Publications by authors named "Huifeng Jiang"

59 Publications

Clinicopathological analysis and genomic profiling of a rare histiocyte-rich rhabdomyoblastic tumor: A case report.

Medicine (Baltimore) 2021 Jun;100(24):e26105

Department of General Surgery, Shenzhen University General Hospital & Carson International Cancer Research Centre, Shenzhen, P.R. China.

Rationale: Skeletal muscle tumors are traditionally classified as rhabdomyomas or rhabdomyosarcomas. However, some soft tissue tumors cannot easily be identified as benign or malignant. We report a case of a histiocyte-rich rhabdomyoblastic tumor, with pathologic characteristics distinct from either rhabdomyoma or rhabdomyosarcoma. In contrast to rhabdomyosarcomas, the tumor cells exhibited low mitotic activity, lacking obvious morphologic atypia. Clinically, the tumor followed a very indolent course. Overall, the tumor did not fit classification criteria for either benign or malignant.

Patient Concerns: A 58-year-old Chinese man was admitted to Qilu Hospital on September 8, 2018, with a >20 year history of a mass in the middle of the left thigh. A few months prior to admission, he had experienced the pain from the mass extending to the distal left lower extremity. He had no prior history of significant disease or relevant family history.

Diagnoses: Microscopically, numerous histiocytes and foamy cells covered the actual tumor cells that were positive for desmin, MyoD1, and myogenin, suggesting striated skeletal muscle cell differentiation. However, cross-striations were not detected in the tumor cells. The tumor was characterized by a non-infiltrative growth pattern and a low level of Ki67. A diagnosis of histiocyte-rich rhabdomyoblastic tumor was suggested.

Interventions: The thigh mass was surgically resected September 12, 2018.

Outcomes: The patient recovered well postoperatively, and was free of tumor recurrence or metastasis, followed to September 12, 2020 (23 months).

Lessons: Histiocyte-rich rhabdomyoblastic tumor cells have minor atypia, indicating possible malignant potential. However, the tumor behavior was quit indolent. Due to the conflicting clinical and pathologic aspects of the tumor, to label it as rhabdomyosarcoma seemed inaccurate, potentially prompting over treatment. Interestingly, mutations were detected in NF1, AXIN2, CHEK2, DNMT3A, KMT2D, and RB1 through next-generation sequencing. These mutations suggest disruptions in Ras signaling, the Wnt pathway, methyltransferases, and the cell cyclepotentially influencing the development of this histiocyte-rich rhabdomyoblastic tumor. This unusual tumor should be incorporated into the WHO Classification of Soft Tissue Tumors owing to its unique characteristics.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/MD.0000000000026105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8213239PMC
June 2021

Biosynthesis of Polydatin in .

J Agric Food Chem 2021 Jun 21;69(21):5917-5925. Epub 2021 May 21.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Polydatin, with better structural stability and biological activities than resveratrol, is mainly extracted from the traditional Chinese medicinal plant . In this study, based on the transcriptome analysis of , we identified the key glycosyltransferase of resveratrol and achieved the biosynthesis of polydatin from glucose by incorporation with the resveratrol biosynthesis module, UDP-glucose supply module, and glycosyltransferase expression module. Through metabolic engineering and fermentation optimization, the production of polydatin reached 545 mg/L, and the dry cell weight was 27.83 mg/g DCW, which was about twice that of extracted from the root (11.404 mg/g DCW). Therefore, it is possible to replace the production mode of polydatin from plant extraction to microbial chassis in the future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jafc.1c01557DOI Listing
June 2021

PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking.

Synth Syst Biotechnol 2021 Jun 24;6(2):102-109. Epub 2021 Apr 24.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.

Plant cytochrome P450s play key roles in the diversification and functional modification of plant natural products. Although over 200,000 plant P450 gene sequences have been recorded, only seven crystalized P450 genes severely hampered the functional characterization, gene mining and engineering of important P450s. Here, we combined Rosetta homologous modeling and MD-based refinement to construct a high-resolution P450 structure prediction process (PCPCM), which was applied to 181 plant P450s with identified functions. Furthermore, we constructed a ligand docking process (PCPLD) that can be applied for plant P450s virtual screening. 10 examples of virtual screening indicated the process can reduce about 80% screening space for next experimental verification. Finally, we constructed a plant P450 database (PCPD: http://p450.biodesign.ac.cn/), which includes the sequences, structures and functions of the 181 plant P450s, and a web service based on PCPCM and PCPLD. Our study not only developed methods for the P450-specific structure analysis, but also introduced a universal approach that can assist the mining and functional analysis of P450 enzymes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.synbio.2021.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8094579PMC
June 2021

Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway.

Mol Plant 2021 Jul 2;14(7):1199-1209. Epub 2021 May 2.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.

Taxus, commonly known as yew, is a well-known gymnosperm with great ornamental and medicinal value. In this study, by assembling a chromosome-level genome of the Himalayan yew (Taxus wallichiana) with 10.9 Gb in 12 chromosomes, we revealed that tandem duplication acts as the driving force of gene family evolution in the yew genome, resulting in the main genes for paclitaxel biosynthesis, i.e. those encoding the taxadiene synthase, P450s, and transferases, being clustered on the same chromosome. The tandem duplication may also provide genetic resources for the nature to sculpt the core structure of taxoids at different positions and subsequently establish the complex pathway of paclitaxel by neofunctionalization. Furthermore, we confirmed that there are two genes in the cluster encoding isoenzymes of a known enzyme in the paclitaxel biosynthetic pathway. The reference genome of the Himalayan yew will serve as a platform for decoding the complete biosynthetic pathway of paclitaxel and understanding the chemodiversity of taxoids in gymnosperms.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molp.2021.04.015DOI Listing
July 2021

Biocatalytic C-C Bond Formation for One Carbon Resource Utilization.

Int J Mol Sci 2021 Feb 14;22(4). Epub 2021 Feb 14.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

The carbon-carbon bond formation has always been one of the most important reactions in C1 resource utilization. Compared to traditional organic synthesis methods, biocatalytic C-C bond formation offers a green and potent alternative for C1 transformation. In recent years, with the development of synthetic biology, more and more carboxylases and C-C ligases have been mined and designed for the C1 transformation in vitro and C1 assimilation in vivo. This article presents an overview of C-C bond formation in biocatalytic C1 resource utilization is first provided. Sets of newly mined and designed carboxylases and ligases capable of catalyzing C-C bond formation for the transformation of CO, formaldehyde, CO, and formate are then reviewed, and their catalytic mechanisms are discussed. Finally, the current advances and the future perspectives for the development of catalysts for C1 resource utilization are provided.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms22041890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7918591PMC
February 2021

Directed Evolution of Propionyl-CoA Carboxylase for Succinate Biosynthesis.

Trends Biotechnol 2021 04 22;39(4):330-331. Epub 2021 Feb 22.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China. Electronic address:

Due to low carboxylase activity, CO biotransformation is challenging to achieve using natural CO fixation pathways. Liu et al. have improved the activity of propionyl-CoA carboxylase (PCC) 94-fold, enabling the efficient synthesis of succinate from acetyl-CoA and paving the way for CO assimilation via the 3-hydroxypropionate (3-HP) bicycle or 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tibtech.2021.02.006DOI Listing
April 2021

Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes.

Cell 2021 Mar 4;184(5):1377-1391.e14. Epub 2021 Feb 4.

BGI-Shenzhen, Shenzhen 518083, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. Electronic address:

Rich fossil evidence suggests that many traits and functions related to terrestrial evolution were present long before the ancestor of lobe- and ray-finned fishes. Here, we present genome sequences of the bichir, paddlefish, bowfin, and alligator gar, covering all major early divergent lineages of ray-finned fishes. Our analyses show that these species exhibit many mosaic genomic features of lobe- and ray-finned fishes. In particular, many regulatory elements for limb development are present in these fishes, supporting the hypothesis that the relevant ancestral regulation networks emerged before the origin of tetrapods. Transcriptome analyses confirm the homology between the lung and swim bladder and reveal the presence of functional lung-related genes in early ray-finned fishes. Furthermore, we functionally validate the essential role of a jawed vertebrate highly conserved element for cardiovascular development. Our results imply the ancestors of jawed vertebrates already had the potential gene networks for cardio-respiratory systems supporting air breathing.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2021.01.046DOI Listing
March 2021

The origin and evolution of the diosgenin biosynthetic pathway in yam.

Plant Commun 2021 Jan 2;2(1):100079. Epub 2020 Jun 2.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Diosgenin, mainly produced by species, is a traditional precursor of most hormonal drugs in the pharmaceutical industry. The mechanisms that underlie the origin and evolution of diosgenin biosynthesis in plants remain unclear. After sequencing the whole genome of , we revealed the evolutionary trajectory of the diosgenin biosynthetic pathway in and demonstrated the biosynthesis of diosgenin in a yeast cell factory. First, we found that P450 gene duplication and neo-functionalization, driven by positive selection, played important roles in the origin of the diosgenin biosynthetic pathway. Subsequently, we found that the enrichment of diosgenin in the yam lineage was regulated by CpG islands, which evolved to regulate gene expression in the diosgenin pathway and balance the carbon flux between the biosynthesis of diosgenin and starch. Finally, by integrating genes from plants, animals, and yeast, we heterologously synthesized diosgenin to 10 mg/l in genetically-engineered yeast. Our study not only reveals the origin and evolutionary mechanisms of the diosgenin biosynthetic pathway in , but also introduces an alternative approach for the production of diosgenin through synthetic biology.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.xplc.2020.100079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7816074PMC
January 2021

Nicotinamide as Additive for Microcrystalline and Defect Passivated Perovskite Solar Cells with 21.7% Efficiency.

ACS Appl Mater Interfaces 2020 Nov 10;12(47):52500-52508. Epub 2020 Nov 10.

Institute of Photovoltaic, Southwest Petroleum University, Chengdu 610500. P.R. China.

Passivation of electronic defects on the surface and at grain boundaries (GBs) of perovskite films has become one of the most effective tactics to suppress charge recombination in perovskite solar cells. It is demonstrated that trap states can be effectively passivated by Lewis acid or base functional groups. In this work, nicotinamide (NTM, commonly known as vitamin B3 or vitamin PP) serving as a Lewis base additive is introduced into the PbI and/or FAI: MABr: MACl precursor solution to obtain NTM modified perovskite films. It has been found that the NTM in the perovskite film can well passivate surface and GBs defects, control the film morphology and enhance the crystallinity via its interaction with a lone pair of electrons in nitrogen. In the presence of the NTM additive, we obtained enlarged perovskite crystal grain about 3.6 μm and a champion planar perovskite solar cell with efficiency of 21.72% and negligible hysteresis. Our findings provide an effective route for crystal growth and defect passivation to bring further increases on both efficiency and stability of perovskite solar cells.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acsami.0c12030DOI Listing
November 2020

Oxidization-Free Spiro-OMeTAD Hole-Transporting Layer for Efficient CsPbIBr Perovskite Solar Cells.

ACS Appl Mater Interfaces 2020 Nov 10;12(47):52779-52787. Epub 2020 Nov 10.

Institute of Photovoltaic, Southwest Petroleum University, Chengdu 610500. P. R. China.

The inorganic CsPbIBr perovskite faces serious challenges of low phase stability and high moisture sensitivity. The moisture controllable process of a hole-transporting layer (HTL) is crucial for the development of stable and efficient inorganic perovskite solar cells (IPSCs). In this work, we proposed an oxidization-free spiro-OMeTAD hole-transport layer (HTL) with a preoxidized spiro-OMeTAD solution to prevent moisture and completely avoid the phase transition of CsPbIBr from the α-phase to β-phase. The oxidization-free HTL exhibited improved surface hydrophobic properties, smoother morphology, and optimized energy-level alignment compared with a traditional HTL. As a result, the CsPbIBr-based IPSCs achieved an efficiency of up to 14.2 and 86.6% of the initial power conversion efficiency (PCE) with 2000 h storage. Meanwhile, this oxidization-free HTL was applied in CHNHPbI-based PSCs and obtained 13.8% PCE enhancement, which proved the universality of the solution preoxidization tactic. We believe that the oxidization-free HTL could be an efficient strategy to replace traditional HTLs and can be widely used in perovskite solar cells, especially in moisture-sensitive PSCs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acsami.0c16355DOI Listing
November 2020

Synthesis of Ligustrazine from Acetaldehyde by a Combined Biological-Chemical Approach.

ACS Synth Biol 2020 11 6;9(11):2902-2908. Epub 2020 Nov 6.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.

Ligustrazine is an important active alkaloid in medicine and in the food industry. Here, we developed a combined biological-chemical approach to produce ligustrazine from acetaldehyde. First, we constructed a whole-cell biocatalytic system to produce the precursor acetoin from acetaldehyde by overexpressing formolase (FLS). Second, a two-step strategy was developed to enhance protein expression of FLS by codon usage optimization at the first 14 codons and the introduction of an overlapping gene before the start codon. Through expression optimization and directed evolution of FLS, we improved the titer of acetoin about 40 fold when the concentration of acetaldehyde was 1.5 M. Finally, after reaction conditions optimization, the titer of acetoin and ligustrazine reached 222 g L and 94 g L, with a 86.5% and 48% conversion rate from acetaldehyde, respectively. The developed one-pot synthesis for acetoin and ligustrazine is expected to be applied to industrial production in the future with the advantages of a green process, high efficiency, and low cost.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acssynbio.0c00113DOI Listing
November 2020

Biosynthesis of Multiple Pinocembrin Derivatives in .

ACS Synth Biol 2020 11 27;9(11):3042-3051. Epub 2020 Oct 27.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Pinocembrin derived flavones are the major bioactive compounds presented in the Lamiaceae plants that have long been of interest due to their great pharmaceutical and economical significance. Modifications on the central skeleton of the flavone moiety have a huge impact on their biological activities. However, the enzymes responsible for structure modification of most flavones are either inefficient or remain unidentified. By integrating omics analysis of and synthetic biology tools in yeast chassis, we characterized a novel gene encoding flavone 7--methyltransferase (F7OMT) and discovered a new flavone 8-hydroxylase (F8H) with increased activity. We also identified a series of flavone 6-hydroxylases (F6Hs) and flavone 8--methyltransferases (F8OMTs) in this study. Subsequently, we constructed the biosynthetic pathway for chrysin production by assembling catalytic elements from different species and improved the titer to 10.06 mg/L. Using the established chrysin production platform, we achieved the biosynthesis of baicalein, baicalin, norwogonin, wogonin, isowogonin, and moslosooflavone in yeast. Our results indicated that the combination of omics and synthetic biology can greatly speed up the efficiency of gene mining in plants and the engineered yeasts established an alternative way for the production of pinocembrin derivatives.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acssynbio.0c00289DOI Listing
November 2020

Origin and Evolution of Fusidane-Type Antibiotics Biosynthetic Pathway through Multiple Horizontal Gene Transfers.

Genome Biol Evol 2020 10;12(10):1830-1840

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.

Fusidane-type antibiotics represented by fusidic acid, helvolic acid, and cephalosporin P1 have very similar core structures, but they are produced by fungi belonging to different taxonomic groups. The origin and evolution of fusidane-type antibiotics biosynthetic gene clusters (BGCs) in different antibiotics producing strains remained an enigma. In this study, we investigated the distribution and evolution of the fusidane BGCs in 1,284 fungal genomes. We identified 12 helvolic acid BGCs, 4 fusidic acid BGCs, and 1 cephalosporin P1 BGC in Pezizomycotina fungi. Phylogenetic analyses indicated six horizontal gene transfer (HGT) events in the evolutionary trajectory of the BGCs, including 1) three transfers across Eurotiomycetes and Sordariomycetes classes; 2) one transfer between genera under Sordariomycetes class; and 3) two transfers within Aspergillus genus under Eurotiomycetes classes. Finally, we proposed that the ancestor of fusidane BGCs would be originated from the Zoopagomycota by ancient HGT events according to the phylogenetic trees of key enzymes in fusidane BGCs (OSC and P450 genes). Our results extensively clarify the evolutionary trajectory of fusidane BGCs by HGT among distantly related fungi and provide new insights into the evolutionary mechanisms of metabolic pathways in fungi.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/gbe/evaa163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7750971PMC
October 2020

Primary breast diffuse large B-cell lymphoma in a patient with systemic lupus erythematosus: A case report and review of the literature.

Medicine (Baltimore) 2020 Aug;99(33):e21736

Department of Pathology, Luohu District People's Hospital, Shenzhen, China.

Rationale: Pilot studies have reported that patients with systemic lupus erythematosus (SLE) appear more likely to develop into neoplasia, especially lymphatic hyperplasia diseases. To our knowledge, this is the first case report of the concomitant onset of SLE and primary breast diffuse large B-cell lymphoma (PB-DLBCL).

Patient Concerns: We reported an unusual case of the occurrence of primary breast diffuse large B-cell lymphoma in a 25-year-old female patient who had been diagnosed with SLE and treated with immunosuppressive drugs for about 4 years. She presented a 7-week history of a painless mass above the left breast and no history suggestive of any nipple discharge, fever, and weight loss.

Diagnosis: Ultrasonography of the breast showed that there was 1 mass in the left breast. After breast mass surgical resection, histopathological examinations were performed and revealed that it was primary breast diffuse large B-cell lymphoma.

Interventions: Treatment strategy with vincristine and dexamethasone was used to improve symptoms. However, the patient's renal function deteriorated and the blood potassium rose continuously and she and their family members refused the follow-up treatments.

Outcomes: The patient died 8 months after she was discharged from the hospital.

Lessons: PB-DLBCL is a rare occurrence in SLE patients. Therefore, a careful examination is very important in SLE cohort, as activity of the disease and malignancy may mimic each other. Meanwhile, when symptoms cannot be explained or insensitive to treatment, the occurrence of malignant tumors must be highly considered.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/MD.0000000000021736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7437807PMC
August 2020

Combining protein and metabolic engineering to construct efficient microbial cell factories.

Curr Opin Biotechnol 2020 12 12;66:27-35. Epub 2020 Jul 12.

Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.

Microbial cell factories offer great opportunities for the feasible biosynthesis of various value-added products from renewable resources. In recent years, protein engineering has served as a powerful approach for generating enzymes or proteins with desirable properties. As an effective toolbox, many efforts have been employed into protein engineering for the improvement of biological networks by enhancing, regulating, expanding, and innovating metabolic pathways. In combination with traditional metabolic engineering strategies, protein engineering has demonstrated tremendous promise in facilitating the production of many bio-based products. In this review, we present recent trends and strategies available for protein engineering, and highlight the successful interplay between protein and metabolic engineering in boosting the production of target compounds using diverse microbial cell factories. The perspectives for protein design in metabolic engineering are also briefly discussed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.copbio.2020.06.001DOI Listing
December 2020

Discovery and modification of cytochrome P450 for plant natural products biosynthesis.

Synth Syst Biotechnol 2020 Sep 1;5(3):187-199. Epub 2020 Jul 1.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.

Cytochrome P450s are widespread in nature and play key roles in the diversification and functional modification of plant natural products. Over the last few years, there has been remarkable progress in plant P450s identification with the rapid development of sequencing technology, "omics" analysis and synthetic biology. However, challenges still persist in respect of crystal structure, heterologous expression and enzyme engineering. Here, we reviewed several research hotspots of P450 enzymes involved in the biosynthesis of plant natural products, including P450 databases, gene mining, heterologous expression and protein engineering.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.synbio.2020.06.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7332504PMC
September 2020

[Biocatalysis of formaldehyde to L-xylose].

Sheng Wu Gong Cheng Xue Bao 2020 May;36(5):942-948

Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

It is of great significance to use biosynthesis to transform the inorganic substance formaldehyde into organic sugars. Most important in this process was to find a suitable catalyst combination to achieve the dimerization of formaldehyde. In a recent report, an engineered glycolaldehyde synthase was reported to catalyze this reaction. It could be combined with engineered D-fructose-6-phosphate aldolase, a "one-pot enzyme" method, to synthesize L-xylose using formaldehyde and the conversion rate could reach up to 64%. This process also provides a reference for the synthesis of other sugars. With the increasing consumption of non-renewable resources, it was of great significance to convert formaldehyde into sugar by biosynthesis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.13345/j.cjb.190554DOI Listing
May 2020

Raising the production of phloretin by alleviation of by-product of chalcone synthase in the engineered yeast.

Sci China Life Sci 2020 Nov 27;63(11):1734-1743. Epub 2020 Apr 27.

Center for Ecology and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China.

Phloretin is an important skin-lightening and depigmenting agent from the peel of apples. Although de novo production of phloretin has been realized in microbes using the natural pathway from plants, the efficiency of phloretin production is still not enough for industrial application. Here, we established an artificial pathway in the yeast to produce phloretin via assembling two genes of p-coumaroyl-CoA ligase (4CL) and chalcone synthase (CHS). CHS is a key enzyme which conventionally condenses a CoA-tethered starter with three molecules of malonyl-CoA to form the backbone of flavonoids. However, there was 33% of by-product generated via CHS by condensing two molecules of malonyl-CoA during the fermentation process. Hence, we introduced a more efficient CHS and improved the supply of malonyl-CoA through two pathways; the by-product ratio was decreased from 33% to 17% and the production of phloretin was improved from 48 to 83.2 mg L. Finally, a fed-batch fermentation process was optimized and the production of phloretin reached 619.5 mg L, which was 14-fold higher than that of the previous studies. Our work established a platform for the biosynthesis of phloretin from the low-cost raw material 3-(4-hydroxyphenyl) propanoic acid and also illustrated the potential for industrial scale bio-manufacturing of phloretin.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11427-019-1634-8DOI Listing
November 2020

[A high efficiency cloning approach of multi-points combinational mutagenesis].

Sheng Wu Gong Cheng Xue Bao 2020 Feb;36(2):309-319

Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

The combination of high-quality mutagenesis and effective screening can improve the efficiency of enzyme directed evolution. In this study, a high efficiency cloning construction method of Multi-points Combinational Mutagenesis (MCM) was developed. Efficient multi-point combination mutations were performed in this MCM method by introducing DNA assembly, fusion PCR and hybridization techniques. After optimization, the efficiency of MCM was tested by directed evolution of benzoylformate decarboxylase. The obtained number of Colony Forming Units (CFUs) by electroporation to competent cells E. coli Trelief™ 5α exceeded 10⁶ CFUs/μg DNA. Test results show that 90/100 clones were precisely assembled. The efficiency of simultaneous mutation at 5 sites (L109, L110, H281, Q282 and A460) was up to 88%. Finally, a mutant enzyme (L109Y, L110D, H281G, Q282V and A460M) with a 10-fold increase in kcat/Km was obtained. Therefore, this method can effectively create diverse mutant libraries and promote the rapid development of enzyme directed evolution.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.13345/j.cjb.190147DOI Listing
February 2020

Assembly and Analysis of the Genome Sequence of the Yeast CBS 7540.

Microorganisms 2019 Oct 26;7(11). Epub 2019 Oct 26.

Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007 Uppsala, Sweden.

is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of CBS 7540. The genome of CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/microorganisms7110489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6921048PMC
October 2019

A first case report of primary epithelial myoepithelial carcinoma-like renal tumor showing a perivascular pseudorosette-like pattern: Description of morphologic, immunohistochemical, and genetic features.

Medicine (Baltimore) 2019 Sep;98(39):e17245

Department of Pathology.

Rationale: Over the past decade, although several new entities of renal tumors have emerged, a form of renal cell carcinoma (RCC) that morphologically resembles epithelial-myoepithelial carcinoma has not been reported thus far. Herein, we describe a case of an unusual renal tumor that remained unclassified under a current RCC subtype, and briefly present its morphologic, immunophenotypic, and genetic features.

Patient Concerns: The patient was an 85-year-old man who presented with hematuria and flank pain. Imaging studies revealed a left renal mass without enlarged lymph nodes. There were no abnormal masses or nodules in other organs.

Diagnoses: The patient underwent no other treatment except the left radical nephrectomy under a clinical diagnosis of invasive urothelial carcinoma and was discharged on the thirteenth day. Histologically, the renal tumor showed biphasic proliferation of epithelial (strongly cytokeratin-positive; P63, P40, and vimentin-negative) and myoepithelial (strongly vimentin-positive; focal P63 and P40-positive; and weakly cytokeratin-positive) cells arranged in a perivascular pseudorosette-like pattern. No mutations were detected in multiple gene tests. According to the pathological structure, the patient was diagnosed as primary epithelial myoepithelial carcinoma-like renal tumor.

Interventions: To the best of our knowledge, the present tumor has not been previously described, and thus, this variant has not been integrated into a known form of PCC. Therefore, we cannot diagnose this type of tumor with other types of kidney tumors.

Outcomes: Three years after primary diagnosis, the patient died of multiple organ failure result from multiple distant metastases.

Lessons: We present the first case of carcinoma of the kidney with EMC-like features and a perivascular pseudorosette-like growth pattern. Clinicians should be aware of the features of this uncommon variant of RCC to avoid diagnostic delays or misdiagnosis and prevent unnecessary or inappropriate treatment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/MD.0000000000017245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6775372PMC
September 2019

Systematic design and in vitro validation of novel one-carbon assimilation pathways.

Metab Eng 2019 12 3;56:142-153. Epub 2019 Sep 3.

Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.

The utilization of one-carbon (C) assimilation pathways to produce chemicals and fuels from low-cost C compounds could greatly reduce the substrate-related production costs, and would also alleviate the pressure of the resource supply for bio-manufacturing. However, the natural C assimilation pathways normally involve ATP consumption or the loss of carbon resources as CO, resulting in low product yields, making the design of novel pathways highly pertinent. Here we present several new ATP-independent and carbon-conserving C assimilation cycles with 100% theoretical carbon yield, which were discovered by computational analysis of metabolic reaction set with 6578 natural reactions from MetaCyc database and 73 computationally predicted aldolase reactions from ATLAS database. Then, kinetic evaluation of these cycles was conducted and the cycles without kinetic traps were chosen for further experimental verification. Finally, we used the two engineered enzymes Gals and TalB for the artificial reactions to construct a novel C assimilation pathway in vitro and optimized the pathway to achieve 88% carbon yield. These results demonstrate the usefulness of computational design in finding novel metabolic pathways for the efficient utilization of C compounds and shedding light on other promising pathways.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymben.2019.09.001DOI Listing
December 2019

Lysine Mutation of the Claw-Arm-Like Loop Accelerates Catalysis by Cellobiohydrolases.

J Am Chem Soc 2019 09 3;141(36):14451-14459. Epub 2019 Sep 3.

State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China.

Searching for viable strategies to accelerate the catalytic cycle of glycoside hydrolase family 7 (GH7) cellobiohydrolase I (CBHI)-the workhorse cellulose-degrading enzymes, we have performed a total of 12-μs molecular dynamics simulations on GH7 CBHI, which brought to light a new mechanism for cellobiose expulsion, coined "claw-arm" action. The loop flanking the product binding site plays the role of a flexible "arm" extending toward cellobiose, and residue Thr389 of this loop acts as a "claw" that captures cellobiose. Five mutations of residue Thr389 were considered to enhance the loop-cellobiose interaction. The lysine mutant was found to significantly accelerate cellobiose expulsion and facilitate polysaccharide-chain translocation. Lysine mutation of Thr393 in CBHI (Cel7A) performed similarly. Lysine approaches the catalytic area and stabilizes the Michaelis complex, potentially affecting glycosylation, the rate-limiting step of the catalytic cycle. QM/MM calculations indicate that lysine replacement diminishes the barrier against proton transfer, the crucial step of glycosylation, by 2.3 kcal/mol. Experimental validation was performed using the full-length wild-type (WT) of Cel7A and its mutants, recombinantly expressed in , to degrade the substrates. Compared with the WT, the lysine mutant revealed an associated higher enzymatic reaction rate. Furthermore, cellobiose yield was also increased by lysine mutation, indicating that dissociation of the enzyme from cellulose was accelerated, which largely stems from the enhanced flexibility of the "arm". The present work is envisioned to help design strategies for improving enzymatic activity, while decreasing enzyme cost.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/jacs.9b08477DOI Listing
September 2019

Combining Protein and Metabolic Engineering Strategies for High-Level Production of O-Acetylhomoserine in Escherichia coli.

ACS Synth Biol 2019 05 22;8(5):1153-1167. Epub 2019 Apr 22.

Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China.

O-acetylhomoserine (OAH) is a promising platform chemical for the production of l-methionine and other valuable compounds. However, the relative low titer and yield of OAH greatly limit its industrial production and cost-effective application. In this study, we successfully constructed an efficient OAH-producing strain with high titer and yield by combining protein and metabolic engineering strategies in E. coli. Initially, an OAH-producing strain was created by reconstruction of biosynthetic pathway and deletion of degradation and competitive pathways, which accumulated 1.68 g/L of OAH. Subsequently, several metabolic engineering strategies were implemented to improve the production of OAH. The pathway flux of OAH was enhanced by eliminating byproduct accumulation, increasing oxaloacetate supply and promoting the biosynthesis of precursor homoserine, resulting in a 1.79-fold increase in OAH production. Moreover, protein engineering was applied to improve the properties of the rate-limiting enzyme homoserine acetyltransferase (MetXlm) based on evolutionary conservation analysis and structure-guided engineering. The resulting triple F147L-M182I-M240A mutant of MetXlm exhibited a 12.15-fold increase in specific activity, and the optimized expression of the MetXlm mutant led to a 57.14% improvement in OAH production. Furthermore, the precursor acetyl-CoA supply and NADPH generation were also enhanced to facilitate the biosynthesis of OAH by promoting CoA biosynthesis, overexpressing heterogeneous acetyl-CoA synthetase (ACS), and introducing NADP-dependent pyruvate dehydrogenase (PDH). Finally, the engineered strain OAH-7 produced 62.7 g/L of OAH with yield and productivity values of 0.45 g/g glucose and 1.08 g/L/h, respectively, in a 7.5 L fed-batch fermenter, which was the highest OAH production ever reported.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acssynbio.9b00042DOI Listing
May 2019

Primary pulmonary hepatoid adenocarcinoma: A case report and review of the literature.

Medicine (Baltimore) 2019 Apr;98(14):e15053

Department of Pathology, Qilu Hospital, Shandong University, Qingdao, China.

Rationale: Hepatoid adenocarcinoma of lung (HAL) is a rare malignant tumor, which can be defined as a primary alpha-fetoprotein (AFP)-producing lung carcinoma. The majority of hepatoid adenocarcinoma (HAC) expressed AFP in tumor cells, but AFP expression is not required for its diagnosis according to the modified diagnostic criteria. Despite that HAC exhibits a poor prognosis and ineffective treatment options, early diagnosis and aggressive treatment can result in long-term survival.

Patient Concerns: We report a 70-year-old Chinese male patient with alcoholic intake over 30 years and smoking history of 60 cigarettes per day for 40 years. He sought medical consultation for productive cough and hemoptysis sputum.

Diagnoses And Interventions: Chest CT scan revealed a mass (6.4 × 5.5 cm) in the left lower lobe of the lung. The patient underwent curative surgical resection, and subsequently diagnosed as HAL.

Outcomes: Eighteen months after primary diagnosis, the patient died of multiple organ failure caused by distant metastases.

Lessons: Familiarizing with the clinical features and modified diagnostic criteria of this rare tumor may increase awareness of the disease among clinicians and pathologists, thereby avoiding misdiagnosis and mistreatment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/MD.0000000000015053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6455993PMC
April 2019

Constructing a synthetic pathway for acetyl-coenzyme A from one-carbon through enzyme design.

Nat Commun 2019 03 26;10(1):1378. Epub 2019 Mar 26.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China.

Acetyl-CoA is a fundamental metabolite for all life on Earth, and is also a key starting point for the biosynthesis of a variety of industrial chemicals and natural products. Here we design and construct a Synthetic Acetyl-CoA (SACA) pathway by repurposing glycolaldehyde synthase and acetyl-phosphate synthase. First, we design and engineer glycolaldehyde synthase to improve catalytic activity more than 70-fold, to condense two molecules of formaldehyde into one glycolaldehyde. Second, we repurpose a phosphoketolase to convert glycolaldehyde into acetyl-phosphate. We demonstrated the feasibility of the SACA pathway in vitro, achieving a carbon yield ~50%, and confirmed the SACA pathway by C-labeled metabolites. Finally, the SACA pathway was verified by cell growth using glycolaldehyde, formaldehyde and methanol as supplemental carbon source. The SACA pathway is proved to be the shortest, ATP-independent, carbon-conserving and oxygen-insensitive pathway for acetyl-CoA biosynthesis, opening possibilities for producing acetyl-CoA-derived chemicals from one-carbon resources in the future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-019-09095-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6435721PMC
March 2019

Engineering the 5' UTR-Mediated Regulation of Protein Abundance in Yeast Using Nucleotide Sequence Activity Relationships.

ACS Synth Biol 2018 12 13;7(12):2709-2714. Epub 2018 Dec 13.

Key Laboratory of Systems Microbial Biotechnology , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308 , China.

The 5' untranslated region (5'UTR) plays a key role in post-transcriptional regulation, but interaction between nucleotides and directed evolution of 5'UTRs as synthetic regulatory elements remain unclear. By constructing a library of synthesized random 5'UTRs of 24 nucleotides in Saccharomyces cerevisiae, we observed strong epistatic interactions among bases from different positions in the 5'UTR. Taking into account these base interactions, we constructed a mathematical model to predict protein abundance with a precision of R = 0.60. On the basis of this model, we developed an approach to engineer 5'UTRs according to nucleotide sequence activity relationships (NuSAR), in which 5'UTRs were engineered stepwise through repeated cycles of backbone design, directed screening, and model reconstruction. After three rounds of NuSAR, the predictive accuracy of our model was improved to R = 0.71, and a strong 5'UTR was obtained with 5-fold higher protein abundance than the starting 5'UTR. Our findings provide new insights into the mechanism of 5'UTR regulation and  contribute to a new translational elements engineering approach in synthetic biology.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acssynbio.8b00127DOI Listing
December 2018

[Enzymatic synthesis of xylulose from formaldehyde].

Sheng Wu Gong Cheng Xue Bao 2018 Jul;34(7):1128-1136

Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Xylulose as a metabolic intermediate is the precursor of rare sugars, and its unique pattern of biological activity plays an important role in the fields of food, health, medicine and so on. The aim of this study was to design a new pathway for xylulose synthesis from formaldehyde, which is one of the most simple and basic organic substrate. The pathway was comprised of 3 steps: (1) formaldehyde was converted to glycolaldehyde by benzoylformate decarboxylase mutant BFD-M3 (from Pseudomonas putida); (2) formaldehyde and glycolaldehyde were converted to dihydroxyacetone by BFD-M3 as well; (3) glycolaldehyde and dihydroxyacetone were converted to xylulose by transaldolase mutant TalB-F178Y (from Escherichia coli). By adding formaldehyde (5 g/L), BFD-M3 and TalB-F178Y in one pot, xylulose was produced at a conversion rate of 0.4%. Through optimizing the concentration of formaldehyde, the conversion rate of xylulose was increased to 4.6% (20 g/L formaldehyde), which is 11.5 folds higher than the initial value. In order to further improve the xylulose conversion rate, we employed Scaffold Self-Assembly technique to co-immobilize BFD-M3 and TalB-F178Y. Finally, the xylulose conversion rate reached 14.02%. This study provides a new scheme for the biosynthesis of rare sugars.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.13345/j.cjb.170466DOI Listing
July 2018

Engineering yeast for the production of breviscapine by genomic analysis and synthetic biology approaches.

Nat Commun 2018 01 31;9(1):448. Epub 2018 Jan 31.

Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.

The flavonoid extract from Erigeron breviscapus, breviscapine, has increasingly been used to treat cardio- and cerebrovascular diseases in China for more than 30 years, and plant supply of E. breviscapus is becoming insufficient to satisfy the growing market demand. Here we report an alternative strategy for the supply of breviscapine by building a yeast cell factory using synthetic biology. We identify two key enzymes in the biosynthetic pathway (flavonoid-7-O-glucuronosyltransferase and flavone-6-hydroxylase) from E. breviscapus genome and engineer yeast to produce breviscapine from glucose. After metabolic engineering and optimization of fed-batch fermentation, scutellarin and apigenin-7-O-glucuronide, two major active ingredients of breviscapine, reach to 108 and 185 mg l, respectively. Our study not only introduces an alternative source of these valuable compounds, but also provides an example of integrating genomics and synthetic biology knowledge for metabolic engineering of natural compounds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-018-02883-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5792594PMC
January 2018

Parallel Evolution of Chromatin Structure Underlying Metabolic Adaptation.

Mol Biol Evol 2017 Nov;34(11):2870-2878

Division of Nutritional Sciences, Cornell University, Ithaca, NY.

Parallel evolution occurs when a similar trait emerges in independent evolutionary lineages. Although changes in protein coding and gene transcription have been investigated as underlying mechanisms for parallel evolution, parallel changes in chromatin structure have never been reported. Here, Saccharomyces cerevisiae and a distantly related yeast species, Dekkera bruxellensis, are investigated because both species have independently evolved the capacity of aerobic fermentation. By profiling and comparing genome sequences, transcriptomic landscapes, and chromatin structures, we revealed that parallel changes in nucleosome occupancy in the promoter regions of mitochondria-localized genes led to concerted suppression of mitochondrial functions by glucose, which can explain the metabolic convergence in these two independent yeast species. Further investigation indicated that similar mutational processes in the promoter regions of these genes in the two independent evolutionary lineages underlay the parallel changes in chromatin structure. Our results indicate that, despite several hundred million years of separation, parallel changes in chromatin structure, can be an important adaptation mechanism for different organisms. Due to the important role of chromatin structure changes in regulating gene expression and organism phenotypes, the novel mechanism revealed in this study could be a general phenomenon contributing to parallel adaptation in nature.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msx220DOI Listing
November 2017
-->