Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics

Elucidating metabolic pathways through genomic analysis in highly heavy metal-resistant Halobacterium salinarum strains

The annotated and predicted genomes of five archaeal strains (AS1, AS2, AS8, AS11 and AS19), isolated from Sfax solar saltern sediments (Tunisia) and affiliated with Halobacterium salinarum, were performed by RAST webserver (Rapid Annotation using Subsystem Technology) and NCBI prokaryotic genome annotation pipeline (PGAP). The results showed the ability of strains to use a reduced semi-phosphorylative Entner-Doudoroff pathway for glucose degradation and an Embden-Meyerhof one for gluconeogenesis. They could use glucose, fructose, glycerol, and acetate as sole source of carbon and energy. ATP synthase, various cytochromes and aerobic respiration proteins were encoded. All strains showed fermentation capability through the arginine deiminase pathway and facultative anaerobic respiration using electron acceptors (Dimethyl sulfoxide and trimethylamine N-oxide). Several biosynthesis pathways for many amino acids were identified. Comparative and pangenome analyses between the strains and the well-studied halophilic archaea Halobacterium NRC-1 highlighted a notable dissimilarity. Besides, the strains shared a core genome of 1973 genes and an accessory genome of 767 genes. 129, 94, 67, 15 and 29 unique genes were detected in the AS1, AS2, AS8, AS11 and AS19 genomes, respectively. Most of these unique genes code for hypothetical proteins. The strains displayed plant-growth promoting characteristics under heavy metal stress (Ammonium assimilation, phosphate solubilization, chemotaxis, cell motility and production of indole acetic acid, siderophore and phenazine). Therefore, they could be used as a biofertilizer to promote plant growth. The genomes encoded numerous biotechnologically relevant genes responsible for vitamin biosynthesis, including cobalamin, folate, biotin, pantothenate, riboflavin, thiamine, menaquinone, nicotinate, and nicotinamide. The carotenogenetic pathway of the studied strains was also predicted. Consequently, the findings of this study contribute to a better understanding of the halophilic archaea metabolism providing valuable insights into their ecophysiology as well as relevant biotechnological applications.

Assessment of rapid initiators and long-lasting nutrients for developing biological permeable reactive barriers to treat mine-contaminated groundwater

The formation of mine-contaminated groundwater as a result of acidic mine drainage from the oxidation of sulfur-containing minerals entering the groundwater. Biological permeable reactive barrier (Bio-PRB) technology is excellent for the remediation of mine-contaminated groundwater. Usually, the organic substrates utilized in Bio-PRB are a combination of rapid initiators, which are readily bioavailable, and long-lasting nutrients, which are more difficult to degrade. Herein, we investigated the effectiveness of three rapid initiators and three long-lasting nutrients to remove sulfate from simulated mine-contaminated groundwater via simulated column experiments. The rapid initiators comprised crude glycerol, sodium acetate, and industrial syrup (IS), and the long-lasting nutrients included biodiesel emulsified oil, soybean oil emulsified oil, and high-carbon alcohol emulsified oil (HO). Microorganisms were stimulated using IS to create a sulfate reduction system owing to its high total organic carbon content (24.30 g L-1), achieving optimal sulfate removal rate (1.69 mmol dm-3 d-1). The fastest (2.93 mmol dm-3 d-1) and highest (88%) sulfate removal rates were achieved using HO, which is probably associated with the ability of HO to provide the most suitable C/N ratio (111.75) and induce the growth of sulfate-reducing bacteria (SRB) for substrate degradation. Conversely, a high concentration of sulfate reduction products inhibited SRB growth in the HO column. The addition of organic materials promoted SRB growth and various organic substrate-degrading bacteria. Furthermore, the competitive growth of methanogens (86.6%) may be responsible for the decrease in the relative abundance of SRB during the later stages of the experiment in the HO column.

Utilization of carbon catabolite repression for efficiently biotransformation of anthraquinone O-glucuronides by Streptomyces coeruleorubidus DM

Carbon catabolite repression (CCR) is a highly conserved mechanism that regulates carbon source utilization in Streptomyces. CCR has a negative impact on secondary metabolite fermentation, both in industrial and research settings. In this study, CCR was observed in the daunorubicin (DNR)-producing strain Streptomyces coeruleorubidus DM, which was cultivated in high concentration of carbohydrates. Unexpectedly, DM exhibited a high ability for anthraquinone glucuronidation biotransformation under CCR conditions with a maximum bioconversion rate of 95% achieved at pH 6, 30°C for 24 h. The co-utilization of glucose and sucrose resulted in the highest biotransformation rate compared to other carbon source combinations. Three novel anthraquinone glucuronides were obtained, with purpurin-O-glucuronide showing significantly improved water solubility, antioxidant activity, and antibacterial bioactivity. Comparative transcript analysis revealed that glucose and sucrose utilization were significantly upregulated as DM cultivated under CCR condition, which strongly enhance the biosynthetic pathway of the precursors Uridine diphosphate glucuronic acid (UDPGA). Meanwhile, the carbon metabolic flux has significantly enhanced the fatty acid biosynthesis, the exhaust of acetyl coenzyme A may lead to the complete repression of the biosynthesis of DNR, Additionally, the efflux transporter genes were simultaneously downregulated, which may contribute to the anthraquinones intracellular glucuronidation. Overall, our findings demonstrate that utilizing CCR can be a valuable strategy for enhancing the biotransformation efficiency of anthraquinone O-glucuronides by DM. This approach has the potential to improve the bioavailability and therapeutic potential of these compounds, opening up new possibilities for their pharmaceutical applications.

Identification and characterization of a novel type of ketohexokinase from the haloarchaeon Haloferax volcanii

Ketohexokinase (KHK) catalyzes the ATP-dependent phosphorylation of fructose, forming fructose-1-phosphate and ADP. The enzyme is well studied in Eukarya, in particular in humans and other vertebrates, but homologs have not been identified in Bacteria and Archaea. Here we report the identification of a novel type of KHK from the haloarchaeon Haloferax volcanii (HvKHK). The encoding gene khk was identified as HVO_1812. The gene was expressed as a 90-kDa homodimeric protein, catalyzing the phosphorylation of fructose with a Vmax value of 59 U/mg and apparent KM values for ATP and fructose of 0.47 and 1.29 mM, respectively. Homologs of HvKHK were only identified in a few haloarchaea and halophilic Bacteria. The protein showed low sequence identity to characterized KHKs from Eukarya and phylogenetic analyses indicate that haloarchaeal KHKs are largely separated from eukaryal KHKs. This is the first report of the identification of KHKs in prokaryotes that form a novel cluster of sugar kinases within the ribokinase/pfkB superfamily.

Optimization of bacterioruberin production from Halorubrum ruber and assessment of its antioxidant potential

Haloarchaea produce bacterioruberin, a major C50 carotenoid with antioxidant properties that allow for its potential application in the food, cosmetic, and pharmaceutical industries. This study aimed to optimize culture conditions for total carotenoid, predominantly comprising bacterioruberin, production using Halorubrum ruber MBLA0099. A one-factor-at-a-time and statistically-based experimental design were applied to optimize the culture conditions. Culture in the optimized medium caused an increase in total carotenoid production from 0.496 to 1.966 mg L- 1 Maximal carotenoid productivity was achieved in a 7-L laboratory-scale fermentation and represented a 6.05-fold increase (0.492 mg L-1 d-1). The carotenoid extracts from strain MBLA0099 exhibited a 1.8-10.3-fold higher antioxidant activity in vitro, and allowed for a higher survival rate of Caenorhabditis elegans under oxidative stress conditions. These results demonstrated that Hrr. ruber MBLA0099 has significant potential as a haloarchaon for the commercial production of bacterioruberin.

Cellulose metabolism in halo(natrono)archaea: a comparative genomics study

Extremely halophilic archaea are one of the principal microbial community components in hypersaline environments. The majority of cultivated haloarchaea are aerobic heterotrophs using peptides or simple sugars as carbon and energy sources. At the same time, a number of novel metabolic capacities of these extremophiles were discovered recently among which is a capability of growing on insoluble polysaccharides such as cellulose and chitin. Still, polysaccharidolytic strains are in minority among cultivated haloarchaea and their capacities of hydrolyzing recalcitrant polysaccharides are hardly investigated. This includes the mechanisms and enzymes involved in cellulose degradation, which are well studied for bacterial species, while almost unexplored in archaea and haloarchaea in particular. To fill this gap, a comparative genomic analysis of 155 cultivated representatives of halo(natrono)archaea, including seven cellulotrophic strains belonging to the genera Natronobiforma, Natronolimnobius, Natrarchaeobius, Halosimplex, Halomicrobium and Halococcoides was performed. The analysis revealed a number of cellulases, encoded in the genomes of cellulotrophic strains but also in several haloarchaea, for which the capacity to grow on cellulose was not shown. Surprisingly, the cellulases genes, especially of GH5, GH9 and GH12 families, were significantly overrepresented in the cellulotrophic haloarchaea genomes in comparison with other cellulotrophic archaea and even cellulotrophic bacteria. Besides cellulases, the genes for GH10 and GH51 families were also abundant in the genomes of cellulotrophic haloarchaea. These results allowed to propose the genomic patterns, determining the capability of haloarchaea to grow on cellulose. The patterns helped to predict cellulotrophic capacity for several halo(natrono)archaea, and for three of them it was experimentally confirmed. Further genomic search revealed that glucose and cellooligosaccharides import occurred by means of porters and ABC (ATP-binding cassette) transporters. Intracellular glucose oxidation occurred through glycolysis or the semi-phosphorylative Entner-Dudoroff pathway which occurrence was strain-specific. Comparative analysis of CAZymes toolbox and available cultivation-based information allowed proposing two possible strategies used by haloarchaea capable of growing on cellulose: so-called specialists are more effective in degradation of cellulose while generalists are more flexible in nutrient spectra. Besides CAZymes profiles the groups differed in genome sizes, as well as in variability of mechanisms of import and central metabolism of sugars.

Molecular analysis of sugar transporters and glycolysis pathways in Ettlia sp. under heterotrophy using fructose and glucose

Fructophilic behavior in microalgae is a rare trait that could benefit biorefineries by enabling substitution of carbon source with fructose, and our previous study identified that Ettlia sp. prefers fructose relative to glucose. In this study, by analyzing the transcription levels of genes related to sugar transport and the glycolysis pathway, the fructose utilization of Ettlia sp. was investigated. In a fructose-containing medium, the expression levels of fructokinase (EttFRK3) and glucokinase (EttGCK1 and EttGCK2) genes were significantly upregulated in heterotrophic cultivation of Ettlia sp. under fructose supplementation conditions. Further, a sugar transporter (EttSTF11) was significantly upregulated by 3.2-fold in 1 day, and this increase was analogous to the specific growth rate exhibited by the species. Subsequent cultivation tests with multi-sugar sources also showed a significant upregulation of EttSTF11 relative to other treatments without fructose. A phylogenetic tree derived from the analysis of different transporters of interest identified that EttSTF11 was adjacent to reference fructose transporters with a high bootstrap value of 71. Given that the transmembrane domains of EttSTF11 were analogous to those of reference fructose transporter genes, EttSTF11 appeared to play a critical role in fructose consumption and metabolism in Ettlia sp.

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.

Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase

Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature.

Effects of nutrient and oxygen limitation, salinity and type of salt on the accumulation of poly(3-hydroxybutyrate) in Bacillus megaterium uyuni S29 with sucrose as a carbon source

Due to high manufacturing costs, industrial production and application of bio-based polyhydroxyalkanoates (PHA) as bioplastics remain below the expected potential. Improving yields and productivities during biotechnological production will contribute to eliminating existing shortcomings and should therefore be a priority in process development with new strains and substrates. The present study investigates key parameters such as different nutrient and oxygen limitation strategies and the salinity and type of salt to determine their impact on growth and poly(3-hydroxybutyrate) (P(3HB)) formation behaviour of Bacillus megaterium. The oxygen-limiting conditions applied resulted in a longer process duration and were found to be least effective with regard to P(3HB) content in the biomass. A higher P(3HB) content of 0.42 g g^-1 was achieved when nitrogen was limited compared to 0.34 g g^-1 under phosphate-limiting conditions; however, sucrose utilization was better when phosphate was limited. Replacing NaCl by KCl and evaluating different concentrations ranging from 0.08 to 1.7 mol L^-1 in the process medium showed that B. megaterium has a higher tolerance to KCl as the biomass and P(3HB) formation was increased to 0.48 g g^-1 compared to 0.36 g g^-1. The combination of applying KCl instead of NaCl together with phosphorous limitation significantly increased P(3HB) productivity to 0.25 g L^-1 h^-1 compared to 0.09 g L^-1 h^-1. It can be concluded that the effective utilization of sucrose as a carbon source requires a combination of high nitrogen and low phosphorous concentration and a salt content of 0.6 g L^-1 KCl for P(3HB) production with B. megaterium uyuni S29.

Dibutyl phthalate contamination accelerates the uptake and metabolism of sugars by microbes in black soil

Dibutyl phthalate (DBP) is widely used as plasticizer and has been detected in the environment, posing a threat to animal health. However, the effects of DBP on agricultural microbiomes are not known. In this study, DBP levels in black soil were evaluated, and the impact of DBP contamination on the uptake and metabolism of sugars in microbes was assessed by glucose absorption tests, metaproteomics, metabolomics, enzyme activity assays and computational simulation analysis. The results indicated that DBP contamination accelerated glucose consumption and upregulated the expression of porins and periplasmic monosaccharide ATP-binding cassette (ABC) transporter solute-binding proteins (SBPs). DBP and its metabolic intermediates (carboxymuconate and butanol) may form a stable complex with sugar transporters and enhance the rigidity and stability of these proteins. Sugar metabolism resulting in the generation of ATP and reducing agent (NADPH), as well as the expression of some key enzymes (dehydrogenases) were also upregulated by DBP treatment. Moreover, a diverse bacterial community appears to utilize sugar, suggesting that there are widespread effects of DBP contamination on soil microbial ecosystems. The results of this study provide a theoretical basis for investigating the toxicological effects of DBP on microbes in black soil.