaea.

Traversing the "Omic" landscape of microbial halotolerance for key molecular processes and new insights

Post-2005, the biology of the salt afflicted habitats is predominantly studied employing high throughput "Omic" approaches comprising metagenomics, transcriptomics, metatranscriptomics, metabolomics, and proteomics. Such "Omic-based" studies have deciphered the unfamiliar details about microbial salt-stress biology. The MAGs (Metagenome-assembled genomes) of uncultured halophilic microbial lineages such as Nanohaloarchaea and haloalkaliphilic members within CPR (Candidate Phyla Radiation) have been reconstructed from diverse hypersaline habitats. The study of MAGs of such uncultured halophilic microbial lineages has unveiled the genomic basis of salt stress tolerance in "yet to culture" microbial lineages. Furthermore, functional metagenomic approaches have been used to decipher the novel genes from uncultured microbes and their possible role in microbial salt-stress tolerance. The present review focuses on the new insights into microbial salt-stress biology gained through different "Omic" approaches. This review also summarizes the key molecular processes that underlie microbial salt-stress response, and their role in microbial salt-stress tolerance has been confirmed at more than one "Omic" levels.

Investigation into archaeal extremophilic lifestyles through comparative proteogenomic analysis

Archaea are a group of primary life forms on Earth and could thrive in many unique environments. Their successful colonization of extreme niches requires corresponding adaptations at proteogenomic level in order to maintain stable cellular structures and active physiological functions. Although some studies have already investigated the extremophilic lifestyles of archaeal species based on genomic features and protein structures, there is a lack of comparative proteogenomic analysis in a large scale. In this study, we explored 686 high-quality archaeal genomes (proteomes) sourced from the Pathosystems Resource Integration Center (PATRIC) database. General patterns of genomic features such as genome size, coding capacity (coding genes and non-coding regions), and G + C contents were re-confirmed. Protein domain distribution patterns were then identified across archaeal species. Domains with unknown functions (DUFs) and mini proteins were investigated in terms of their distributions due to their importance in archaeal physiological functions. In addition, physicochemical properties of protein sequences, such as stability, hydrophobicity, isoelectric point, aromaticity and amino acid compositions in corresponding archaeal groups were compared. Unique features associated with extremophilic lifestyles were observed, which suggested that evolutionary adaptations to different extreme environments had intrinsic impacts on archaeal protein features. Taken together, this systematic study facilitates a better understanding of the mechanisms behind the extremophilic lifestyles of archaeal species, which will further contribute to the evolutionary explorations of archaeal adaptations both experimentally and theoretically in the future studies.Communicated by Ramaswamy H. Sarma.

A potassium chloride to glycine betaine osmoprotectant switch in the extreme halophile Halorhodospira halophila

Halophiles utilize two distinct osmoprotection strategies. The accumulation of organic compatible solutes such as glycine betaine does not perturb the functioning of cytoplasmic components, but represents a large investment of energy and carbon. KCl is an energetically attractive alternative osmoprotectant, but requires genome-wide modifications to establish a highly acidic proteome. Most extreme halophiles are optimized for the use of one of these two strategies. Here we examine the extremely halophilic Proteobacterium Halorhodospira halophila and report that medium K⁺ concentration dramatically alters its osmoprotectant use. When grown in hypersaline media containing substantial K⁺ concentrations, H. halophila accumulates molar concentrations of KCl. However, at limiting K⁺ concentrations the organism switches to glycine betaine as its major osmoprotectant. In contrast, the closely related organism Halorhodospira halochloris is limited to using compatible solutes. H. halophila performs both de novo synthesis and uptake of glycine betaine, matching the biosynthesis and transport systems encoded in its genome. The medium K⁺ concentration (~10 mM) at which the KCl to glycine betaine osmoprotectant switch in H. halophila occurs is near the K⁺ content of the lake from which it was isolated, supporting an ecological relevance of this osmoprotectant strategy.

New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea

Hypersaline aquatic and terrestrial ecosystems display a cosmopolitan distribution. These environments teem with microbes and harbor a plethora of prokaryotic lineages that evaded ecological characterization due to the prior inability to cultivate them or to access their genomic information. In order to close the current knowledge gap, we performed two sampling and isolation campaigns in the saline soils of the Odiel Saltmarshes and the salterns of Isla Cristina (Huelva, Spain). From the isolated haloarchaeal strains subjected to high-throughput phylogenetic screening, two were chosen (F15B^T and F9-27^T) for physiological and genomic characterization due of their relatedness to the genus Halonotius. Comparative genomic analyses were carried out between the isolated strains and the genomes of previously described species Halonotius pteroides CECT 7525^T, Halonotius aquaticus F13-13^T and environmentaly recovered metagenome-assembled representatives of the genus Halonotius. The topology of the phylogenomic tree showed agreement with the phylogenetic ones based on 16S rRNA and rpoB' genes, and together with average amino acid and nucleotide identities suggested the two strains as novel species within the genus. We propose the names Halonotius terrestris sp. nov. (type strain F15B^T = CECT 9688^T = CCM 8954^T) and Halonotius roseus sp. nov. (type strain F9-27^T = CECT 9745^T = CCM 8956^T) for these strains. Comparative genomic analyses within the genus highlighted a typical salt-in signature, characterized by acidic proteomes with low isoelectric points, and indicated heterotrophic aerobic lifestyles. Genome-scale metabolic reconstructions revealed that the newly proposed species encode all the necessary enzymatic reactions involved in cobalamin (vitamin B₁₂) biosynthesis. Based on the worldwide distribution of the genus and its abundance in hypersaline habitats we postulate that its members perform a critical function by being able to provide "expensive" commodities (i.e., vitamin B₁₂) to the halophilic microbial communities at large.

Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome

BACKGROUND

The adaptation of a marine prokaryote to live in freshwater environments or vice versa is generally believed to be an unusual and evolutionary demanding process. However, the reasons are not obvious given the similarity of both kinds of habitats.

RESULTS

We have found major differences at the level of the predicted metaproteomes of marine and freshwater habitats with more acidic values of the isoelectric points (pI) in marine microbes. Furthermore, by comparing genomes of marine-freshwater phylogenetic relatives, we have found higher pI values (basic shift) in the freshwater ones. This difference was sharper in secreted > cytoplasmic > membrane proteins. The changes are concentrated on the surface of soluble proteins. It is also detectable at the level of total amino acid composition and involves similarly core and flexible genome- encoded proteins.

CONCLUSIONS

The marked changes at the level of protein amino acid composition and pI provide a tool to predict the preferred habitat of a culture or a metagenome-assembled genome (MAG). The exact physiological explanation for such variations in the pIs and electrostatic surface potentials is not known yet. However, these changes might reflect differences in membrane bioenergetics derived from the absence of significant Na⁺ concentrations in most freshwater habitats. In any case, the changes in amino acid composition in most proteins imply that a long evolutionary time is required to adapt from one type of habitat to the other.

Molecular Adaptations of Bacterial Mercuric Reductase to the Hypersaline Kebrit Deep in the Red Sea

The hypersaline Kebrit Deep brine pool in the Red Sea is characterized by high levels of toxic heavy metals. Here, we describe two structurally related mercuric reductases (MerAs) from this site which were expressed in Escherichia coli Sequence similarities suggest that both genes are derived from proteobacteria, most likely the Betaproteobacteria or Gammaproteobacteria We show that one of the enzymes (K35NH) is strongly inhibited by NaCl, while the other (K09H) is activated in a NaCl-dependent manner. We infer from this difference that the two forms might support the detoxification of mercury in bacterial microorganisms that employ the compatible solutes and salt-in strategies, respectively. Three-dimensional structure modeling shows that all amino acid substitutions unique to each type are located outside the domain responsible for formation of the active MerA homodimer, and the vast majority of these are found on the surface of the molecule. Moreover, K09H exhibits the predominance of acidic over hydrophobic side chains that is typical of halophilic salt-dependent proteins. These findings enhance our understanding of how selection pressures imposed by two environmental stressors have endowed MerA enzymes with catalytic properties that can potentially function in microorganisms that utilize distinct mechanisms for osmotic balance in hypersaline environments.IMPORTANCE Analysis of two structurally homologous but catalytically distinct mercuric reductases from the Kebrit Deep brine in the Red Sea sheds light on the adaptations that enable microorganisms to cope simultaneously with extreme salinity and toxic mercury compounds. One is strongly inhibited by high NaCl concentrations, while the other exhibits NaCl-dependent activation. Their different activity profiles imply that they may derive from bacterial microorganisms that utilize compatible solutes and salt-in strategies, respectively, to maintain osmotic balance. Three-dimensional modeling reveals that regions not involved in formation of the active homodimer are conserved between the two. However, in the NaCl-dependent form, distinct amino acid substitutions are found in areas that are critical for stability in high salt. The work provides insights into how two environmental stressors have shaped the structure of orthologous enzymes through selection and adaptation, enabling them to retain their catalytic function in what may be very different cellular contexts.

NaCl-saturated brines are thermodynamically moderate, rather than extreme, microbial habitats

NaCl-saturated brines such as saltern crystalliser ponds, inland salt lakes, deep-sea brines and liquids-of-deliquescence on halite are commonly regarded as a paradigm for the limit of life on Earth. There are, however, other habitats that are thermodynamically more extreme. Typically, NaCl-saturated environments contain all domains of life and perform complete biogeochemical cycling. Despite their reduced water activity, ∼0.755 at 5 M NaCl, some halophiles belonging to the Archaea and Bacteria exhibit optimum growth/metabolism in these brines. Furthermore, the recognised water-activity limit for microbial function, ∼0.585 for some strains of fungi, lies far below 0.755. Other biophysical constraints on the microbial biosphere (temperatures of >121°C; pH > 12; and high chaotropicity; e.g. ethanol at >18.9% w/v (24% v/v) and MgCl2 at >3.03 M) can prevent any cellular metabolism or ecosystem function. By contrast, NaCl-saturated environments contain biomass-dense, metabolically diverse, highly active and complex microbial ecosystems; and this underscores their moderate character. Here, we survey the evidence that NaCl-saturated brines are biologically permissive, fertile habitats that are thermodynamically mid-range rather than extreme. Indeed, were NaCl sufficiently soluble, some halophiles might grow at concentrations of up to 8 M. It may be that the finite solubility of NaCl has stabilised the genetic composition of halophile populations and limited the action of natural selection in driving halophile evolution towards greater xerophilicity. Further implications are considered for the origin(s) of life and other aspects of astrobiology.

Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis

Fluctuations in environmental osmolarity are ubiquitous stress factors in many natural habitats of microorganisms, as they inevitably trigger osmotically instigated fluxes of water across the semi-permeable cytoplasmic membrane. Under hyperosmotic conditions, many microorganisms fend off the detrimental effects of water efflux and the ensuing dehydration of the cytoplasm and drop in turgor through the accumulation of a restricted class of organic osmolytes, the compatible solutes. Ectoine and its derivative 5-hydroxyectoine are prominent members of these compounds and are synthesized widely by members of the Bacteria and a few Archaea and Eukarya in response to high salinity/osmolarity and/or growth temperature extremes. Ectoines have excellent function-preserving properties, attributes that have led to their description as chemical chaperones and fostered the development of an industrial-scale biotechnological production process for their exploitation in biotechnology, skin care, and medicine. We review, here, the current knowledge on the biochemistry of the ectoine/hydroxyectoine biosynthetic enzymes and the available crystal structures of some of them, explore the genetics of the underlying biosynthetic genes and their transcriptional regulation, and present an extensive phylogenomic analysis of the ectoine/hydroxyectoine biosynthetic genes. In addition, we address the biochemistry, phylogenomics, and genetic regulation for the alternative use of ectoines as nutrients.

Compatible Solute Synthesis and Import by the Moderate Halophile Spiribacter salinus: Physiology and Genomics

Members of the genus Spiribacter are found worldwide and are abundant in ecosystems possessing intermediate salinities between seawater and saturated salt concentrations. Spiribacter salinus M19-40 is the type species of this genus and its first cultivated representative. In the habitats of S. salinus M19-40, high salinity is a key determinant for growth and we therefore focused on the cellular adjustment strategy to this persistent environmental challenge. We coupled these experimental studies to the in silico mining of the genome sequence of this moderate halophile with respect to systems allowing this bacterium to control its potassium and sodium pools, and its ability to import and synthesize compatible solutes. S. salinus M19-40 produces enhanced levels of the compatible solute ectoine, both under optimal and growth-challenging salt concentrations, but the genes encoding the corresponding biosynthetic enzymes are not organized in a canonical ectABC operon. Instead, they are scrambled (ectAC; ectB) and are physically separated from each other on the S. salinus M19-40 genome. Genomes of many phylogenetically related bacteria also exhibit a non-canonical organization of the ect genes. S. salinus M19-40 also synthesizes trehalose, but this compatible solute seems to make only a minor contribution to the cytoplasmic solute pool under osmotic stress conditions. However, its cellular levels increase substantially in stationary phase cells grown under optimal salt concentrations. In silico genome mining revealed that S. salinus M19-40 possesses different types of uptake systems for compatible solutes. Among the set of compatible solutes tested in an osmostress protection growth assay, glycine betaine and arsenobetaine were the most effective. Transport studies with radiolabeled glycine betaine showed that S. salinus M19-40 increases the pool size of this osmolyte in a fashion that is sensitively tied to the prevalent salinity of the growth medium. It was amassed in salt-stressed cells in unmodified form and suppressed the synthesis of ectoine. In conclusion, the data presented here allow us to derive a genome-scale picture of the cellular adjustment strategy of a species that represents an environmentally abundant group of ecophysiologically important halophilic microorganisms.

With a pinch of extra salt-Did predatory protists steal genes from their food?

The cellular adjustment of Bacteria and Archaea to high-salinity habitats is well studied and has generally been classified into one of two strategies. These are to accumulate high levels either of ions (the “salt-in” strategy) or of physiologically compliant organic osmolytes, the compatible solutes (the “salt-out” strategy). Halophilic protists are ecophysiological important inhabitants of salt-stressed ecosystems because they are not only very abundant but also represent the majority of eukaryotic lineages in nature. However, their cellular osmostress responses have been largely neglected. Recent reports have now shed new light on this issue using the geographically widely distributed halophilic heterotrophic protists Halocafeteria seosinensis, Pharyngomonas kirbyi, and Schmidingerothrix salinarum as model systems. Different approaches led to the joint conclusion that these unicellular Eukarya use the salt-out strategy to cope successfully with the persistent high salinity in their habitat. They accumulate various compatible solutes, e.g., glycine betaine, myo-inositol, and ectoines. The finding of intron-containing biosynthetic genes for ectoine and hydroxyectoine, their salt stress–responsive transcription in H. seosinensis, and the production of ectoine and its import by S. salinarum come as a considerable surprise because ectoines have thus far been considered exclusive prokaryotic compatible solutes. Phylogenetic considerations of the ectoine/hydroxyectoine biosynthetic genes of H. seosinensis suggest that they have been acquired via lateral gene transfer by these bacterivorous Eukarya from ectoine/hydroxyectoine-producing food bacteria that populate the same habitat.

Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists

Halophilic microbes living in hypersaline environments must counteract the detrimental effects of low water activity and salt interference. Some halophilic prokaryotes equilibrate their intracellular osmotic strength with the extracellular milieu by importing inorganic solutes, mainly potassium. These "salt-in" organisms characteristically have proteins that are highly enriched with acidic and hydrophilic residues. In contrast, "salt-out" halophiles accumulate large amounts of organic solutes like amino acids, sugars and polyols, and lack a strong signature of halophilicity in the amino acid composition of cytoplasmic proteins. Studies to date have examined halophilic prokaryotes, yeasts, or algae, thus virtually nothing is known about the molecular adaptations of the other eukaryotic microbes, that is, heterotrophic protists (protozoa), that also thrive in hypersaline habitats. We conducted transcriptomic investigations to unravel the molecular adaptations of two obligately halophilic protists, Halocafeteria seosinensis and Pharyngomonas kirbyi Their predicted cytoplasmic proteomes showed increased hydrophilicity compared with marine protists. Furthermore, analysis of reconstructed ancestral sequences suggested that, relative to mesophiles, proteins in halophilic protists have undergone fewer substitutions from hydrophilic to hydrophobic residues since divergence from their closest relatives. These results suggest that these halophilic protists have a higher intracellular salt content than marine protists. However, absence of the acidic signature of salt-in microbes suggests that Haloc. seosinensis and P. kirbyi utilize organic osmolytes to maintain osmotic equilibrium. We detected increased expression of enzymes involved in synthesis and transport of organic osmolytes, namely hydroxyectoine and myo-inositol, at maximal salt concentration for growth in Haloc. seosinensis, suggesting possible candidates for these inferred organic osmolytes.

Structural evidence for solvent-stabilisation by aspartic acid as a mechanism for halophilic protein stability in high salt concentrations

Halophilic organisms have adapted to survive in high salt environments, where mesophilic organisms would perish. One of the biggest challenges faced by halophilic proteins is the ability to maintain both the structure and function at molar concentrations of salt. A distinct adaptation of halophilic proteins, compared to mesophilic homologues, is the abundance of aspartic acid on the protein surface. Mutagenesis and crystallographic studies of halophilic proteins suggest an important role for solvent interactions with the surface aspartic acid residues. This interaction, between the regions of the acidic protein surface and the solvent, is thought to maintain a hydration layer around the protein at molar salt concentrations thereby allowing halophilic proteins to retain their functional state. Here we present neutron diffraction data of the monomeric zwitterionic form of aspartic acid solutions at physiological pH in 0.25 M and 2.5 M concentration of potassium chloride, to mimic mesophilic and halophilic-like environmental conditions. We have used isotopic substitution in combination with empirical potential structure refinement to extract atomic-scale information from the data. Our study provides structural insights that support the hypothesis that carboxyl groups on acidic residues bind water more tightly under high salt conditions, in support of the residue-ion interaction model of halophilic protein stabilisation. Furthermore our data show that in the presence of high salt the self-association between the zwitterionic form of aspartic acid molecules is reduced, suggesting a possible mechanism through which protein aggregation is prevented.

Hans Georg Trüper (1936-2016) and His Contributions to Halophile Research

Prof. Hans Georg Trüper, one of the most important scientists in the field of halophile research, passed away on 9 March 2016 at the age of 79. I here present a brief obituary with special emphasis on Prof. Trüper's contributions to our understanding of the halophilic prokaryotes and their adaptations to life in hypersaline environments. He has pioneered the study of the halophilic anoxygenic phototrophic sulfur bacteria of the Ectothiorhodospira-Halorhodospira group. Some of the species he and his group isolated from hypersaline and haloalkaline environments have become model organisms for the study of the mechanisms of haloadaptation: the functions of three major organic compounds - glycine betaine, ectoine, and trehalose - known to serve as "compatible solutes" in halophilic members of the Bacteria domain, were discovered during studies of these anoxygenic phototrophs. Prof. Trüper's studies of hypersaline alkaline environments in Egypt also led to the isolation of the first known extremely halophilic archaeon (Natronomonas pharaonis). The guest editors dedicate this special volume of Life to the memory of Prof. Hans Georg Trüper.

Strangers in the archaeal world: osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus

Ectoine and hydroxyectoine are compatible solutes widely synthesized by members of the Bacteria to cope with high osmolarity surroundings. Inspection of 557 archaeal genomes revealed that only 12 strains affiliated with the Nitrosopumilus, Methanothrix or Methanobacterium genera harbour ectoine/hydroxyectoine gene clusters. Phylogenetic considerations suggest that these Archaea have acquired these genes through horizontal gene transfer events. Using the Thaumarchaeon 'Candidatus Nitrosopumilus maritimus' as an example, we demonstrate that the transcription of its ectABCD genes is osmotically induced and functional since it leads to the production of both ectoine and hydroxyectoine. The ectoine synthase and the ectoine hydroxylase were biochemically characterized, and their properties resemble those of their counterparts from Bacteria. Transcriptional analysis of osmotically stressed 'Ca. N. maritimus' cells demonstrated that they possess an ectoine/hydroxyectoine gene cluster (hyp-ectABCD-mscS) different from those recognized previously since it contains a gene for an MscS-type mechanosensitive channel. Complementation experiments with an Escherichia coli mutant lacking all known mechanosensitive channel proteins demonstrated that the (Nm)MscS protein is functional. Hence, 'Ca. N. maritimus' cells cope with high salinity not only through enhanced synthesis of osmostress-protective ectoines but they already prepare themselves simultaneously for an eventually occurring osmotic down-shock by enhancing the production of a safety-valve (NmMscS).

Salt resistance genes revealed by functional metagenomics from brines and moderate-salinity rhizosphere within a hypersaline environment

Hypersaline environments are considered one of the most extreme habitats on earth and microorganisms have developed diverse molecular mechanisms of adaptation to withstand these conditions. The present study was aimed at identifying novel genes from the microbial communities of a moderate-salinity rhizosphere and brine from the Es Trenc saltern (Mallorca, Spain), which could confer increased salt resistance to Escherichia coli. The microbial diversity assessed by pyrosequencing of 16S rRNA gene libraries revealed the presence of communities that are typical in such environments and the remarkable presence of three bacterial groups never revealed as major components of salt brines. Metagenomic libraries from brine and rhizosphere samples, were transferred to the osmosensitive strain E. coli MKH13, and screened for salt resistance. Eleven genes that conferred salt resistance were identified, some encoding for well-known proteins previously related to osmoadaptation such as a glycerol transporter and a proton pump, whereas others encoded proteins not previously related to this function in microorganisms such as DNA/RNA helicases, an endonuclease III (Nth) and hypothetical proteins of unknown function. Furthermore, four of the retrieved genes were cloned and expressed in Bacillus subtilis and they also conferred salt resistance to this bacterium, broadening the spectrum of bacterial species in which these genes can function. This is the first report of salt resistance genes recovered from metagenomes of a hypersaline environment.

Molecular adaptation and salt stress response of Halobacterium salinarum cells revealed by neutron spectroscopy

Halobacterium salinarum is an extreme halophile archaeon with an absolute requirement for a multimolar salt environment. It accumulates molar concentrations of KCl in the cytosol to counterbalance the external osmotic pressure imposed by the molar NaCl. As a consequence, cytosolic proteins are permanently exposed to low water activity and highly ionic conditions. In non-adapted systems, such conditions would promote protein aggregation, precipitation, and denaturation. In contrast, in vitro studies showed that proteins from extreme halophilic cells are themselves obligate halophiles. In this paper, adaptation via dynamics to low-salt stress in H. salinarum cells was measured by neutron scattering experiments coupled with microbiological characterization. The molecular dynamic properties of a proteome represent a good indicator for environmental adaptation and the neutron/microbiology approach has been shown to be well tailored to characterize these modifications. In their natural setting, halophilic organisms often have to face important variations in environmental salt concentration. The results showed deleterious effects already occur in the H. salinarum proteome, even when the external salt concentration is still relatively high, suggesting the onset of survival mechanisms quite early when the environmental salt concentration decreases.

Halophiles and their enzymes: negativity put to good use

Halophilic microorganisms possess stable enzymes that function in very high salinity, an extreme condition that leads to denaturation, aggregation, and precipitation of most other proteins. Genomic and structural analyses have established that the enzymes of halophilic Archaea and many halophilic Bacteria are negatively charged due to an excess of acidic over basic residues, and altered hydrophobicity, which enhance solubility and promote function in low water activity conditions. Here, we provide an update on recent bioinformatic analysis of predicted halophilic proteomes as well as experimental molecular studies on individual halophilic enzymes. Recent efforts on discovery and utilization of halophiles and their enzymes for biotechnology, including biofuel applications are also considered.

Is there a common water-activity limit for the three domains of life?

Archaea and Bacteria constitute a majority of life systems on Earth but have long been considered inferior to Eukarya in terms of solute tolerance. Whereas the most halophilic prokaryotes are known for an ability to multiply at saturated NaCl (water activity (a(w)) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650-0.605 a(w). Here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for Halanaerobium lacusrosei (0.748), Halobacterium strain 004.1 (0.728), Halobacterium sp. NRC-1 and Halococcus morrhuae (0.717), Haloquadratum walsbyi (0.709), Halococcus salifodinae (0.693), Halobacterium noricense (0.687), Natrinema pallidum (0.681) and haloarchaeal strains GN-2 and GN-5 (0.635 a(w)). Furthermore, extrapolation of growth curves (prone to giving conservative estimates) indicated theoretical minima down to 0.611 aw for extreme, obligately halophilic Archaea and Bacteria. These were compared with minima for the most solute-tolerant Bacteria in high-sugar (or other non-saline) media (Mycobacterium spp., Tetragenococcus halophilus, Saccharibacter floricola, Staphylococcus aureus and so on) and eukaryotic microbes in saline (Wallemia spp., Basipetospora halophila, Dunaliella spp. and so on) and high-sugar substrates (for example, Xeromyces bisporus, Zygosaccharomyces rouxii, Aspergillus and Eurotium spp.). We also manipulated the balance of chaotropic and kosmotropic stressors for the extreme, xerophilic fungi Aspergillus penicilloides and X. bisporus and, via this approach, their established water-activity limits for mycelial growth (∼0.65) were reduced to 0.640. Furthermore, extrapolations indicated theoretical limits of 0.632 and 0.636 a(w) for A. penicilloides and X. bisporus, respectively. Collectively, these findings suggest that there is a common water-activity limit that is determined by physicochemical constraints for the three domains of life.

Structural changes in halophilic and non-halophilic proteases in response to chaotropic reagents

Halophilic enzymes have been established for their stability and catalytic abilities under harsh operational conditions. These have been documented to withstand denaturation at high temperature, pH, organic solvents, and chaotropic agents. However, this stability is modulated by salt. The present study targets an important aspect in understanding protein-urea/GdmCl interactions using proteases from halophilic Bacillus sp. EMB9 and non-halophilic subtilisin (Carlsberg) from Bacillus licheniformis as model systems. While, halophilic protease containing 1 % (w/v) NaCl (0.17 M) retained full activity towards urea (8 M), non-halophilic protease lost about 90 % activity under similar conditions. The secondary and tertiary structure were lost in non-halophilic but preserved for halophilic protein. This effect could be due to the possible charge screening and shielding of the protein surface by Ca(2+) and Na(+) ions rendering it stable against denaturation. The dialyzed halophilic protease almost behaved like the non-halophilic counterpart. Incorporation of NaCl (up to 5 %, w/v or 0.85 M) in dialyzed EMB9 protease containing urea/GdmCl, not only helped regain of proteolytic activity but also evaded denaturing action. Deciphering the basis of this salt modulated stability amidst a denaturing milieu will provide guidelines and templates for engineering stable proteins/enzymes for biotechnological applications.

Water and temperature relations of soil Actinobacteria

Actinobacteria perform essential functions within soils, and are dependent on available water to do so. We determined the water-activity (aw ) limits for cell division of Streptomyces albidoflavus, Streptomyces rectiviolaceus, Micromonospora grisea and Micromonospora (JCM 3050) over a range of temperatures, using culture media supplemented with a biologically permissive solute (glycerol). Each species grew optimally at 0.998 aw (control; no added glycerol) and growth rates were near-optimal in the range 0.971-0.974 (1 M glycerol) at permissive temperatures. Each was capable of cell division at 0.916-0.924 aw (2 M glycerol), but only S. albidoflavus grew at 0.895 or 0.897 aw (3 M glycerol, at 30 and 37°C respectively). For S. albidoflavus, however, no growth occurred on media at ≤ 0.870 (4 M glycerol) during the 40-day assessment period, regardless of temperature, and a theoretical limit of 0.877 aw was derived by extrapolation of growth curves. This level of solute tolerance is high for non-halophilic bacteria, but is consistent with reported limits for the growth and metabolic activities of soil microbes. The limit, within the range 0.895-0.870 aw , is very much inferior to those for obligately halophilic bacteria and extremely halophilic or xerophilic fungi, and is inconsistent with earlier reports of cell division at 0.500 aw . These findings are discussed in relation to planetary protection policy for space exploration and the microbiology of arid soils.

Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response

Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

The ability to adjust to changing osmotic conditions (osmoadaptation) is crucial to the survival of organisms across the tree of life. However, significant gaps still exist in our understanding of this important phenomenon. To help fill some of these gaps, we have produced high-quality draft genomes for 59 osmoadaptation “experts” (extreme halophiles of the euryarchaeal family Halobacteriaceae). We describe the dispersal of osmoadaptive protein families across the haloarchaeal evolutionary tree. We use this data to suggest a generalized model for haloarchaeal ion transport in response to changing osmotic conditions, including proposed new mechanisms for magnesium and chloride accumulation. We describe the evolutionary expansion and differentiation of haloarchaeal general transcription factor families and discuss their potential for enabling rapid adaptation to environmental fluxes. Lastly, we challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. This result highlights the power of our dataset for making evolutionary inferences, a feature which will make it useful to the broader evolutionary community. We distribute our genomic dataset through a user-friendly graphical interface.

Dissection of hexosyl- and sialyltransferase domains in the bifunctional capsule polymerases from Neisseria meningitidis W and Y defines a new sialyltransferase family

Crucial virulence determinants of disease causing Neisseria meningitidis species are their extracellular polysaccharide capsules. In the serogroups W and Y, these are heteropolymers of the repeating units (→6)-α-d-Gal-(1→4)-α-Neu5Ac-(2→)n in NmW and (→6)-α-d-Glc-(1→4)-α-Neu5Ac-(2→)n in NmY. The capsule polymerases, SiaDW and SiaDY, which synthesize these highly unusual polymers, are composed of two predicted GT-B fold domains separated by a large stretch of amino acids (aa 399-762). We recently showed that residues critical to the hexosyl- and sialyltransferase activity are found in the predicted N-terminal (aa 1-398) and C-terminal (aa 763-1037) GT-B fold domains, respectively. Here we use a mutational approach and synthetic fluorescent substrates to define the boundaries of the hexosyl- and sialyltransferase domains. Our results reveal that the active sialyltransferase domain extends well beyond the predicted C-terminal GT-B domain and defines a new glycosyltransferase family, GT97, in CAZy (Carbohydrate-Active enZYmes Database).

Draft Genome Sequence of the Extremely Halophilic Phototrophic Purple Sulfur Bacterium Halorhodospira halochloris

Halorhodospira halochloris is an extremely halophilic bacterium isolated from hypersaline Wadi Nantrun lakes in Egypt. Here we report the draft genome sequence of this gammaproteobacteria (GI number: 589289709, GenBank Accession number: CP007268). The 3.5-Mb genome encodes for photosynthesis and biosynthesis of organic osmoprotectants. Comparison with the genome of H.halophila promises to yield insights into the evolution of halophilic adaptations.