Effects of co-overexpression of the genes of Rubisco and transketolase on photosynthesis in rice

Metabolome analyses have indicated an accumulation of sedoheptulose 7-phosphate in transgenic rice plants with overproduction of Rubisco (Suzuki et al. in Plant Cell Environ 35:1369-1379, 2012. doi: 10.1111/j.1365-3040.2012.02494.x ). Since Rubisco overproduction did not quantitatively enhance photosynthesis even under CO₂-limited conditions, it is suspected that such an accumulation of sedoheptulose 7-phosphate hampers the improvement of photosynthetic capacity. In the present study, the gene of transketolase, which is involved in the metabolism of sedoheptulose 7-phosphate, was co-overexpressed with the Rubisco small subunit gene in rice. Rubisco and transketolase were successfully overproduced in comparison with those in wild-type plants by 35-53 and 39-84 %, respectively. These changes in the amounts of the proteins were associated with those of the mRNA levels. However, the rate of CO₂ assimilation under high irradiance and different [CO₂] did not differ between co-overexpressed plants and wild-type plants. Thus, co-overproduction of Rubisco and transketolase did not improve photosynthesis in rice. Transketolase was probably not a limiting factor of photosynthesis as overproduction of transketolase alone by 80-94 % did not affect photosynthesis.

Complete genome sequence of high-yield strain S. lincolnensis B48 and identification of crucial mutations contributing to lincomycin overproduction

The lincosamide family antibiotic lincomycin is a widely used antibacterial pharmaceutical generated by Streptomyces lincolnensis, and the high-yield strain B48 produces 2.5 g/L lincomycin, approximately 30-fold as the wild-type strain NRRL 2936. Here, the genome of S. lincolnensis B48 was completely sequenced, revealing a ~10.0 Mb single chromosome with 71.03% G + C content. Based on the genomic information, lincomycin-related primary metabolism network was constructed and the secondary metabolic potential was analyzed. In order to dissect the overproduction mechanism, a comparative genomic analysis with NRRL 2936 was performed. Three large deletions (LDI-III), one large inverted duplication (LID), one long inversion and 80 small variations (including 50 single nucleotide variations, 13 insertions and 17 deletions) were found in B48 genome. Then several crucial mutants contributing to higher production phenotype were validated. Deleting of a MarR-type regulator-encoding gene slinc377 from LDI, and the whole 24.7 kb LDII in NRRL 2936 enhanced lincomycin titer by 244% and 284%, respectively. Besides, lincomycin production of NRRL 2936 was increased to 7.7-fold when a 71 kb supercluster BGC33 from LDIII was eliminated. As for the duplication region, overexpression of the cluster situated genes lmbB2 and lmbU, as well as two novel transcriptional regulator-encoding genes (slinc191 and slinc348) elevated lincomycin titer by 77%, 75%, 114% and 702%, respectively. Furthermore, three negative correlation genes (slinc6156, slinc4481 and slinc6011) on lincomycin biosynthesis, participating in regulation were found out. And surprisingly, inactivation of RNase J-encoding gene slinc6156 and TPR (tetratricopeptide repeat) domain-containing protein-encoding gene slinc4481 achieved lincomycin titer equivalent to 83% and 68% of B48, respectively, to 22.4 and 18.4-fold compared to NRRL 2936. Therefore, the comparative genomics approach combined with confirmatory experiments identified that large fragment deletion, long sequence duplication, along with several mutations of genes, especially regulator genes, are crucial for lincomycin overproduction.

Phosphate limitation increases coenzyme Q10 production in industrial Rhodobacter sphaeroides HY01

Coenzyme Q₁₀ (CoQ₁₀) is an important component of the respiratory chain in humans and some bacteria. As a high-value-added nutraceutical antioxidant, CoQ₁₀ has excellent capacity to prevent cardiovascular disease. The content of CoQ₁₀ in the industrial Rhodobacter sphaeroides HY01 is hundreds of folds higher than normal physiological levels. In this study, we found that overexpression or optimization of the synthetic pathway failed CoQ₁₀ overproduction in the HY01 strain. Moreover, under phosphate- limited conditions (decreased phosphate or in the absence of inorganic phosphate addition), CoQ₁₀ production increased significantly by 12% to220 mg/L, biomass decreased by 12%, and the CoQ₁₀ productivity of unit cells increased by 27%. In subsequent fed-batch fermentation, CoQ₁₀ production reached 272 mg/L in the shake-flask fermentation and 1.95 g/L in a 100-L bioreactor under phosphate limitation. Furthermore, to understand the mechanism associated with CoQ₁₀ overproduction under phosphate- limited conditions, the comparatve transcriptome analysis was performed. These results indicated that phosphate limitation combined with glucose fed-batch fermentation represented an effective strategy for CoQ₁₀ production in the HY01. Phosphate limitation induced a pleiotropic effect on cell metabolism, and that improved CoQ₁₀ biosynthesis efficiency was possibly related to the disturbance of energy metabolism and redox potential.

Enhancing scleroglucan production by Sclerotium rolfsii WSH-G01 through a pH-shift strategy based on kinetic analysis

As a stable microbial polysaccharide, scleroglucan has extensive application in the food, medicine, and cosmetics industries. However, its large-scale industrial application is limited by its high production cost, low yield, long production time, etc. This study aims to enhance scleroglucan production by Sclerotium rolfsii WSH-G01. Based on the analysis of batch fermentation kinetics parameters, a pH-shift strategy was adopted. Through systematic kinetics analysis, a 32.4 g/L scleroglucan was accomplished. The kinetic model of the pH-shift batch fermentation process was established using a logistic equation, Luedeking-Piret equation, and a Luedeking-Piret-like equation. As decreased glucose concentration could cause decreased scleroglucan synthesis rates during the batch fermentation process, 30 g/L glucose was fed in the later phase of fermentation. As a result, scleroglucan production increased to 42 g/L, with a productivity of 0.5 g/L·h. Thus, the pH-shift strategy and feeding approach could be useful for industrial scleroglucan production.

Comparative functional genomics of the acarbose producers reveals potential targets for metabolic engineering

The α-glucosidase inhibitor acarbose is produced in large-scale by strains derived from Actinoplanes sp. SE50 and used widely for the treatment of type-2 diabetes. Compared with the wild-type SE50, a high-yield derivative Actinoplanes sp. SE50/110 shows 2-fold and 3–7-fold improvement of acarbose yield and acb cluster transcription, respectively. The genome of SE50 was fully sequenced and compared with that of SE50/110, and 11 SNVs and 4 InDels, affecting 8 CDSs, were identified in SE50/110. The 8 CDSs were individually inactivated in SE50. Deletions of ACWT_4325 (encoding alcohol dehydrogenase) resulted in increases of acarbose yield by 25% from 1.87 to 2.34 g/L, acetyl-CoA concentration by 52.7%, and PEP concentration by 22.7%. Meanwhile, deletion of ACWT_7629 (encoding elongation factor G) caused improvements of acarbose yield by 36% from 1.87 to 2.54 g/L, transcription of acb cluster, and ppGpp concentration to 2.2 folds. Combined deletions of ACWT_4325 and ACWT_7629 resulted in further improvement of acarbose to 2.83 g/L (i.e. 76% of SE50/110), suggesting that the metabolic perturbation and improved transcription of acb cluster caused by these two mutations contribute substantially to the acarbose overproduction. Enforced application of similar strategies was performed to manipulate SE50/110, resulting in a further increase of acarbose titer from 3.73 to 4.21 g/L. Therefore, the comparative genomics approach combined with functional verification not only revealed the acarbose overproduction mechanisms, but also guided further engineering of its high-yield producers.

Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in Saccharopolyspora erythraea

Background

Erythromycin A (Er-A) produced by the actinomycete Saccharopolyspora erythraea is an important antibiotic extensively used in human medicine. Dissecting of transcriptional regulators and their target genes associated with erythromycin biosynthesis is crucial to obtain erythromycin overproducer strains through engineering of relevant regulatory elements in S. erythraea.

Results

Here, we identified a TetR family transcriptional regulator (TFR), SACE_5754, negatively controlling erythromycin production. SACE_5754 indirectly repressed the transcription of ery cluster and cannot regulate itself and its adjacent gene SACE_5753. RNA-seq coupled with EMSAs and qRT-PCR was performed to identify the targets of SACE_5754, and confirmed that transcription of SACE_0388 (encoding a pyruvate, water diknase), SACE_3599 (encoding an antibiotic resistance macrolide glycosyltransferase) and SACE_6149 (encoding a FAD-binding monooxygenase) were directly repressed by SACE_5754. A consensus palindromic sequence TYMAGG-n2/n4/n11-KKTKRA (Y: C/T, M: A/C, K: T/G, R: A/G) was proved to be essential for SACE_5754 binding using DNase I footprinting and EMSAs. During the three target genes of SACE_5754, SACE_0388 and SACE_6149 exhibited the positive effect on erythromycin production. Overexpression of either SACE_0388 or SACE_6149 in ∆SACE_5754 further increased the Er-A production. By engineering the industrial strain S. erythraea WB with deletion of SACE_5754 combined with overexpression of either SACE_0388 or SACE_6149, Er-A production in WB∆SACE_5754/pIB139–0388 and WB∆SACE_5754/pIB139–6149 was successively increased by 42 and 30% compared to WB. Co-overexpression of SACE_0388 and SACE_6149 in WB∆SACE_5754 resulted in enhanced Er-A production by 64% relative to WB. In a 5-L fermenter, WB∆SACE_5754/pIB139–0388-6149 produced 4998 mg/L Er-A, a 48% increase over WB.

Conclusion

We have identified a TFR, SACE_5754, as a negative regulator of erythromycin biosynthesis, and engineering of SACE_5754 and its target genes, SACE_0388 and SACE_6149, resulted in enhanced erythromycin production in both wild-type and industrial S. erythraea strains. The strategy demonstrated here may be valuable to facilitate the manipulation of transcriptional regulators and their targets for production improvement of antibiotics in industrial actinomycetes.

Electronic supplementary material

The online version of this article (10.1186/s13036-018-0135-2) contains supplementary material, which is available to authorized users.

Impact of overproduced heterologous protein characteristics on physiological response in Yarrowia lipolytica steady-state-maintained continuous cultures

Overproduction of recombinant secretory proteins triggers numerous physiological perturbations. Depending on a given heterologous protein characteristics, the producer cell is faced with different challenges which lead to varying responses in terms of its physiology and the target protein production rate. In the present study, we used steady-state-maintained Yarrowia lipolytica cells to investigate the impact of different heterologous proteins on the physiological behavior of the host cells. Such an approach allowed to uncouple the impact of the overproduction of a particular protein from the phenomena that result from growth phase or are caused by the heterogeneity of the analyzed populations. Altogether, eight variants of recombinant strains, individually overproducing heterologous proteins of varying molecular weight (27-65 kDa) and reporting activity (enzymatic and fluorescent) were subjected to chemostat cultivations. The steady-state-maintained cells were analyzed in terms of the substrate utilization, biomass and metabolites production, as well as the reporter protein synthesis. Simplified distribution of carbon and nitrogen between the respective products, as well as expression analysis of the heterologous genes were conducted. The here-obtained data suggest that using a more transcriptionally active promoter results in channeling more C flux towards the target protein, giving significantly higher specific amounts and production rates of the target polypeptide, at the cost of biomass accumulation, and with no significant impact on the polyols production. The extent of the reporter protein's post-translational modifications, i.e., the number of disulfide bonds and glycosylation pattern, strongly impacts the synthesis process. Specific responses in terms of the protein formation kinetics, the gene expression levels, and transcript-to-protein linearity were observed.Key Points• Eight expression systems, producing different reporter proteins were analyzed.• The cells were maintained in steady-state by continuous chemostat culturing.• Protein- and promoter-specific effects were observed.

In Vivo Platforms for Terpenoid Overproduction and the Generation of Chemical Diversity

Terpenoids represent a highly diverse group of natural products with wide applications. Engineering approaches have been used to increase titers of many value-added terpenoids, such as farnesene, taxadiene, lycopene, and astaxanthin. In this chapter, we review the in vitro reconstitution-based targeted engineering of terpenoids, as well as approaches for the mining of terpene cyclases and for increasing the chemical diversity. Information gained from in vitro reconstitution extends our understanding of the mechanisms underlying terpenoid biosynthesis, the contributions of enzymes and cofactors, and key enzymes and rate-limiting steps for the development of an ideal biosynthetic production system. The in vitro reconstitution-based targeted engineering strategy provides a rational and accurate engineering approach for terpenoid overproduction with high efficiency. Furthermore, an efficient terpenoid overproduction platform can accelerate the entire process for the mining of terpene cyclases and the discovery of novel terpenoids and can substantially increase the chemical diversity of these kinds of terpenoids.

Pseudomonas stutzeri as an alternative host for membrane proteins

Background

Studies on membrane proteins are often hampered by insufficient yields of the protein of interest. Several prokaryotic hosts have been tested for their applicability as production platform but still Escherichia coli by far is the one most commonly used. Nevertheless, it has been demonstrated that in some cases hosts other than E. coli are more appropriate for certain target proteins.

Results

Here we have developed an expression system for the heterologous production of membrane proteins using a single plasmid-based approach. The gammaproteobacterium Pseudomonas stutzeri was employed as a new production host. We investigated several basic microbiological features crucial for its handling in the laboratory. The organism belonging to bio-safety level one is a close relative of the human pathogen Pseudomonas aeruginosa. Pseudomonas stutzeri is comparable to E. coli regarding its growth and cultivation conditions. Several effective antibiotics were identified and a protocol for plasmid transformation was established. We present a workflow including cloning of the target proteins, small-scale screening for the best production conditions and finally large-scale production in the milligram range. The GFP folding assay was used for the rapid analysis of protein folding states. In summary, out of 36 heterologous target proteins, 20 were produced at high yields. Additionally, eight transporters derived from P. aeruginosa could be obtained with high yields. Upscaling of protein production and purification of a Gluconate:H⁺ Symporter (GntP) family transporter (STM2913) from Salmonella enterica to high purity was demonstrated.

Conclusions

Pseudomonas stutzeri is an alternative production host for membrane proteins with success rates comparable to E. coli. However, some proteins were produced with high yields in P. stutzeri but not in E. coli and vice versa. Therefore, P. stutzeri extends the spectrum of useful production hosts for membrane proteins and increases the success rate for highly produced proteins. Using the new pL2020 vector no additional cloning is required to test both hosts in parallel.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0771-0) contains supplementary material, which is available to authorized users.

A host-vector toolbox for improved secretory protein overproduction in Bacillus subtilis

Abstract

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.

Key points

• Construction of a versatile Bacillus subtilis gene expression toolbox.

• Verification of the toolbox by the secretory overproduction of two difficult-to-express proteins.

• Fermentation strategy for an acetoin-controlled overproduction of heterologous proteins.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-12062-2.

Comparative genomics and analysis of the mechanism of PQQ overproduction in Methylobacterium

Methylobacterium sp. CLZ was isolated from soil contaminated with chemical wastewater. This strain simultaneously synthesizes Pyrroloquinoline quinone (PQQ), Coenzyme Q10 (CoQ10), and carotenoids by utilizing methanol as a carbon source. Comparative genomic analysis was performed for five Methylobacterium strains. As per the outcomes, the Methylobacterium CLZ strain showed the smallest genome size and the lowest number of proteins. Thus, it can serve as an ideal cell model for investigating the biological process of Methylobacterium and constructing genetically engineered Methylobacterium. The Methylobacterium CLZ strain's pqqL gene, which does not occur in other Methylobacterium strains but plays a crucial role in PQQ synthesis. This was a surprising finding for the study of PQQ biosynthesis in Methylobacterium. Methylobacterium sp. NI91 strain was generated by random mutagenesis of CLZ strain, and NI91 strain showed a 72.44% increase in PQQ yield. The mutation in the mxaJ gene involved in the methanol dehydrogenase (MDH) synthesis was identified through comparative genomic analysis of the whole genome of mutant strain NI91 and wild-type strain CLZ. The mxaJ gene was found to be upregulated in the NI91 strain. Thus, the up-regulation of the mxaJ gene could be correlated with the high yield of PQQ, and it could provide valuable clues for strain engineering to improve PQQ production.

Overproduction of PIB-Type ATPases

Understanding of the functions and mechanisms of fundamental processes in the cell requires structural information. Structural studies of membrane proteins typically necessitate large amounts of purified and preferably homogenous target protein. Here, we describe a rapid overproduction and purification strategy of a bacterial PIB-type ATPase for isolation of milligrams of target protein per liter Escherichia coli cell culture, with a final quality of the sample which is sufficient for generating high-resolution crystals.

Overproduction of Clavulanic Acid by UV Mutagenesis of Streptomyces clavuligerus

Clavulanic acid is produced industrially by fermentation of Streptomyces clavuligerus and researches have increased its production by strain improvement, recombinant DNA technology, and media composition and growth condition optimization. The main objective of this study was to increase the level of clavulanic acid production from Streptomyces clavuligerus (DSM 738), using UV irradiation. After incubation, the spores and aerial mycelia were scraped off the agar plate by a sterile loop. After passing through a cotton wool, the serially diluted spore suspension was spread on GYM- agar containing caffeine. The plates were irradiated with UV light, wrapped in aluminum foil and incubated. The colonies were sub-cultured again to express the mutations. An aliquot of the spore suspension prepared from the resulted culture was poured in GYM agar plates and incubated. The plates were overlaid with nutrient-agar containing penicillin G and Klebsiela pneumoniae, and incubated. The inhibition zone diameter was measured and compared with the wild type colony. Repeating this procedure, the overproducer mutants were selected. Concentration of clavulanic acid was determined by HPLC analysis. It was concluded that secondary metabolites, mainly antibiotics containing clavulanic acid, were produced about 6-7 days after the growth, and concentration of clavulanic acid was increased up to two-folds after UV mutagenesis.

Toxicity of the model protein 3×GFP arises from degradation overload, not from aggregate formation

Although protein aggregation can cause cytotoxicity, such aggregates can also form to mitigate cytotoxicity from misfolded proteins, although the nature of these contrasting aggregates remains unclear. We previously found that overproduction (op) of a three green fluorescent protein-linked protein (3×GFP) induces giant aggregates and is detrimental to growth. Here, we investigated the mechanism of growth inhibition by 3×GFP-op using non-aggregative 3×MOX-op as a control in Saccharomyces cerevisiae. The 3×GFP aggregates were induced by misfolding, and 3×GFP-op had higher cytotoxicity than 3×MOX-op because it perturbed the ubiquitin-proteasome system. Static aggregates formed by 3×GFP-op dynamically trapped Hsp70 family proteins (Ssa1 and Ssa2 in yeast), causing the heat-shock response. Systematic analysis of mutants deficient in the protein quality control suggested that 3×GFP-op did not cause a critical Hsp70 depletion and aggregation functioned in the direction of mitigating toxicity. Artificial trapping of essential cell cycle regulators into 3×GFP aggregates caused abnormalities in the cell cycle. In conclusion, the formation of the giant 3×GFP aggregates itself is not cytotoxic, as it does not entrap and deplete essential proteins. Rather, it is productive, inducing the heat-shock response while preventing an overload to the degradation system.

Natural overproduction of catalase by Kocuria sp. ASB 107: extraction and semi-purification

BACKGROUND AND OBJECTIVES

Because of importance of catalase in various industries, efforts have been made to find more suitable bacterial sources for catalase production. Kocuria is one of well-known catalase-producing genus. This is the first report about a new catalase-overproducing bacterial strain, Kocuria sp. ASB 107.

MATERIALS AND METHODS

Kocuria sp. ASB 107 had been isolated from Abe-Siah Spring in Ramsar in our previous report. The bacterial biomass freezed, thawed and then lysed by three different operations separately: ultrasound, lysing buffer and enzymatic digestion. The crude extract was subjected to ammonium sulfate precipitation (40 and 60% saturation). Quality and quantity of the semi-purification was checked by electrophoresis and measuring specific activity, respectively.

RESULTS

Kocuria sp. ASB 107 can be lysed by a freeze-thaw stage followed by lysozyme digestion and not by lysing buffer and not by ultrasound. Surprisingly specific activity of catalase in crude extract from Kocuria sp. ASB 107 was measured to be 195, 370 U/mg protein which is too much higher than other bacterial strains. The bacterium showed a relatively long growth curve about 40 hours. Semi-purification using ammonium sulfate precipitation was led in an increased specific activity up to about 7×10⁶ U/mg protein implying more than 3.6-fold purification.

CONCLUSION

We have showed natural catalase-overproducing ability of Kocuria sp. ASB 107. Yield and purity of catalase from Kocuria sp. ASB 107 showed great potential in industrial application suggesting the strain as good source for mass production of catalase for treatment of H₂O₂-containing wastewater in comparison to other bacterial sources.

Yeast cell wall mannan structural features, biological activities, and production strategies

Mannan and outer structural yeast cell wall polysaccharides have recently garnered attention for their health defense and cosmetic applications. In addition, many studies have confirmed that yeast cell wall mannans exhibit various biological activities, such as antioxidant, immune regulation, reducing hyperlipidemia, and gut health promotion. This paper elucidates yeast cell wall mannan structural features, biological activities, underlying molecular mechanisms, and biosynthesis. Moreover, mannan-overproducing strategies through yeast strain engineering are emphasized and discussed. This review will provide a scientific basis for yeast cell wall mannan research and industrial applications.

Effects of multiwalled carbon nanotubes on the dissolved organic matter released by Prorocentrum donghaiense: Results of spectroscopic studies

Many reports have investigated the effects of carbon nanotubes (CNTs) on the properties of terrestrial dissolved organic matter (DOM), which could significantly altered its binding affinity for contaminants. However, the effects of CNTs on algogenic DOM are largely unknown. To address this issue, the properties of algogenic DOM released by Prorocentrum donghaiense (P. donghaiense-DOM) under the stress from 0.1 to 10.0 mg/L graphitized multiwalled CNTs were nondestructively characterized by the use of UV-visible absorption and fluorescence excitation-emission matrices with parallel factor analysis. The results showed that the changes in the properties of P. donghaiense-DOM were highly dependent on the CNTs concentration. The properties of P. donghaiense-DOM under 0.1 mg/L CNTs treatment showed no obvious differences compared to the control. The addition of 0.5-10.0 mg/L CNTs changed the release pathways of P. donghaiense-DOM, resulting in significant alterations to the properties of P. donghaiense-DOM. The aromaticity, molecular weight, protein-like and humic-like components were enhanced under stress from 0.5 to 1.0 mg/L CNTs on day 4, which can be ascribed to the overproduction of extracellular DOM (EDOM) that occurred in response to the significant increase in intracellular ROS levels. CNTs at 5.0 and 10.0 mg/L significantly induced membrane damage to P. donghaiense on day 4, which led to the leakage of intracellular DOM (IDOM) and then increased the molecular weight and protein-like components but decreased the aromaticity and humic-like components. After the P. donghaiense recovered to its normal growth under 0.5-10.0 mg/L CNTs treatments, the changes in the properties of P. donghaiense-DOM were attributed to the release pathways of P. donghaiense-DOM that were governed by the production of EDOM and the leakage of IDOM in the stationary and declining phases, respectively.