1
|
Wu Y, Lei S, Lu C, Li J, Du G, Liu Y. Enhanced Ribonucleic Acid Production by High-Throughput Screening Based on Fluorescence Activation and Transcriptomic-Guided Fermentation Optimization in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6673-6680. [PMID: 37071119 DOI: 10.1021/acs.jafc.3c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Currently, the primary source of ribonucleic acids (RNAs), which is used as a flavor enhancer and nutritional supplement in the food manufacturing and processing industries, for large-scale industrial production is yeast, where the challenge is to optimize the cellular RNA content. Here, we developed and screened yeast strains yielding abundant RNAs via various methods. The novel Saccharomyces cerevisiae strain H1 with a 45.1% higher cellular RNA content than its FX-2 parent was successfully generated. Comparative transcriptomic analysis elucidated the molecular mechanisms underlying RNA accumulation in H1. Upregulation of genes encoding the hexose monophosphate and sulfur-containing amino acid biosynthesis pathways promoted RNA accumulation in the yeast, particularly in the presence of glucose as the sole carbon source. Feeding methionine into the bioreactor resulted in 145.2 mg/g dry cell weight and 9.6 g/L of cellular RNA content, which is the highest volumetric productivity of RNAs achieved in S. cerevisiae. This strategy of breeding S. cerevisiae strain with a higher capacity of accumulating abundant RNAs did not employ any genetic modification and thus will be favored by the food industry.
Collapse
Affiliation(s)
- Yexu Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Angel Yeast Co. Ltd., Chengdong Avenue 168, Yichang 443003, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Senlin Lei
- Angel Yeast Co. Ltd., Chengdong Avenue 168, Yichang 443003, China
| | - Chuanchuan Lu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
2
|
Blaabjerg K, Nørgaard JV, Nielsen B, Cantor MD, Derkx P, Sehested J, Poulsen HD. Transport of valine across the small intestinal epithelium in pigs fed different valine levels and Bacillus subtilis. J Anim Physiol Anim Nutr (Berl) 2017; 102:e856-e863. [PMID: 29193328 DOI: 10.1111/jpn.12846] [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: 03/27/2017] [Accepted: 11/05/2017] [Indexed: 11/29/2022]
Abstract
Mutants of Bacillus subtilis overproducing valine (B. subtilis VAL) could be an approach to supply pigs dietary valine (Val). In the study, 18 gilts were fed: (i) negative diet with a standardized ileal digestible (SID) Val:Lys of 0.63:1 (Neg); (ii) Neg added B. subtilis VAL (1.28 × 1011 cfu/kg as-fed) or; (iii) Neg added L-Val to a Val:Lys of 0.69:1. Using the Ussing chamber method, the study aimed to investigate whether (i) the diets affect intestinal transport of additions of 0, 5, 10 or 20 mmol Val/L from the mucosal to the serosal side and (ii) the B. subtilis VAL contributes to a net transport of Val produced in situ. The results showed that the Isc (ΔIscVal ) and release of Val to the serosal side solution (Srel ; μmol cm-2 min-1 ) increased with Val addition (linear and quadratic, p < .0001) but was similar for 5, 10 or 20 mmol Val/L and not affected by diet. No net transport of in situ produced Val by B. subtilis VAL was detected. In conclusion, feeding a Val-deficient diet with or without B. subtilis VAL or a Val sufficient diet did not affect the Val transport across intestinal epithelia. No in situ Val production by B. subtilis VAL was observed in the Ussing chambers.
Collapse
Affiliation(s)
- K Blaabjerg
- Department of Animal Science, Aarhus University, Foulum, Tjele, Denmark
| | - J V Nørgaard
- Department of Animal Science, Aarhus University, Foulum, Tjele, Denmark
| | | | | | - P Derkx
- Chr. Hansen A/S, Hørsholm, Denmark
| | - J Sehested
- Department of Animal Science, Aarhus University, Foulum, Tjele, Denmark
| | - H D Poulsen
- Department of Animal Science, Aarhus University, Foulum, Tjele, Denmark
| |
Collapse
|
3
|
Abstract
Mutants of Bacillus subtilis can be developed to overproduce Val in vitro. It was hypothesized that addition of Bacillus subtilis mutants to pig diets can be a strategy to supply the animal with Val. The objective was to investigate the effect of Bacillus subtilis mutants on growth performance and blood amino acid (AA) concentrations when fed to piglets. Experiment 1 included 18 pigs (15.0±1.1 kg) fed one of three diets containing either 0.63 or 0.69 standardized ileal digestible (SID) Val : Lys, or 0.63 SID Val : Lys supplemented with a Bacillus subtilis mutant (mutant 1). Blood samples were obtained 0.5 h before feeding and at 1, 2, 3, 4, 5 and 6 h after feeding and analyzed for AAs. In Experiment 2, 80 piglets (9.1±1.1 kg) were fed one of four diets containing 0.63 or 0.67 SID Val : Lys, or 0.63 SID Val : Lys supplemented with another Bacillus subtilis mutant (mutant 2) or its parent wild type. Average daily feed intake, daily weight gain and feed conversion ratio were measured on days 7, 14 and 21. On day 17, blood samples were taken and analyzed for AAs. On days 24 to 26, six pigs from each dietary treatment were fitted with a permanent jugular vein catheter, and blood samples were taken for AA analysis 0.5 h before feeding and at 1, 2, 3, 4, 5 and 6 h after feeding. In experiment 1, Bacillus subtilis mutant 1 tended (P<0.10) to increase the plasma levels of Val at 2 and 3 h post-feeding, but this was not confirmed in Experiment 2. In Experiment 2, Bacillus subtilis mutant 2 and the wild type did not result in a growth performance different from the negative and positive controls. In conclusion, results obtained with the mutant strains of Bacillus subtilis were not better than results obtained with the wild-type strain, and for both strains, the results were not different than the negative control.
Collapse
|
4
|
Canibe N, Poulsen HV, Nørgaard JV, Nielsen B, Cantor MD, Derkx P, Poulsen HD, Blaabjerg K, Jensens BB. Growth of and valine production by a Bacillus subtilis mutant in the small intestine of pigs1. J Anim Sci 2016. [DOI: 10.2527/jas.2015-9813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
5
|
Torres-Pitarch A, Nielsen B, Canibe N, Jensen BB, Derkx P, Cantor MD, Blaabjerg K, Poulsen HD, Nørgaard JV. Tryptophan provision by dietary supplementation of a Bacillus subtilismutant strain in piglets. ACTA AGR SCAND A-AN 2016. [DOI: 10.1080/09064702.2015.1131326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
6
|
Shin JH, Lee SY. Metabolic engineering of microorganisms for the production of L-arginine and its derivatives. Microb Cell Fact 2014; 13:166. [PMID: 25467280 PMCID: PMC4258820 DOI: 10.1186/s12934-014-0166-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 11/15/2014] [Indexed: 12/18/2022] Open
Abstract
L-arginine (ARG) is an important amino acid for both medicinal and industrial applications. For almost six decades, the research has been going on for its improved industrial level production using different microorganisms. While the initial approaches involved random mutagenesis for increased tolerance to ARG and consequently higher ARG titer, it is laborious and often leads to unwanted phenotypes, such as retarded growth. Discovery of L-glutamate (GLU) overproducing strains and using them as base strains for ARG production led to improved ARG production titer. Continued effort to unveil molecular mechanisms led to the accumulation of detailed knowledge on amino acid metabolism, which has contributed to better understanding of ARG biosynthesis and its regulation. Moreover, systems metabolic engineering now enables scientists and engineers to efficiently construct genetically defined microorganisms for ARG overproduction in a more rational and system-wide manner. Despite such effort, ARG biosynthesis is still not fully understood and many of the genes in the pathway are mislabeled. Here, we review the major metabolic pathways and its regulation involved in ARG biosynthesis in different prokaryotes including recent discoveries. Also, various strategies for metabolic engineering of bacteria for the overproduction of ARG are described. Furthermore, metabolic engineering approaches for producing ARG derivatives such as L-ornithine (ORN), putrescine and cyanophycin are described. ORN is used in medical applications, while putrescine can be used as a bio-based precursor for the synthesis of nylon-4,6 and nylon-4,10. Cyanophycin is also an important compound for the production of polyaspartate, another important bio-based polymer. Strategies outlined here will serve as a general guideline for rationally designing of cell-factories for overproduction of ARG and related compounds that are industrially valuable.
Collapse
Affiliation(s)
- Jae Ho Shin
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Republic of Korea.
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Republic of Korea. .,BioProcess Engineering Research Center, KAIST, Daejeon, 305-701, Republic of Korea. .,BioInformatics Research Center, KAIST, Daejeon, 305-701, Republic of Korea.
| |
Collapse
|
7
|
Nørgaard J, Canibe N, Nielsen B, Carlson D, Knap I, Cantor M, Poulsen H. First studies on a new concept for amino acid provision through B. subtilis in situ valine production in young pigs. Livest Sci 2012. [DOI: 10.1016/j.livsci.2012.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
8
|
Ochiai A, Itoh T, Kawamata A, Hashimoto W, Murata K. Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization. Appl Environ Microbiol 2007; 73:3803-13. [PMID: 17449691 PMCID: PMC1932723 DOI: 10.1128/aem.00147-07] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 04/16/2007] [Indexed: 11/20/2022] Open
Abstract
Plant cell wall degradation is a premier event when Bacillus subtilis, a typical saprophytic bacterium, invades plants. Here we show the degradation system of rhamnogalacturonan type I (RG-I), a component of pectin from the plant cell wall, in B. subtilis strain 168. Strain 168 cells showed a significant growth on plant cell wall polysaccharides such as pectin, polygalacturonan, and RG-I as a carbon source. DNA microarray analysis indicated that three gene clusters (yesOPQRSTUVWXYZ, ytePQRST, and ybcMOPST-ybdABDE) are inducibly expressed in strain 168 cells grown on RG-I. Cells of an industrially important bacterium, B. subtilis strain natto, fermenting soybeans also express the gene cluster including the yes series during the assimilation of soybean used as a carbon source. Among proteins encoded in the yes cluster, YesW and YesX were found to be novel types of RG lyases releasing disaccharide from RG-I. Genetic and enzymatic properties of YesW and YesX suggest that strain 168 cells secrete YesW, which catalyzes the initial cleavage of the RG-I main chain, and the resultant oligosaccharides are converted to disaccharides through the extracellular exotype YesX reaction. The disaccharide is finally degraded into its constituent monosaccharides through the reaction of intracellular unsaturated galacturonyl hydrolases YesR and YteR. This enzymatic route for RG-I degradation in strain 168 differs significantly from that in plant-pathogenic fungus Aspergillus aculeatus. This is, to our knowledge, the first report on the bacterial system for complete RG-I main chain degradation.
Collapse
Affiliation(s)
- Akihito Ochiai
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | | | | | | | | |
Collapse
|
9
|
Chaudhuri A, Mishra AK, Nanda G. Variation of antimetabolite sensitivity with different carbon sources in Bacillus subtilis. Folia Microbiol (Praha) 1982; 27:73-5. [PMID: 6806159 DOI: 10.1007/bf02879762] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The susceptibility of Bacillus subtilis to amino acid analogues was found to be markedly influenced by the carbon source used in the test media. Thialysine inhibited the bacterium with a greater number of carbon sources than the other two analogues tested. 5-Hydroxylysine was inhibitory with glycerol, lactose, D-xylose, L-arabinose and soluble starch while ethionine showed toxicity with lactose, D-xylose and L-arabinose. None of these analogues were toxic at the levels tested when D-galactose was used as carbon source. The bacterium was not susceptible to thialysine with glycerol, to 5-hydroxylysine with L-arabinose and to ethionine with lactose.
Collapse
|