Halobacterium Halobium Research Articles

Supplementary Tables for "Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC-1"

Supplementary Tables for "Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC-1"

Denovo designing: a novel signal peptide for tat translocation pathway to transport activin A to the periplasmic space of E. coli.

The twin-arginine translocation (Tat) pathway is one of the bacterial secretory strategies which exports folded proteins across the cytoplasmic membrane. In the present study, we designed a novel Tat-signal peptide for secretion of human activin A used as a recombinant protein model here. In doing so, Haloferax volcanii, Halobacterium salinarum, and Escherichia coli Tat specific signal peptides were aligned by ClustalW program to determine conserved and more frequently used residues. After making the initial signal peptide sequence and doing some mutations, efficiency of this designed signal peptide was evaluated using a set of well-known software programs such as TatP, PRED-TAT, and Phobius. Then the best complex between TatC as an initiator protein in Tat secretory machine and the new designed signal peptide connected to activin A with the lowest binding energy was constructed by HADDOCK server, and ΔΔG value of - 5.5kcal/mol was calculated by FoldX module. After that, efficiency of this novel signal peptide for secretion of human activin A to the periplasmic space of E. coli Rosetta-gami (DE3) strain was experimentally evaluated; to scrutinize the activity of the novel signal peptide, Iranian Bacillus Licheniformis α-Amylase enzyme signal peptide as a Sec pathway signal peptide was used as a positive control. The quantitative analysis of western blotting bands by ImageJ software confirmed the high secretion ability of the new designed signal peptide; translocation of 69% of the produced recombinant activin A to the periplasmic space of E. coli. Circular Dichroism (CD) spectroscopy technique also approved the proper secondary structure of activin A secreted to the periplasmic space. The biological activity of activin A was also confirmed by differentiation of K562 erythroleukemia cells to the red blood cell by measuring the amount of hemoglobin or Fe2+ ion using ICP method. In conclusion, this novel designed signal peptide can be used to secrete any other recombinant proteins to the periplasmic space of E. coli efficiently.

The Stain of the Original Salt: Red Heats on Chrome Tanned Leathers and Purple Spots on Ancient Parchments Are Two Sides of the Same Ecological Coin.

Animal hides are one of man’s earliest and mostly used materials; many rawhide products, primarily leather, have for centuries been used for several purposes. The peculiar mechanical properties of leather depend on the hide composition, a dense collagen feltwork. Unfortunately, due to their proteic composition, rawhides may undergo microbial attack and biodeterioration. Over centuries, different processes and treatments (brining, vegetal or chrome tanning, tawing, etc.) were set up to face the biological attack and modify/stabilise the hide’s mechanical properties. Nevertheless, even present-day rawhides are subjected to biological colonisation, and traces of this colonisation are clearly shown in Chrome(III) tanned leathers (in the wet blue stage), with obvious economic damages. The colonisation traces on tanned leathers consist of isolated or coalescent red patches, known as red heat deterioration. Parchments are rawhide products, too; they derive from another manufacturing procedure. Even parchments undergo microbial attack; the parchment biodeterioration seems comparable to leather red heat deterioration and is known as purple spots. Recently, an ecological succession model explained the process of historical parchment purple spot deterioration; the haloarchaea Halobacterium salinarum is the pioneer organism triggering this attack. The marine salt used to prevent rawhide rotting is the carrier of haloarchaea colonisers (Migliore et al., 2019). The aim of this study was to investigate the dynamics of biodeterioration on Chrome(III) tanned leathers and its effects on the stability/integrity of collagen structure. To this end, standard cultivation methods were integrated with three updated technologies, Next-Generation Sequencing (NGS), Raman spectroscopy, and Light Transmitted Analysis (LTA). A bioinformatic comparison between chrome tanned leather vs. historical parchment colonisers was performed to evaluate if leather and parchment share common culprits; furthermore, the effect of the biodeterioration on the physical properties of the hide product was evaluated.

The extremely halophilic archaeon Halobacterium salinarum ETD5 from the solar saltern of Sfax (Tunisia) produces multiple halocins

The extremely halophilic archaeon Halobacterium salinarum strain ETD5 was previously isolated from the solar saltern of Sfax (Tunisia) and shown to encode and express halocin S8. The Hbt. salinarum ETD5 culture supernatant was shown here to exhibit high antimicrobial activity against several halophilic archaea and bacteria of different genera, showing a cross-domain inhibition. The antimicrobial activity was destroyed by proteases, thus pointing to halocins. A bioguided purification procedure was applied using two chromatography steps and antimicrobial assays directed against Halorubrum chaoviator ETR14. In-gel screening assay showed the presence of two antimicrobial bands of approximately 8 and 14 kDa, for which characterization was investigated by N-terminal sequencing and mass spectrometry. The full-length form of halocin S8 that contains 81 amino acids and differs from the 36 amino acid short-length halocin S8 previously described from an uncharacterized haloarchaeon S8a, was identified in the 8 kDa halocin band. A novel halocin that we termed halocin S14 was found in the 14 kDa band. It exhibits amino acid sequence identities with the N-terminally truncated region of the archaeal Mn-superoxide dismutase. These results show that Hbt. salinarum ETD5 produces multiple halocins, a feature that had not been described until now in the domain Archaea.

Structural study of two different forms of SmAP from Halobacterium salinarum which have a different RNA-binding ability

Structural study of two different forms of SmAP from <i>Halobacterium salinarum</i> which have a different RNA-binding ability

Energy Transfer Induced by Dye Encapsulation in a Hybrid Nanoparticle‐Purple Membrane Reversible Assembly

AbstractThe purple membrane (PM) isolated from the bacteria Halobacterium salinarum (H. salinarum) arranges the transmembrane proton pump bacteriorhodopsin (bR) in a 2D hexagonal crystalline lattice. Here, PM sheets containing native bR bend into tube‐like structures with open edges under acidic pH conditions. When decorated with gold nanoparticles (AuNPs), these same PM sheets yield a sealed tube assembly. Upon Rhodamine B (Rh B) sequestration inside the sealed tube, a dramatic decrease in Rh B fluorescence lifetime (τf) from 1.5 ns (unencapsulated) to 14 ps (encapsulated) is observed. The dramatic decrease in lifetime is attributed to energy transfer between AuNPs and Rh B. Subsequent release from the AuNP–PM capsules triggered by an increase in pH shows that 93% of Rh B is recovered (τ = 14 min) due to the capsules' unfolding. The hybrid AuNP–PM material highlights the utility of multicomponent ensembles (i.e., lipid bilayer, protein array, and NPs) by demonstrating that complex, multistimuli 3D responses can lead to multiplexed functions such as controlling energy transfer in the confined, encapsulated state and breaking the energy pair via molecular release in response to a change in pH.

Insights into the mechanism of ATP-driven rotary motors from direct torque measurement.

Motor proteins are molecular machines that convert chemical energy into mechanical work. In addition to existing studies performed on the linear motors found in eukaryotic cells, researchers in biophysics have also focused on rotary motors such as F1-ATPase. Detailed studies on the rotary F1-ATPase motor have correlated all chemical states to specific mechanical events at the single-molecule level. Recent studies showed that there exists another ATP-driven protein motor in life: the rotary machinery that rotates archaeal flagella (archaella). Rotation speed, stepwise movement, and variable directionality of the motor of Halobacterium salinarum were described in previous studies. Here we review recent experimental work discerning the molecular mechanism underlying how the archaellar motor protein FlaI drives rotation by generation of motor torque. In combination, those studies found that rotation slows as the viscous drag of markers increases, but torque remains constant at 160 pN·nm independent of rotation speed. Unexpectedly, the estimated work done in a single rotation is twice the expected energy that would come from hydrolysis of six ATP molecules in the FlaI hexamer. To reconcile the apparent contradiction, a new and general model for the mechanism of ATP-driven rotary motors is discussed.

Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR.

Interactions between proteins and DNA are crucial for all biological systems. Many studies have shown the dependence of protein–DNA interactions on the surrounding salt concentration. How these interactions are maintained in the hypersaline environments that halophiles inhabit remains puzzling. Towards solving this enigma, we identified the DNA motif recognized by the Halobactrium salinarum ROS-dependent transcription factor (hsRosR), determined the structure of several hsRosR–DNA complexes and investigated the DNA-binding process under extreme high-salt conditions. The picture that emerges from this work contributes to our understanding of the principles underlying the interplay between electrostatic interactions and salt-mediated protein–DNA interactions in an ionic environment characterized by molar salt concentrations.

The Genome Sequence of the Halobacterium salinarum Type Strain Is Closely Related to That of Laboratory Strains NRC-1 and R1.

High-coverage long-read sequencing of the Halobacterium salinarum type strain (91-R6) revealed a 2.17-Mb chromosome and two large plasmids (148 and 102 kb). Population heterogeneity and long repeats were observed. Strain 91-R6 and laboratory strain R1 showed 99.63% sequence identity in common chromosomal regions and only 38 strain-specific segments. This information resolves the previously uncertain relationship between type and laboratory strains.

Lidocaine turns the surface charge of biological membranes more positive and changes the permeability of blood-brain barrier culture models

The surface charge of brain endothelial cells forming the blood-brain barrier (BBB) is highly negative due to phospholipids in the plasma membrane and the glycocalyx. This negative charge is an important element of the defense systems of the BBB. Lidocaine, a cationic and lipophilic molecule which has anaesthetic and antiarrhytmic properties, exerts its actions by interacting with lipid membranes. Lidocaine when administered intravenously acts on vascular endothelial cells, but its direct effect on brain endothelial cells has not yet been studied. Our aim was to measure the effect of lidocaine on the charge of biological membranes and the barrier function of brain endothelial cells. We used the simplified membrane model, the bacteriorhodopsin (bR) containing purple membrane of Halobacterium salinarum and culture models of the BBB. We found that lidocaine turns the negative surface charge of purple membrane more positive and restores the function of the proton pump bR. Lidocaine also changed the zeta potential of brain endothelial cells in the same way. Short-term lidocaine treatment at a 10 μM therapeutically relevant concentration did not cause major BBB barrier dysfunction, substantial change in cell morphology or P-glycoprotein efflux pump inhibition. Lidocaine treatment decreased the flux of a cationic lipophilic molecule across the cell layer, but had no effect on the penetration of hydrophilic neutral or negatively charged markers. Our observations help to understand the biophysical background of the effect of lidocaine on biological membranes and draws the attention to the interaction of cationic drug molecules at the level of the BBB.

Culturable bacteriorhodopsin-producing haloarchaea of Tuz Lake (Turkey)

Lake Tuz, the largest hypersaline lake in Turkey, has a great variety of microbial communities that adapted to its extreme environment and produce many industrially important compounds such as photosensitive bacteriorhodopsins. So far, the information about the bacteriorhodopsin-producing haloarchaea species of the lake is still limited. In the present study, archaeal bacteriorhodopsin producers were isolated from three locations of the lake. Their bacteriorhodopsin-producing capability was validated by the purification and SDS-PAGE analysis of the delipidated bacteriorhodopsin molecule. The active isolates were identified by the sequencing of partial 16S rDNA gene regions. According to the results, 11 bacteriorhodopsin-producing isolates grouped in Halobacterium salinarum (4), Halobacterium sp. (3), Haloarcula salaria (2), Haloarcula sp. (1) and Halorubrum sp. (1). Our research demonstrated that Lake Tuz is an important natural source of bacteriorhodopsin-producing haloarchaea and the isolates can be valuable for the related technological applications.

N-Glycosylation Is Important for Halobacterium salinarum Archaellin Expression, Archaellum Assembly and Cell Motility.

Halobacterium salinarum are halophilic archaea that display directional swimming in response to various environmental signals, including light, chemicals and oxygen. In Hbt. salinarum, the building blocks (archaellins) of the archaeal swimming apparatus (the archaellum) are N-glycosylated. However, the physiological importance of archaellin N-glycosylation remains unclear. Here, a tetrasaccharide comprising a hexose and three hexuronic acids decorating the five archaellins was characterized by mass spectrometry. Such analysis failed to detect sulfation of the hexuronic acids, in contrast to earlier reports. To better understand the physiological significance of Hbt. salinarum archaellin N-glycosylation, a strain deleted of aglB, encoding the archaeal oligosaccharyltransferase, was generated. In this ΔaglB strain, archaella were not detected and only low levels of archaellins were released into the medium, in contrast to what occurs with the parent strain. Mass spectrometry analysis of the archaellins in ΔaglB cultures did not detect N-glycosylation. ΔaglB cells also showed a slight growth defect and were impaired for motility. Quantitative real-time PCR analysis revealed dramatically reduced transcript levels of archaellin-encoding genes in the mutant strain, suggesting that N-glycosylation is important for archaellin transcription, with downstream effects on archaellum assembly and function. Control of AglB-dependent post-translational modification of archaellins could thus reflect a previously unrecognized route for regulating Hbt. salinarum motility.

Investigation of factors influencing oxygen content in Halobacterium salinarum growth medium for improved bacteriorhodopsin production

Improving production of bacteriorhodopsin in the culture medium of Halobacterium salinarum confronts indeterminacy related to culture conditions. Several studies have revealed that high oxygen content increases the growth of Halobacterium salinarum whereas it down-regulates the expression of genes responsible for bacteriorhodopsin production. The focus of this study was to clarify this contradictory role of oxygen in bacteriorhodopsin production and to indirectly regulate the oxygen content of the culture medium at a level that would increase the final concentration of bacteriorhodopsin. Oxygen consumption evaluation showed tha in a typical growth of Halobacterium salinarum at aerobic condition, the decrease in oxygen demand was concurrent with a sharp increase in bacteriorhodopsin production. Further investigation on culture conditions revealed that agitation rate and filling volume had a linear correlation with the cell growth and bacteriorhodopsin production by each cell, however, a two-factor interaction model described the relationship between the culture condition and overall bacteriorhodopsin concentration. It was concluded that although each cell of Halobacterium salinarum produced high amount of bacteriorhodopsin at low turbulence condition, the low yield of biomass production at this condition caused a low overall bacteriorhodopsin concentration. The highest overall bacteriorhodopsin concentration was obtained from high turbulence condition, in which cell numbers were high enough to compensate for low production of bacteriorhodopsin by each cell.

Improved GFP Variants to Study Gene Expression in Haloarchaea.

The study of promoter activities in haloarchaea is carried out exclusively using enzymes as reporters. An alternative reporter is the gene encoding the Green Fluorescent Protein (GFP), a simple and fast tool for investigating promoter strengths. However, the GFP variant smRS-GFP, used to analyze protein stabilities in haloarchaea, is not suitable to quantify weak promoter activities, since the fluorescence signal is too low. We enhanced the fluorescence of smRS-GFP 3.3-fold by introducing ten amino acid substitutions, resulting in mGFP6. Using mGFP6 as reporter, we studied six haloarchaeal promoters exhibiting different promoter strengths. The strongest activity was observed with the housekeeping promoters Pfdx of the ferredoxin gene and P2 of the ribosomal 16S rRNA gene. Much lower activities were determined for the promoters of the p-vac region driving the expression of gas vesicle protein (gvp) genes in Halobacterium salinarum PHH1. The basal promoter strength dropped in the order PpA, PpO > PpF, PpD. All promoters showed a growth-dependent activity pattern. The GvpE-induced activities of PpA and PpD were high, but lower compared to the Pfdx or P2 promoter activities. The mGFP6 reporter was also used to investigate the regulatory effects of 5′-untranslated regions (5′-UTRs) of three different gvp mRNAs. A deletion of the 5′-UTR always resulted in an increased expression, implying a negative effect of the 5′-UTRs on translation. Our experiments confirmed mGFP6 as simple, fast and sensitive reporter to study gene expression in haloarchaea.

Motor torque measurement of Halobacterium salinarum archaellar suggests a general model for ATP-driven rotary motors

It is unknown how the archaellum—the rotary propeller used by Archaea for motility—works. To further understand the molecular mechanism by which the hexameric ATPase motor protein FlaI drives rotation of the membrane-embedded archaellar motor, we determined motor torque by imposition of various loads on Halobacterium salinarum archaella. Markers of different sizes were attached to single archaella, and their trajectories were quantified using three-dimensional tracking and high-speed recording. We show that rotation slows as the viscous drag of markers increases, but torque remains constant at 160 pN·nm independent of rotation speed. Notably, the estimated work done in a single rotation is twice the expected energy that would come from hydrolysis of six ATP molecules in the hexamer, indicating that more ATP molecules are required for one rotation of archaellum. To reconcile the apparent contradiction, we suggest a new and general model for the mechanism of ATP-driven rotary motors.

Remarkably enhanced photoelectrical efficiency of bacteriorhodopsin in quantum dot – Purple membrane complexes under two-photon excitation

The photosensitive protein bacteriorhodopsin (bR) has been shown to be a promising material for optoelectronic applications, but it cannot effectively absorb and utilize light energy in the near-infrared (NIR) region of the optical spectrum. Semiconductor quantum dots (QDs) have two-photon absorption cross-sections two orders of magnitude larger than those of bR and can effectively transfer the up-converted energy of two NIR photons to bR via the Förster resonance energy transfer (FRET). In this study, we have engineered a photoelectrochemical cell based on a hybrid material consisting of QDs and bR-containing purple membranes (PMs) of Halobacterium salinarum and demonstrated that this cell can generate an electrical signal under the two-photon laser excitation. We have shown that the efficiency of light conversion by the PM–QD hybrid material under two-photon excitation is up to 4.3 times higher than the efficiency of conversion by PMs alone. The QD integration into the bR-containing PMs significantly improves the bR capacity for utilizing light upon two-photon laser excitation, thus paving the way to the engineering of biologically inspired hybrid NIR nonlinear optoelectronic elements. The nonlinear nature of two-photon excitation may provide considerable advantages, such as a sharp sensitivity threshold and the possibility of precise three-dimensional location of excitation in holography and optical computing.

The Blue-Green Sensory Rhodopsin SRM from Haloarcula marismortui Attenuates Both Phototactic Responses Mediated by Sensory Rhodopsin I and II in Halobacterium salinarum

Haloarchaea utilize various microbial rhodopsins to harvest light energy or to mediate phototaxis in search of optimal environmental niches. To date, only the red light-sensing sensory rhodopsin I (SRI) and the blue light-sensing sensory rhodopsin II (SRII) have been shown to mediate positive and negative phototaxis, respectively. In this work, we demonstrated that a blue-green light-sensing (504 nm) sensory rhodopsin from Haloarcula marismortui, SRM, attenuated both positive and negative phototaxis through its sensing region. The H. marismortui genome encodes three sensory rhodopsins: SRI, SRII and SRM. Using spectroscopic assays, we first demonstrated the interaction between SRM and its cognate transducer, HtrM. We then transformed an SRM-HtrM fusion protein into Halobacterium salinarum, which contains only SRI and SRII, and observed that SRM-HtrM fusion protein decreased both positive and negative phototaxis of H. salinarum. Together, our results suggested a novel phototaxis signalling system in H. marismortui comprised of three sensory rhodopsins in which the phototactic response of SRI and SRII were attenuated by SRM.

The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1.

Antisense RNAs (asRNAs) are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon Halobacterium salinarum NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSSs) and inferred the probable 3′ ends of these transcripts. We analyzed the resulting asRNAs according to the size, location, function of genes on the opposite strand, expression levels and conservation. We show that at least 21% of the genes contain asRNAs in H. salinarum. Most of these asRNAs are expressed at low levels. They are located antisense to genes related to distinctive characteristics of H. salinarum, such as bacteriorhodopsin, gas vesicles, transposases and other important biological processes such as translation. We provide evidence to support asRNAs in type II toxin–antitoxin systems in archaea. We also analyzed public Ribosome profiling (Ribo-seq) data and found that ~10% of the asRNAs are ribosome-associated non-coding RNAs (rancRNAs), with asRNAs from transposases overrepresented. Using a comparative transcriptomics approach, we found that ~19% of the asRNAs annotated in H. salinarum belong to genes with an ortholog in Haloferax volcanii, in which an aTSS could be identified with positional equivalence. This shows that most asRNAs are not conserved between these halophilic archaea.

“Fitness Cost of Two Inteins in Halobacterium salinarum”

Halobacterium salinarum is from the domain Archaea and an obligate inhabitant of extremely saline conditions, including saturated brines. Its PolII and Cdc21a genes are both interrupted by an intein. Inteins are genetic elements within an organism's genome, which, at the protein level, self‐catalyze their own excision to concomitantly form a functional protein. We previously showed that protein splicing of these inteins depends on high salt concentrations, requiring a minimum of 2.0 M NaCl to be active. This suggests that the intein may be active in the native cellular environment of H. salinarum, allowing for production of functional protein, and that its presence might not be detrimental to its host. Conversely, a study by Naor et al. (PNAS (2016) 113(32), E4654) showed that in another halophilic archaeon, Haloferax volcanii, there is a &gt; 7% fitness cost for maintaining the polB‐c intein. We are interested in whether the inteins in H. salinarum exert a similar fitness cost, and will test this using a growth‐competition assay between wild type and intein‐less strains of H. salinarum.Support or Funding InformationThis work was supported by NASA (grant NNX15AM09G to RTP), the National Science Foundation (grants MCB‐1517138 to KVM) and the Dreyfus Foundation (KVM).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Conditional Protein Splicing of Inteins from Extremophiles

Protein splicing is a post‐translational process facilitated by an intein, by which the intein catalyzes its own excision from flanking polypeptides (the exteins), concomitant with ligation of the exteins. Many inteins are themselves interrupted by homing endonuclease domains that can facilitate homing into intein‐less alleles. We have discovered inteins from extremophiles that can be expressed in E. coli, purified as unspliced precursors, and induced to splice by cues such as incubation under reducing conditions, at high temperature, or at high ionic strength. We have shown that the activity and folding of inteins from the extreme halophiles Halobacterium salinarum and Haloquadratum walsbyi demonstrate variable dependence on salt concentration, and we have designed transgenic organisms lacking inteins to test the physiological role of splicing. We have solved the structure of an intein from the extreme thermophile Pyrococcus abyssi, and studied the influence of structural elements on its stability at high temperature and pressure. We also have discovered that the splicing and nuclease activity of inteins from extreme thermophiles can be influenced by pressures consistent with those found at the seafloor.Support or Funding InformationThis work was supported by grants from the National Science Foundation (grants MCB1244089 and MCB1517138) and the Camille and Henry Dreyfus Foundation.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.