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Target proteins in biotechnological applications are highly diverse. Therefore, versatile flexible expression systems for their functional overproduction are required. In order to find the right heterologous gene expression strategy, suitable host-vector systems, which combine different genetic circuits, are useful. In this study, we designed a novel Bacillus subtilis expression toolbox, which allows the overproduction and secretion of potentially toxic enzymes. This toolbox comprises a set of 60 expression vectors, which combine two promoter variants, four strong secretion signals, a translation-enhancing downstream box, and three plasmid backbones. This B. subtilis toolbox is based on a tailor-made, clean deletion mutant strain, which is protease and sporulation deficient and exhibits reduced autolysis and secondary metabolism. The appropriateness of this alternative expression platform was tested for the overproduction of two difficult-to-produce eukaryotic model proteins. These included the sulfhydryl oxidase Sox from Saccharomyces cerevisiae, which forms reactive hydrogen peroxide and undesired cross-linking of functional proteins, and the human interleukin-1β, a pro-inflammatory cytokine. For the best performing Sox and interleukin, overproducing and secreting variants of these new B. subtilis toolbox fermentation strategies were developed and tested. This study demonstrates the suitability of the prokaryotic B. subtilis host-vector system for the extracellular production of two eukaryotic proteins with biotechnological relevance.
Summary
Outer membrane extensions are common in many marine bacteria. However, the function of these surface enlargements or extracellular compartments is poorly understood. Using a combined approach of microscopy and subproteome analyses, we therefore examined Pseudoalteromonas distincta ANT/505, an Antarctic polysaccharide degrading gamma‐proteobacterium. P. distincta produced outer membrane vesicles (MV) and vesicle chains (VC) on polysaccharide and non‐polysaccharide carbon sources during the exponential and stationary growth phase. Surface structures of carbohydrate‐grown cells were equipped with increased levels of highly substrate‐specific proteins. At the same time, proteins encoded in all other polysaccharide degradation‐related genomic regions were also detected in MV and VC samples under all growth conditions, indicating a basal expression. In addition, two alkaline phosphatases were highly abundant under non‐limiting phosphate conditions. Surface structures may thus allow rapid sensing and fast responses in nutritionally deprived environments. It may also facilitate efficient carbohydrate processing and reduce loss of substrates and enzymes by diffusion as important adaptions to the aquatic ecosystem.
Marine bacteria represent the most diverse organisms in the marine environment. The majority of these microbes is unknown and unculturable. Algae represent the main nutrient source for bacteria. Macro- and microalgae can consist to 70% of polysaccharides. The metabolic degradation of marine polysaccharides is underexplored and thus these mechanisms have to be investigated. These mechanisms are of high importance to generate defined oligosaccharides for the medical and pharmaceutical applications. The specific structure of marine poly- and oligosaccharides show antiviral activities, e.g. carrageenans from red algae are used for the inhibition of human papillomavirus. Another alginate derived marine polysaccharide show inhibition of the replication of the human immunodeficiency virus (HIV). The degradation mechanisms of marine CAZymes and the structure of marine polysaccharides should be further investigated for their high potential of antiviral activities and the creation of new marine drugs.
Many marine bacteria produce membrane extension like membrane vesicles or appendages but the function of these is poorly understood. In order to investigate their function, especially concerning polysaccharide utilization, proteomic analyses of subcellular compartments were performed. Microscopy analyses revealed that, beside MV, P. distincta forms different appendages, vesicle chains (VC) and thin filaments which were dedicated to extracellular polymeric substance. The formation of MV and VC was independent of growth phase or carbon source. The proteomic data showed that transporters end enzymes for the initial degradation of pectin and alginate were highly abundant in these membrane extensions and that there could be a kind of sorting for proteins in the membrane extensions. Additionally, two PUL encoded alkaline phosphatases and other phosphate acquiring enzymes were abundant in the MV and VC fractions. This indicates, that P. distincta constitutively produces enzymes for phosphate uptake, which would be necessary in the phosphate-limiting environment of the Southern Ocean. On the one hand marine bacteria produce membrane extensions in order to create a larger surface in the nutrient limiting marine environment for an increased chance to get in contact to nutrients and on the other hand the results indicate an accumulation of enzymes responsible for uptake and degradation of carbohydrates and phosphates in the MV and VC. Therefore, the membrane extensions act as nutrient traps and this might be beneficial for the bacteria in the diffuse aquatic environment.
The microbial community structure and the metabolism of bacteria in the Southern Ocean are very poorly investigated. The SO is a harsh environment for all organism but nevertheless, the SO is of high importance for the climate in the world due to the high carbon dioxide uptake. In this study water samples from two different sampling sites (S1 and S2) in the SO were investigated. With a metagenomic and metaproteomic approach the key players and the metabolic activity were analyzed. Additionally, the surface water was inoculated with pectin and incubated for several days in order to analyze polysaccharide utilization loci for pectin degradation and to isolate new pectin degraders. 16S-rDNA analyses revealed the bacterial community from the genomic data. Bacteria were separated in particle-associated and free-living bacteria. The overall particle associated bacterial community at both sampling sites was comparable, with Bacteroidetes and Gammaproteobacteria as the abundant phylum. Within the Gammaproteobacteria the Alteromonadaceae and Colwelliaceae were more abundant at S2 than at S1. The free-living bacteria at S1 were dominated by the Alphaproteobacteria, especially the SAR11 clade I. Metagenomic analyses showed that both sampling sites had comparable PUL composition, but taxonomical classification of PULs was differently. The metaproteome data revealed that PUL encoded enzymes were not highly abundant. Only few CAZymes were found, mostly TonB-dependent transporters belonged to the detected PUL proteins. Taxonomical classification of proteins showed differences between the sampling sites. At S2 the genus Colwellia and Arcobacter were highly increased compared to S1. At this location Candidatus Pelagibacter, Planktomarina and Polaribacter were the abundant taxa. The functional classification at both sampling sites was comparable. The only difference was the high abundance of Epsilonproteobacteria at S2 referable to the Arcobacter species. Nevertheless, the notably taxonomical differences could not be explained by the proteomic data and the functional classification, because no specific metabolic function could be highly addressed to these bacteria. These results assumed that different abundance of the key players could be explained by different environmental conditions. The pectin enriched cultured at both sampling sites were investigated for the functional potential of pectin degrading enzymes. No metaproteomic approach could be performed due to less sampling material. Only one PUL for the degradation of rhamnogalacturonan, a component of pectin, was found at S1. In contrast, bacteria grown on pectin could be isolated from these samples. Genome sequencing of five isolates showed that functional potential of pectin degradation is available. Due to the limitations of sequence alignments, it was not possible to detect a PUL responsible for pectin utilization in the metagenomic data. The results show that the polysaccharide degradation mechanism in the Southern Ocean has to be more investigated to get knowledge about the bacterial activity in the ocean’s surface and the carbon turnover in this underexplored environment.
Metabolic engineering enables Bacillus licheniformis to grow on the marine polysaccharide ulvan
(2022)
Background
Marine algae are responsible for half of the global primary production, converting carbon dioxide into organic compounds like carbohydrates. Particularly in eutrophic waters, they can grow into massive algal blooms. This polysaccharide rich biomass represents a cheap and abundant renewable carbon source. In nature, the diverse group of polysaccharides is decomposed by highly specialized microbial catabolic systems. We elucidated the complete degradation pathway of the green algae-specific polysaccharide ulvan in previous studies using a toolbox of enzymes discovered in the marine flavobacterium Formosa agariphila and recombinantly expressed in Escherichia coli.
Results
In this study we show that ulvan from algal biomass can be used as feedstock for a biotechnological production strain using recombinantly expressed carbohydrate-active enzymes. We demonstrate that Bacillus licheniformis is able to grow on ulvan-derived xylose-containing oligosaccharides. Comparative growth experiments with different ulvan hydrolysates and physiological proteogenomic analyses indicated that analogues of the F. agariphila ulvan lyase and an unsaturated β-glucuronylhydrolase are missing in B. licheniformis. We reveal that the heterologous expression of these two marine enzymes in B. licheniformis enables an efficient conversion of the algal polysaccharide ulvan as carbon and energy source.
Conclusion
Our data demonstrate the physiological capability of the industrially relevant bacterium B. licheniformis to grow on ulvan. We present a metabolic engineering strategy to enable ulvan-based biorefinery processes using this bacterial cell factory. With this study, we provide a stepping stone for the development of future bioprocesses with Bacillus using the abundant marine renewable carbon source ulvan.