Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2

Type III CRISPR-Cas systems provide adaptive immunity against foreign mobile genetic elements through RNA-guided interference. Sequence-specific recognition of RNA targets by the type III effector complex triggers the generation of cyclic oligoadenylate (cOA) second messengers that activate ancillary effector proteins, thus reinforcing the host immune response. The ancillary nuclease Can2 is activated by cyclic tetra-AMP (cA4); however, the mechanisms underlying cA4-mediated activation and substrate selectivity remain elusive. Here we report crystal structures of Thermoanaerobacter brockii Can2 (TbrCan2) in substrate- and product-bound complexes. We show that TbrCan2 is a single strand-selective DNase and RNase that binds substrates via a conserved SxTTS active site motif, and reveal molecular interactions underpinning its sequence preference for CA dinucleotides. Furthermore, we identify a molecular interaction relay linking the cA4 binding site and the nuclease catalytic site to enable divalent metal cation coordination and catalytic activation. These findings provide key insights into the molecular mechanisms of Can2 nucleases in type III CRISPR-Cas immunity and may guide their technological development for nucleic acid detection applications.

Characterization of ferredoxins from the thermophilic, acetogenic bacterium Thermoanaerobacter kivui

A major electron carrier involved in energy and carbon metabolism in the acetogenic model organism Thermoanaerobacter kivui is ferredoxin, an iron-sulfur-containing, electron-transferring protein. Here, we show that the genome of T. kivui encodes four putative ferredoxin-like proteins (TKV_c09620, TKV_c16450, TKV_c10420 and TKV_c19530). All four genes were cloned, a His-tag encoding sequence was added and the proteins were produced from a plasmid in T. kivui. The purified proteins had an absorption peak at 430 nm typical for ferredoxins. The determined iron-sulfur content is consistent with the presence of two predicted [4Fe4S] clusters in TKV_c09620 and TKV_c19530 or one predicted [4Fe4S] cluster in TKV_c16450 and TKV_c10420 respectively. The reduction potential (Em ) for TKV_c09620, TKV_c16450, TKV_c10420 and TKV_c19530 was determined to be -386 ± 4 mV, -386 ± 2 mV, -559 ± 10 mV and -557 ± 3 mV, respectively. TKV_c09620 and TKV_c16450 served as electron carriers for different oxidoreductases from T. kivui. Deletion of the ferredoxin genes led to only a slight reduction of growth on pyruvate or autotrophically on H2  + CO2 . Transcriptional analysis revealed that TKV_c09620 was upregulated in a ΔTKV_c16450 mutant and vice versa TKV_c16450 in a ΔTKV_c09620 mutant, indicating that TKV_c09620 and TKV_c16450 can replace each other. In sum, our data are consistent with the hypothesis that TKV_c09620 and TKV_c16450 are ferredoxins involved in autotrophic and heterotrophic metabolism of T. kivui.

Cross-feeding and wheat straw extractives enhance growth of Clostridium thermocellum-containing co-cultures for consolidated bioprocessing

Co-cultures consisting of three thermophilic and lignocellulolytic bacteria, namely Clostridium thermocellum, C. stercorarium, and Thermoanaerobacter thermohydrosulfuricus, degrade lignocellulosic material in a synergistic manner. When cultured in a defined minimal medium two of the members appeared to be auxotrophic and unable to grow, but the growth of all species was observed in all co-culture combinations, indicating cross-feeding of unidentified growth factors between the members. Growth factors also appeared to be present in water-soluble extractives obtained from wheat straw, allowing for the growth of the auxotrophic monocultures in the defined minimal medium. Cell enumeration during growth on wheat straw in this medium revealed different growth profiles of the members that varied between the co-cultures. End-product profiles also varied substantially between the cultures, with significantly higher ethanol production in all co-cultures compared to the mono-cultures. Understanding interactions between co-culture members, and the additional nutrients provided by lignocellulosic substrates, will aid us in consolidated bioprocessing design.

A biological process effective for the conversion of CO-containing industrial waste gas to acetate

Acetogens have often been observed to be inhibited by CO above an inhibition threshold concentration. In this study, a two-stage culture consisting of carboxydotrophic archaea and homoacetogenic bacteria is found to be effective in converting industrial waste gas derived from a steel mill process. In the first stage, Thermococcus onnurineus could grow on the Linz-Donawitz converter gas (LDG) containing ca. 56% CO as a sole energy source, converting the CO into H2 and CO2. Then, in the second stage, Thermoanaerobacter kivui could grow on the off-gas from the first stage culture, consuming the H2 and CO in the off-gas completely and producing acetate as a main product. T. kivui alone could not grow on the LDG gas. This work represents the first demonstration of acetate production using steel mill waste gas by a two-stage culture of carboxydotrophic hydrogenogenic microbes and homoacetogenic bacteria.

Carbon Isotope Fractionation during Catabolism and Anabolism in Acetogenic Bacteria Growing on Different Substrates

Homoacetogenic bacteria are versatile microbes that use the acetyl coenzyme A (acetyl-CoA) pathway to synthesize acetate from CO2 and hydrogen. Likewise, the acetyl-CoA pathway may be used to incorporate other 1-carbon substrates (e.g., methanol or formate) into acetate or to homoferment monosaccharides completely to acetate. In this study, we analyzed the fractionation of pure acetogenic cultures grown on different carbon substrates. While the fractionation of Sporomusa sphaeroides grown on C1 compounds was strong (εC1, -49‰ to -64‰), the fractionation of Moorella thermoacetica and Thermoanaerobacter kivui using glucose (εGlu= -14.1‰) was roughly one-third as strong, suggesting a contribution of less-depleted acetate from fermentative processes. ForM. thermoacetica, this could indeed be validated by the addition of nitrate, which inhibited the acetyl-CoA pathway, resulting in fractionation during fermentation (εferm= -0.4‰). In addition, we determined the fractionation into microbial biomass of T. kivui grown on H2/CO2(εanabol.= -28.6‰) as well as on glucose (εanabol.= +2.9‰).

Conformational Rearrangements of Individual Nucleotides during RNA-Ligand Binding Are Rate-Differentiated

A pronounced rate differentiation has been found for conformational rearrangements of individual nucleobases that occur during ligand recognition of the preQ1 class-I riboswitch aptamer from Thermoanaerobacter tengcongensis. Rate measurements rely on the 2ApFold approach by analyzing the fluorescence response of riboswitch variants, each with a single, strategically positioned 2-aminopurine nucleobase substitution. Observed rate discrimination between the fastest and the slowest conformational adaption is 22-fold, with the largest rate observed for the rearrangement of a nucleoside directly at the binding site and the smallest rate observed for the 3'-unpaired nucleoside that stacks onto the pseudo-knot-closing Watson-Crick base pair. Our findings provide novel insights into how compact, prefolded RNAs that follow the induced-fit recognition mechanism adapt local structural elements in response to ligand binding on a rather broad time scale and how this process culminates in a structural signal that is responsible for efficient downregulation of ribosomal translation.

Characterization of Electrical Current-Generation Capabilities from Thermophilic Bacterium Thermoanaerobacter pseudethanolicus Using Xylose, Glucose, Cellobiose, or Acetate with Fixed Anode Potentials

Thermoanaerobacter pseudethanolicus 39E (ATCC 33223), a thermophilic, Fe(III)-reducing, and fermentative bacterium, was evaluated for its ability to produce current from four electron donors-xylose, glucose, cellobiose, and acetate-with a fixed anode potential (+ 0.042 V vs SHE) in a microbial electrochemical cell (MXC). Under thermophilic conditions (60 °C), T. pseudethanolicus produced high current densities from xylose (5.8 ± 2.4 A m(-2)), glucose (4.3 ± 1.9 A m(-2)), and cellobiose (5.2 ± 1.6 A m(-2)). It produced insignificant current when grown with acetate, but consumed the acetate produced from sugar fermentation to produce electrical current. Low-scan cyclic voltammetry (LSCV) revealed a sigmoidal response with a midpoint potential of -0.17 V vs SHE. Coulombic efficiency (CE) varied by electron donor, with xylose at 34.8% ± 0.7%, glucose at 65.3% ± 1.0%, and cellobiose at 27.7% ± 1.5%. Anode respiration was sustained over a pH range of 5.4-8.3, with higher current densities observed at higher pH values. Scanning electron microscopy showed a well-developed biofilm of T. pseudethanolicus on the anode, and confocal laser scanning microscopy demonstrated a maximum biofilm thickness (Lf) greater than ~150 μm for the glucose-fed biofilm.

Continuous Ethanol Fermentation of Pretreated Lignocellulosic Biomasses, Waste Biomasses, Molasses and Syrup Using the Anaerobic, Thermophilic Bacterium Thermoanaerobacter italicus Pentocrobe 411

Lignocellosic ethanol production is now at a stage where commercial or semi-commercial plants are coming online and, provided cost effective production can be achieved, lignocellulosic ethanol will become an important part of the world bio economy. However, challenges are still to be overcome throughout the process and particularly for the fermentation of the complex sugar mixtures resulting from the hydrolysis of hemicellulose. Here we describe the continuous fermentation of glucose, xylose and arabinose from non-detoxified pretreated wheat straw, birch, corn cob, sugar cane bagasse, cardboard, mixed bio waste, oil palm empty fruit bunch and frond, sugar cane syrup and sugar cane molasses using the anaerobic, thermophilic bacterium Thermoanaerobacter Pentocrobe 411. All fermentations resulted in close to maximum theoretical ethanol yields of 0.47–0.49 g/g (based on glucose, xylose, and arabinose), volumetric ethanol productivities of 1.2–2.7 g/L/h and a total sugar conversion of 90–99% including glucose, xylose and arabinose. The results solidify the potential of Thermoanaerobacter strains as candidates for lignocellulose bioconversion.

Spore-Forming Thermophilic Bacterium within Artificial Meteorite Survives Entry into the Earth's Atmosphere on FOTON-M4 Satellite Landing Module

One of the key conditions of the lithopanspermia hypothesis is that microorganisms situated within meteorites could survive hypervelocity entry from space through the Earth's atmosphere. So far, all experimental proof of this possibility has been based on tests with sounding rockets which do not reach the transit velocities of natural meteorites. We explored the survival of the spore-forming thermophilic anaerobic bacterium, Thermoanaerobacter siderophilus, placed within 1.4-cm thick basalt discs fixed on the exterior of a space capsule (the METEORITE experiment on the FOTON-M4 satellite). After 45 days of orbital flight, the landing module of the space vehicle returned to Earth. The temperature during the atmospheric transit was high enough to melt the surface of basalt. T. siderophilus survived the entry; viable cells were recovered from 4 of 24 wells loaded with this microorganism. The identity of the strain was confirmed by 16S rRNA gene sequence and physiological tests. This is the first report on the survival of a lifeform within an artificial meteorite after entry from space orbit through Earth's atmosphere at a velocity that closely approached the velocities of natural meteorites. The characteristics of the artificial meteorite and the living object applied in this study can serve as positive controls in further experiments on testing of different organisms and conditions of interplanetary transport.

A genome-guided analysis of energy conservation in the thermophilic, cytochrome-free acetogenic bacterium Thermoanaerobacter kivui

BACKGROUND

Acetogenic bacteria are able to use CO2 as terminal electron acceptor of an anaerobic respiration, thereby producing acetate with electrons coming from H2. Due to this feature, acetogens came into focus as platforms to produce biocommodities from waste gases such as H2+CO2 and/or CO. A prerequisite for metabolic engineering is a detailed understanding of the mechanisms of ATP synthesis and electron-transfer reactions to ensure redox homeostasis. Acetogenesis involves the reduction of CO2 to acetate via soluble enzymes and is coupled to energy conservation by a chemiosmotic mechanism. The membrane-bound module, acting as an ion pump, was of special interest for decades and recently, an Rnf complex was shown to couple electron flow from reduced ferredoxin to NAD+ with the export of Na+ in Acetobacterium woodii. However, not all acetogens have rnf genes in their genome. In order to gain further insights into energy conservation of non-Rnf-containing, thermophilic acetogens, we sequenced the genome of Thermoanaerobacter kivui.

RESULTS

The genome of Thermoanaerobacter kivui comprises 2.9 Mbp with a G+C content of 35% and 2,378 protein encoding orfs. Neither autotrophic growth nor acetate formation from H2+CO2 was dependent on Na+ and acetate formation was inhibited by a protonophore, indicating that H+ is used as coupling ion for primary bioenergetics. This is consistent with the finding that the c subunit of the F1FO ATP synthase does not have the conserved Na+ binding motif. A search for potential H+-translocating, membrane-bound protein complexes revealed genes potentially encoding two different proton-reducing, energy-conserving hydrogenases (Ech).

CONCLUSIONS

The thermophilic acetogen T. kivui does not use Na+ but H+ for chemiosmotic ATP synthesis. It does not contain cytochromes and the electrochemical proton gradient is most likely established by an energy-conserving hydrogenase (Ech). Its thermophilic nature and the efficient conversion of H2+CO2 make T. kivui an interesting acetogen to be used for the production of biocommodities in industrial micobiology. Furthermore, our experimental data as well as the increasing number of sequenced genomes of acetogenic bacteria supported the new classification of acetogens into two groups: Rnf- and Ech-containing acetogens.

Scalable production of microbially mediated zinc sulfide nanoparticles and application to functional thin films

A series of semiconducting zinc sulfide (ZnS) nanoparticles were scalably, reproducibly, controllably and economically synthesized with anaerobic metal-reducing Thermoanaerobacter species. These bacteria reduced partially oxidized sulfur sources to sulfides that extracellularly and thermodynamically incorporated with zinc ions to produce sparingly soluble ZnS nanoparticles with ∼5nm crystallites at yields of ∼5gl(-1)month(-1). A predominant sphalerite formation was facilitated by rapid precipitation kinetics, a low cation/anion ratio and a higher zinc concentration compared to background to produce a naturally occurring hexagonal form at the low temperature, and/or water adsorption in aqueous conditions. The sphalerite ZnS nanoparticles exhibited narrow size distribution, high emission intensity and few native defects. Scale-up and emission tunability using copper doping were confirmed spectroscopically. Surface characterization was determined using Fourier transform infrared and X-ray photoelectron spectroscopies, which confirmed amino acid as proteins and bacterial fermentation end products not only maintaining a nano-dimensional average crystallite size, but also increasing aggregation. The application of ZnS nanoparticle ink to a functional thin film was successfully tested for potential future applications.

Ethanol production from glucose and xylose by immobilized Thermoanaerobacter pentosaceus at 70 °C in an up-flow anaerobic sludge blanket (UASB) reactor

The newly isolated extreme thermophilic ethanologen Thermoanaerobacter pentosaceus was immobilized in different support materials in order to improve its ethanol production ability. In batch fermentation, a maximum ethanol yield of 1.36 mol mol(-1) consumed sugars was obtained by T. pentosaceus immobilized on rapeseed straw. Additionally, immobilized T. pentosaceus' ethanol production was improved by 11% in comparison to free cells. In continuous mode, it was shown that hydraulic retention time (HRT) affected ethanol yield, and a dramatic shift from ethanol to acetate and lactate production occurred at an HRT of 6 h. The maximum ethanol yield and concentration, 1.50 mol mol(-1) consumed sugars and 12.4 g l(-1), were obtained with an HRT of 12 h. The latter represented an improvement of 60% in relation to previously obtained results. This indicates that immobilization of T. pentosaceus is an effective strategy to improve its ethanol production ability.

Recombinant thermostable AP exonuclease from Thermoanaerobacter tengcongensis: cloning, expression, purification, properties and PCR application

Apurinic/apyrimidinic (AP) sites in DNA are considered to be highly mutagenic and must be corrected to preserve genetic integrity, especially at high temperatures. The gene encoding a homologue of AP exonuclease was cloned from the thermophilic anaerobic bacterium Thermoanaerobacter tengcongensis and transformed into Escherichia coli. The protein product showed high identity (80%) to human Ape1 nuclease, whereas to E. coli exonuclease III - 78%. This is the first prokaryotic AP nuclease that exhibits such high identity to human Ape1 nuclease. The very high expression level (57% of total soluble proteins) of fully active and soluble His6-tagged Tte AP enzyme with His6-tag on C-terminal end was obtained in Escherichia coli Rosetta (DE3) pLysS. The active enzyme was purified up to 98% homogeneity in one chromatographic step using metal-affinity chromatography on Ni(2+)-IDA-Sepharose resin. The yield was 90 mg (14000 kU) of pure His6-tagged Tte AP (153 kU/mg) from 1 liter of culture. The optimal conditions of Tte AP endo-, exonuclease and 3'-nuclease activity were investigated using fluorescein labeled dsDNA with inserted AP sites and ssDNA. Optimal Tte AP endonuclease activity was observed at 70-75 degrees C, pH 8.0 and at low Mg2+ concentration (0.5 mM). Higher Mg2+ concentration (> 1 mM) enhanced 3'-5' exonuclease activity and at Mg2+ concentration > 2.0 mM 3' nuclease activity was observed. Because of the endonuclease activity of Tte AP exonuclease, the enzyme was applied in PCR amplification of long DNA templates. Tte AP exonuclease eliminated AP-sites in DNA template and improved the efficiency of DNA amplification.

Hexagonal platelet-like magnetite as a biosignature of thermophilic iron-reducing bacteria and its applications to the exploration of the modern deep, hot biosphere and the emergence of iron-reducing bacteria in early precambrian oceans

Dissimilatory iron-reducing bacteria are able to enzymatically reduce ferric iron and couple to the oxidation of organic carbon. This mechanism induces the mineralization of fine magnetite crystals characterized by a wide distribution in size and irregular morphologies that are indistinguishable from authigenic magnetite. Thermoanaerobacter are thermophilic iron-reducing bacteria that predominantly inhabit terrestrial hot springs or deep crusts and have the capacity to transform amorphous ferric iron into magnetite with a size up to 120 nm. In this study, I first characterize the formation of hexagonal platelet-like magnetite of a few hundred nanometers in cultures of Thermoanaerobacter spp. strain TOR39. Biogenic magnetite with such large crystal sizes and unique morphology has never been observed in abiotic or biotic processes and thus can be considered as a potential biosignature for thermophilic iron-reducing bacteria. The unique crystallographic features and strong ferrimagnetic properties of these crystals allow easy and rapid screening for the previous presence of iron-reducing bacteria in deep terrestrial crustal samples that are unsuitable for biological detection methods and, also, the search for biogenic magnetite in banded iron formations that deposited only in the first 2 billion years of Earth with evidence of life.

Is histidine dissociation a critical component of the NO/H-NOX signaling mechanism? Insights from X-ray absorption spectroscopy

The H-NOX (Heme-Nitric oxide/OXygen binding) family of diatomic gas sensing hemoproteins has attracted great interest. Soluble guanylate cyclase (sGC), the well-characterized eukaryotic nitric oxide (NO) sensor is an H-NOX family member. When NO binds sGC at the ferrous histidine-ligated protoporphyrin-IX, the proximal histidine ligand dissociates, resulting in a 5-coordinate (5c) complex; formation of this 5c complex is viewed as necessary for activation of sGC. Characterization of other H-NOX family members has revealed that while most also bind NO in a 5c complex, some bind NO in a 6-coordinate (6c) complex or as a 5c/6c mixture. To gain insight into the heme pocket structural differences between 5c and 6c Fe(ii)-NO H-NOX complexes, we investigated the extended X-ray absorption fine structure (EXAFS) of the Fe(II)-unligated and Fe(II)-NO complexes of H-NOX domains from three species, Thermoanaerobacter tengcongensis, Shewanella woodyi, and Pseudoalteromonas atlantica. Although the Fe(II)-NO complex of TtH-NOX is formally 6c, we found the Fe-N(His) bond is substantially lengthened. Furthermore, although NO binds to SwH-NOX and PaH-NOX as a 5c complex, consistent with histidine dissociation, the EXAFS data do not exclude a very weakly associated histidine. Regardless of coordination number, upon NO-binding, the Fe-N(porphyrin) bond lengths in all three H-NOXs contract by ~0.07 Å. This study reveals that the overall heme structure of 5c and 6c Fe(II)-NO H-NOX complexes are substantially similar, suggesting that formal histidine dissociation may not be required to trigger NO/H-NOX signal transduction. The study has refined our understanding of the molecular mechanisms underlying NO/H-NOX signaling.

Hydrogen and volatile fatty acid production during fermentation of cellulosic substrates by a thermophilic consortium at 50 and 60 °C

The purpose of this study was to characterize the effect of temperature and cellulosic substrates on fermentative metabolites, H(2) production, and community successions in an anaerobic, cellulolytic consortium, TC60. Pyrosequencing analysis indicated that the consortium was predominated by Thermoanaerobacter and Clostridium spp. Metabolite production was analyzed with four cellulosic substrates at 4 kg/m(3). Triplicate cultures of each substrate were incubated at 50 or 60 °C. The main fermentation products (H(2), CO(2), ethanol, and acetate) were monitored over time. The ANOVA model for production rates showed a significant temperature effect (P<0.05) on all products. Increased temperature promoted higher H(2), CO(2), and ethanol yields while acetate yields were only affected prior to 24h of incubation. In addition to individual effects discerned in the model, ANOVA indicated significant interactions between the substrate and temperature. These interactions have not been previously recognized in the literature for cellulolytic and hydrogen-producing microorganisms.

Reassessment of hydrogen tolerance in Caldicellulosiruptor saccharolyticus

BACKGROUND

Caldicellulosiruptor saccharolyticus has the ability to produce hydrogen (H2) at high yields from a wide spectrum of carbon sources, and has therefore gained industrial interest. For a cost-effective biohydrogen process, the ability of an organism to tolerate high partial pressures of H2 (PH2) is a critical aspect to eliminate the need for continuous stripping of the produced H2 from the bioreactor.

RESULTS

Herein, we demonstrate that, under given conditions, growth and H2 production in C. saccharolyticus can be sustained at PH2 up to 67 kPa in a chemostat. At this PH2, 38% and 16% of the pyruvate flux was redirected to lactate and ethanol, respectively, to maintain a relatively low cytosolic NADH/NAD ratio (0.12 mol/mol). To investigate the effect of the redox ratio on the glycolytic flux, a kinetic model describing the activity of the key glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), was developed. Indeed, at NADH/NAD ratios of 0.12 mol/mol (Ki of NADH = 0.03 ± 0.01 mM) GAPDH activity was inhibited by only 50% allowing still a high glycolytic flux (3.2 ± 0.4 mM/h). Even at high NADH/NAD ratios up to 1 mol/mol the enzyme was not completely inhibited. During batch cultivations, hydrogen tolerance of C. saccharolyticus was dependent on the growth phase of the organism as well as the carbon and energy source used. The obtained results were analyzed, based on thermodynamic and enzyme kinetic considerations, to gain insight in the mechanism underlying the unique ability of C. saccharolyticus to grow and produce H2 under relatively high PH2.

CONCLUSION

C. saccharolyticus is able to grow and produce hydrogen at high PH2, hence eliminating the need of gas sparging in its cultures. Under this condition, it has a unique ability to fine tune its metabolism by maintaining the glycolytic flux through regulating GAPDH activity and redistribution of pyruvate flux. Concerning the later, xylose-rich feedstock should be preferred over the sucrose-rich one for better H2 yield.

[Characterization of an acidotolerant, thermophilic Thermoanaerobacter sp. xyl-d with a high xylose conversion]

OBJECTIVE

We screened a thermophilic xylolytic bacterium that produced fuel ethanol from a high-temperature oil reservoir, and provided microbial resources to genetic engineering strains construction and consolidated bioprocessing.

METHODS

We adopted Hungate anaerobic technique to isolate strain xyl-d from oil reservoir water sample enriched for two years from Shengli Oilfield in China, and we identified strain xyl-d with morphological, physiological, biochemical and phylogenetic analysis.

RESULTS

Strain xyl-d was gram-negative, rod-shaped, spore-forming and strictly anaerobic. The growth temperature ranged from 30 degrees C to 85 degrees C (optimum 65 degrees C) and the pH ranged from 3.0 to 10.0 (optimum 7.5) and salt concentration was 0% - 4% (optimum at 2.0%). It converted D-xylose into ethanol, acetate, CO2, trace amount of iso-butanol and propionate. The genomic DNA G + C contents of strain xyl-d was 45.6 mol%. Based on 16S rRNA gene sequence, strain xyl-d was most close to Thermoanaerobacter wiegelii DSM10319(T) and Thermoanaerobacter ethanolicus DSM 2246(T) both with the 99.3% similarity. It produced more ethanol and less acetate at initial pH 8.5 than other pH. Ethanol yield was increased significantly with yeast extract, and ethanol became the main end product. In addition, growth of strain xyl-d was inhibited obviously with ethanol concentration more than 7% (V/V). In the optimum growth conditions, xylose degradation rates reached to 91.37%.

CONCLUSION

Strain xyl-d was thermophilic, high xylose conversion rate, acidotolerant anaerobe. It was a potential bacterium that can be used for consolidated bioprocessing.

The Thermoanaerobacter glycobiome reveals mechanisms of pentose and hexose co-utilization in bacteria

Thermoanaerobic bacteria are of interest in cellulosic-biofuel production, due to their simultaneous pentose and hexose utilization (co-utilization) and thermophilic nature. In this study, we experimentally reconstructed the structure and dynamics of the first genome-wide carbon utilization network of thermoanaerobes. The network uncovers numerous novel pathways and identifies previously unrecognized but crucial pathway interactions and the associated key junctions. First, glucose, xylose, fructose, and cellobiose catabolism are each featured in distinct functional modules; the transport systems of hexose and pentose are apparently both regulated by transcriptional antiterminators of the BglG family, which is consistent with pentose and hexose co-utilization. Second, glucose and xylose modules cooperate in that the activity of the former promotes the activity of the latter via activating xylose transport and catabolism, while xylose delays cell lysis by sustaining coenzyme and ion metabolism. Third, the vitamin B₁₂ pathway appears to promote ethanologenesis through ethanolamine and 1, 2-propanediol, while the arginine deiminase pathway probably contributes to cell survival in stationary phase. Moreover, by experimentally validating the distinct yet collaborative nature of glucose and xylose catabolism, we demonstrated that these novel network-derived features can be rationally exploited for product-yield enhancement via optimized timing and balanced loading of the carbon supply in a substrate-specific manner. Thus, this thermoanaerobic glycobiome reveals novel genetic features in carbon catabolism that may have immediate industrial implications and provides novel strategies and targets for fermentation and genome engineering.

Renewable liquid fuels derived from lignocellulosic biomass could alleviate global energy shortage and climate change. Cellulose and hemicellulose are the main components of lignocellulosic biomass. Therefore, the ability to simultaneously utilize pentose and hexose (i.e., co-utilization) has been a crucial challenge for industrial microbes producing lignocellulosic biofuels. Certain thermoanaerobic bacteria demonstrate this unusual talent, but the genetic foundation and molecular mechanism of this process remain unknown. In this study, we reconstructed the structure and dynamics of the first genome-wide carbon utilization network of thermoanaerobes. This transcriptome-based co-expression network reveals that glucose, xylose, fructose, and cellobiose catabolism are each featured on distinct functional modules. Furthermore, the dynamics of the network suggests a distinct yet collaborative nature between glucose and xylose catabolism. In addition, we experimentally demonstrated that these novel network-derived features can be rationally exploited for product-yield enhancement via optimized timing and balanced loading of the carbon supply in a substrate-specific manner. Thus, the newly discovered modular and precisely regulated network elucidates unique features of thermoanaerobic glycobiomes and reveals novel perturbation strategies and targets for the enhanced thermophilic production of lignocellulosic biofuels.

Mechanisms of enhanced cellulosic bioethanol fermentation by co-cultivation of Clostridium and Thermoanaerobacter spp

Engineering microbial consortia capable of efficient ethanolic fermentation of cellulose is a strategy for the development of consolidated bioprocessing for bioethanol production. Co-cultures of cellulolytic Clostridium thermocellum with non-cellulolytic Thermoanaerobacter strains (X514 and 39E) significantly improved ethanol production by 194-440%. Strain X514 enhanced ethanolic fermentation much more effectively than strain 39E in co-cultivation, with ethanol production in X514 co-cultures at least 62% higher than that of 39E co-cultures. Comparative genome sequence analysis revealed that the higher ethanolic fermentation efficiency in strain X514 was associated with the presence of a complete vitamin B(12) biosynthesis pathway, which is incomplete in strain 39E. The significance of the vitamin B(12)de novo biosynthesis capacity was further supported by the observation of improved ethanol production in strain 39E by 203% following the addition of exogenous vitamin B(12). The vitamin B(12) biosynthesis pathway provides a valuable biomarker for selecting metabolically robust strains for bioethanol production.

Crystallite sizes and lattice parameters of nano-biomagnetite particles

Average crystallite sizes of microbially synthesized pure, metal-, and lanthanide-substituted magnetite (bio-magnetite) were determined for a variety of incubation times and temperatures, substitutional elements and amounts, bacterial species, and precursor types. The intriguing difference between nanoparticle bio-magnetite and chemically synthesized magnetite (chem-magnetite) was that powder X-ray diffraction (XRD) data showed that the bio-magnetite exhibited slightly smaller lattice parameters, however, Raman Spectroscopy exhibited no difference in Fe-O bonding. These results indicate that bio-magnetite likely exhibits a more compact crystal structure with less uncoordinated iron on the surface suppressing negative pressure effects. The bio-magnetite with decreased lattice parameters could have potential technological advantages over current commercial chemically synthesized magnetites.

[Isolation and identification of a thermophilic anaerobic bacterium]

OBJECTIVE

To find new microbial resources from a high-temperature oil reservoir.

METHODS

Strain HL-3 was isolated by Hungate Anaerobic Technique from oil reservoir water sampled from Dagang oilfield, China. Through physiological, biochemical and phylogenetic analysis, the strain HL-3 was classified.

RESULTS

Cells were Gram-positive. The temperature range for growth was 40 degrees C-75 degrees C (optimum at 60 degrees C) and the pH range was 5.0-8.0 (optimum at 6.5). The isolate could grow in the presence of 0%-3.2% NaCl (optimum at 0.25%). Glucose, ribose, mannose, xylose and cellobiose could be metabolized. Metabolites of glucose were ethanol, acetate, CO2 and trace amount of propionate and butanol. The G + C content of DNA was 33.9 mol%. Based on 16S rRNA studies,strain HL-3 was most close to T. uzonensis DSM 18761T (EF530067) with 98.8% similarity and to T. sulfurigignens DSM 17917T (AF234164) with the 98.1% similarity. Strain HL-3 tolerated to high sulfite (0. 1mol/L) ions and extremely high concentration of thiosulfate (0.8 mol/L). When the concentration of thiosulfate was higher than 0.075 mol/L, the cell would generate S element granular. The presence of H2S gas was detected inside of space at the top of serum bottle. Strain HL-3 together with T. uzonensis DSM 18761T differed greatly in toleration of thiosulfate and sulfite. The toleration of strain HL-3 to thiosulfate and sulfite was most close to T. sulfurigignens DSM 17917T (AF234164). In addition, strain HL-3 to metabolite thiosulfate and sulfite was also similar with T. sulfurigignens DSM 17917T (AF234164). However, it differs largely from both of them to metabolize glucose.

CONCLUSION

Therefore, strain HL-3 may be a new spieces of the Thermoanaerobacter, and the definitive classification positioning is still awaiting for further verified with the method of determination of whole-genome DNA-DNA similarity

[Cellulose degradation and ethanol production of different Clostridium strain]

Cellulose degradation and ethanol production of two types of cellulosic materials with different concentration were evaluated in batch system of mono-cultures of cellulolytic ethanol producing strains (Clostridium thermocellum strain LQRI and Clostridium thermocellum strain VPI), and co-cultures of LQRI or VPI in combination with one of the non-cellulolytic ethanol producing strains (Thermoanaerobacter ethanolicus strains X514 or Thermoanaerobacter ethanolicus 39E). Results demonstrated that higher cellulose degradation abilities about 1.2 times were detected in LQRI mono-culture than in VPI mono-culture, while no significant difference of ethanol yields was found between the two mono-cultures. Abilities of cellulose degradation and ethanol production decreased significantly with the increasing of substrate cellulose concentration (1%, 2%, 5%). In the co-culture system, cellulose degradation abilities of LQRI were also significantly higher than VPI, the former is 1.28-1.58 times of the latter. Cellulose degradation rate of LQRI + Thermoanaerobacter and VPI + Thermoanaerobacter decreased gradually with the increasing of substrate cellulose concentration, while the absolute value of cellulose degradation was also affected by the partner Thermoanaerobacter strain. Additionally, the ethanol yields in the co-cultures of LQRI + Thermoanaerobacter were significantly higher than that in the co-cultures of VPI + Thermoanaerobacter with same Thermoanaerobaeter partner, the former is 1.27-1.77 times of the latter. However, ethanol yields in the co-cultures have not significantly declined with the increasing of substrate cellulose concentration.

Thermoanaerobacter spp. control ethanol pathway via transcriptional regulation and versatility of key enzymes

Ethanologenic Thermoanaerobacter species produce ethanol from lignocellulose derived substrates at temperatures above 70 degrees C. In the final steps of ethanol formation, two bifunctional acetaldehyde/alcohol dehydrogenases, AdhB and AdhE, and an alcohol dehydrogenase, AdhA, catalyze redox reactions between acetyl-CoA and ethanol via an acetaldehyde intermediate. DNA cloning and analysis revealed that the dehydrogenase genes and their transcriptional regulatory regions were highly conserved in these species. As determined by real-time PCR, the transcription of adhE was activated by ethanol, while adhB was transcribed without ethanol; however, all of their transcription was reduced at higher ethanol concentrations. Under imitating physiological conditions, AdhE played a crucial role in ethanol formation, and AdhB favored ethanol consumption when ethanol concentration was high e.g. 1%. Thus, the ethanol titer of fermentation is controlled via transcriptional regulation and the properties of specific enzymes in Thermoanaerobacter. These results provide evidence for an ethanol balance model and offer the possibility to raise the ethanol titer by metabolic engineering.

[Enhanced role of the co-culture of thermophilic anaerobic bacteria on cellulosic ethanol]

Fermentation of the type of cellulosic materials to ethanol was evaluated in batch system of mono-cultures of cellulolytic ethanol producing strains (Clostridium thermocellum strain LQRI), and co-cultures of LQRI in combination with one of the non-cellulolytic ethanol producing strains (Thermoanaerobacter pseudoethanolicus strains X514 or Thermoanaerobacter ethanolicus 39E). Results showed that ethanol yields and cellulose degradation abilities were significantly improved by the establishment of co-cultures consisting of LQRI and Thermoanaerobacter ethanolicus partner. A factorial experimental comparison revealed that the co-culture of LQRI + X514 provided the higher ethanol yield than the co-culture of LQRI + 39E, but no significant difference on cellulose degradation by LQRI was found in these co-cultures. In the absence of yeast extract, the highest ethanol concentrations in the co-cultures of LQRI + X514 and LQRI + 39E were about 71 mmol/L and 36.5 mmol/L, which were approximately 5-11 and 3-5 times higher than that of the mono-culture LQRI under the same concentration substrate, respectively. In the presence of 0.6% yeast extract, the highest ethanol concentrations in the co-cultures of LQRI + X514 and LQRI + 39E were rapidly improved and reached 263.5 mmol/L and 143.5 mmol/L, which were approximately 8-22 and 8-12 times higher than that of the mono-culture LQRI under the same concentrations substrate, respectively. The maximum ethanol concentration reached about 263.5 mmol/L (1.2%) in the co-culture of LQRI + X514 grown on 5% Solka Floc in the presence of 0.6% yeast extract, while the maximum ethanol concentration reached 143.5 mmol/L (1.2%) in the co-culture of LQRI + 39E grown on 2% Solka Floc in the presence of 0.6% yeast extract.

Characterization of the impact of acetate and lactate on ethanolic fermentation by Thermoanaerobacter ethanolicus

Ethanolic fermentation of simple sugars is an important step in the production of bioethanol as a renewable fuel. Significant levels of organic acids, which are generally considered inhibitory to microbial metabolism, could be accumulated during ethanolic fermentation, either as a fermentation product or as a by-product generated from pre-treatment steps. To study the impact of elevated concentrations of organic acids on ethanol production, varying levels of exogenous acetate or lactate were added into cultures of Thermoanaerobacter ethanolicus strain 39E with glucose, xylose or cellobiose as the sole fermentation substrate. Our results found that lactate was in general inhibitory to ethanolic fermentation by strain 39E. However, the addition of acetate showed an unexpected stimulatory effect on ethanolic fermentation of sugars by strain 39E, enhancing ethanol production by up to 394%. Similar stimulatory effects of acetate were also evident in two other ethanologens tested, T. ethanolicus X514, and Clostridium thermocellum ATCC 27405, suggesting the potentially broad occurrence of acetate stimulation of ethanolic fermentation. Analysis of fermentation end product profiles further indicated that the uptake of exogenous acetate as a carbon source might contribute to the improved ethanol yield when 0.1% (w/v) yeast extract was added as a nutrient supplement. In contrast, when yeast extract was omitted, increases in sugar utilization appeared to be the likely cause of higher ethanol yields, suggesting that the characteristics of acetate stimulation were growth condition-dependent. Further understanding of the physiological and metabolic basis of the acetate stimulation effect is warranted for its potential application in improving bioethanol fermentation processes.

The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain

Riboswitches are RNA elements that control gene expression through metabolite binding. The preQ(1) riboswitch exhibits the smallest known ligand-binding domain and is of interest for its economical organization and high affinity interactions with guanine-derived metabolites required to confer tRNA wobbling. Here we present the crystal structure of a preQ(1) aptamer domain in complex with its precursor metabolite preQ(0). The structure is highly compact with a core that features a stem capped by a well organized decaloop. The metabolite is recognized within a deep pocket via Watson-Crick pairing with C15. Additional hydrogen bonds are made to invariant bases U6 and A29. The ligand-bound state confers continuous helical stacking throughout the core fold, thus providing a platform to promote Watson-Crick base pairing between C9 of the decaloop and the first base of the ribosome-binding site, G33. The structure offers insight into the mode of ribosome-binding site sequestration by a minimal RNA fold stabilized by metabolite binding and has implications for understanding the molecular basis by which bacterial genes are regulated.

Novel ssDNA-binding properties of SSB2 and SSB3 from Thermoanaerobacter tengcongensis

OBJECTIVE

SSB2 and SSB3 are ssDNA-binding proteins of Thermoanaerobacter tengcongensis. This work aimed to disclose novel properties of both proteins.

METHODS

We performed electrophoretic mobility shift assays (EMSAs) using oligonucleotides spanning the replication origin of T. tengcongensis and non-denaturing polyacrylamide gels. Western blotting assays were used to study the expression patterns of both proteins.

RESULTS

SSB2 bound to 35-nt, 59-nt and 70-nt ssDNA spanning the replication origin and formed one,two or three DNA-protein complexes. The number of the SSB2-DNA complexes was determined by both the length of the ssDNA and the concentration of SSB2. SSB3 formed one more DNA-protein complex with 59-nt or 70-nt ssDNA in comparison with SSB2. Storage of the proteins at -70 degrees C led to the disappearance of one SSB2-(70-nt) complex, or two SSB3-(59-nt) complexes or three SSB3-(70-nt) complexes in the EMSA, indicating the distinct loss of the SSBs's conformations. Moreover,SSB2 and SSB3 displayed different expression patterns at variable incubation temperatures in vivo.

CONCLUSION

SSB2 and SSB3 could bind ssDNA with various conformations that were determined by the length of ssDNA, the concentration of the proteins, as well as the temperature of treatment. To our knowledge, this is the first disclosure of the characteristics of SSB2 and SSB3 on 35-70 nt oligonucleotides.

[Isolation and characterization of Thermoanaerobacter mathranii SC-2 from oil-field water]

OBJECTIVE

We studied physiological, biochemical properties and metabolites of Thermoanaerobacter mathranii SC-2 from oil-field water in Shengli oilfield.

METHODS

Strain SC-2 was isolated by Hungate anaerobic technique. Through physiological, biochemical and phylogenetic analysis, the strain was identified. Metabolites were analyzed by gas chromatogram.

RESULTS

The cells were Gram-negative, rod-shaped, spore-forming. Growth was observed in the temperature range from 40 to 75degrees C (optimum 70 degrees C) and pH range from 5.5 to 9.5 (optimum 6.5). The isolate grew in the presence of 0%-5% NaCl with an optimum without NaCl at pH 7.0 and 65 degrees C. Strain SC-2 used many carbohydrates as carbon sources, including glucose and xylose. Metabolites of glucose were ethanol, acetate, propionate, lactate, CO2 and H2. Based on 16S rDNA studies, strain SC-2 was most close to T. mathranii subsp. mathranii11246T with 99.85% similarity. More ethanol and acetate were produced at initial pH 8.0 than yields at other pH. Yeast extract could significantly increase ethanol and acetate yields. In addition, ethanol (4%) added in the medium obviously inhibited its growth.

CONCLUSION

Strain SC-2 was extremely thermophilic, halotolerant anaerobe.

Replication initiator DnaA interacts with an anti-terminator NusG in T. tengcongensis

DnaA plays a central role in initiation of DNA replication at oriC in bacteria, and is also a transcription regulator which interacts with the DnaA box relative to a specific gene. Through screening the interaction between TtDnaA and the transcription machinery in Thermoanaerobacter tengcongensis by yeast two-hybrid assays, we found for the first time that the TtDnaA could interact with an anti-terminator, TtNusG2, in this thermophilic bacterium. The direct interaction between TtDnaA and TtNusG2 was verified by surface plasmon resonance (SPR) assay in vitro, and was further confirmed by co-immunoprecipitation assay in vivo. Moreover, we demonstrated that domain I and domain III of TtDnaA were responsible for the interaction with TtNusG2. These findings might expand our understanding of cooperation of two fundamental processes, replication and transcription, in this bacterium.

An ability of isolated strains to efficiently cooperate in ethanolic fermentation of agricultural plant refuse under initially aerobic thermophilic conditions: oxygen deletion process appended to consolidated bioprocessing (CBP)

For bioconversion of bean curd refuse, a processing by-product of bean curd, ethanol-producing anaerobic thermophiles (strains kpu03 and kpu04) were newly isolated. Both of them degraded hemicellulose, but not cellulose at all. Phylogenetically, strains kpu03 and kpu04 belong to the Clostridium and Thermoanaerobacterium genus, respectively. Aerobic thermophiles degrading cellulose were also isolated newly. Among them, strain kpuB3 particularly enhanced ethanol production by anaerobic strain kpu04 in the aerobic bean curd refuse medium. Strain kpuB3 belongs to the Geobacillus genus phylogenetically. The co-culture also significantly reduced CH(3)SH production, leading to the prevention of offensive odor. These results demonstrate that cellulolytic aerobe cooperated with hemicellulolytic anaerobe in ethanolic fermentation by not only synergistic effect but also deletion of oxygen from the vessels, providing a new model of oxygen deletion process appended to consolidated bioprocessing (CBP).

Effect of temperature on ethanol tolerance of a thermophilic anaerobic ethanol producerThermoanaerobacter A10: Modeling and simulation

The low ethanol tolerance of thermophilic anaerobic bacteria (<2%, v/v) is a major obstacle for their industrial exploitation for ethanol production. The ethanol tolerance of the thermophilic anaerobic ethanol-producing strain Thermoanaerobacter A10 was studied during batch tests of xylose fermentation at a temperature range of 50-70 degrees C with exogenously added ethanol up to approximately 6.4% (v/v). At the optimum growth temperature of 70 degrees C, the strain was able to tolerate 4.7% (v/v) ethanol, and growth was completely inhibited at 5.6% (v/v). A higher ethanol tolerance was found at lower temperatures. At 60 degrees C, the strain was able to tolerate at least 5.1% (v/v) ethanol. A generalized form of Monod kinetic equation proposed by Levenspiel was used to describe the ethanol (product) inhibition. The model predicted quite well the experimental data for the temperature interval 50-70 degrees C, and the maximum specific growth rate and the toxic power (n), which describes the order of ethanol inhibition at each temperature, were estimated. The toxic power (n) was 1.33 at 70 degrees C, and corresponding critical inhibitory product concentration (P(crit)) above which no microbial growth occurs was determined to be 5.4% (v/v). An analysis of toxic power (n) and P(crit) showed that the optimum temperature for combined microbial growth and ethanol tolerance was 60 degrees C. At this temperature, the toxic power (n), and P(crit) were 0.50, and 6.5% (v/v) ethanol, respectively. From a practical point of view, the model may be applied to compare the ethanol inhibition (ethanol tolerance) on microbial growth of different thermophilic anaerobic bacterial strains.

In situ analysis of sulfur species in sulfur globules produced from thiosulfate by Thermoanaerobacter sulfurigignens and Thermoanaerobacterium thermosulfurigenes

The Firmicutes Thermoanaerobacter sulfurigignens and Thermoanaerobacterium thermosulfurigenes convert thiosulfate, forming sulfur globules inside and outside cells. X-ray absorption near-edge structure analysis revealed that the sulfur consisted mainly of sulfur chains with organic end groups similar to sulfur formed in purple sulfur bacteria, suggesting the possibility that the process of sulfur globule formation by bacteria is an ancient feature.

Evaluation of continuous ethanol fermentation of dilute-acid corn stover hydrolysate using thermophilic anaerobic bacterium Thermoanaerobacter BG1L1

Dilute sulfuric acid pretreated corn stover is potential feedstock of industrial interest for second generation fuel ethanol production. However, the toxicity of corn stover hydrolysate (PCS) has been a challenge for fermentation by recombinant xylose fermenting organisms. In this work, the thermophilic anaerobic bacterial strain Thermoanaerobacter BG1L1 was assessed for its ability to ferment undetoxified PCS hydrolysate in a continuous immobilized reactor system at 70 degrees C. The tested strain showed significant resistance to PCS, and substrate concentrations up to 15% total solids (TS) were fermented yielding ethanol of 0.39-0.42 g/g-sugars consumed. Xylose was nearly completely utilized (89-98%) for PCS up to 10% TS, whereas at 15% TS, xylose conversion was lowered to 67%. The reactor was operated continuously for 135 days, and no contamination was seen without the use of any agent for preventing bacterial infections. This study demonstrated that the use of immobilized thermophilic anaerobic bacteria for continuous ethanol fermentation could be promising in a commercial ethanol process in terms of system stability to process hardiness and reactor contamination. The tested microorganism has considerable potential to be a novel candidate for lignocellulose bioconversion into ethanol.

Thermoanaerobacter sulfurigignens sp. nov., an anaerobic thermophilic bacterium that reduces 1 M thiosulfate to elemental sulfur and tolerates 90 mM sulfite

Two anaerobic thermophilic bacteria, designated strains JW/SL824 and JW/SL-NZ826(T), were isolated from an acidic volcanic steam outlet on White Island, New Zealand. Cells were rod-shaped, spore-forming, motile and Gram-stain negative, but contained Gram-type positive cell wall. Strain JW/SL-NZ826(T) utilized various carbohydrates including xylose and glucose. The fermentation end products produced from glucose in the absence of thiosulfate were lactate, ethanol, acetate, CO(2) and H(2). The temperature range for growth was 34-72 degrees C, with an optimum at 63-67 degrees C. The pH(60 degrees C) range for growth was 4.0-8.0, with an optimum at 5.0-6.5. The doubling time of strain JW/SL-NZ826(T) under optimal growth conditions was 2.4 h. The DNA G+C content was 34-35 mol% (HPLC). The two strains reduced up to 1 M thiosulfate to elemental sulfur without sulfide formation, which is a trend typically observed among species belonging to the genus Thermoanaerobacterium. Sulfur globules containing short and long sulfur chains but no S(8)-ring sulfur were produced inside and outside the cells. Up to 90 mM sulfite was tolerated. This tolerance is assumed to be an adaptation to the geochemistry of the environment of White Island. The 16S rRNA gene sequence analysis, however, indicated that the two strains belonged to the genus Thermoanaerobacter, with similarities in the range 95.6-92.7 %. Therefore, strains JW/SL-NZ824 and JW/SL-NZ826(T) represent a novel taxon, for which the name Thermoanaerobacter sulfurigignens sp. nov. is proposed, with strain JW/SL-NZ826(T) (=ATCC 700320(T)=DSM 17917(T)) as the type strain. Based on this and previous studies, an emended description of the genus Thermoanaerobacter is given.

Microbial formation of lanthanide-substituted magnetites by Thermoanaerobacter sp. TOR-39

The potentially toxic effects of soluble lanthanide (L) ions, although microbially induced mineralization can facilitate the formation of tractable materials, has been one factor preventing the more widespread use of L-ions in biotechnology. Here, we propose a new mixed-L precursor method as compared to the traditional direct addition technique. L (Nd, Gd, Tb, Ho and Er)-substituted magnetites, L( y )Fe(3 - y )O(4) were microbially produced using L-mixed precursors, L( x )Fe(1 - x )OOH, where x = 0.01-0.2. By combining lanthanides into the akaganeite precursor phase, we were able to mitigate some of the toxicity, enabling the microbial formation of L-substituted magnetites using a metal reducing bacterium, Thermoanaerobacter sp. TOR-39. The employment of L-mixed precursors enabled the microbial formation of L-substituted magnetite, nominal composition up to L(0.06)Fe(2.94)O(4), with at least tenfold higher L-concentration than could be obtained when the lanthanides were added as soluble salts. This mixed-precursor method can be used to extend the application of microbially produced L-substituted magnetite, while also mitigating their toxicity.

The proteomic alterations of Thermoanaerobacter tengcongensis cultured at different temperatures

Thermoanaerobacter tengcongensis, one of many thermophilic organisms, survives harsh living conditions in temperatures ranging from 50 to 80 degrees C. In this comprehensive analysis, we present a robust approach, 2-DE and MALDI-TOF MS, to compare and identify the bacterial proteins responding to the temperature stress. In total, 164 spots of 2-DE were found with the significant changes in spot volume at three culture temperatures, 55, 75, and 80 degrees C, respectively; furthermore, 87 unique proteins were characterized by MS. Our results reveal that the electrophoretic images of the bacterial proteins, extracted from two culture temperatures (55 and 75 degrees C), had similar patterns; however, the bacteria cultured at 80 degrees C had dramatically decreased their spot volumes. Additionally, the temperature-sensitive proteins are broadly divided into two groups: specific expression at certain temperatures and consistent changes of expression responsive to temperature. For instance, three proteins closely related with redox regulation, dihydrolipoamide acyltransferase, NADH:ubiquinone oxidoreductase, and ferredoxin, were only detected in the bacteria cultured at 55 degrees C. Whereas, two chaperonins, GroES and GroEL, were found to show a consistent increase during the elevated temperatures with the determinations, either by MS or Western blot. The proteomic information, thus expedites our understanding of the molecular mechanisms regarding how thermophilic bacteria adapt to the alterations in living environment.

Characterization of enzymes involved in the ethanol production of Moorella sp. HUC22-1

Since the thermophilic bacterium Moorella sp. HUC22-1 produces 120 mM acetate and 5.2 mM ethanol from H(2)-CO(2), several candidate genes, which were predicted to code for three alcohol dehydrogenases (AdhA, B, C) and one acetaldehyde dehydrogenase (Aldh), were cloned from HUC22-1. The cloned genes were subcloned into a His-tagged expression vector and expressed in Escherichia coli. Recombinant AdhA and B were both dependent on NADP(H) but independent of NAD(H), and their reduction activities from aldehyde to alcohol were higher than their oxidation activities. In contrast with AdhA and B, no activity of AdhC was observed in either reaction. On the other hand, Aldh was active toward both NADP(H) and NAD(H). The enzyme activity of Aldh was directed toward the thioester cleavage and the thioester condensation. When 50 microg of AdhA and 50 microg Aldh were added to the buffer solution (pH 8.0) containing NADPH, NADH and acetyl-CoA at 60 degrees C, 1.6 mM ethanol was produced from 3 mM acetyl-CoA after 90 min. Expression analysis of the mRNAs revealed that the expression level of aldh was threefold higher in the H(2)-CO(2) culture than that in the fructose culture, but levels of adhA, B and C were decreased.

Electrotransformation of Thermoanaerobacter ethanolicus JW200

Electrotransformation of Thermoanaerobacter ethanolicus JW200 was achieved using the plasmid, pTE16, and a pUC-based suicide vector, pTEA2. The construct pTE16 is based on the Escherichia coli-Clostridium perfringens shuttle vector pJIR715 and contains a thermostable chloramphenicol (Cm) resistance cassette. Evidence supporting transformation was provided by extracting plasmid pTE16 from presumptive transformants of T. ethanolicus and by PCR specific to the chloramphenicol acetyltransferase (cat) gene on the vector pTEA2. Transformation frequencies of plasmid pTE16 and pTEA2 were 50 +/- 7.4 and 30 +/- 4.2 transformants per mug plasmid DNA. The results provide the first unequivocal gene transfer method functional in T. ethanolicus.

Structure of the S-adenosylmethionine riboswitch regulatory mRNA element

Riboswitches are cis-acting genetic regulatory elements found in the 5'-untranslated regions of messenger RNAs that control gene expression through their ability to bind small molecule metabolites directly. Regulation occurs through the interplay of two domains of the RNA: an aptamer domain that responds to intracellular metabolite concentrations and an expression platform that uses two mutually exclusive secondary structures to direct a decision-making process. In Gram-positive bacteria such as Bacillus species, riboswitches control the expression of more than 2% of all genes through their ability to respond to a diverse set of metabolites including amino acids, nucleobases and protein cofactors. Here we report the 2.9-angstroms resolution crystal structure of an S-adenosylmethionine (SAM)-responsive riboswitch from Thermoanaerobacter tengcongensis complexed with S-adenosylmethionine, an RNA element that controls the expression of several genes involved in sulphur and methionine metabolism. This RNA folds into a complex three-dimensional architecture that recognizes almost every functional group of the ligand through a combination of direct and indirect readout mechanisms. Ligand binding induces the formation of a series of tertiary interactions with one of the helices, serving as a communication link between the aptamer and expression platform domains.

Role of conserved surface amino acids in binding of SmpB protein to SsrA RNA

Bacteria possess a unique salvage mechanism for rescuing ribosomes stalled on aberrant mRNAs. A complex of SmpB protein and SsrA RNA orchestrates this salvage process. The specific and direct binding of SmpB facilitates recognition and delivery of SsrA RNA to stalled ribosomes. The SmpB protein is conserved throughout the bacterial kingdom and contains several conserved amino acid sequence motifs. We present evidence to demonstrate that amino acid residues Glu-31, Leu-91, and Lys-124, which are highly conserved and clustered along an exposed surface of the protein, play a crucial role in the SsrA-mediated peptide tagging process. Our analysis suggests that the peptide-tagging defect exhibited by these SmpB variants is due to their inability to facilitate the delivery of SsrA RNA to stalled ribosomes. Moreover, we present evidence to demonstrate that the ribosome association defect of these variants is due to their reduced SsrA binding affinity. Consistent with these findings, we present biochemical evidence to demonstrate that residues Glu-31, Leu-91, and Lys-124 are essential for the SsrA binding activity of SmpB protein. Furthermore, we have investigated the interactions of SmpB.SsrA orthologues from the thermophilic bacterium Thermoanaerobacter tengcongensis. Our investigations demonstrate an analogous role for the equivalent T. tengcongensis residues in SmpB.SsrA interactions, hence further validating our findings for the Escherichia coli SmpB.SsrA system. These results demonstrate the functional significance of this cluster of conserved residues in SmpB binding to SsrA RNA, suggesting they might represent a core contact surface for recognition of SsrA RNA.

[Dynamic analysis of the heat shock protein 60 and its gene expression in Thermoanaerobacter tengcongensis induced by temperature increase]

Heat shock protein 60 (HSP60) is one of the important chaperonins, which can assist proper protein folding and configuration,and can prevent denaturation and degradation of proteins as well. It was found that HSP60 in Thermoanaerobacter tengcongensis (T. tengcongensis) was typically temperature-dependent with the highest protein expression at 80 degrees C. To understand the molecular mechanisms of thermophiles in their responding to heat stress, further investigation was conducted to examine the dynamic expression of HSP60 gene induced by higher temperature. The T. tengcongensis cells cultured at optimal temperature (75 degrees C) were transferred to 80 degrees C followed by taking the aliquots at different time intervals. To monitor the expression levels of HSP60 mRNA and protein, these bacterial gene products were analyzed by two-dimensional electrophoresis, MALDI-TOF, HPLC-MS/MS, Western blot and quantitative PCR. The experimental data were calculated statistically and quantitatively, which indicate that the HSP60 protein increases steadily and significantly within 4h period after temperature raised, but its mRNA level is shown as a peak shape change within 1h. Obviously, the expression response of HSP60 protein to heat stress is significantly slower than that of its mRNA expression. Additionally, the expression extent of HSP60 mRNA and protein induced by raised-temperature is very different. In E. coli strains, the expression of HSP60 is usually regulated by the sigma32 factor, which disassociates with DnaK immediately when the environmental temperature elevated. Since the genome of T. tengcongensis contains two sigma32 genes, thus, it is likely that both bacteria share the similar mechanisms which regulate HSP60 transcription responding to the changes of temperature. Interestingly, the mRNA of HSP60 drops down about 70% within 30m responding to heat shock, but goes to the increased expression after then. Although this phenomenon is hard to explain based upon the current theory, it is plausible that the transcription in T. tengcongensis is temporally inhibited due to the culture temperature sharply raised.

Domain II plays a crucial role in the function of ribosome recycling factor

RRF (ribosome recycling factor) consists of two domains, and in concert with EF-G (elongation factor-G), triggers dissociation of the post-termination ribosomal complex. However, the function of the individual domains of RRF remains unclear. To clarify this, two RRF chimaeras, EcoDI/TteDII and TteDI/EcoDII, were created by domain swaps between the proteins from Escherichia coli and Thermoanaerobacter tengcongensis. The ribosome recycling activity of the RRF chimaeras was compared with their wild-type RRFs by using in vivo and in vitro activity assays. Like wild-type TteRRF (T. tengcongensis RRF), the EcoDI/TteDII chimaera is non-functional in E. coli, but both wild-type TteRRF, and EcoDI/TteDII can be activated by coexpression of T. tengcongensis EF-G in E. coli. By contrast, like wild-type E. coli RRF (EcoRRF), TteDI/EcoDII is fully functional in E. coli. These findings suggest that domain II of RRF plays a crucial role in the concerted action of RRF and EF-G for the post-termination complex disassembly, and the specific interaction between RRF and EF-G on ribosomes mainly depends on the interaction between domain II of RRF and EF-G. This study provides direct genetic and biochemical evidence for the function of the individual domains of RRF.

Screening of Thermophilic Anaerobic Bacteria for Solid Substrate Cultivation on Lignocellulosic Substrates

Interest in solid substrate cultivation (SSC) techniques is gaining for biochemical production from renewable resources; however, heat and mass transfer problems may limit application of this technique. The use of anaerobic thermophiles in SSC offers a unique solution to overcoming these challenges. The production potential of nine thermophilic anaerobic bacteria was examined on corn stover, sugar cane bagasse, paper pulp sludge, and wheat bran in submerged liquid cultivation (SmC) and SSC. Production of acetate, ethanol, and lactate was measured over a 10 day period, and total product concentrations were used to compare the performance of different organism-substrate combinations using the two cultivation methods. Overall microbial activity in SmC and SSC was dependent on the organism and growth substrate. Clostridium thermocellum strains JW20, LQRI, and 27405 performed significantly better in SSC when grown on sugar cane bagasse and paper pulp sludge, producing at least 70 and 170 mM of total products, respectively. Growth of C. thermocellum strains in SSC on paper pulp sludge proved to be most favorable, generating at least twice the concentration of total products produced in SmC (p-value < 0.05). Clostridium thermolacticum TC21 demonstrated growth on all substrates producing 30-80 and 60-116 mM of total product in SmC and SSC, respectively. Bacterial species with optimal growth temperatures of 70 degrees C grew best on wheat bran in SmC, producing total product concentrations of 45-75 mM. For some of the organism-substrate combinations total end product concentrations in SSC exceeded those in SmC, indicating that SSC may be a promising alternative for microbial activity and value-added biochemical production.

Kinetic modeling of acetophenone reduction catalyzed by alcohol dehydrogenase from Thermoanaerobacter sp

NADPH-dependent alcohol dehydrogenase (ADH) from Thermoanaerobacter sp. was kinetically characterized using reduction of acetophenone as a model. To achieve 98% conversion of acetophenone, cofactor regeneration by oxidation of 2-propanol with the same enzyme was used. The enzyme was stable in the batch reactor. It was enantioselective towards (S)-1-phenylethanol (ee>99.5%). Due to its high deactivation in continuously operated stirred tank reactor (kd=0.0141 min-1) there was no way to keep high conversion of acetophenone at 98%. The deactivation occurred in the repetitive batch as well. A mathematical model for the acetophenone reduction with cofactor regeneration describing the behaviour in a batch, repetitive-batch and continuously stirred tank reactor was developed.

Expression in Escherichia coli, Purification and Characterization of Thermoanaerobacter tengcongensis Ribosome Recycling Factor

A very promising approach to understanding the mechanism of protein thermostability is to investigate the structure-function relationship of homologous proteins with different thermostabilities. Ribosome recycling factor (RRF), which is an essential factor for protein synthesis in bacteria, may be a good candidate for such study. In this report, a ribosome recycling factor from Thermoanaerobacter tengcongensis was expressed and characterized. This protein contains 184 residues, shows 51.4% identity to that of Escherichia coli RRF, and has very strong antigenic cross-reactivity with antibody to E. coli RRF. In vivo activity assay shows that weak residual activity may remain in TteRRF in E. coli cells. Circular dichroism spectral analysis shows that TteRRF has a very similar secondary structure to that of E. coli RRF, implying that they have similar tertiary structures. However, their thermostabilities are significantly different. To find which domain of RRF is mainly responsible for maintaining stability, TteDI/EcoDII and EcoDI/TteDII RRF chimeras were created. Their domain I and domain II are from E. coli and T. tengcongensis RRFs, respectively. The results of GdnHCl and heat induced denaturation of the chimeric RRFs suggest that the domain I plays a major role in maintaining the stability of the RRF molecule.

Characterization of a thermostable UvrD helicase and its participation in helicase-dependent amplification

Helicase-dependent amplification (HDA) is an isothermal in vitro DNA amplification method based upon the coordinated actions of helicases to separate double-stranded DNA and DNA polymerases to synthesize DNA. Previously, a mesophilic form of HDA (mHDA) utilizing the Escherichia coli UvrD helicase, DNA polymerase I Klenow fragment, two accessory proteins, MutL and single-stranded DNA-binding protein (SSB), was developed (1). In an effort to improve the specificity and performance of HDA, we have cloned and purified a thermostable UvrD helicase (Tte-UvrD) and the mutL homolog (Tte-MutL) from Thermoanaerobacter tengcongensis. Characterization of the Tte-UvrD helicase shows that it is stable and active from 45 to 65 degrees C. We have found that the Tte-UvrD helicase unwinds blunt-ended DNA duplexes as well as substrates possessing 3'- or 5'-ssDNA tails. Tte-UvrD was used to develop athermophilichelicase-dependent amplification (tHDA) system to selectively amplify target sequences at 60-65 degrees C. The tHDA system is more efficient than mHDA, displaying heightened amplification sensitivity without the need for the MutL and SSB accessory proteins. Amplification independent of MutL corresponds with studies demonstrating that maximal Tte-UvrD helicase activity does not require the mutL homolog. The tHDA system allows for rapid amplification and detection of targets present in genomic DNA. The expeditious nature and simplistic design of the tHDA platform makes the technology ideal for use in diagnostic applications requiring rapid identification of organisms at the point-of-need.

Ethanol production from H2 and CO2 by a newly isolated thermophilic bacterium, Moorella sp. HUC22-1

The thermophilic bacterium, Moorella sp. HUC22-1, newly isolated from a mud sample, produced ethanol from H(2) and CO(2) during growth at 55 degrees C. In batch cultures in serum bottles, 1.5 mM ethanol was produced from 270 mM H(2) and 130 mM CO(2) after 156 h, whereas less than 1 mM ethanol was produced from 23 mM fructose after 33 h. Alcohol dehydrogenase and acetaldehyde dehydrogenase activities were higher in cells grown with H(2) and CO(2) than those grown with fructose. The NADH/NAD(+) and NADPH/NADP(+) ratios in cells grown with H(2) and CO(2) were also higher than those in cells grown with fructose. When the culture pH was controlled at 5 with H(2) and CO(2) in a fermenter, ethanol production was 3.7-fold higher than that in a pH-uncontrolled culture after 220 h.

[Prevalence of nonmevalonate and mevalonate pathways for isoprenoid biosynthesis among bacteria of different systematic groups]

The effect of fosmidomycin and mevinoline, inhibitors of the nonmevalonate and the mevalonate pathway of isoprenoid biosynthesis, respectively, on the growth of 34 anaerobic and 10 aerobic prokaryotic strains was studied. Fosmidomycin at the concentrations used was shown to inhibit the growth of 9 (of 10) representatives of the family Microbacteriaceae, 4 (of 5) strains of Thermoanaerobacter, and 11 (of 12) strains of Clostridium, whereas mevinoline inhibited the growth of lactobacilli (Carnobacterium), methanogenic and sulfate-reducing bacteria insensitive to fosmidomycin. During the late growth phase, four strains of actinobacteria (of nine) accumulate the compound, which, upon oxidation, generates a long-lived free radical; three strains synthesize 2-C-methyl-D-erythritol-2,4-cyclopyrophosphate (MEC). It was concluded that the difference in the sensitivity of the organisms to fosmidomycin and mevinoline might serve as a test to differentiate several representatives of the family Microbacteriaceae. The use of mevinoline for inhibiting methanogens in ecological investigations seems to be promising.

Acetate and ethanol production from H2 and CO2by Moorella sp. using a repeated batch culture

The growth inhibition of Moorella sp. HUC22-1 by undissociated acetic acid was analyzed using a non-competitive inhibition model coupled with a pH inhibition model. In the cells grown on H2 and CO2, the inhibition constant, K(p) of the undissociated acetic acid was 6.2 mM (164 mM as the total acetate at pH 6.2, pKa = 4.795, 55 degrees C), which was 1.5-fold higher than that obtained in cells grown on fructose. When a pH-controlled batch culture was performed using a fermentor at pH 6.2 with H2 and CO2, a maximum of 0.92 g/l of dry cell weight and 339 mM of acetate were produced after 220 h, which were 4.4- and 6.8-fold higher than those produced in the pH-uncontrolled batch culture, respectively. In order to reduce acetate inhibition in the culture medium, a repeated batch culture with cell recycling was performed at a constant pH with H2 and CO2. At a pH of 6.2, the total acetate production reached 840 mmol/l-reactor with 4.7 mmol/l-reactor of total ethanol production after 420 h. When the culture pH was maintained at 5.8, which was the optimum for ethanol production, the total ethanol production reached 15.4 mmol/l-reactor after 430 h, although the total acetate production was decreased to 675 mmol/l-reactor.