Abstract:Industrial bioprocess is one of the most important research fields supports the promoting of biological manufacturing industry in China, and guarantee the implementation of bioscience and biotechnology research results into the industrial applications. For improving the interconnection between academic researchers and industrial stuffs and pushing research achievement into industrial implementation, bioprocess modelling and control committee of Chinese Society for Microbiology organized two tandem conferences separately in 2012 and 2014 on the topic of “Industrial bioprocess technology”, focusing mainly technique front of industrial bioprocess. A special session on industrial technique applications was hold to stimulate cooperation. The conference received many good submissions from academic and industrial sectors. This special issue is based on selected excellent papers from the submissions, together with free submissions. The special issue consists of reviews and original papers, mainly involving the aspects closely related to the bio-industrial sectors including, i) high yield strain constructing and high throughput screening; ii) optimization and modification of industrial enzymes, and iii) bioprocess modelling and high efficient scale-up method.

Abstract:Methane monooxygenases (MMO), regarded as “an amazing biomolecular machine”, catalyze the oxidation of methane to methanol under aerobic conditions. MMO catalyze the oxidation of methane elaborately, which is a novel way to catalyze methane to methanol. Furthermore, MMO can inspire the biomolecular machine design. In this review, we introduced MMO including structure, gene and catalytic mechanism. The history and the taxonomy of MMO were also introduced.

Abstract:As a protein originally found in plant pathogenic bacteria, transcription activator-like effectors (TALEs) can fuse with the cleaving domain of restriction endonuclease (For example FokⅠ) to form artificial nucleases named TALENs. These proteins are dependent on variable numbers of tandem Repeats of TALEs to recognize and bind DNA sequences. Each of these repeats consists of a set of approximately 34 amino acids, composed of about 32 conserved amino acids and 2 highly variable amino acids called repeat variant di-residues (RVDs). RVDs distinguish one TALE from another and can make TALEs have a simple cipher for the one-to-one recognition for proteins and DNA bases. Based on this, in theory, artificially constructed TALENs could recognize and break DNA sites specifically and arbitrarily to perform gene knockout, insertion or modification. We reviewed the development of this technology in multi-level and multi species, and its advantages and disadvantages compared with ZFNs and CRISPR/Cas technology. We also address its special advantages in industrial microbe breeding, vector construction, targeting precision, high efficiency of editing and biological safety.

Abstract:Although heterologous biosynthesis of polyketide erythromycin has been successfully achieved in Escherichia coli, the titer remains at a very low level (~10 mg/L). In this study, based on genome-scale metabolic model of E. coli, in silico method flux distribution comparison analysis was used to discover novel potential targets for heterologous 6-dEB biosynthesis. Synthetic small regulatory RNAs (sRNAs) was used to experimentally test 12 down-regulated targets. The results showed that repression of each of these target genes e.g. lsrC and ackA led to significantly improve heterologous 6-dEB biosynthesis. Using co-repression of lsrC and ackA, 6-dEB titer was improved by 59.9 % in shake-flask with a maximum yield of 22.8 mg/L. This study indicates that combined flux distribution comparison analysis and synthetic small regulatory RNAs is an effective strategy to improve 6-dEB production in E. coli.

Abstract:Rhamnolipid biosurfactant is mainly produced by Pseudomonas aeruginosa that is the opportunistic pathogenic strain and not suitable for future industrial development. In order to develop a relatively safe microbial strain for the production of rhamnolipid biosurfactant, we constructed engineered Escherichia coli strains for rhamnolipid production by expressing different copy numbers of rhamnosyltransferase (rhlAB) gene with the constitutive synthetic promoters of different strengths in E. coli ATCC 8739. We further studied the combinatorial regulation of rhlAB gene and rhaBDAC gene cluster for dTDP-l-rhamnose biosynthesis with different synthetic promoters, and obtained the best engineered strain—E. coli TIB-RAB226. Through the optimization of culture temperature, the titer of rhamnolipd reached 124.3 mg/L, 1.17 fold higher than that under the original condition. Fed-batch fermentation further improved the production of rhamnolipid and the titer reached the highest 209.2 mg/L within 12 h. High performance liquid chromatography-mass spectrometry (LC-MS) analysis showed that there are total 5 mono-rhamnolipid congeners with different nuclear mass ratio and relative abundance. This study laid foundation for heterologous biosynthesis of rhanomilipd.

Abstract:To develop a genetic transformation method of Aureobasidium pullulans and T-DNA insertion for high-efficient screening of polymalic acid (PMA) producing strain. Agrobacterium tumefaciens-AGL1, containing the selection genes encoding hygromycin B phosphotase or phosphinothricin acetyltranferase, was used to transform Aureobasidium pullulans CCTCC M2012223 and transformants were confirmed by colony PCR method. Transferred DNA (T-DNA) insertional mutants were cultured in microwell plate, and screened for high-titer PMA producing strain according to the pH response model. DNA walking was used to detect the insertion sites in the mutant. Results show that the selection markers could stably generated in the transformants, and 80 to 120 transformants could be found per 107 single cells. A high-titer PMA mutant H27 was obtained, giving a good PMA production caused by the disruption of phosphoglycerate mutase, that increased by 24.5% compared with the control. Agrobacterium tumefaciens-mediated transformation and high-efficient screening method were successfully developed, which will be helpful for genetic transformation of Aureobasidium pullulans and its functional genes discovery.

Abstract:Isoprene is an important precursor of synthetic rubber material. In our previous study, metabolic engineered Escherichia coli strain (BW-01) was constructed and used to produce isoprene. Based on the theory of protein budget, using synthetic biology strategies including the increased copy number of genes and rare codons, we regulated the expression of key enzyme to improve isoprene production in Escherichia coli strain. Under shake-flask conditions, isoprene productivity of the engineered strain (BW-07) increased by 73% compared with BW-01, reached 761.1 mg/L. It provides a reference for further studies.

Abstract:Anidulafungin is an effective antifungal medicine, which can inhibit activities of candida in vitro and in vivo. Echinocandin B (ECB) is the key precursor of Anidulafungin, thus the price and market prospect of Anidulafungin is directly due to the fermentation titer of ECB. In this study, Aspergillus nidulans was used for ECB fermentation, and the influence of adding microparticles on ECB fermentation was studied, such as talcum powder, Al2O3, and glass beads. The particle size and concentration were the key factors for mycelium morphology and ECB production, and ECB production could reach 1263 mg/L and 1 344 mg/L by adding talcum powder of 20 g/L (d50 = 14.2 μm) and 7 glass beads (6 mm), an increase by 33.2% and 41.7%, respectively. The results indicated that the mycelium morphology of filamentous microorganisms and the product yield of fermentation could be improved by adding microparticles remarkably, and it provide an important method for the fermentative optimization of filamentous microorganisms.

Abstract:Carbon-limited continuous culture was used to study the relationship between the growth of Aspergillus niger and the production of glucoamylase. The result showed that when the specific growth rate was lower than 0.068 h–1, the production of glucoamylase was growth-associated, when the specific growth rate was higher than 0.068 h–1, the production of glucoamylase was not growth-associated. Based on the result of continuous culture, the Monod dynamics model of glucose consumption of A. niger was constructed, Combining Herbert-Pirt equation of glucose and oxygen consumption with Luedeking-Piret equation of enzyme production, the black-box model of Aspergillus niger for enzyme production was established. The exponential fed-batch culture was designed to control the specific growth rate at 0.05 h–1 by using this model and the highest yield for glucoamylase production by A. niger reached 0.127 g glucoamylase/g glucose. The black-box model constructed in this study successfully described the glucoamylase production by A. niger and the result of the model fitted the measured value well. The black-box model could guide the design and optimization of glucoamylase production by A. niger.

Abstract:Agitator is one of the essential factors to realize high efficient fermentation for high aerobic and viscous microorganisms, and the influence of different impeller combination on the fermentation process is very important. Welan gum is a microbial exopolysaccharide produced by Alcaligenes sp. under high aerobic and high viscos conditions. Computational fluid dynamics (CFD) numerical simulation was used for analyzing the distribution of velocity, shear rate and gas holdup in the welan fermentation reactor under six different impeller combinations. The best three combinations of impellers were applied to the fermentation of welan. By analyzing the fermentation performance, the MB-4-6 combination had better effect on dissolved oxygen and velocity. The content of welan was increased by 13%. Furthermore, the viscosity of production were also increased.

Abstract:In industrial application of NAD(P)H-dependent dehydrogenases, NAD(H) has the advantages over NADP(H) in higher stability, lower price and wider recycling system. Recently, a meso-2,6-diaminopimelate dehydrogenase from Symbiobacterium thermophilum (StDAPDH) has been found to be a useful biocatalyst for the production of D-amino acids, but it requires NADP(H) as co-enzyme. To switch the co-enzyme specificity from NADP(H) to NAD(H), we studied the effect of Y76 on the co-enzyme specificity of StDAPDH, because the crystal structural analysis indicated that residue Y76 is near the adenine ring. The mutation of Y76 exerted significant effect on the co-enzyme specificity. Furthermore, the double mutant R35S/R36V significantly lowered the specific activity toward NADP+, and the combination of R35S/R36V with some of the Y76 mutants resulted in mutant enzymes favorable NAD+ over NADP+. This study should provide useful guidance for the further development of highly active NAD+-dependent StDAPDH by enzyme engineering.

Abstract:To improve bond selectivity of recombinant β-glucuronidase in Escherichia coli (PGUS-E), based on the PGUS-E structure guidance, three key points R329, T369 and N467 were identified to be responsible for the bond selectivity of PGUS-E, and further saturation mutagenesis was conducted. Two positive mutants R329K and T369V were obtained by a combined selection technique of thin-layer chromatography and high performance liquid chromatography. Compared to PGUS-E, the bond selectivity of mutants R329K and T369V increased by 26.9% and 34.3%, respectively; whereas the biochemical properties such as pH and temperature profile were unchanged. Nevertheless, the activity was decreased compared to PGUS-E. These results further confirmed that sites R329 and T369 played important roles for the bond selectivity and activity. In summary, this study significantly increased the bond selectivity of PGUS-E by structure guided saturation mutagenesis, providing experimental support for elucidating the relationship between the structure and function of PGUS-E.

Abstract:Most main oilfields in China have already entered a “double high” development stage (high water cut, high recovery degree). To further enhance oil recovery in reservoirs after polymer flooding (RAPFs), an efficient activator formulation for promoting metabolism of endogenous microorganism was studied by aerogenic experiments, physical simulation experiments, electron microscopy scanning and pyrophosphate sequencing. Results show that the activator could activate the endogenous microorganisms in the injected water and make the pressurized gas reach 2 MPa after 60 d static culture of the activator in a high pressure vessel. The oil recovery efficiency of natural core physical simulation flooding can be improved by more than 3.0% (OOIP) in RAPFs when injected 0.35 PV activator with 1.8% mass concentration, and a lot of growth and reproduction of activated endogenous microorganism in the core was observed by electron microscopy scanning. Field trial with 1 injector and 4 producers was carried out in the east of south Ⅱblock of Sa Nan in December 2011. By monitoring four effective production wells, changes of carbon isotope δ13C (PDB) content of methane and carbon dioxide were –45‰ to –54‰ and 7‰ to 12‰. Compared with east Ⅱof Sa Nan block, the oil amount increased by 35.9%, water cut stabled at 94%. The incremental oil was 5 957 t during the three and a half years, which provides an alternative approach for further improving oil recovery in similar reservoirs.