1
|
Bo X, Chen J, Mu J, Dong X, Ren Z, Liu J, Wang S. Quercetin promotes the secretion of musk by regulating the hormone level and microbial structure of forest musk deer. Integr Zool 2024; 19:596-611. [PMID: 37789560 DOI: 10.1111/1749-4877.12763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Musk is a scarce and precious medical resource secreted by male forest musk deer (FMD). Current research to promote musk secretion in FMD has used almost exclusively hormone injections, but this approach can be detrimental to the health of FMD. In order to conserve this endangered species as much as possible while increasing the production of musk, this study first used bioinformatics methods to predict the function of quercetin, a flavonoid that promotes testosterone (T) production and prevents late-onset male hypogonadism. On the basis of good prediction effect, different concentrations of quercetin were added to the diet of FMD. The results showed that quercetin could change the levels of T, luteinizing hormone releasing hormone, luteinizing hormone, and estradiol, and regulate the structure of intestinal microorganisms and musk microorganisms of FMD. Moreover, there is a correlation among musk components, hormones, intestinal microorganisms, and musk microorganisms, which indicates that the production of musk may be regulated by these three at the same time, and the addition of quercetin with 800 mg per kg diet could significantly increase the yield of muscone (P < 0.05), the most effective ingredient in musk. In addition, quercetin decreased the high level of cortisol during musk secretion, which may relieve the stress on FMD in this process. This may help to protect the health of FMD. Combined with the results of software prediction, we finally proposed a possible mechanism for the complex process of musk secretion in FMD with a view to providing ideas for further studies.
Collapse
Affiliation(s)
- Xinyu Bo
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Jialing Chen
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Jinzhan Mu
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Xianggui Dong
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Zhanjun Ren
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Jinyao Liu
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| |
Collapse
|
2
|
Steinhoff H, Finger M, Osthege M, Golze C, Schito S, Noack S, Büchs J, Grünberger A. Experimental k S estimation: A comparison of methods for Corynebacterium glutamicum from lab to microfluidic scale. Biotechnol Bioeng 2023; 120:1288-1302. [PMID: 36740737 DOI: 10.1002/bit.28345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/16/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
Knowledge about the specific affinity of whole cells toward a substrate, commonly referred to as kS , is a crucial parameter for characterizing growth within bioreactors. State-of-the-art methodologies measure either uptake or consumption rates at different initial substrate concentrations. Alternatively, cell dry weight or respiratory data like online oxygen and carbon dioxide transfer rates can be used to estimate kS . In this work, a recently developed substrate-limited microfluidic single-cell cultivation (sl-MSCC) method is applied for the estimation of kS values under defined environmental conditions. This method is benchmarked with two alternative microtiter plate methods, namely high-frequency biomass measurement (HFB) and substrate-limited respiratory activity monitoring (sl-RA). As a model system, the substrate affinity kS of Corynebacterium glutamicum ATCC 13032 regarding glucose was investigated assuming a Monod-type growth response. A kS of <70.7 mg/L (with 95% probability) with HFB, 8.55 ± 1.38 mg/L with sl-RA, and 2.66 ± 0.99 mg/L with sl-MSCC was obtained. Whereas HFB and sl-RA are suitable for a fast initial kS estimation, sl-MSCC allows an affinity estimation by determining tD at concentrations less or equal to the kS value. Thus, sl-MSCC lays the foundation for strain-specific kS estimations under defined environmental conditions with additional insights into cell-to-cell heterogeneity.
Collapse
Affiliation(s)
- Heiko Steinhoff
- Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Maurice Finger
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Michael Osthege
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.,Institute of Bio- and Geoscience, IBG-1: Biotechnology, Jülich, Germany
| | - Corinna Golze
- Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany
| | - Simone Schito
- Institute of Bio- and Geoscience, IBG-1: Biotechnology, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geoscience, IBG-1: Biotechnology, Jülich, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld, Germany.,Microsystems in Bioprocess Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| |
Collapse
|
3
|
Li H, Zhang J, Zhao Y, Yang W. Predicting Corynebacterium glutamicum promoters based on novel feature descriptor and feature selection technique. Front Microbiol 2023; 14:1141227. [PMID: 36937275 PMCID: PMC10018189 DOI: 10.3389/fmicb.2023.1141227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
The promoter is an important noncoding DNA regulatory element, which combines with RNA polymerase to activate the expression of downstream genes. In industry, artificial arginine is mainly synthesized by Corynebacterium glutamicum. Replication of specific promoter regions can increase arginine production. Therefore, it is necessary to accurately locate the promoter in C. glutamicum. In the wet experiment, promoter identification depends on sigma factors and DNA splicing technology, this is a laborious job. To quickly and conveniently identify the promoters in C. glutamicum, we have developed a method based on novel feature representation and feature selection to complete this task, describing the DNA sequences through statistical parameters of multiple physicochemical properties, filtering redundant features by combining analysis of variance and hierarchical clustering, the prediction accuracy of the which is as high as 91.6%, the sensitivity of 91.9% can effectively identify promoters, and the specificity of 91.2% can accurately identify non-promoters. In addition, our model can correctly identify 181 promoters and 174 non-promoters among 400 independent samples, which proves that the developed prediction model has excellent robustness.
Collapse
Affiliation(s)
- HongFei Li
- College of Life Science, Northeast Forestry University, Harbin, China
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Jingyu Zhang
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuming Zhao
- College of Life Science, Northeast Forestry University, Harbin, China
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
- *Correspondence: Yuming Zhao, ; Wen Yang,
| | - Wen Yang
- International Medical Center, Shenzhen University General Hospital, Shenzhen, China
- *Correspondence: Yuming Zhao, ; Wen Yang,
| |
Collapse
|
4
|
Lin K, Han S, Zheng S. Application of Corynebacterium glutamicum engineering display system in three generations of biorefinery. Microb Cell Fact 2022; 21:14. [PMID: 35090458 PMCID: PMC8796525 DOI: 10.1186/s12934-022-01741-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/09/2022] [Indexed: 11/29/2022] Open
Abstract
The fermentation production of platform chemicals in biorefineries is a sustainable alternative to the current petroleum refining process. The natural advantages of Corynebacterium glutamicum in carbon metabolism have led to C. glutamicum being used as a microbial cell factory that can use various biomass to produce value-added platform chemicals and polymers. In this review, we discussed the use of C. glutamicum surface display engineering bacteria in the three generations of biorefinery resources, and analyzed the C. glutamicum engineering display system in degradation, transport, and metabolic network reconstruction models. These engineering modifications show that the C. glutamicum engineering display system has great potential to become a cell refining factory based on sustainable biomass, and further optimizes the inherent properties of C. glutamicum as a whole-cell biocatalyst. This review will also provide a reference for the direction of future engineering transformation.
Collapse
Affiliation(s)
- Kerui Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
| |
Collapse
|
5
|
Advances in metabolic engineering of Corynebacterium glutamicum to produce high-value active ingredients for food, feed, human health, and well-being. Essays Biochem 2021; 65:197-212. [PMID: 34096577 PMCID: PMC8313993 DOI: 10.1042/ebc20200134] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022]
Abstract
The soil microbe Corynebacterium glutamicum is a leading workhorse in industrial biotechnology and has become famous for its power to synthetise amino acids and a range of bulk chemicals at high titre and yield. The product portfolio of the microbe is continuously expanding. Moreover, metabolically engineered strains of C. glutamicum produce more than 30 high value active ingredients, including signature molecules of raspberry, savoury, and orange flavours, sun blockers, anti-ageing sugars, and polymers for regenerative medicine. Herein, we highlight recent advances in engineering of the microbe into novel cell factories that overproduce these precious molecules from pioneering proofs-of-concept up to industrial productivity.
Collapse
|
6
|
Graf M, Haas T, Teleki A, Feith A, Cerff M, Wiechert W, Nöh K, Busche T, Kalinowski J, Takors R. Revisiting the Growth Modulon of Corynebacterium glutamicum Under Glucose Limited Chemostat Conditions. Front Bioeng Biotechnol 2020; 8:584614. [PMID: 33178676 PMCID: PMC7594717 DOI: 10.3389/fbioe.2020.584614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
Increasing the growth rate of the industrial host Corynebacterium glutamicum is a promising target to rise productivities of growth coupled product formation. As a prerequisite, detailed knowledge about the tight regulation network is necessary for identifying promising metabolic engineering goals. Here, we present comprehensive metabolic and transcriptional analysis of C. glutamicum ATCC 13032 growing under glucose limited chemostat conditions with μ = 0.2, 0.3, and 0.4 h–1. Intermediates of central metabolism mostly showed rising pool sizes with increasing growth. 13C-metabolic flux analysis (13C-MFA) underlined the fundamental role of central metabolism for the supply of precursors, redox, and energy equivalents. Global, growth-associated, concerted transcriptional patterns were not detected giving rise to the conclusion that glycolysis, pentose-phosphate pathway, and citric acid cycle are predominately metabolically controlled under glucose-limiting chemostat conditions. However, evidence is found that transcriptional regulation takes control over glycolysis once glucose-rich growth conditions are installed.
Collapse
Affiliation(s)
- Michaela Graf
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Thorsten Haas
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - André Feith
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Martin Cerff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| |
Collapse
|
7
|
Bowya T, Balachandar D. Rhizosphere engineering through exogenous growth-regulating small molecules improves the colonizing efficiency of a plant growth-promoting rhizobacterium in rice. 3 Biotech 2020; 10:277. [PMID: 32537377 DOI: 10.1007/s13205-020-02275-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/23/2020] [Indexed: 11/27/2022] Open
Abstract
Enhancing the rhizosphere colonization and persistence of plant growth-promoting rhizobacteria (PGPR) is necessary for maximizing PGPR-mediated benefits for crop growth and fitness in environmentally friendly agriculture. In the present investigation, we attempted manipulation of the rice rhizosphere by spraying of low molecular weight plant-regulating metabolites on the foliage of rice plants to in turn enhance the colonizing efficiency of soil-inoculated PGPR strain. The green fluorescent protein gene-tagged rhizobacterial strain, Pseudomonas chlororaphis ZSB15-M2, was inoculated in sterile plant growth medium (vermiculite coco peat mixture) and non-autoclaved agricultural soil. We sprayed different plant growth-regulating small molecules on the foliage of rice seedlings and monitored the colonizing efficiency of ZSB15-M2 in the rice rhizosphere. Among the chemicals assessed, salicylic acid (SA) at 1 mM or Corynebacterium glutamicum cell extract (CGCE, 0.2% w/v) or Saccharomyces cerevisiae cell extract (SCCE, 0.2% w/v) showed a tenfold increase in rhizosphere colony-forming units of ZSB15-M2 compared to control with a significant decline in non-rhizosphere bulk soil population. Foliar spray of CGCE enhanced soil organic carbon, microbial biomass carbon and soil protein by 21.86%, 9.68% and 11.57% respectively in the rice rhizosphere as compared to mock control. Additionally, CGCE spray enhanced the key soil enzymes, viz., dehydrogenase and acid- and alkaline phosphatase in the rhizosphere ranging 15-36%. The cumulative effect of this engineered rhizosphere resulted in the elevation of nitrogen, phosphorus, potassium and zinc availability by 21.83%, 28.83%, 23.95% and 61.94%, respectively, in rice rhizosphere as compared to control. On the other hand, SCCE and SA spray had an equal influence on the rhizosphere's biological attributes, which is lower than that of GCGE and higher than that of mock control. From the study, we propose that the aboveground management of rice with microbial-based small molecules will modulate the rice rhizosphere to attract more beneficial PGPR-based inoculants, thus improving the crop and soil health.
Collapse
Affiliation(s)
- Thangamuthu Bowya
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003 India
| |
Collapse
|
8
|
Graf M, Zieringer J, Haas T, Nieß A, Blombach B, Takors R. Physiological Response of Corynebacterium glutamicum to Increasingly Nutrient-Rich Growth Conditions. Front Microbiol 2018; 9:2058. [PMID: 30210489 PMCID: PMC6123352 DOI: 10.3389/fmicb.2018.02058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/13/2018] [Indexed: 01/31/2023] Open
Abstract
To ensure economic competitiveness, bioprocesses should achieve maximum productivities enabled by high growth rates (μ) and equally high substrate consumption rates (qS) as a prerequisite of sufficient carbon-to-product conversion. Both traits were investigated and improved via bioprocess engineering approaches studying the industrial work horse Corynebacterium glutamicum. Standard minimal medium CGXII with glucose as sole carbon source was supplemented with complex brain-heart-infusion (BHI) or amino acid (AA) cocktails. Maximum μ of 0.67 h-1 was exclusively observed in 37 g BHI L-1 whereas only minor growth stimulation was found after AA supplementation (μ = 0.468 h-1). Increasing glucose consumption rates (qGlc) were solely observed in certain dosages of BHI (1-10 g L-1), while 37 g BHI L-1 and AA addition revealed qGlc below the reference experiments. Moreover, BHI supplementation revealed Monod-type saturation kinetics of μ (KBHI = 2.73 g BHI L-1) referring to the preference of non-AAs as key boosting nutrients. ATP-demands under reference, 1 g BHI L-1, and AA conditions were nearly constant but halved in BHI concentrations above 5 g L-1 reflecting the energetic advantage of consuming complex nutrient components in addition to "simple" building blocks such as AAs. Furthermore, C. glutamicum revealed maximum biomass per carbon yields of about 18 gCDW C-mol-1 irrespective of the medium. In AA supplementation experiments, simultaneous uptake of 17 AAs was observed, maximum individual consumption rates determined, and L-asparagine and L-glutamine were distinguished as compounds with the highest consumption rates. Employment of the expanded stoichiometric model iMG481 successfully reproduced experimental results and revealed the importance of C. glutamicum's transaminase network to compensate needs of limiting AA supply. Model-based sensitivity studies attributed the highest impact on μ to AAs with high ATP and NADPH demands such as L-tryptophan or L-phenylalanine.
Collapse
Affiliation(s)
| | | | | | | | | | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| |
Collapse
|
9
|
Kitade Y, Hashimoto R, Suda M, Hiraga K, Inui M. Production of 4-Hydroxybenzoic Acid by an Aerobic Growth-Arrested Bioprocess Using Metabolically Engineered Corynebacterium glutamicum. Appl Environ Microbiol 2018; 84:e02587-17. [PMID: 29305513 PMCID: PMC5835730 DOI: 10.1128/aem.02587-17] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/14/2017] [Indexed: 12/22/2022] Open
Abstract
Corynebacterium glutamicum was metabolically engineered to produce 4-hydroxybenzoic acid (4-HBA), a valuable aromatic compound used as a raw material for the production of liquid crystal polymers and paraben. C. glutamicum was found to have a higher tolerance to 4-HBA toxicity than previously reported hosts used for the production of genetically engineered 4-HBA. To obtain higher titers of 4-HBA, we employed a stepwise overexpression of all seven target genes in the shikimate pathway in C. glutamicum Specifically, multiple chromosomal integrations of a mutated aroG gene from Escherichia coli, encoding a 3-deoxy-d-arabinoheptulosonic acid 7-phosphate (DAHP) synthase, and wild-type aroCKB from C. glutamicum, encoding chorismate synthase, shikimate kinase, and 3-dehydroquinate synthase, were effective in increasing product titers. The last step of the 4-HBA biosynthesis pathway was recreated in C. glutamicum by expressing a highly 4-HBA-resistant chorismate pyruvate-lyase (UbiC) from the intestinal bacterium Providencia rustigianii To enhance the yield of 4-HBA, we reduced the formation of by-products, such as 1,3-dihydroxyacetone and pyruvate, by deleting hdpA, a gene coding for a haloacid dehalogenase superfamily phosphatase, and pyk, a gene coding for a pyruvate kinase, from the bacterial chromosome. The maximum concentration of 4-HBA produced by the resultant strain was 36.6 g/liter, with a yield of 41% (mol/mol) glucose after incubation for 24 h in minimal medium in an aerobic growth-arrested bioprocess using a jar fermentor. To our knowledge, this is the highest concentration of 4-HBA produced by a metabolically engineered microorganism ever reported.IMPORTANCE Since aromatic compound 4-HBA has been chemically produced from petroleum-derived phenol for a long time, eco-friendly bioproduction of 4-HBA from biomass resources is desired in order to address environmental issues. In microbial chemical production, product toxicity often causes problems, but we confirmed that wild-type C. glutamicum has high tolerance to the target 4-HBA. A growth-arrested bioprocess using this microorganism has been successfully used for the production of various compounds, such as biofuels, organic acids, and amino acids. However, no production method has been applied for aromatic compounds to date. In this study, we screened for a novel final reaction enzyme possessing characteristics superior to those in previously employed microbial 4-HBA production. We demonstrated that the use of the highly 4-HBA-resistant UbiC from the intestinal bacterium P. rustigianii is very effective in increasing 4-HBA production.
Collapse
Affiliation(s)
- Yukihiro Kitade
- Molecular Microbiology and Biotechnology Group, Research Institute of Innovative Technology for the Earth (RITE), Kizugawa, Kyoto, Japan
- Green Phenol Development Co., Ltd., Kizugawa, Kyoto, Japan
| | | | - Masako Suda
- Molecular Microbiology and Biotechnology Group, Research Institute of Innovative Technology for the Earth (RITE), Kizugawa, Kyoto, Japan
- Green Phenol Development Co., Ltd., Kizugawa, Kyoto, Japan
| | - Kazumi Hiraga
- Molecular Microbiology and Biotechnology Group, Research Institute of Innovative Technology for the Earth (RITE), Kizugawa, Kyoto, Japan
- Green Phenol Development Co., Ltd., Kizugawa, Kyoto, Japan
| | - Masayuki Inui
- Molecular Microbiology and Biotechnology Group, Research Institute of Innovative Technology for the Earth (RITE), Kizugawa, Kyoto, Japan
- Green Phenol Development Co., Ltd., Kizugawa, Kyoto, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| |
Collapse
|
10
|
Vertès AA. Methods and practices to diversify cell-based products. Regen Med 2017; 12:997-1013. [PMID: 29243940 DOI: 10.2217/rme-2017-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Medicinal signaling cell (MSC)-based products represent emerging treatments in various therapeutic areas including cardiometabolic, inflammation, autoimmunity, orthopedics, wound healing and oncology. Exploring innovation beyond minimally manipulated plastic-adherent ex vivo expanded allogeneic MSCs enables product delineation. Product delineation is on the critical path to maximize clinical benefits and market access. An innovation framework is presented here along various innovation dimensions comprising composition-of-matter by means of positive cell surface markers, formulation varying for example the cell dose or the preservation mode and medium, manufacturing to adapt the secretome of MSCs to the condition of interest, the mode of delivery and corresponding delivery devices, as well as molecular engineering and biomarkers. The rationale of the innovation space thus described applies generally to all cell-based therapies.
Collapse
Affiliation(s)
- Alain A Vertès
- London Business School, UK & NxR Biotechnologies GmbH, Basel, Switzerland
| |
Collapse
|
11
|
Yang J, Yang S. Comparative analysis of Corynebacterium glutamicum genomes: a new perspective for the industrial production of amino acids. BMC Genomics 2017; 18:940. [PMID: 28198668 PMCID: PMC5310272 DOI: 10.1186/s12864-016-3255-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Corynebacterium glutamicum is a non-pathogenic bacterium widely used in industrial amino acid production and metabolic engineering research. Although the genome sequences of some C. glutamicum strains are available, comprehensive comparative genome analyses of these species have not been done. Six wild type C. glutamicum strains were sequenced using next-generation sequencing technology in our study. Together with 20 previously reported strains, we present a comprehensive comparative analysis of C. glutamicum genomes. Results By average nucleotide identity (ANI) analysis, we show that 10 strains, which were previously classified either in the genus Brevibacterium, or as some other species within the genus Corynebacterium, should be reclassified as members of the species C. glutamicum. C. glutamicum has an open pan-genome with 2359 core genes. An additional NAD+/NADP+ specific glutamate dehydrogenase (GDH) gene (gdh) was identified in the glutamate synthesis pathway of some C. glutamicum strains. For analyzing variations related to amino acid production, we have developed an efficient pipeline that includes three major steps: multi locus sequence typing (MLST), phylogenomic analysis based on single nucleotide polymorphisms (SNPs), and a thorough comparison of all genomic variation amongst ancestral or closely related wild type strains. This combined approach can provide new perspectives on the industrial use of C. glutamicum. Conclusions This is the first comprehensive comparative analysis of C. glutamicum genomes at the pan-genomic level. Whole genome comparison provides definitive evidence for classifying the members of this species. Identifying an aditional gdh gene in some C. glutamicum strains may accelerate further research on glutamate synthesis. Our proposed pipeline can provide a clear perspective, including the presumed ancestor, the strain breeding trajectory, and the genomic variations necessary to increase amino acid production in C. glutamicum. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3255-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Junjie Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.,Shanghai Research Center of Industrial Biotechnology, Shanghai, 201201, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, 211816, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China. .,Shanghai Research Center of Industrial Biotechnology, Shanghai, 201201, China. .,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, 211816, China.
| |
Collapse
|
12
|
Hasunuma T, Kondo A. Production of Fuels and Chemicals from Biomass by Integrated Bioprocesses. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Tomohisa Hasunuma
- Kobe University; Graduate School of Science, Technology and Innovation; 1-1 Rokkodai Nada Kobe 657-8501 Japan
| | - Akihiko Kondo
- RIKEN; Biomass Engineering Program; 1-7-22 Suehiro-cho, Tsurumi Yokohama 230-0045 Japan
| |
Collapse
|
13
|
Guo W, Chen Z, Zhang X, Xu G, Zhang X, Shi J, Xu Z. A novel aceE mutation leading to a better growth profile and a higher l-serine production in a high-yield l-serine-producing Corynebacterium glutamicum strain. ACTA ACUST UNITED AC 2016; 43:1293-301. [DOI: 10.1007/s10295-016-1801-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022]
Abstract
Abstract
A comparative genomic analysis was performed to study the genetic variations between the l-serine-producing strain Corynebacterium glutamicum SYPS-062 and the mutant strain SYPS-062-33a, which was derived from SYPS-062 by random mutagenesis with enhanced l-serine production. Some variant genes between the two strains were reversely mutated or deleted in the genome of SYPS-062-33a to verify the influences of the gene mutations introduced by random mutagenesis. It was found that a His-594 → Tyr mutation in aceE was responsible for the more accumulation of by-products, such as l-alanine and l-valine, in SYPS-062-33a. Furthermore, the influence of this point mutation on the l-serine production was investigated, and the results suggested that this point mutation led to a better growth profile and a higher l-serine production in the high-yield strain 33a∆SSAAI, which was derived from SYPS-062-33a by metabolic engineering with the highest l-serine production to date.
Collapse
Affiliation(s)
- Wen Guo
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi People’s Republic of China
| | - Ziwei Chen
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi People’s Republic of China
| | - Xiaomei Zhang
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi People’s Republic of China
| | - Guoqiang Xu
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University 214122 Wuxi People’s Republic of China
| | - Xiaojuan Zhang
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
| | - Jinsong Shi
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi People’s Republic of China
| | - Zhenghong Xu
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi People’s Republic of China
| |
Collapse
|
14
|
Shah A, Eikmanns BJ. Transcriptional Regulation of the β-Type Carbonic Anhydrase Gene bca by RamA in Corynebacterium glutamicum. PLoS One 2016; 11:e0154382. [PMID: 27119954 PMCID: PMC4847777 DOI: 10.1371/journal.pone.0154382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/12/2016] [Indexed: 11/25/2022] Open
Abstract
Carbonic anhydrase catalyzes the reversible hydration of carbon dioxide to bicarbonate and maintains the balance of CO2/HCO3- in the intracellular environment, specifically for carboxylation/decarboxylation reactions. In Corynebacterium glutamicum, two putative genes, namely the bca (cg2954) and gca (cg0155) genes, coding for β-type and γ-type carbonic anhydrase, respectively, have been identified. We here analyze the transcriptional organization of these genes. The transcriptional start site (TSS) of the bca gene was shown to be the first nucleotide "A" of its putative translational start codon (ATG) and thus, bca codes for a leaderless transcript. The TSS of the gca gene was identified as an "A" residue located at position -20 relative to the first nucleotide of the annotated translational start codon of the cg0154 gene, which is located immediately upstream of gca. Comparative expression analysis revealed carbon source-dependent regulation of the bca gene, with 1.5- to 2-fold lower promoter activity in cells grown on acetate as compared to glucose as sole carbon source. Based on higher expression of bca in a mutant deficient of the regulator of acetate metabolism RamA as compared to the wild-type of C. glutamicum and based on the binding of His-tagged RamA protein to the bca promoter region, we here present evidence that RamA negatively regulates expression of bca in C. glutamicum. Functional characterization of a gca deletion mutant of C. glutamicum revealed the same growth characteristics of C. glutamicum ∆gca as that of wild-type C. glutamicum and no effect on expression of the bca gene.
Collapse
Affiliation(s)
- Adnan Shah
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| | - Bernhard J. Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069 Ulm, Germany
| |
Collapse
|
15
|
Yamamoto K, Tsuchisaka A, Yukawa H. Branched-Chain Amino Acids. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 159:103-128. [PMID: 27872960 DOI: 10.1007/10_2016_28] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Branched-chain amino acids (BCAAs), viz., L-isoleucine, L-leucine, and L-valine, are essential amino acids that cannot be synthesized in higher organisms and are important nutrition for humans as well as livestock. They are also valued as synthetic intermediates for pharmaceuticals. Therefore, the demand for BCAAs in the feed and pharmaceutical industries is increasing continuously. Traditional industrial fermentative production of BCAAs was performed using microorganisms isolated by random mutagenesis. A collection of these classical strains was also scientifically useful to clarify the details of the BCAA biosynthetic pathways, which are tightly regulated by feedback inhibition and transcriptional attenuation. Based on this understanding of the metabolism of BCAAs, it is now possible for us to pursue strains with higher BCAA productivity using rational design and advanced molecular biology techniques. Additionally, systems biology approaches using augmented omics information help us to optimize carbon flux toward BCAA production. Here, we describe the biosynthetic pathways of BCAAs and their regulation and then overview the microorganisms developed for BCAA production. Other chemicals, including isobutanol, i.e., a second-generation biofuel, can be synthesized by branching the BCAA biosynthetic pathways, which are also outlined.
Collapse
Affiliation(s)
- Keisuke Yamamoto
- Green Earth Institute Co., Ltd, Hongo, Tokyo, Japan
- Green Earth Research Center, Kisarazu, Chiba, Japan
| | - Atsunari Tsuchisaka
- Green Earth Institute Co., Ltd, Hongo, Tokyo, Japan
- Green Earth Research Center, Kisarazu, Chiba, Japan
| | - Hideaki Yukawa
- Green Earth Institute Co., Ltd, Hongo, Tokyo, Japan.
- Green Earth Research Center, Kisarazu, Chiba, Japan.
| |
Collapse
|
16
|
Rider SD, Morgan MS, Arlian LG. Draft genome of the scabies mite. Parasit Vectors 2015; 8:585. [PMID: 26555130 PMCID: PMC4641413 DOI: 10.1186/s13071-015-1198-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/05/2015] [Indexed: 12/11/2022] Open
Abstract
Background The disease scabies, caused by the ectoparasitic mite, Sarcoptes scabiei, causes significant morbidity in humans and other mammals worldwide. However, there is limited data available regarding the molecular basis of host specificity and host-parasite interactions. Therefore, we sought to produce a draft genome for S. scabiei and use this to identify molecular markers that will be useful for phylogenetic population studies and to identify candidate protein-coding genes that are critical to the unique biology of the parasite. Methods S. scabiei var. canis DNA was isolated from living mites and sequenced to ultra-deep coverage using paired-end technology. Sequence reads were assembled into gapped contigs using de Bruijn graph based algorithms. The assembled genome was examined for repetitive elements and gene annotation was performed using ab initio, and homology-based methods. Results The draft genome assembly was about 56.2 Mb and included a mitochondrial genome contig. The predicted proteome contained 10,644 proteins, ~67 % of which appear to have clear orthologs in other species. The genome also contained more than 140,000 simple sequence repeat loci that may be useful for population-level studies. The mitochondrial genome contained 13 protein coding loci and 20 transfer RNAs. Hundreds of candidate salivary gland protein genes were identified by comparing the scabies mite predicted proteome with sialoproteins and transcripts identified in ticks and other hematophagous arthropods. These include serpins, ferritins, reprolysins, apyrases and new members of the macrophage migration inhibitory factor (MIF) gene family. Numerous other genes coding for salivary proteins, metabolic enzymes, structural proteins, proteins that are potentially immune modulating, and vaccine candidates were identified. The genes encoding cysteine and serine protease paralogs as well as mu-type glutathione S-transferases are represented by gene clusters. S. scabiei possessed homologs for most of the 33 dust mite allergens. Conclusion The draft genome is useful for advancing our understanding of the host-parasite interaction, the biology of the mite and its phylogenetic relationship to other Acari. The identification of antigen-producing genes, candidate immune modulating proteins and pathways, and genes responsible for acaricide resistance offers opportunities for developing new methods for diagnosing, treating and preventing this disease. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-1198-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- S Dean Rider
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA.
| | - Marjorie S Morgan
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA.
| | - Larry G Arlian
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH, 45435, USA.
| |
Collapse
|
17
|
Toyoda K, Inui M. Regulons of global transcription factors in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2015; 100:45-60. [DOI: 10.1007/s00253-015-7074-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/03/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
|
18
|
Unthan S, Baumgart M, Radek A, Herbst M, Siebert D, Brühl N, Bartsch A, Bott M, Wiechert W, Marin K, Hans S, Krämer R, Seibold G, Frunzke J, Kalinowski J, Rückert C, Wendisch VF, Noack S. Chassis organism from Corynebacterium glutamicum--a top-down approach to identify and delete irrelevant gene clusters. Biotechnol J 2015; 10:290-301. [PMID: 25139579 PMCID: PMC4361050 DOI: 10.1002/biot.201400041] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/25/2014] [Accepted: 08/19/2014] [Indexed: 01/05/2023]
Abstract
For synthetic biology applications, a robust structural basis is required, which can be constructed either from scratch or in a top-down approach starting from any existing organism. In this study, we initiated the top-down construction of a chassis organism from Corynebacterium glutamicum ATCC 13032, aiming for the relevant gene set to maintain its fast growth on defined medium. We evaluated each native gene for its essentiality considering expression levels, phylogenetic conservation, and knockout data. Based on this classification, we determined 41 gene clusters ranging from 3.7 to 49.7 kbp as target sites for deletion. 36 deletions were successful and 10 genome-reduced strains showed impaired growth rates, indicating that genes were hit, which are relevant to maintain biological fitness at wild-type level. In contrast, 26 deleted clusters were found to include exclusively irrelevant genes for growth on defined medium. A combinatory deletion of all irrelevant gene clusters would, in a prophage-free strain, decrease the size of the native genome by about 722 kbp (22%) to 2561 kbp. Finally, five combinatory deletions of irrelevant gene clusters were investigated. The study introduces the novel concept of relevant genes and demonstrates general strategies to construct a chassis suitable for biotechnological application.
Collapse
Affiliation(s)
- Simon Unthan
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Andreas Radek
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Marius Herbst
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Daniel Siebert
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Natalie Brühl
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Anna Bartsch
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Kay Marin
- Evonik Degussa GmbHHalle/Westphalia, Germany
| | | | - Reinhard Krämer
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Gerd Seibold
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld UniversityBielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld UniversityBielefeld, Germany
| | - Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| |
Collapse
|
19
|
Eikmanns BJ, Blombach B. The pyruvate dehydrogenase complex of Corynebacterium glutamicum: an attractive target for metabolic engineering. J Biotechnol 2014; 192 Pt B:339-45. [PMID: 24486441 DOI: 10.1016/j.jbiotec.2013.12.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/12/2013] [Accepted: 12/16/2013] [Indexed: 11/18/2022]
Abstract
The pyruvate dehydrogenase complex (PDHC) catalyzes the oxidative thiamine pyrophosphate-dependent decarboxylation of pyruvate to acetyl-CoA and CO2. Since pyruvate is a key metabolite of the central metabolism and also the precursor for several relevant biotechnological products, metabolic engineering of this multienzyme complex is a promising strategy to improve microbial production processes. This review summarizes the current knowledge and achievements on metabolic engineering approaches to tailor the PDHC of Corynebacterium glutamicum for the bio-based production of l-valine, 2-ketosiovalerate, pyruvate, succinate and isobutanol and to improve l-lysine production.
Collapse
Affiliation(s)
- Bernhard J Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, 89069 Ulm, Germany
| | - Bastian Blombach
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany.
| |
Collapse
|
20
|
Hasunuma T, Okazaki F, Okai N, Hara KY, Ishii J, Kondo A. A review of enzymes and microbes for lignocellulosic biorefinery and the possibility of their application to consolidated bioprocessing technology. BIORESOURCE TECHNOLOGY 2013. [PMID: 23195654 DOI: 10.1016/j.biortech.2012.10.047] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The biorefinery manufacturing process for producing chemicals and liquid fuels from biomass is a promising approach for securing energy and resources. To establish cost-effective fermentation of lignocellulosic biomass, the consolidation of sacccharification and fermentation processes is a desirable strategy, but requires the development of microorganisms capable of cellulose/hemicellulose hydrolysis and target chemical production. Such an endeavor requires a large number of prerequisites to be realized, including engineering microbial strains with high cellulolytic activity, high product yield, productivities, and titers, ability to use many carbon sources, and resistance to toxic compounds released during the pretreatment of lignocellulosic biomass. Researchers have focused on either engineering naturally cellulolytic microorganisms to improve product-related properties or modifying non-cellulolytic organisms with high product yields to become cellulolytic. This article reviews recent advances in the development of microorganisms for the production of renewable chemicals and advanced biofuels, as well as ethanol, from lignocellulosic materials through consolidated bioprocessing.
Collapse
Affiliation(s)
- Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | | | | | | | | | | |
Collapse
|
21
|
Vasco-Cárdenas MF, Baños S, Ramos A, Martín JF, Barreiro C. Proteome response of Corynebacterium glutamicum to high concentration of industrially relevant C₄ and C₅ dicarboxylic acids. J Proteomics 2013; 85:65-88. [PMID: 23624027 DOI: 10.1016/j.jprot.2013.04.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 03/05/2013] [Accepted: 04/09/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED More than fifty years of industrial and scientific developments on the amino acid-producer strain Corynebacterium glutamicum has generated an extremely huge knowledge highly applicable to the development of new products. Despite the production of dicarboxylic acids has already been engineered in C. glutamicum, the effect caused by these acids at competitive industrial levels has not yet been described. Thus, aspartic, fumaric, itaconic, malic and succinic acids have been tested on the growth of C. glutamicum to obtain their minimal inhibitory concentrations and their intracellular effects analyzed by 2D-DIGE. This analysis showed the modification of the central metabolism of C. glutamicum, the cross-regulation between malic acid and glucose as well as the aspartic acid utilization as nitrogen source. The analysis of the transcriptional regulators involved in the control of the detected proteins pointed to the ramB gene as a candidate for strain improvement. The analysis of the ΔramB mutant demonstrated its function as an enhancer of the growth speed or resistance level against aspartic, fumaric, itaconic and malic acids in C. glutamicum. BIOLOGICAL SIGNIFICANCE The effect of dicarboxylic acids addition to the C. glutamicum culture broth has been described. This proteome response is detailed and the deletion of a global regulator (ramB) has been described as a possible improving method for industrial strains. In addition, the consumption of aspartic acid as nitrogen source has been described for the first time in C. glutamicum, as well as, the cross-regulation between malic acid and glucose through the F0F1 respiratory system.
Collapse
Affiliation(s)
- María F Vasco-Cárdenas
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | | | | | | | | |
Collapse
|
22
|
Stes E, Francis I, Pertry I, Dolzblasz A, Depuydt S, Vereecke D. The leafy gall syndrome induced byRhodococcus fascians. FEMS Microbiol Lett 2013; 342:187-94. [DOI: 10.1111/1574-6968.12119] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 12/20/2022] Open
Affiliation(s)
- Elisabeth Stes
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Gent; Belgium
| | - Isolde Francis
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Gent; Belgium
| | - Ine Pertry
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Gent; Belgium
| | - Alicja Dolzblasz
- Institute of Experimental Biology; Department of Plant Developmental Biology; Wrocław University; Wrocław; Poland
| | | | - Danny Vereecke
- Department of Plant Production; University College Ghent; Ghent University; Gent; Belgium
| |
Collapse
|
23
|
Cell envelope of corynebacteria: structure and influence on pathogenicity. ISRN MICROBIOLOGY 2013; 2013:935736. [PMID: 23724339 PMCID: PMC3658426 DOI: 10.1155/2013/935736] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 12/31/2012] [Indexed: 11/18/2022]
Abstract
To date the genus Corynebacterium comprises 88 species. More than half of these are connected to human and animal infections, with the most prominent member of the pathogenic species being Corynebacterium diphtheriae, which is also the type species of the genus. Corynebacterium species are characterized by a complex cell wall architecture: the plasma membrane of these bacteria is followed by a peptidoglycan layer, which itself is covalently linked to a polymer of arabinogalactan. Bound to this, an outer layer of mycolic acids is found which is functionally equivalent to the outer membrane of Gram-negative bacteria. As final layer, free polysaccharides, glycolipids, and proteins are found. The composition of the different substructures of the corynebacterial cell envelope and their influence on pathogenicity are discussed in this paper.
Collapse
|
24
|
Pátek M, Holátko J, Busche T, Kalinowski J, Nešvera J. Corynebacterium glutamicum promoters: a practical approach. Microb Biotechnol 2013; 6:103-17. [PMID: 23305350 PMCID: PMC3917453 DOI: 10.1111/1751-7915.12019] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/05/2012] [Accepted: 11/08/2012] [Indexed: 11/27/2022] Open
Abstract
Transcription initiation is the key step in gene expression in bacteria, and it is therefore studied for both theoretical and practical reasons. Promoters, the traffic lights of transcription initiation, are used as construction elements in biotechnological efforts to coordinate ‘green waves’ in the metabolic pathways leading to the desired metabolites. Detailed analyses of Corynebacterium glutamicum promoters have already provided large amounts of data on their structures, regulatory mechanisms and practical capabilities in metabolic engineering. In this minireview the main aspects of promoter studies, the methods developed for their analysis and their practical use in C. glutamicum are discussed. These include definitions of the consensus sequences of the distinct promoter classes, promoter localization and characterization, activity measurements, the functions of transcriptional regulators and examples of practical uses of constitutive, inducible and modified promoters in biotechnology. The implications of the introduction of novel techniques, such as in vitro transcription and RNA sequencing, to C. glutamicum promoter studies are outlined.
Collapse
Affiliation(s)
- Miroslav Pátek
- Institute of Microbiology AS CR, vvi, Prague 4, Czech Republic.
| | | | | | | | | |
Collapse
|
25
|
Wieschalka S, Blombach B, Bott M, Eikmanns BJ. Bio-based production of organic acids with Corynebacterium glutamicum. Microb Biotechnol 2012. [PMID: 23199277 PMCID: PMC3917452 DOI: 10.1111/1751-7915.12013] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The shortage of oil resources, the steadily rising oil prices and the impact of its use on the environment evokes an increasing political, industrial and technical interest for development of safe and efficient processes for the production of chemicals from renewable biomass. Thus, microbial fermentation of renewable feedstocks found its way in white biotechnology, complementing more and more traditional crude oil-based chemical processes. Rational strain design of appropriate microorganisms has become possible due to steadily increasing knowledge on metabolism and pathway regulation of industrially relevant organisms and, aside from process engineering and optimization, has an outstanding impact on improving the performance of such hosts. Corynebacterium glutamicum is well known as workhorse for the industrial production of numerous amino acids. However, recent studies also explored the usefulness of this organism for the production of several organic acids and great efforts have been made for improvement of the performance. This review summarizes the current knowledge and recent achievements on metabolic engineering approaches to tailor C. glutamicum for the bio-based production of organic acids. We focus here on the fermentative production of pyruvate, L- and D-lactate, 2-ketoisovalerate, 2-ketoglutarate, and succinate. These organic acids represent a class of compounds with manifold application ranges, e.g. in pharmaceutical and cosmetics industry, as food additives, and economically very interesting, as precursors for a variety of bulk chemicals and commercially important polymers.
Collapse
Affiliation(s)
- Stefan Wieschalka
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | | | | | | |
Collapse
|