Isolation of levoglucosan-assimilating microorganisms from soil and an investigation of their levoglucosan kinases

Comparing levoglucosan and mannosan ratios in sediments and corresponding aerosols from recent Australian fires

The monosaccharide anhydrides levoglucosan, mannosan, and galactosan are known as 'fire sugars' as they are powerful proxies used to trace fire events. Despite their increasing use, their application is not completely understood, especially in the context of tracing past fire events using sediment samples. There are many uncertainties about fire sugar formation, partitioning, transport, complexation, and stability along all stages of the source-to-sink pathway. While these uncertainties exist, the efficacy of fire sugars as fire tracers remains limited. This study compared high-resolution fire sugar fluxes in freshwater sediment cores to known fire records in Tasmania, Australia. Past fire events correlated with fire sugar flux increases down-core, with the magnitude of the flux inversely proportional to the distance of the fires from the study site. For the first time, fire sugar ratios (levoglucosan/mannosan, L/M) in aerosols were compared with those in sediments from the same time-period. The L/M ratio in surface sediments (1.42-2.58) were significantly lower than in corresponding aerosols (5.08-15.62). We propose two hypotheses that may explain the lower average L/M of sediments. Firstly, the degradation rate of levoglucosan is higher than mannosan in the water column, sediment-water interface, and/or sediment. Secondly, the L/M ratio of non-atmospheric emissions during fires may be lower than that of atmospheric emissions from the same fire. Due to the uncertainties about transport partitioning (atmospheric versus non-atmospheric emissions) and fire sugar degradation along all stages of the source-to-sink pathway, we advise caution when inferring vegetation type (e.g. softwood, hardwood, or grasses) based purely on fire sugar ratios in sediments (e.g. L/M ratio). Future investigations are required to increase the efficacy of fire sugars as a complimentary, or standalone, fire tracer in sediments.

Omics analysis coupled with gene editing revealed potential transporters and regulators related to levoglucosan metabolism efficiency of the engineered Escherichia coli

Background

Bioconversion of levoglucosan, a promising sugar derived from the pyrolysis of lignocellulose, into biofuels and chemicals can reduce our dependence on fossil-based raw materials. However, this bioconversion process in microbial strains is challenging due to the lack of catalytic enzyme relevant to levoglucosan metabolism, narrow production ranges of the native strains, poor cellular transport rate of levoglucosan, and inhibition of levoglucosan metabolism by other sugars co-existing in the lignocellulose pyrolysate. The heterologous expression of eukaryotic levoglucosan kinase gene in suitable microbial hosts like Escherichia coli could overcome the first two challenges to some extent; however, no research has been dedicated to resolving the last two issues till now.

Results

Aiming to resolve the two unsolved problems, we revealed that seven ABC transporters (XylF, MalE, UgpB, UgpC, YtfQ, YphF, and MglA), three MFS transporters (KgtP, GntT, and ActP), and seven regulatory proteins (GalS, MhpR, YkgD, Rsd, Ybl162, MalM, and IraP) in the previously engineered levoglucosan-utilizing and ethanol-producing E. coli LGE2 were induced upon exposure to levoglucosan using comparative proteomics technique, indicating these transporters and regulators were involved in the transport and metabolic regulation of levoglucosan. The proteomics results were further verified by transcriptional analysis of 16 randomly selected genes. Subsequent gene knockout and complementation tests revealed that ABC transporter XylF was likely to be a levoglucosan transporter. Molecular docking showed that levoglucosan can bind to the active pocket of XylF by seven H-bonds with relatively strong strength.

Conclusion

This study focusing on the omics discrepancies between the utilization of levoglucosan and non-levoglucosan sugar, could provide better understanding of levoglucosan transport and metabolism mechanisms by identifying the transporters and regulators related to the uptake and regulation of levoglucosan metabolism. The protein database generated from this study could be used for further screening and characterization of the transporter(s) and regulator(s) for downstream enzymatic/genetic engineering work, thereby facilitating more efficient microbial utilization of levoglucosan for biofuels and chemicals production in future.

Both levoglucosan kinase activity and transport capacity limit the utilization of levoglucosan in Saccharomyces cerevisiae

Manufacturing fuels and chemicals from cellulose materials is a promising strategy to achieve carbon neutralization goals. In addition to the commonly used enzymatic hydrolysis by cellulase, rapid pyrolysis is another way to degrade cellulose. The sugar obtained by fast pyrolysis is not glucose, but rather its isomer, levoglucosan (LG). Here, we revealed that both levoglucosan kinase activity and the transportation of levoglucosan are bottlenecks for LG utilization in Saccharomyces cerevisiae, a widely used cell factory. We revealed that among six heterologous proteins that had levoglucosan kinase activity, the 1,6-anhydro-N-acetylmuramic acid kinase from Rhodotorula toruloides was the best choice to construct levoglucosan-utilizing S. cerevisiae strain. Furthermore, we revealed that the amino acid residue Q341 and W455, which were located in the middle of the transport channel closer to the exit, are the sterically hindered barrier to levoglucosan transportation in Gal2p, a hexose transporter. The engineered yeast strain expressing the genes encoding the 1,6-anhydro-N-acetylmuramic acid kinase from R. toruloides and transporter mutant Gal2p^Q341A or Gal2p^W455A consumed ~ 4.2 g L⁻¹ LG in 48 h, which is the fastest LG-utilizing S. cerevisiae strain to date.

Isolation and Characterization of Levoglucosan Metabolizing Bacteria

Bacteria were isolated from wastewater and soil containing charred wood remnants based on their ability to use levoglucosan as a sole carbon source and on their levoglucosan dehydrogenase (LGDH) activity. On the basis of their 16S rRNA gene sequences, these bacteria represented diverse genera of Microbacterium, Paenibacillus, Shinella, and Klebsiella. Genomic sequencing of the isolates verified that two isolates represented novel species, Paenibacillus athensensis MEC069^T and Shinella sumterensis MEC087^T, while the remaining isolates were closely related to either Microbacterium lacusdiani or Klebsiella pneumoniae. The genetic sequence of LGDH, lgdA, was found in the genomes of these four isolates as well as Pseudarthrobacter phenanthrenivorans Sphe3. The identity of the P. phenanthrenivorans LGDH was experimentally verified following recombinant expression in E. coli. Comparison of the putative genes surrounding lgdA in the isolate genomes indicated that several other gene products facilitate the bacterial catabolism of levoglucosan, including a putative sugar isomerase and several transport proteins. Importance Levoglucosan is the most prevalent soluble carbohydrate remaining after high temperature pyrolysis of lignocellulosic biomass, but it is not fermented by typical production microbes such as Escherichia coli and Saccharomyces cerevisiae. A few fungi metabolize levoglucosan via the enzyme levoglucosan kinase, while several bacteria metabolize levoglucosan via levoglucosan dehydrogenase. This study describes the isolation and characterization of four bacterial species which degrade levoglucosan. Each isolate is shown to contain several genes within an operon involved in levoglucosan degradation, furthering our understanding of bacteria which metabolize levoglucosan.

Aspergillus niger as a Secondary Metabolite Factory

Aspergillus niger, one of the most common and important fungal species, is ubiquitous in various environments. A. niger isolates possess a large number of cryptic biosynthetic gene clusters (BGCs) and produce various biomolecules as secondary metabolites with a broad spectrum of application fields covering agriculture, food, and pharmaceutical industry. By extensive literature search, this review with a comprehensive summary on biological and chemical aspects of A. niger strains including their sources, BGCs, and secondary metabolites as well as biological properties and biosynthetic pathways is presented. Future perspectives on the discovery of more A. niger-derived functional biomolecules are also provided in this review.

New insights into a hot environment for early life

Investigating the physical-chemical setting of early life is a challenging task. In this contribution, the author attempted to introduce a provocative concept from cosmology - cosmic microwave background (CMB), which is the residual thermal radiation from a hot early Universe - to the field. For this purpose, the author revisited a recently deduced biomarker, the 1,6-anhydro bond of sugars in bacteria. In vitro, the 1,6-anhydro bond of sugars reflects and captures residual thermal radiation in thermochemical processes and therefore is somewhat analogous to CMB. In vivo, the formation process of the 1,6-anhydro bond of sugars on the peptidoglycan of prokaryotic cell wall is parallel to in vitro processes, suggesting that the 1,6-anhydro bond is an ideal CMB-like analogue that suggests a hot setting for early life. The CMB-like 1,6-anhydro bond is involved in the life cycle of viruses and the metabolism of eukaryotes, underlying this notion. From a novel perspective, the application of the concept of the CMB to microbial ecology may give new insights into a hot environment, such as hydrothermal vents, supporting early life and providing hypotheses to test in molecular palaeontology.

Bioconversion of anhydrosugars: Emerging concepts and strategies

As methods for the use of anhydrosugars in chemical and biofuel production continue to develop, our collective knowledge of anhydrosugar processing enzymes continues to improve, including their mechanistic details, structural dynamics and modes of substrate binding. Of particular interest, anhydrosugar kinases, such as levoglucosan kinase (LGK) and 1,6-anhydro-N-acetylmuramic acid kinase (AnmK), utilize an unusual mechanism whereby the sugar substrate is both cleaved and phosphorylated. The phosphorylated sugar can then be routed to other metabolic pathways, thereby allowing its further bioconversion. Advanced engineering efforts to improve the catalytic efficiency and stability of LGK have been steadily progressing. Other enzymes that cleave the glycosidic bond of disaccharide sugars containing an anhydrosugar component are also being identified and characterized. Accordingly, the potential future use of these enzymes in large-scale production strategies is becoming increasingly viable. Here, a mini-review of the observed characteristics of anhydrosugar processing enzymes is presented along with recent developments in the bioconversion of these sugars. © 2016 IUBMB Life 68(9):700-708, 2016.

Identification of Soil Microbes Capable of Utilizing Cellobiosan

Approximately 100 million tons of anhydrosugars, such as levoglucosan and cellobiosan, are produced through biomass burning every year. These sugars are also produced through fast pyrolysis, the controlled thermal depolymerization of biomass. While the microbial pathways associated with levoglucosan utilization have been characterized, there is little known about cellobiosan utilization. Here we describe the isolation and characterization of six cellobiosan-utilizing microbes from soil samples. Each of these organisms is capable of using both cellobiosan and levoglucosan as sole carbon source, though both minimal and rich media cellobiosan supported significantly higher biomass production than levoglucosan. Ribosomal sequencing was used to identify the closest reported match for these organisms: Sphingobacterium multivorum, Acinetobacter oleivorans JC3-1, Enterobacter sp SJZ-6, and Microbacterium sps FXJ8.207 and 203 and a fungal species Cryptococcus sp. The commercially-acquired Enterobacter cloacae DSM 16657 showed growth on levoglucosan and cellobiosan, supporting our isolate identification. Analysis of an existing database of 16S rRNA amplicons from Iowa soil samples confirmed the representation of our five bacterial isolates and four previously-reported levoglucosan-utilizing bacterial isolates in other soil samples and provided insight into their population distributions. Phylogenetic analysis of the 16S rRNA and 18S rRNA of strains previously reported to utilize levoglucosan and our newfound isolates showed that the organisms isolated in this study are distinct from previously described anhydrosugar-utilizing microbial species.

Computational analysis of AnmK-like kinase: New insights into the cell wall metabolism of fungi

1,6-Anhydro-N-acetylmuramic acid kinase (AnmK) is the unique enzyme that marks the recycling of the cell wall of Escherichia coli. Here, 81 fungal AnmK-like kinase sequences from 57 fungal species were searched in the NCBI database and a phylogenetic tree was constructed. The three-dimensional structure of an AnmK-like kinase, levoglucosan kinase (LGK) of the yeast Lipomyces starkeyi, was modeled; molecular docking revealed that AnmK and LGK are conserved proteins, and 187Asp, 212Asp are enzymatic residues, respectively. Analysis suggests that 1,6-anhydro-N-acetylglucosamine (anhGlcNAc) and/or 1,6-anhydro-β-d-glucosamine (anhGlcN) would be the appropriate substrates of AnmK-like kinases. Also, the counterparts of other characteristic enzymes of cell wall recycling of bacteria were found in fungi. Taken together, it is proposed that a putative recycling of anhGlcNAc/anhGlcN, which is associated with the hydrolysis of cell walls, exists in fungi. This computational analysis will provide new insights into the metabolism of fungal cell walls.

Fermentation of levoglucosan with oleaginous yeasts for lipid production

This paper reports the production of lipids from non-hydrolyzed levoglucosan (LG) by oleaginous yeasts Rhodosporidium toruloides and Rhodotorula glutinis. Enzyme activity tests of LG kinases from both yeasts indicated that the phosphorylation pathway of LG to glucose-6-phosphate existed. The highest enzyme activity obtained for R. glutinis was 0.22 U/mg of protein. The highest cell mass and lipid production by R. glutinis were 6.8 and 2.7 g/L, respectively from pure LG, and 3.3 and 0.78 g/L from a pyrolytic LG aqueous phase detoxified by ethyl acetate extraction, rotary evaporation and activated carbon. This corresponded to a lipid yield of 13.5 wt.% for pure LG and only 3.9 wt.% for LG in pyrolysis oil.

Novel molecular fossils of bacteria: insights into hydrothermal origin of life

Hydrothermal vents, in particular, alkaline submarine vents, are potential systems for the origin of life. Early hydrothermal vents may have imprinted on biochemical processes and housekeeping proteins of life and have hallmarked key molecules. This essay introduces new information to this discussion by focusing on newly identified sulfur-modified DNA and a heretofore ignored anhydro bond of the cell wall peptidoglycan in bacteria. It is suggested that they are novel molecular fossils that are relevant to the settings of alkaline submarine vents and harbor clues of early life. As DNA and the cell wall are bound up with genetic information and the integrity of cell, respectively, these two molecular fossils may provide insights into hydrothermal origin of life from a new angle.