1
|
Liu Y, Wang S, Wang L, Lu H, Zhang T, Zeng W. Characterization of Genomic, Physiological, and Probiotic Features of Lactiplantibacillus plantarum JS21 Strain Isolated from Traditional Fermented Jiangshui. Foods 2024; 13:1082. [PMID: 38611386 PMCID: PMC11011416 DOI: 10.3390/foods13071082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
This study aimed to understand the genetic and metabolic traits of a Lactiplantibacillus plantarum JS21 strain and its probiotic abilities through laboratory tests and computer analysis. L. plantarum JS21 was isolated from a traditional fermented food known as "Jiangshui" in Hanzhong city. In this research, the complete genetic makeup of JS21 was determined using Illumina and PacBio technologies. The JS21 genome consisted of a 3.423 Mb circular chromosome and five plasmids. It was found to contain 3023 protein-coding genes, 16 tRNA genes, 64 rRNA operons, 40 non-coding RNA genes, 264 pseudogenes, and six CRISPR array regions. The GC content of the genome was 44.53%. Additionally, the genome harbored three complete prophages. The evolutionary relationship and the genome collinearity of JS21 were compared with other L. plantarum strains. The resistance genes identified in JS21 were inherent. Enzyme genes involved in the Embden-Meyerhof-Parnas (EMP) and phosphoketolase (PK) pathways were detected, indicating potential for facultative heterofermentative pathways. JS21 possessed bacteriocins plnE/plnF genes and genes for polyketide and terpenoid assembly, possibly contributing to its antibacterial properties against Escherichia coli (ATCC 25922), Escherichia coli (K88), Staphylococcus aureus (CMCC 26003), and Listeria monocytogenes (CICC 21635). Furthermore, JS21 carried genes for Na+/H+ antiporters, F0F1 ATPase, and other stress resistance genes, which may account for its ability to withstand simulated conditions of the human gastrointestinal tract in vitro. The high hydrophobicity of its cell surface suggested the potential for intestinal colonization. Overall, L. plantarum JS21 exhibited probiotic traits as evidenced by laboratory experiments and computational analysis, suggesting its suitability as a dietary supplement.
Collapse
Affiliation(s)
- Yang Liu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
| | - Shanshan Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001, China
| | - Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Shaanxi University of Technology, Hanzhong 723001, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Shaanxi University of Technology, Hanzhong 723001, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi Province Key Laboratory of Bio-Resources, Shaanxi University of Technology, Hanzhong 723001, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (Y.L.); (W.Z.)
- Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Shaanxi University of Technology, Hanzhong 723001, China
| |
Collapse
|
2
|
Choi JW, Song NE, Hong SP, Rhee YK, Hong HD, Cho CW. Engineering Bacillus subtilis J46 for efficient utilization of galactose through adaptive laboratory evolution. AMB Express 2024; 14:14. [PMID: 38282124 PMCID: PMC10822834 DOI: 10.1186/s13568-024-01666-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024] Open
Abstract
Efficient utilization of galactose by microorganisms can lead to the production of valuable bio-products and improved metabolic processes. While Bacillus subtilis has inherent pathways for galactose metabolism, there is potential for enhancement via evolutionary strategies. This study aimed to boost galactose utilization in B. subtilis using adaptive laboratory evolution (ALE) and to elucidate the genetic and metabolic changes underlying the observed enhancements. The strains of B. subtilis underwent multiple rounds of adaptive laboratory evolution (approximately 5000 generations) in an environment that favored the use of galactose. This process resulted in an enhanced specific growth rate of 0.319 ± 0.005 h-1, a significant increase from the 0.03 ± 0.008 h-1 observed in the wild-type strains. Upon selecting the evolved strain BSGA14, a comprehensive whole-genome sequencing revealed the presence of 63 single nucleotide polymorphisms (SNPs). Two of them, located in the coding sequences of the genes araR and glcR, were found to be the advantageous mutations after reverse engineering. The strain with these two accumulated mutations, BSGALE4, exhibited similar specific growth rate on galactose to the evolved strain BSGA14 (0.296 ± 0.01 h-1). Furthermore, evolved strain showed higher productivity of protease and β-galactosidase in mock soybean biomass medium. ALE proved to be a potent tool for enhancing galactose metabolism in B. subtilis. The findings offer valuable insights into the potential of evolutionary strategies in microbial engineering and pave the way for industrial applications harnessing enhanced galactose conversion.
Collapse
Affiliation(s)
- Jae Woong Choi
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Nho-Eul Song
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Sang-Pil Hong
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Young Kyoung Rhee
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Hee-Do Hong
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Chang-Won Cho
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea.
| |
Collapse
|
3
|
Yin Y, Wang P, Wang X, Wen J. Construction of Bacillus subtilis for efficient production of fengycin from xylose through CRISPR-Cas9. Front Microbiol 2024; 14:1342199. [PMID: 38249479 PMCID: PMC10797001 DOI: 10.3389/fmicb.2023.1342199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
Fengycin is a multifunctional peptide antibiotic produced mainly by Bacillus species and the purpose of this research was to construct a Bacillus subtilis strain that can produce fengycin with the xylose as the substrate with CRSIPR-Cas9. Hence, at the beginning of this study, functional sfp and degQ were expressed in B. subtilis 168 strain to give the strain the ability to produce the fengycin with the titer of 71.21 mg/L. Subsequently, the native promoter PppsA of the cluster responsible for the fengycin synthesis was replaced by the Pveg promoter, resulting in a further 5.22-fold increase in fengycin titer. To confer xylose utilization capacity to B. subtilis, deletion of araR and constitutive overexpression of araE were performed, and the xylose consumption rate of the engineered strain BSUY06 reached 0.29 g/L/h, which is about 6.25-fold higher than that of the parent strain BSUY04-1. In the final phase of this study, the fermentation characteristics were observed and the initial xylose concentration was optimized. In this study, 40 g/L xylose was proved to be the most suitable initial concentration for growth and fengycin fermentation, which leading to a fengycin titer of 430.86 mg/L. This study demonstrated that lignocellulose, the clean and sustainable substrate with xylose as the second largest sugar, is a potential substrate for the production of fengycin.
Collapse
Affiliation(s)
- Ying Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Pan Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Xin Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| |
Collapse
|
4
|
Xia L, Wen J. Available strategies for improving the biosynthesis of surfactin: a review. Crit Rev Biotechnol 2023; 43:1111-1128. [PMID: 36001039 DOI: 10.1080/07388551.2022.2095252] [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: 01/04/2022] [Accepted: 06/04/2022] [Indexed: 11/03/2022]
Abstract
Surfactin is an excellent biosurfactant with a wide range of application prospects in many industrial fields. However, its low productivity and high cost have largely limited its commercial applications. In this review, the pathways for surfactin synthesis in Bacillus strains are summarized and discussed. Further, the latest strategies for improving surfactin production, including: medium optimization, genome engineering methods (rational genetic engineering, genome reduction, and genome shuffling), heterologous synthesis, and the use of synthetic biology combined with metabolic engineering approaches to construct high-quality artificial cells for surfactin production using xylose, are described. Finally, the prospects for improving surfactin synthesis are discussed in detail.
Collapse
Affiliation(s)
- Li Xia
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- National Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, People's Republic of China
- Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin, People's Republic of China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- National Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, People's Republic of China
- Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin, People's Republic of China
| |
Collapse
|
5
|
Koreeda A, Taguchi R, Miyamoto K, Kuwahara Y, Hirooka K. Protein expression systems combining a flavonoid-inducible promoter and T7 RNA polymerase in Bacillus subtilis. Biosci Biotechnol Biochem 2023; 87:1017-1028. [PMID: 37279445 DOI: 10.1093/bbb/zbad072] [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] [Received: 04/19/2023] [Accepted: 05/30/2023] [Indexed: 06/08/2023]
Abstract
Recombinant protein production must be tightly controlled when overproduction adversely affects the host bacteria. We developed a flavonoid-inducible T7 expression system in Bacillus subtilis using the qdoI promoter to control the T7 RNA polymerase gene (T7 pol). Using the egfp reporter gene controlled by the T7 promoter in a multicopy plasmid, we confirmed that this expression system is tightly regulated by flavonoids, such as quercetin and fisetin. Altering the qdoI promoter for T7 pol control to its hybrid derivative increased the expression level by 6.6-fold at maximum values upon induction. However, faint expression leakage was observed under a noninducing condition. Therefore, the two expression systems with the original qdoI promoter and the hybrid construct can be used selectively, depending on the high control accuracy or production yield required.
Collapse
Affiliation(s)
- Ami Koreeda
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, Fukuyama, Hiroshima, Japan
| | - Rina Taguchi
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, Fukuyama, Hiroshima, Japan
| | - Kanon Miyamoto
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, Fukuyama, Hiroshima, Japan
| | - Yuna Kuwahara
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, Fukuyama, Hiroshima, Japan
| | - Kazutake Hirooka
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, Fukuyama, Hiroshima, Japan
| |
Collapse
|
6
|
Bidart GN, Gharabli H, Welner DH. Functional characterization of the phosphotransferase system in Parageobacillus thermoglucosidasius. Sci Rep 2023; 13:7131. [PMID: 37130962 PMCID: PMC10154347 DOI: 10.1038/s41598-023-33918-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/20/2023] [Indexed: 05/04/2023] Open
Abstract
Parageobacillus thermoglucosidasius is a thermophilic bacterium characterized by rapid growth, low nutrient requirements, and amenability to genetic manipulation. These characteristics along with its ability to ferment a broad range of carbohydrates make P. thermoglucosidasius a potential workhorse in whole-cell biocatalysis. The phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) catalyzes the transport and phosphorylation of carbohydrates and sugar derivatives in bacteria, making it important for their physiological characterization. In this study, the role of PTS elements on the catabolism of PTS and non-PTS substrates was investigated for P. thermoglucosidasius DSM 2542. Knockout of the common enzyme I, part of all PTSs, showed that arbutin, cellobiose, fructose, glucose, glycerol, mannitol, mannose, N-acetylglucosamine, N-acetylmuramic acid, sorbitol, salicin, sucrose, and trehalose were PTS-dependent on translocation and coupled to phosphorylation. The role of each putative PTS was investigated and six PTS-deletion variants could not grow on arbutin, mannitol, N-acetylglucosamine, sorbitol, and trehalose as the main carbon source, or showed diminished growth on N-acetylmuramic acid. We concluded that PTS is a pivotal factor in the sugar metabolism of P. thermoglucosidasius and established six PTS variants important for the translocation of specific carbohydrates. This study lays the groundwork for engineering efforts with P. thermoglucosidasius towards efficient utilization of diverse carbon substrates for whole-cell biocatalysis.
Collapse
Affiliation(s)
- Gonzalo N Bidart
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Hani Gharabli
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Ditte Hededam Welner
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark.
| |
Collapse
|
7
|
Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:microorganisms10122355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
Collapse
Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
| | - Mohammad J. Taherzadeh
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
- Correspondence:
| |
Collapse
|
8
|
Liang J, van Kranenburg R, Bolhuis A, Leak DJ. Removing carbon catabolite repression in Parageobacillus thermoglucosidasius DSM 2542. Front Microbiol 2022; 13:985465. [PMID: 36338101 PMCID: PMC9631020 DOI: 10.3389/fmicb.2022.985465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Parageobacillus thermoglucosidasius is a thermophilic bacterium of interest for lignocellulosic biomass fermentation. However, carbon catabolite repression (CCR) hinders co-utilization of pentoses and hexoses in the biomass substrate. Hence, to optimize the fermentation process, it is critical to remove CCR in the fermentation strains with minimal fitness cost. In this study, we investigated whether CCR could be removed from P. thermoglucosidasius DSM 2542 by mutating the Ser46 regulatory sites on HPr and Crh to a non-reactive alanine residue. It was found that neither the ptsH1 (HPr-S46A) nor the crh1 (Crh-S46A) mutation individually eliminated CCR in P. thermoglucosidasius DSM 2542. However, it was not possible to generate a ptsH1 crh1 double mutant. While the Crh-S46A mutation had no obvious fitness effect in DSM 2542, the ptsH1 mutation had a negative impact on cell growth and sugar utilization under fermentative conditions. Under these conditions, the ptsH1 mutation was associated with the production of a brown pigment, believed to arise from methylglyoxal production, which is harmful to cells. Subsequently, a less directed adaptive evolution approach was employed, in which DSM 2542 was grown in a mixture of 2-deoxy-D-glucose(2-DG) and xylose. This successfully removed CCR from P. thermoglucosidasius DSM 2542. Two selection strategies were applied to optimize the phenotypes of evolved strains. Genome sequencing identified key mutations affecting the PTS components PtsI and PtsG, the ribose operon repressor RbsR and adenine phosphoribosyltransferase APRT. Genetic complementation and bioinformatics analysis revealed that the presence of wild type rbsR and apt inhibited xylose uptake or utilization, while ptsI and ptsG might play a role in the regulation of CCR in P. thermoglucosidasius DSM 2542.
Collapse
Affiliation(s)
- Jinghui Liang
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Centre for Sustainable and Circular Technologies (CSCT), University of Bath, Bath, United Kingdom
- *Correspondence: Jinghui Liang
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
- Corbion, Gorinchem, Netherlands
| | - Albert Bolhuis
- Department of Pharmacy and Pharmacology, Centre for Therapeutic Innovation, University of Bath, Bath, United Kingdom
| | - David J. Leak
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Centre for Sustainable and Circular Technologies (CSCT), University of Bath, Bath, United Kingdom
| |
Collapse
|
9
|
Geng B, Jia X, Peng X, Han Y. Biosynthesis of value-added bioproducts from hemicellulose of biomass through microbial metabolic engineering. Metab Eng Commun 2022; 15:e00211. [PMID: 36311477 PMCID: PMC9597109 DOI: 10.1016/j.mec.2022.e00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Hemicellulose is the second most abundant carbohydrate in lignocellulosic biomass and has extensive applications. In conventional biomass refinery, hemicellulose is easily converted to unwanted by-products in pretreatment and therefore can't be fully utilized. The present study aims to summarize the most recent development of lignocellulosic polysaccharide degradation and fully convert it to value-added bioproducts through microbial and enzymatic catalysis. Firstly, bioprocess and microbial metabolic engineering for enhanced utilization of lignocellulosic carbohydrates were discussed. The bioprocess for degradation and conversion of natural lignocellulose to monosaccharides and organic acids using anaerobic thermophilic bacteria and thermostable glycoside hydrolases were summarized. Xylose transmembrane transporting systems in natural microorganisms and the latest strategies for promoting the transporting capacity by metabolic engineering were summarized. The carbon catabolite repression effect restricting xylose utilization in microorganisms, and metabolic engineering strategies developed for co-utilization of glucose and xylose were discussed. Secondly, the metabolic pathways of xylose catabolism in microorganisms were comparatively analyzed. Microbial metabolic engineering for converting xylose to value-added bioproducts based on redox pathways, non-redox pathways, pentose phosphate pathway, and improving inhibitors resistance were summarized. Thirdly, strategies for degrading lignocellulosic polysaccharides and fully converting hemicellulose to value-added bioproducts through microbial metabolic engineering were proposed. Hemicellulose is the main carbohydrate of biomass and has valuable applications. Hemicellulose is underutilized in conventional biomass refinery and pretreatment. Microbial and enzymatic catalysis were applied for hemicellulose utilization. Xylose is converted to value-added bioproducts by metabolic engineering.
Collapse
Affiliation(s)
- Biao Geng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China,Corresponding author. National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
| |
Collapse
|
10
|
Zhu X, Fan F, Qiu H, Shao M, Li D, Yu Y, Bi C, Zhang X. New xylose transporters support the simultaneous consumption of glucose and xylose in Escherichia coli. MLIFE 2022; 1:156-170. [PMID: 38817680 PMCID: PMC10989795 DOI: 10.1002/mlf2.12021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/11/2022] [Accepted: 04/14/2022] [Indexed: 06/01/2024]
Abstract
Glucose and xylose are two major components of lignocellulose. Simultaneous consumption of glucose and xylose is critical for engineered microorganisms to produce fuels and chemicals from lignocellulosic biomass. Although many production limitations have been resolved, glucose-induced inhibition of xylose transport remains a challenge. In this study, a cell growth-based screening strategy was designed to identify xylose transporters uninhibited by glucose. The glucose pathway was genetically blocked in Escherichia coli so that glucose functions only as an inhibitor and cells need xylose as the carbon source for survival. Through adaptive evolution, omics analysis and reverse metabolic engineering, a new phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS) galactitol transporter (GalABC, encoded by EcolC_1640, EcolC_1641, and EcolC_1642 genes) that is not inhibited by glucose was identified. Inactivation of adenylate cyclase led to increased expression of the EcolC_1642 gene, and a point mutation in gene EcolC_1642 (N13S) further enhanced xylose transport. During the second round of gene mining, AraE and a new ABC transporter (AraFGH) of xylose were identified. A point mutation in the transcription regulator araC (L156I) caused increased expression of araE and araFGH genes without arabinose induction, and a point mutation in araE (D223Y) further enhanced xylose transport. These newly identified xylose transporters can support the simultaneous consumption of glucose and xylose and have potential use in producing chemicals from lignocellulose.
Collapse
Affiliation(s)
- Xinna Zhu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Feiyu Fan
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Huanna Qiu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- College of BiotechnologyTianjin University of Sciences and TechnologyTianjinChina
| | - Mengyao Shao
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- College of BiotechnologyTianjin University of Sciences and TechnologyTianjinChina
| | - Di Li
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- College of BiotechnologyTianjin University of Sciences and TechnologyTianjinChina
| | - Yong Yu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- University of Chinese Academy of SciencesBeijingChina
| | - Changhao Bi
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Xueli Zhang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| |
Collapse
|
11
|
Banerjee S, Sen S, Bhakat A, Bhowmick A, Sarkar K. The lipopeptides Fengycin and Iturin are involved in the anticandidal activity of endophytic Bacillus sp. as determined by experimental and in-silico analysis. Lett Appl Microbiol 2022; 75:450-459. [PMID: 35620862 DOI: 10.1111/lam.13750] [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: 03/01/2022] [Revised: 04/28/2022] [Accepted: 05/21/2022] [Indexed: 11/28/2022]
Abstract
In this study, an endophytic Bacillus sp. strain (K7) was isolated from the medicinally important ornamental plant, Jasminum officinale. Biochemical analyses were conducted to evaluate the nature of the extracted product, which displayed strong anticandidal activity against Candida albicans SC5314, as evident from the results obtained in agar-cup diffusion tests, phase contrast microscopy, scanning electron microscopy, and minimum inhibitory concentration assays. After confirming the presence of the gene clusters encoding the lipopeptides iturins and fengycin in the genome of K7, their corresponding molecular ions were identified using MALDI-TOF-MS. 3D structures of the lipopeptides were downloaded from specific databases and molecular docking was performed against a vital C. albicans enzyme, Exo 1, 3- beta-glucanase, involved in cell wall remodeling, adhesion to polymer materials, and biofilm formation. The docking score of iturins was found to be -8.6 and -8.2 kcal mol-1 and for fengycin it was -9.4 kcal mol-1 , indicating a strong affinity of these cyclic lipopeptides towards Exo 1, 3- beta-glucanase. The combined in vitro and in-silico anticandidal studies suggested that these secreted lipopeptides from Bacillus sp. may be used as potential therapeutics against opportunistic and complicated infections of Candida albicans.
Collapse
Affiliation(s)
- Saikat Banerjee
- Department of Microbiology, University of Kalyani, Kalyani, West Bengal, India
| | - Samya Sen
- Department of Microbiology, University of Kalyani, Kalyani, West Bengal, India.,Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India
| | - Ankika Bhakat
- Department of Microbiology, University of Kalyani, Kalyani, West Bengal, India
| | - Arpita Bhowmick
- Department of Microbiology, University of Kalyani, Kalyani, West Bengal, India
| | - Keka Sarkar
- Department of Microbiology, University of Kalyani, Kalyani, West Bengal, India
| |
Collapse
|
12
|
Gao W, Yin Y, Wang P, Tan W, He M, Wen J. Production of fengycin from D-xylose through the expression and metabolic regulation of the Dahms pathway. Appl Microbiol Biotechnol 2022; 106:2557-2567. [PMID: 35362719 DOI: 10.1007/s00253-022-11871-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 02/14/2022] [Accepted: 03/05/2022] [Indexed: 12/01/2022]
Abstract
D-Xylose is a key component of lignocellulosic biomass and the second-most abundant carbohydrate on the planet. As one of the most powerful cyclo-lipopeptide antibiotics, fengycin displays strong wide-spectrum antifungal and antiviral, as well as potential anti-cancer activity. Pyruvate is a key metabolite linking the biosynthesis of fatty acids and amino acids, the precursors for fengycin. In this study, the genes encoding the Dahms xylose-utilization pathway were integrated into the amyE site of Bacillus subtilis 168, and based on the metabolic characteristics of the Dahms pathway, the acetate kinase (ackA) and lactate dehydrogenase (ldh) genes were knocked out. Then, the metabolic control module II was designed to convert glycolaldehyde, another intermediate of the Dahms pathway, in addition to pathways for the conversion of acetaldehyde into malic acid and oxaloacetic acid, resulting in strain BSU03. In the presence of module II, the content of acetic and lactic acid decreased significantly, and the xylose uptake efficiency increased. At the same time, the yield of fengycin increased by 87% compared to the original strain. Additionally, the underlying factors for the increase of fengycin titer were revealed through metabonomic analysis. This study therefore demonstrates that this regulation approach can not only optimize the intracellular fluxes for the Dahms pathway, but is also conducive to the synthesis of secondary metabolites similar to fengycin. KEY POINTS: • The expression and effect of the Dahms pathway on the synthesis of fengycin in Bacillus subtilis 168. • The expression of regulatory module II can promote the metabolic rate of the Dahms pathway and increase the synthesis of the fengycin.
Collapse
Affiliation(s)
- Wenting Gao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Ying Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Pan Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Wei Tan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Mingliang He
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China. .,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China.
| |
Collapse
|
13
|
Liang J, Roberts A, van Kranenburg R, Bolhuis A, Leak DJ. Relaxed control of sugar utilization in Parageobacillus thermoglucosidasius DSM 2542. Microbiol Res 2021; 256:126957. [PMID: 35032723 DOI: 10.1016/j.micres.2021.126957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/22/2021] [Accepted: 12/27/2021] [Indexed: 01/08/2023]
Abstract
Though carbon catabolite repression (CCR) has been intensively studied in some more characterised organisms, there is a lack of information of CCR in thermophiles. In this work, CCR in the thermophile, Parageobacillus thermoglucosidasius DSM 2542 has been studied during growth on pentose sugars in the presence of glucose. Physiological studies under fermentative conditions revealed a loosely controlled CCR when DSM 2542 was grown in minimal medium supplemented with a mixture of glucose and xylose. This atypical CCR pattern was also confirmed by studying xylose isomerase expression level by qRT-PCR. Fortuitously, the pheB gene, which encodes catechol 2, 3-dioxygenase was found to have a cre site highly similar to the consensus catabolite-responsive element (cre) at its 3' end and was used to confirm that expression of pheB from a plasmid was under stringent CCR control. Bioinformatic analysis suggested that the CCR regulation of xylose metabolism in P. thermoglucosidasius DSM 2542 might occur primarily via control of expression of pentose transporter operons. Relaxed control of sugar utilization might reflect a lower affinity of the CcpA-HPr (Ser46-P) or CcpA-Crh (Ser46-P) complexes to the cre(s) in these operons.
Collapse
Affiliation(s)
- Jinghui Liang
- Department of Biology and Biochemistry, University of Bath, UK.
| | - Adam Roberts
- Department of Biology and Biochemistry, University of Bath, UK
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, The Netherlands; Corbion, Arkelsedijk 46, 4206 AC, Gorinchem, The Netherlands
| | - Albert Bolhuis
- Department of Pharmacy and Pharmacology, University of Bath, UK
| | - David J Leak
- Department of Biology and Biochemistry, University of Bath, UK
| |
Collapse
|
14
|
Havukainen S, Pujol-Giménez J, Valkonen M, Hediger MA, Landowski CP. Functional characterization of a highly specific L-arabinose transporter from Trichoderma reesei. Microb Cell Fact 2021; 20:177. [PMID: 34496831 PMCID: PMC8425032 DOI: 10.1186/s12934-021-01666-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Lignocellulose biomass has been investigated as a feedstock for second generation biofuels and other value-added products. Some of the processes for biofuel production utilize cellulases and hemicellulases to convert the lignocellulosic biomass into a range of soluble sugars before fermentation with microorganisms such as yeast Saccharomyces cerevisiae. One of these sugars is l-arabinose, which cannot be utilized naturally by yeast. The first step in l-arabinose catabolism is its transport into the cells, and yeast lacks a specific transporter, which could perform this task. Results We identified Trire2_104072 of Trichoderma reesei as a potential l-arabinose transporter based on its expression profile. This transporter was described already in 2007 as d-xylose transporter XLT1. Electrophysiology experiments with Xenopus laevis oocytes and heterologous expression in yeast revealed that Trire2_104072 is a high-affinity l-arabinose symporter with a Km value in the range of \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$\sim$$\end{document}∼ 0.1–0.2 mM. It can also transport d-xylose but with low affinity (Km\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$\sim$$\end{document}∼ 9 mM). In yeast, l-arabinose transport was inhibited slightly by d-xylose but not by d-glucose in an assay with fivefold excess of the inhibiting sugar. Comparison with known l-arabinose transporters revealed that the expression of Trire2_104072 enabled yeast to uptake l-arabinose at the highest rate in conditions with low extracellular l-arabinose concentration. Despite the high specificity of Trire2_104072 for l-arabinose, the growth of its T. reesei deletion mutant was only affected at low l-arabinose concentrations. Conclusions Due to its high affinity for l-arabinose and low inhibition by d-glucose or d-xylose, Trire2_104072 could serve as a good candidate for improving the existing pentose-utilizing yeast strains. The discovery of a highly specific l-arabinose transporter also adds to our knowledge of the primary metabolism of T. reesei. The phenotype of the deletion strain suggests the involvement of other transporters in l-arabinose transport in this species. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01666-4.
Collapse
Affiliation(s)
- Sami Havukainen
- VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Jonai Pujol-Giménez
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland.,Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland
| | - Mari Valkonen
- VTT Technical Research Center of Finland Ltd, Tietotie 2, 02150, Espoo, Finland
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland.,Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland
| | | |
Collapse
|
15
|
Production of poly-γ-glutamic acid (γ-PGA) from xylose-glucose mixtures by Bacillus amyloliquefaciens C1. 3 Biotech 2021; 11:100. [PMID: 33520585 DOI: 10.1007/s13205-021-02661-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/13/2021] [Indexed: 01/07/2023] Open
Abstract
Due to the promising applications, the demand to enhance poly-γ-glutamic acid (γ-PGA) production while decreasing the cost has increased in the past decade. Here, xylose/glucose mixture and corncob hydrolysate (CCH) was evaluated as alternatives for γ-PGA production by Bacillus amyloliquefaciens C1. Although both have been validated to support cell growth, glucose and xylose were not simutaneously consumed and exhibited a diauxic growth pattern due to carbon catabolite repression (CCR) in B. amyloliquefaciens C1, while the enhanced transcription of araE alleviated the xylose transport bottleneck across a cellular membrane. Additionally, the xyl operon (xylA and xylB), which was responsible for xylose metabolism, was strongly induced by xylose at the transcriptional level. When cultured in a mixed medium, xylR was sharply induced to 3.39-folds during the first 8-h while reduced to the base level similar to that in xylose medium. Finally, pre-treated CCH mainly contained a mixture of glucose and xylose was employed for γ-PGA fermentation, which obtained a final concentration of 6.56 ± 0.27 g/L. Although the glucose utilization rate (84.91 ± 1.81%) was lower than that with chemical substrates, the xylose utilization rate (43.41 ± 2.14%) and the sodium glutamate conversion rate (77.22%) of CCH were acceptable. Our study provided a promising approach for the green production of γ-PGA from lignocellulosic biomass and circumvent excessive non-food usage of glucose.
Collapse
|
16
|
van Tilburg AY, van Heel AJ, Stülke J, de Kok NAW, Rueff AS, Kuipers OP. Mini Bacillus PG10 as a Convenient and Effective Production Host for Lantibiotics. ACS Synth Biol 2020; 9:1833-1842. [PMID: 32551553 PMCID: PMC7372594 DOI: 10.1021/acssynbio.0c00194] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Efficient bacterial cell factories are important for the screening and characterization of potent antimicrobial peptides such as lantibiotics. Although lantibiotic production systems have been established in Lactococcus lactis and Escherichia coli, the industrial workhorse Bacillus subtilis has been left relatively unexplored as a lantibiotic production host. Therefore, we tested different B. subtilis strains for their ability to produce lantibiotic peptides by using the subtilin modification and transport enzymes derived from the natural subtilin producer B. subtilis ATCC 6633. Our study shows that although B. subtilis ATCC 6633 and 168 are able to produce various processed lantibiotic peptides, an evident advantage of using either the 8-fold protease-deficient strain WB800 or the genome-minimized B. subtilis 168 strain PG10 is the lack of extracellular serine protease activity. Consequently, leader processing of lantibiotic precursor peptides is circumvented and thus potential toxicity toward the production host is prevented. Furthermore, PG10 provides a clean secondary metabolic background and therefore appears to be the most promising B. subtilis lantibiotic production host. We demonstrate the production of various lantibiotic precursor peptides by PG10 and show different options for their in vitro activation. Our study thus provides a convenient B. subtilis-based lantibiotic production system, which facilitates the search for novel antimicrobial peptides.
Collapse
Affiliation(s)
- Amanda Y. van Tilburg
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Auke J. van Heel
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Jörg Stülke
- Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, 37077, Germany
| | - Niels A. W. de Kok
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Anne-Stéphanie Rueff
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, 9747AG, The Netherlands
| |
Collapse
|
17
|
Efficient production of surfactin from xylose-rich corncob hydrolysate using genetically modified Bacillus subtilis 168. Appl Microbiol Biotechnol 2020; 104:4017-4026. [DOI: 10.1007/s00253-020-10528-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/28/2020] [Accepted: 03/05/2020] [Indexed: 01/04/2023]
|
18
|
Wu Y, Chen T, Liu Y, Lv X, Li J, Du G, Ledesma-Amaro R, Liu L. CRISPRi allows optimal temporal control of N-acetylglucosamine bioproduction by a dynamic coordination of glucose and xylose metabolism in Bacillus subtilis. Metab Eng 2018; 49:232-241. [DOI: 10.1016/j.ymben.2018.08.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/15/2018] [Accepted: 08/30/2018] [Indexed: 10/28/2022]
|
19
|
Servinsky MD, Renberg RL, Perisin MA, Gerlach ES, Liu S, Sund CJ. Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control in Clostridium acetobutylicum ATCC 824. mSystems 2018; 3:e00064-18. [PMID: 30374459 PMCID: PMC6199471 DOI: 10.1128/msystems.00064-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/13/2018] [Indexed: 12/27/2022] Open
Abstract
Bacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into commodity chemicals by the anaerobic bacterium Clostridium acetobutylicum is a promising alternative source to fossil fuel-derived chemicals. Recently, it was demonstrated that xylose is not appreciably fermented in the presence of arabinose, revealing a hierarchy of pentose utilization in this organism (L. Aristilde, I. A. Lewis, J. O. Park, and J. D. Rabinowitz, Appl Environ Microbiol 81:1452-1462, 2015, https://doi.org/10.1128/AEM.03199-14). The goal of the current study is to characterize the transcriptional regulation that occurs and perhaps drives this pentose hierarchy. Carbohydrate consumption rates showed that arabinose, like glucose, actively represses xylose utilization in cultures fermenting xylose. Further, arabinose addition to xylose cultures led to increased acetate-to-butyrate ratios, which indicated a transition of pentose catabolism from the pentose phosphate pathway to the phosphoketolase pathway. Transcriptome sequencing (RNA-Seq) confirmed that arabinose addition to cells actively growing on xylose resulted in increased phosphoketolase (CA_C1343) mRNA levels, providing additional evidence that arabinose induces this metabolic switch. A significant overlap in differentially regulated genes after addition of arabinose or glucose suggested a common regulation mechanism. A putative open reading frame (ORF) encoding a potential catabolite repression phosphocarrier histidine protein (Crh) was identified that likely participates in the observed transcriptional regulation. These results substantiate the claim that arabinose is utilized preferentially over xylose in C. acetobutylicum and suggest that arabinose can activate carbon catabolite repression via Crh. Furthermore, they provide valuable insights into potential mechanisms for altering pentose utilization to modulate fermentation products for chemical production. IMPORTANCE Clostridium acetobutylicum can ferment a wide variety of carbohydrates to the commodity chemicals acetone, butanol, and ethanol. Recent advances in genetic engineering have expanded the chemical production repertoire of C. acetobutylicum using synthetic biology. Due to its natural properties and genetic engineering potential, this organism is a promising candidate for converting biomass-derived feedstocks containing carbohydrate mixtures to commodity chemicals via natural or engineered pathways. Understanding how this organism regulates its metabolism during growth on carbohydrate mixtures is imperative to enable control of synthetic gene circuits in order to optimize chemical production. The work presented here unveils a novel mechanism via transcriptional regulation by a predicted Crh that controls the hierarchy of carbohydrate utilization and is essential for guiding robust genetic engineering strategies for chemical production.
Collapse
Affiliation(s)
| | | | | | | | - Sanchao Liu
- U.S. Army Research Laboratory, RDRL-SEE-B, Adelphi, Maryland, USA
| | | |
Collapse
|
20
|
Harish BS, Uppuluri KB. Modeling of growth kinetics for an isolated marine bacterium, Oceanimonas sp. BPMS22 during the production of a trypsin inhibitor. Prep Biochem Biotechnol 2018; 48:556-563. [PMID: 29869945 DOI: 10.1080/10826068.2018.1476878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Protease inhibitors significantly control physiologically relevant protease activities. Protease inhibitors from marine microbial sources are unique due to their rough living environmental conditions. In the present study, a protein protease inhibitor (PI) was produced from marine Oceanimonas sp. BPMS22. Seven different media were screened for the growth of the bacterium and production of PI. Different carbon and nitrogen sources were screened and optimized for the specific protease inhibitor activity. Three different growth models were checked for the best fit of the bacterial growth. A modified Gompertz model was selected as the best model for the growth of Oceanimonas sp. BPMS22 with the maximum specific growth rate of 0.165 hr-1 and doubling time of 4.2 hr. The production of PI takes place during the non-growing phase of the bacterial growth. A kinetic model for the production of PI during non-growing phase was used for studying various process parameters. From the model, the maximum trypsin inhibitor formation rate of 0.3802 IU per mg of biomass per hour was observed at 49.91 hr.
Collapse
Affiliation(s)
- B S Harish
- a Bioprospecting Laboratory, School of Chemical and Biotechnology , SASTRA Deemed University , Thanjavur , India
| | - Kiran Babu Uppuluri
- a Bioprospecting Laboratory, School of Chemical and Biotechnology , SASTRA Deemed University , Thanjavur , India
| |
Collapse
|
21
|
Westbrook AW, Ren X, Oh J, Moo-Young M, Chou CP. Metabolic engineering to enhance heterologous production of hyaluronic acid in Bacillus subtilis. Metab Eng 2018; 47:401-413. [PMID: 29698777 DOI: 10.1016/j.ymben.2018.04.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 04/03/2018] [Accepted: 04/20/2018] [Indexed: 12/11/2022]
Abstract
Hyaluronic acid (HA) is a high-value biopolymer that is produced in large scales using attenuated strains ofgroup C streptococci. However, due to the pathogenicity and fastidious nature of these bacteria, the development of bioprocesses for HA production centered on robust 'Generally Recognized as Safe (GRAS)' organisms, such as Bacillus subtilis, is of increased interest. Here, we report metabolic engineering of novel B. subtilis strains in which the carbon flux has been partially diverted from central metabolism, i.e. the pentose phosphate pathway (PPP) and glycolysis, into HA biosynthesis. First, an improved base strain of B. subtilis was engineered for more effective HA production with less susceptibility to catabolite repression when expressing genes from a xylose-inducible promoter. Subsequently, Clustered Regularly Interspaced Palindromic Repeats interference (CRISPRi) was applied to reduce the expression of individual pfkA or zwf in the base strain, leading to substantial improvements to the HA titer with a concomitant decrease in the molecular weight (MW). On the other hand, multiplexed repression of both pfkA and zwf expression resulted in increases to the HA titer of up to 108% and enhancements to the MW, compared to the base strain. Moreover, the addition of exogenous HA monomers, i.e. glucuronic acid (GlcUA) and N-acetyl-glucosamine (GlcNAc), to B. subtilis cultures markedly improved the HA MW but decreased the HA titer, providing insights into the mechanism of HA biosynthesis by streptococcal hyaluronan synthase (SeHAS) in B. subtilis. Our study demonstrates the successful application of metabolic engineering strategies to establish B. subtilis as an effective platform for high-level HA production.
Collapse
Affiliation(s)
- Adam W Westbrook
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada N2L 5B6
| | - Xiang Ren
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada N2L 5B6
| | - Jaewon Oh
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada N2L 5B6
| | - Murray Moo-Young
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada N2L 5B6
| | - C Perry Chou
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada N2L 5B6.
| |
Collapse
|
22
|
Ferreira MJ, Mendes AL, de Sá-Nogueira I. The MsmX ATPase plays a crucial role in pectin mobilization by Bacillus subtilis. PLoS One 2017; 12:e0189483. [PMID: 29240795 PMCID: PMC5730181 DOI: 10.1371/journal.pone.0189483] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/27/2017] [Indexed: 12/20/2022] Open
Abstract
Carbohydrates from plant cell walls are often found as heteropolysaccharides intertwined with each other. For competitive advantage against other microorganisms, and ability to fully exploit available carbon and energy sources, Bacillus subtilis possesses a high number of proteins dedicated to the uptake of mono- and oligosaccharides. Here, we characterize transporter complexes, belonging to the ATP-binding cassette (ABC) superfamily, involved in the uptake of oligosaccharides commonly found in pectin. The uptake of these carbohydrates is shown to be MsmX-dependent, assigning a key role in pectin mobilization for MsmX, a multipurpose ATPase serving several distinct ABC-type I sugar importers. Mutagenesis analysis of the transmembrane domains of the AraNPQ MsmX-dependent importer revealed putative residues for MsmX interaction. Interestingly however, although MsmX is shown to be essential for energizing various ABC transporters we found that a second B. subtilis ATPase, YurJ, is able to complement its function when placed in trans at a different locus of the chromosome.
Collapse
Affiliation(s)
- Mário J. Ferreira
- UCIBIO, REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Aristides L. Mendes
- UCIBIO, REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Isabel de Sá-Nogueira
- UCIBIO, REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
- * E-mail:
| |
Collapse
|
23
|
Enhanced production of xylitol from xylose by expression of Bacillus subtilis arabinose:H + symporter and Scheffersomyces stipitis xylose reductase in recombinant Saccharomyces cerevisiae. Enzyme Microb Technol 2017; 107:7-14. [DOI: 10.1016/j.enzmictec.2017.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/28/2017] [Accepted: 07/29/2017] [Indexed: 11/17/2022]
|
24
|
2,3-Butanediol production from cellobiose using exogenous beta-glucosidase-expressing Bacillus subtilis. Appl Microbiol Biotechnol 2016; 100:5781-9. [DOI: 10.1007/s00253-016-7326-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/04/2023]
|
25
|
Abstract
The acetone–butanol–ethanol fermentation of solventogenic clostridia was operated as a successful, worldwide industrial process during the first half of the twentieth century, but went into decline for economic reasons. The recent resurgence in interest in the fermentation has been due principally to the recognised potential of butanol as a biofuel, and development of reliable molecular tools has encouraged realistic prospects of bacterial strains being engineered to optimise fermentation performance. In order to minimise costs, emphasis is being placed on waste feedstock streams containing a range of fermentable carbohydrates. It is therefore important to develop a detailed understanding of the mechanisms of carbohydrate uptake so that effective engineering strategies can be identified. This review surveys present knowledge of sugar uptake and its control in solventogenic clostridia. The major mechanism of sugar uptake is the PEP-dependent phosphotransferase system (PTS), which both transports and phosphorylates its sugar substrates and plays a central role in metabolic regulation. Clostridial genome sequences have indicated the presence of numerous phosphotransferase systems for uptake of hexose sugars, hexose derivatives and disaccharides. On the other hand, uptake of sugars such as pentoses occurs via non-PTS mechanisms. Progress in characterization of clostridial sugar transporters and manipulation of control mechanisms to optimise sugar fermentation is described.
Collapse
Affiliation(s)
- Wilfrid J Mitchell
- School of Life Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK.
| |
Collapse
|
26
|
Metabolic potential of Bacillus subtilis 168 for the direct conversion of xylans to fermentation products. Appl Microbiol Biotechnol 2015; 100:1501-1510. [PMID: 26559526 DOI: 10.1007/s00253-015-7124-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/30/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
Abstract
Methylglucuronoxylans (MeGXn) and methylglucuronoarabinoxylans (MeGAXn) respectively comprise most of the hemicellulose fractions in dicots and monocots and, next to cellulose, are the major resources for the production of fuels and chemicals from lignocellulosics. With either MeGXn or MeGAXn as a substrate, Bacillus subtilis 168 accumulates acidic methylglucuronoxylotriose as a limit product following the uptake and metabolism of neutral xylooligosaccharides. Secreted GH11 endoxylanase (Xyn11A), GH30 endoxylanase (Xyn30C), and GH43 arabinoxylan arabinofuranohydrolase (Axh43) respectively encoded by the xynA, xynC, and xynD genes collectively contribute to the depolymerization of MeGAXn. Studies here demonstrate the complementary roles of these enzymes in the digestion of MeGAXn. Coordinate expression of the xynD and xynC genes defines an operon accounting for the Axh43-catalyzed release of arabinose followed by Xyn30C and Xyn11A-catalyzed depolymerization of MeGAXn. Both sources generate acetate and lactate as the principal fermentation products, with yields of 26 % acetate and 32 % lactate from MeGXn compared to 22 % acetate and 21 % lactate from MeGAXn. These studies of the GH43/GH30/GH11 system in B. subtilis 168 provide a basis for the further development of B. subtilis and related species as biocatalysts for direct conversion of hemicellulose derived from energy crops as well as agricultural and forest residues to chemical feedstocks.
Collapse
|
27
|
Inverse metabolic engineering of Bacillus subtilis for xylose utilization based on adaptive evolution and whole-genome sequencing. Appl Microbiol Biotechnol 2014; 99:885-96. [DOI: 10.1007/s00253-014-6131-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/23/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
|
28
|
Carbohydrate coating reduces adhesion of biofilm-forming Bacillus subtilis to gold surfaces. Appl Environ Microbiol 2014; 80:5911-7. [PMID: 25038098 DOI: 10.1128/aem.01600-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The growth of bacterial biofilms in pipes and food tanks causes severe problems in industry. Biofilms growing on medical implants or catheters are of great concern, as they can cause serious infections and decrease the functionality of the medical device. The prevention of bacterial adhesion--the first step in colonization and biofilm formation--is therefore very important. Current research comprises alterations in surface properties, the prevention of adhesin biosynthesis, inhibition with receptor analogs, or the development of anti-adhesive vaccines. We present a new approach that allows us to study bacterial adhesion with high sensitivity in real-time while testing several different surfaces in parallel. Using the cantilever-array technique we demonstrate that coating of gold surfaces with mono- or disaccharides results in a reduction of the bacterial adhesion of the biofilm-forming bacterium Bacillus subtilis NCIB 3610 to these gold surfaces. This reduction in bacterial adhesion is independent of the studied carbohydrate. Using several mutant strains, we investigate the underlying molecular interactions, and our results suggest that adhesion to gold surfaces is mediated by thiol groups present in proteins of the bacterial cell membrane or biofilm matrix proteins expressed at low levels by the wild-type strain. Furthermore, our data indicate that the adhesion of B. subtilis NCIB 3610 to carbohydrate-coated gold surfaces is facilitated by interactions between carbohydrates installed on the cantilever gold surface and an exopolysaccharide expressed by this strain. Understanding general and specific contributions of molecular interactions mediating bacterial adhesion will enable its prevention in the future.
Collapse
|
29
|
The LacI-Type transcriptional regulator AraR acts as an L-arabinose-responsive repressor of L-arabinose utilization genes in Corynebacterium glutamicum ATCC 31831. J Bacteriol 2014; 196:2242-54. [PMID: 24706742 DOI: 10.1128/jb.01655-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Corynebacterium glutamicum ATCC 31831 araBDA operon consists of three l-arabinose catabolic genes, upstream of which the galM, araR, and araE genes are located in opposite orientation. araR encodes a LacI-type transcriptional regulator that negatively regulates the l-arabinose-inducible expression of araBDA and araE (encoding an l-arabinose transporter), through a mechanism that has yet to be identified. Here we show that the AraR protein binds in vitro to three sites: one upstream of araBDA and two upstream of araE. We verify that a 16-bp consensus palindromic sequence is essential for binding of AraR, using a series of mutations introduced upstream of araB in electrophoretic mobility shift assays. Moreover, the DNA-binding activity of AraR is reduced by l-arabinose. We employ quantitative reverse transcription-PCR (qRT-PCR) analyses using various mutant strains deficient in l-arabinose utilization genes to demonstrate that the prominent upregulation of araBDA and araE within 5 min of l-arabinose supplementation is dependent on the uptake but independent of the catabolism of l-arabinose. Similar expression patterns, together with the upregulation by araR disruption without l-arabinose, are evident with the apparent galM-araR operon, although attendant changes in expression levels are much smaller than those realized with the expression of araBDA and araE. The AraR-binding site upstream of araB overlaps the -10 region of the divergent galM promoter. These observations indicate that AraR acts as a transcriptional repressor of araBDA, araE, and galM-araR and that l-arabinose acts as an intracellular negative effector of the AraR-dependent regulation.
Collapse
|
30
|
Chen T, Liu WX, Fu J, Zhang B, Tang YJ. Engineering Bacillus subtilis for acetoin production from glucose and xylose mixtures. J Biotechnol 2013; 168:499-505. [DOI: 10.1016/j.jbiotec.2013.09.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 08/25/2013] [Accepted: 09/09/2013] [Indexed: 12/18/2022]
|
31
|
High-level intracellular expression of heterologous proteins in Brevibacillus choshinensis SP3 under the control of a xylose inducible promoter. Microb Cell Fact 2013; 12:12. [PMID: 23374160 PMCID: PMC3582527 DOI: 10.1186/1475-2859-12-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 01/29/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In past years research has focused on the development of alternative Gram positive bacterial expression systems to produce industrially relevant proteins. Brevibacillus choshinensis is an easy to handle non-sporulating bacterium, lacking extracellular proteases, that has been already shown to provide a high level of recombinant protein expression. One major drawback, limiting the applicability of the Brevibacillus expression system, is the absence of expression vectors based on inducible promoters. Here we used the PxylA inducible promoter, commonly employed in other Bacillae expression systems, in Brevibacillus. RESULTS Using GFP, α-amylase and TcdA-GT as model proteins, high level of intracellular protein expression (up to 250 mg/L for the GFP) was achieved in Brevibacillus, using the pHis1522 vector carrying the B. megaterium xylose-inducible promoter (PxylA). The GFP expression yields were more than 25 fold higher than those reported for B. megaterium carrying the same vector. All the tested proteins show significant increment in their expression levels (2-10 folds) than those obtained using the available plasmids based on the P2 constitutive promoter. CONCLUSION Combining the components of two different commercially available Gram positive expression systems, such as Brevibacillus (from Takara Bio) and B. megaterium (from Mobitec), we demonstrate that vectors based on the B. megaterium PxylA xylose inducible promoter can be successfully used to induce high level of intracellular expression of heterologous proteins in Brevibacillus.
Collapse
|
32
|
Abstract
Galactose is a common monosaccharide that can be utilized by all living organisms via the activities of three main enzymes that make up the Leloir pathway: GalK, GalT, and GalE. In Bacillus subtilis, the absence of GalE causes sensitivity to exogenous galactose, leading to rapid cell lysis. This effect can be attributed to the accumulation of toxic galactose metabolites, since the galE mutant is blocked in the final step of galactose catabolism. In a screen for suppressor mutants restoring viability to a galE null mutant in the presence of galactose, we identified mutations in sinR, which is the major biofilm repressor gene. These mutations caused an increase in the production of the exopolysaccharide (EPS) component of the biofilm matrix. We propose that UDP-galactose is the toxic galactose metabolite and that it is used in the synthesis of EPS. Thus, EPS production can function as a shunt mechanism for this toxic molecule. Additionally, we demonstrated that galactose metabolism genes play an essential role in B. subtilis biofilm formation and that the expressions of both the gal and eps genes are interrelated. Finally, we propose that B. subtilis and other members of the Bacillus genus may have evolved to utilize naturally occurring polymers of galactose, such as galactan, as carbon sources. Bacteria switch from unicellular to multicellular states by producing extracellular matrices that contain exopolysaccharides. In such aggregates, known as biofilms, bacteria are more resistant to antibiotics. This makes biofilms a serious problem in clinical settings. The resilience of biofilms makes them very useful in industrial settings. Thus, understanding the production of biofilm matrices is an important problem in microbiology. In studying the synthesis of the biofilm matrix of Bacillus subtilis, we provide further understanding of a long-standing microbiological observation that certain mutants defective in the utilization of galactose became sensitive to it. In this work, we show that the toxicity observed before was because cells were grown under conditions that were not propitious to produce the exopolysaccharide component of the matrix. When cells are grown under conditions that favor matrix production, the toxicity of galactose is relieved. This allowed us to demonstrate that galactose metabolism is essential for the synthesis of the extracellular matrix.
Collapse
|
33
|
Park YC, Jun SY, Seo JH. Construction and characterization of recombinant Bacillus subtilis JY123 able to transport xylose efficiently. J Biotechnol 2012; 161:402-6. [PMID: 22910119 DOI: 10.1016/j.jbiotec.2012.07.192] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 07/25/2012] [Accepted: 07/31/2012] [Indexed: 11/19/2022]
Abstract
It has been known that wild type Bacillus subtilis cannot grow rapidly in a minimal medium containing xylose as a sole carbon source because it does not have a xylose-specific transporter. In this study, the arabinose:H(+) symporter, AraE protein from B. subtilis was expressed in B. subtilis 168 in order to transport xylose efficiently. The AraE expression cassette was constructed to contain the xylose-inducible xylA promoter, araE gene and fba terminator, and integrated into the chromosomal amyE gene in B. subtilis 168. Batch cultures in a defined medium with xylose only or a mixture of xylose and glucose showed that expression of AraE led to fast and complete consumption of initially added xylose and hence a considerable increase in cell growth of the recombinant B. subtilis JY123 expressing AraE. Considering the systematic analysis of cell growth, sugar consumption, respiratory quotient and xylulokinase activity, it was certain that AraE protein could transport xylose into B. subtilis efficiently.
Collapse
Affiliation(s)
- Yong-Cheol Park
- Department of Advanced Fermentation Fusion Science and Technology, Kookmin University, Seoul 136-702, Republic of Korea.
| | | | | |
Collapse
|
34
|
Cheng H, Wang B, Lv J, Jiang M, Lin S, Deng Z. Xylitol production from xylose mother liquor: a novel strategy that combines the use of recombinant Bacillus subtilis and Candida maltosa. Microb Cell Fact 2011; 10:5. [PMID: 21299871 PMCID: PMC3046924 DOI: 10.1186/1475-2859-10-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Accepted: 02/07/2011] [Indexed: 11/10/2022] Open
Abstract
Background Xylose mother liquor has high concentrations of xylose (35%-40%) as well as other sugars such as L-arabinose (10%-15%), galactose (8%-10%), glucose (8%-10%), and other minor sugars. Due to the complexity of this mother liquor, further isolation of xylose by simple method is not possible. In China, more than 50,000 metric tons of xylose mother liquor was produced in 2009, and the management of sugars like xylose that present in the low-cost liquor is a problem. Results We designed a novel strategy in which Bacillus subtilis and Candida maltosa were combined and used to convert xylose in this mother liquor to xylitol, a product of higher value. First, the xylose mother liquor was detoxified with the yeast C. maltosa to remove furfural and 5-hydromethylfurfural (HMF), which are inhibitors of B. subtilis growth. The glucose present in the mother liquor was also depleted by this yeast, which was an added advantage because glucose causes carbon catabolite repression in B. subtilis. This detoxification treatment resulted in an inhibitor-free mother liquor, and the C. maltosa cells could be reused as biocatalysts at a later stage to reduce xylose to xylitol. In the second step, a recombinant B. subtilis strain with a disrupted xylose isomerase gene was constructed. The detoxified xylose mother liquor was used as the medium for recombinant B. subtilis cultivation, and this led to L-arabinose depletion and xylose enrichment of the medium. In the third step, the xylose was further reduced to xylitol by C. maltosa cells, and crystallized xylitol was obtained from this yeast transformation medium. C. maltosa transformation of the xylose-enriched medium resulted in xylitol with 4.25 g L-1·h-1 volumetric productivity and 0.85 g xylitol/g xylose specific productivity. Conclusion In this study, we developed a biological method for the purification of xylose from xylose mother liquor and subsequent preparation of xylitol by C. maltosa-mediated biohydrogenation of xylose.
Collapse
Affiliation(s)
- Hairong Cheng
- Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800# Dongchuan Road, Shanghai, China
| | | | | | | | | | | |
Collapse
|
35
|
A multitask ATPase serving different ABC-type sugar importers in Bacillus subtilis. J Bacteriol 2010; 192:5312-8. [PMID: 20693325 DOI: 10.1128/jb.00832-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis is able to utilize arabinopolysaccharides derived from plant biomass. Here, by combining genetic and physiological analyses we characterize the AraNPQ importer and identify primary and secondary transporters of B. subtilis involved in the uptake of arabinosaccharides. We show that the ABC-type importer AraNPQ is involved in the uptake of α-1,5-arabinooligosaccharides, at least up to four L-arabinosyl units. Although this system is the key transporter for α-1,5-arabinotriose and α-1,5-arabinotetraose, the results indicate that α-1,5-arabinobiose also is translocated by the secondary transporter AraE. This broad-specificity proton symporter is the major transporter for arabinose and also is accountable for the uptake of xylose and galactose. In addition, MsmX is shown to be the ATPase that energizes the incomplete AraNPQ importer. Furthermore, the results suggest the existence of at least one more unidentified MsmX-dependent ABC importer responsible for the uptake of nonlinear α-1,2- and α-1,3-arabinooligosaccharides. This study assigns MsmX as a multipurpose B. subtilis ATPase required to energize different saccharide transporters, the arabinooligosaccharide-specific AraNPQ-MsmX system, a putative MsmX-dependent ABC transporter specific for nonlinear arabinooligosaccharides, and the previously characterized maltodextrin-specific MdxEFG-MsmX system.
Collapse
|
36
|
Sugar transporters in efficient utilization of mixed sugar substrates: current knowledge and outlook. Appl Microbiol Biotechnol 2010; 85:471-80. [PMID: 19838697 DOI: 10.1007/s00253-009-2292-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 10/02/2009] [Accepted: 10/03/2009] [Indexed: 01/04/2023]
Abstract
There is increasing interest in production of transportation fuels and commodity chemicals from lignocellulosic biomass, most desirably through biological fermentation. Considerable effort has been expended to develop efficient biocatalysts that convert sugars derived from lignocellulose directly to value-added products. Glucose, the building block of cellulose, is the most suitable fermentation substrate for industrial microorganisms such as Escherichia coli, Corynebacterium glutamicum, and Saccharomyces cerevisiae. Other sugars including xylose, arabinose, mannose, and galactose that comprise hemicellulose are generally less efficient substrates in terms of productivity and yield. Although metabolic engineering including introduction of functional pentose-metabolizing pathways into pentose-incompetent microorganisms has provided steady progress in pentose utilization, further improvements in sugar mixture utilization by microorganisms is necessary. Among a variety of issues on utilization of sugar mixtures by the microorganisms, recent studies have started to reveal the importance of sugar transporters in microbial fermentation performance. In this article, we review current knowledge on diversity and functions of sugar transporters, especially those associated with pentose uptake in microorganisms. Subsequently, we review and discuss recent studies on engineering of sugar transport as a driving force for efficient bioconversion of sugar mixtures derived from lignocellulose.
Collapse
|
37
|
Sasaki M, Jojima T, Kawaguchi H, Inui M, Yukawa H. Engineering of pentose transport in Corynebacterium glutamicum to improve simultaneous utilization of mixed sugars. Appl Microbiol Biotechnol 2009; 85:105-15. [DOI: 10.1007/s00253-009-2065-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2009] [Revised: 05/29/2009] [Accepted: 05/29/2009] [Indexed: 11/28/2022]
|
38
|
Inácio JM, Correia IL, de Sá-Nogueira I. Two distinct arabinofuranosidases contribute to arabino-oligosaccharide degradation in Bacillus subtilis. MICROBIOLOGY-SGM 2008; 154:2719-2729. [PMID: 18757805 DOI: 10.1099/mic.0.2008/018978-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacillus subtilis produces alpha-l-arabinofuranosidases (EC 3.2.1.55; AFs) capable of releasing arabinosyl oligomers and l-arabinose from plant cell walls. Here, we show by insertion-deletion mutational analysis that genes abfA and xsa(asd), herein renamed abf2, encode AFs responsible for the majority of the intracellular AF activity in B. subtilis. Both enzyme activities were shown to be cytosolic and functional studies indicated that arabino-oligomers are natural substrates for the AFs. The products of the two genes were overproduced in Escherichia coli, purified and characterized. The molecular mass of the purified AbfA and Abf2 was about 58 kDa and 57 kDa, respectively. However, native PAGE gradient gel analysis and cross-linking assays detected higher-order structures (>250 kDa), suggesting a multimeric organization of both enzymes. Kinetic experiments at 37 degrees C, with p-nitrophenyl-alpha-l-arabinofuranoside as substrate, gave an apparent K(m) of 0.498 mM and 0.421 mM, and V(max) of 317 U mg(-1) and 311 U mg(-1) for AbfA and Abf2, respectively. The two enzymes displayed maximum activity at 50 degrees C and 60 degrees C, respectively, and both proteins were most active at pH 8.0. AbfA and Abf2 both belong to family 51 of the glycoside hydrolases but have different substrate specificity. AbfA acts preferentially on (1-->5) linkages of linear alpha-1,5-l-arabinan and alpha-1,5-linked arabino-oligomers, and is much less effective on branched sugar beet arabinan and arabinoxylan and arabinogalactan. In contrast, Abf2 is most active on (1-->2) and (1-->3) linkages of branched arabinan and arabinoxylan, suggesting a concerted contribution of these enzymes to optimal utilization of arabinose-containing polysaccharides by B. subtilis.
Collapse
Affiliation(s)
- José Manuel Inácio
- Laboratory of Microbial Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apt 127, 2781-901 Oeiras, Portugal
| | - Isabel Lopes Correia
- Laboratory of Microbial Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apt 127, 2781-901 Oeiras, Portugal
| | - Isabel de Sá-Nogueira
- Departamento de CiÁncias da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal.,Laboratory of Microbial Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apt 127, 2781-901 Oeiras, Portugal
| |
Collapse
|
39
|
Carbon catabolite repression in Bacillus subtilis: quantitative analysis of repression exerted by different carbon sources. J Bacteriol 2008; 190:7275-84. [PMID: 18757537 DOI: 10.1128/jb.00848-08] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In many bacteria glucose is the preferred carbon source and represses the utilization of secondary substrates. In Bacillus subtilis, this carbon catabolite repression (CCR) is achieved by the global transcription regulator CcpA, whose activity is triggered by the availability of its phosphorylated cofactors, HPr(Ser46-P) and Crh(Ser46-P). Phosphorylation of these proteins is catalyzed by the metabolite-controlled kinase HPrK/P. Recent studies have focused on glucose as a repressing substrate. Here, we show that many carbohydrates cause CCR. The substrates form a hierarchy in their ability to exert repression via the CcpA-mediated CCR pathway. Of the two cofactors, HPr is sufficient for complete CCR. In contrast, Crh cannot substitute for HPr on substrates that cause a strong repression. Determination of the phosphorylation state of HPr in vivo revealed a correlation between the strength of repression and the degree of phosphorylation of HPr at Ser46. Sugars transported by the phosphotransferase system (PTS) cause the strongest repression. However, the phosphorylation state of HPr at its His15 residue and PTS transport activity have no impact on the global CCR mechanism, which is a major difference compared to the mechanism operative in Escherichia coli. Our data suggest that the hierarchy in CCR exerted by the different substrates is exclusively determined by the activity of HPrK/P.
Collapse
|
40
|
Characterization of abn2 (yxiA), encoding a Bacillus subtilis GH43 arabinanase, Abn2, and its role in arabino-polysaccharide degradation. J Bacteriol 2008; 190:4272-80. [PMID: 18408032 DOI: 10.1128/jb.00162-08] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extracellular depolymerization of arabinopolysaccharides by microorganisms is accomplished by arabinanases, xylanases, and galactanases. Here, we characterize a novel endo-alpha-1,5-l-arabinanase (EC 3.2.1.99) from Bacillus subtilis, encoded by the yxiA gene (herein renamed abn2) that contributes to arabinan degradation. Functional studies by mutational analysis showed that Abn2, together with previously characterized AbnA, is responsible for the majority of the extracellular arabinan activity in B. subtilis. Abn2 was overproduced in Escherichia coli, purified from the periplasmic fraction, and characterized with respect to substrate specificity and biochemical and physical properties. With linear-alpha-1,5-l-arabinan as the preferred substrate, the enzyme exhibited an apparent K(m) of 2.0 mg ml(-1) and V(max) of 0.25 mmol min(-1) mg(-1) at pH 7.0 and 50 degrees C. RNA studies revealed the monocistronic nature of abn2. Two potential transcriptional start sites were identified by primer extension analysis, and both a sigma(A)-dependent and a sigma(H)-dependent promoter were located. Transcriptional fusion studies revealed that the expression of abn2 is stimulated by arabinan and pectin and repressed by glucose; however, arabinose is not the natural inducer. Additionally, trans-acting factors and cis elements involved in transcription were investigated. Abn2 displayed a control mechanism at a level of gene expression different from that observed with AbnA. These distinct regulatory mechanisms exhibited by two members of extracellular glycoside hydrolase family 43 (GH43) suggest an adaptative strategy of B. subtilis for optimal degradation of arabinopolysaccharides.
Collapse
|
41
|
Glutamate metabolism in Bacillus subtilis: gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations of the system. J Bacteriol 2008; 190:3557-64. [PMID: 18326565 DOI: 10.1128/jb.00099-08] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glutamate is a central metabolite in all organisms since it provides the link between carbon and nitrogen metabolism. In Bacillus subtilis, glutamate is synthesized exclusively by the glutamate synthase, and it can be degraded by the glutamate dehydrogenase. In B. subtilis, the major glutamate dehydrogenase RocG is expressed only in the presence of arginine, and the bacteria are unable to utilize glutamate as the only carbon source. In addition to rocG, a second cryptic gene (gudB) encodes an inactive glutamate dehydrogenase. Mutations in rocG result in the rapid accumulation of gudB1 suppressor mutations that code for an active enzyme. In this work, we analyzed the physiological significance of this constellation of genes and enzymes involved in glutamate metabolism. We found that the weak expression of rocG in the absence of the inducer arginine is limiting for glutamate utilization. Moreover, we addressed the potential ability of the active glutamate dehydrogenases of B. subtilis to synthesize glutamate. Both RocG and GudB1 were unable to catalyze the anabolic reaction, most probably because of their very high K(m) values for ammonium. In contrast, the Escherichia coli glutamate dehydrogenase is able to produce glutamate even in the background of a B. subtilis cell. B. subtilis responds to any mutation that interferes with glutamate metabolism with the rapid accumulation of extragenic or intragenic suppressor mutations, bringing the glutamate supply into balance. Similarly, with the presence of a cryptic gene, the system can flexibly respond to changes in the external glutamate supply by the selection of mutations.
Collapse
|
42
|
Bocchini DA, Gomes E, Da Silva R. Xylanase Production by Bacillus circulans D1 Using Maltose as Carbon Source. Appl Biochem Biotechnol 2007; 146:29-37. [DOI: 10.1007/s12010-007-8051-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Accepted: 09/05/2007] [Indexed: 11/28/2022]
|
43
|
Ashiuchi M, Nishikawa Y, Matsunaga K, Yamamoto M, Shimanouchi K, Misono H. Genetic design of conditional d-glutamate auxotrophy for Bacillus subtilis: Use of a vector-borne poly-γ-glutamate synthetic system. Biochem Biophys Res Commun 2007; 362:646-50. [PMID: 17720142 DOI: 10.1016/j.bbrc.2007.08.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/03/2007] [Indexed: 11/26/2022]
Abstract
Bacillus subtilis possesses two glutamate racemase isozymes, RacE and YrpC. For the first time, we succeeded in constructing glutamate racemase-gene disruptants of B. subtilis. Phenotypic analysis of their D-glutamate auxotrophy indicated that the RacE-type glutamate racemase is important for ensuring maximum growth rate but dispensable. The YrpC-type glutamate racemase probably operates as an anaplerotic enzyme for RacE, especially under liquid culture conditions. We found novel applicability of RacE-less mutants inheriting only a marginal activity for endogenous D-glutamate supply, viz. the employment for the in vivo identification of D-glutamate-consuming systems. In fact, the genetic induction of a poly-gamma-glutamate synthetic system led a RacE-less mutant to severe growth suppression, which was overcome in the presence of a high concentration of exogenous D-glutamate. The results indicate that a significant amount of D-glutamate is consumed during poly-glutamate biosynthesis. To our knowledge, this is the first report of conditional D-glutamate auxotrophy for B. subtilis.
Collapse
Affiliation(s)
- Makoto Ashiuchi
- Department of Bioresources Science, Kochi University, Nankoku, Kochi 783-8502, Japan.
| | | | | | | | | | | |
Collapse
|
44
|
Franco IS, Mota LJ, Soares CM, de Sá-Nogueira I. Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon. Nucleic Acids Res 2007; 35:4755-66. [PMID: 17617643 PMCID: PMC1950556 DOI: 10.1093/nar/gkm509] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In the absence of arabinose, the AraR transcription factor represses the expression of genes involved in the utilization of arabinose, xylose and galactose in Bacillus subtilis. AraR exhibits a chimeric organization: the N-terminal DNA-binding region belongs to the GntR family and the C-terminal effector-binding domain is homologous to the GalR/LacI family. Here, the AraR-DNA-binding interactions were characterized in vivo and in vitro. The effect of residue substitutions in the AraR N-terminal domain and of base-pair exchanges into an AraR-DNA-binding operator site were examined by assaying for AraR-mediated regulatory activity in vivo and DNA-binding activity in vitro. The results showed that residues K4, R45 and Q61, located in or near the winged-helix DNA-binding motif, were the most critical amino acids required for AraR function. In addition, the analysis of the various mutations in an AraR palindromic operator sequence indicated that bases G9, A11 and T16 are crucial for AraR binding. Moreover, an AraR mutant M34T was isolated that partially suppressed the effect of mutations in the regulatory cis-elements. Together, these findings extend the knowledge on the nature of AraR nucleoprotein complexes and provide insight into the mechanism that underlies the mode of action of AraR and its orthologues.
Collapse
Affiliation(s)
- Irina Saraiva Franco
- Laboratory of Microbial Genetics and Laboratory of Protein Modeling, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. Av. da República, Apt. 127, 2781-901 Oeiras and Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal
| | - Luís Jaime Mota
- Laboratory of Microbial Genetics and Laboratory of Protein Modeling, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. Av. da República, Apt. 127, 2781-901 Oeiras and Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal
| | - Cláudio Manuel Soares
- Laboratory of Microbial Genetics and Laboratory of Protein Modeling, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. Av. da República, Apt. 127, 2781-901 Oeiras and Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal
| | - Isabel de Sá-Nogueira
- Laboratory of Microbial Genetics and Laboratory of Protein Modeling, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. Av. da República, Apt. 127, 2781-901 Oeiras and Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal
- *To whom correspondence should be addressed.+351 21 4469524+351 21 4411277
| |
Collapse
|
45
|
Shipkowski S, Brenchley JE. Bioinformatic, genetic, and biochemical evidence that some glycoside hydrolase family 42 beta-galactosidases are arabinogalactan type I oligomer hydrolases. Appl Environ Microbiol 2006; 72:7730-8. [PMID: 17056685 PMCID: PMC1694227 DOI: 10.1128/aem.01306-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycoside hydrolases are organized into glycoside hydrolase families (GHFs) and within this larger group, the beta-galactosidases are members of four families: 1, 2, 35, and 42. Most genes encoding GHF 42 enzymes are from prokaryotes unlikely to encounter lactose, suggesting a different substrate for these enzymes. In search of this substrate, we analyzed genes neighboring GHF 42 genes in databases and detected an arrangement implying that these enzymes might hydrolyze oligosaccharides released by GHF 53 enzymes from arabinogalactan type I, a pectic plant polysaccharide. Because Bacillus subtilis has adjacent GHF 42 and GHF 53 genes, we used it to test the hypothesis that a GHF 42 enzyme (LacA) could act on the oligosaccharides released by a GHF 53 enzyme (GalA) from galactan. We cloned these genes, plus a second GHF 42 gene from B. subtilis, yesZ, into Escherichia coli and demonstrated that cells expressing LacA with GalA gained the ability to use galactan as a carbon source. We constructed B. subtilis mutants and showed that the increased beta-galactosidase activity generated in response to the addition of galactan was eliminated by inactivating lacA or galA but unaffected by the inactivation of yesZ. As further demonstration, we overexpressed the LacA and GalA proteins in E. coli and demonstrated that these enzymes degrade galactan in vitro as assayed by thin-layer chromatography. Our work provides the first in vivo evidence for a function of some GHF 42 beta-galactosidases. Similar functions for other beta-galactosidases in both GHFs 2 and 42 are suggested by genomic data.
Collapse
Affiliation(s)
- Stephanie Shipkowski
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 209 South Frear, University Park, PA 16802, USA.
| | | |
Collapse
|
46
|
Franco IS, Mota LJ, Soares CM, de Sá-Nogueira I. Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding. J Bacteriol 2006; 188:3024-36. [PMID: 16585763 PMCID: PMC1446991 DOI: 10.1128/jb.188.8.3024-3036.2006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis AraR transcription factor represses at least 13 genes required for the extracellular degradation of arabinose-containing polysaccharides, transport of arabinose, arabinose oligomers, xylose, and galactose, intracellular degradation of arabinose oligomers, and further catabolism of this sugar. AraR exhibits a chimeric organization comprising a small N-terminal DNA-binding domain that contains a winged helix-turn-helix motif similar to that seen with the GntR family and a larger C-terminal domain homologous to that of the LacI/GalR family. Here, a model for AraR was derived based on the known crystal structures of the FadR and PurR regulators from Escherichia coli. We have used random mutagenesis, deletion, and construction of chimeric LexA-AraR fusion proteins to map the functional domains of AraR required for DNA binding, dimerization, and effector binding. Moreover, predictions for the functional role of specific residues were tested by site-directed mutagenesis. In vivo analysis identified particular amino acids required for dimer assembly, formation of the nucleoprotein complex, and composition of the sugar-binding cleft. This work presents a structural framework for the function of AraR and provides insight into the mechanistic mode of action of this modular repressor.
Collapse
Affiliation(s)
- Irina Saraiva Franco
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apt. 127, 2781-901 Oeiras, Portugal
| | | | | | | |
Collapse
|
47
|
Kawaguchi H, Vertès AA, Okino S, Inui M, Yukawa H. Engineering of a xylose metabolic pathway in Corynebacterium glutamicum. Appl Environ Microbiol 2006; 72:3418-28. [PMID: 16672486 PMCID: PMC1472363 DOI: 10.1128/aem.72.5.3418-3428.2006] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 03/08/2006] [Indexed: 11/20/2022] Open
Abstract
The aerobic microorganism Corynebacterium glutamicum was metabolically engineered to broaden its substrate utilization range to include the pentose sugar xylose, which is commonly found in agricultural residues and other lignocellulosic biomass. We demonstrated the functionality of the corynebacterial xylB gene encoding xylulokinase and constructed two recombinant C. glutamicum strains capable of utilizing xylose by cloning the Escherichia coli gene xylA encoding xylose isomerase, either alone (strain CRX1) or in combination with the E. coli gene xylB (strain CRX2). These genes were provided on a high-copy-number plasmid and were under the control of the constitutive promoter trc derived from plasmid pTrc99A. Both recombinant strains were able to grow in mineral medium containing xylose as the sole carbon source, but strain CRX2 grew faster on xylose than strain CRX1. We previously reported the use of oxygen deprivation conditions to arrest cell replication in C. glutamicum and divert carbon source utilization towards product production rather than towards vegetative functions (M. Inui, S. Murakami, S. Okino, H. Kawaguchi, A. A. Vertès, and H. Yukawa, J. Mol. Microbiol. Biotechnol. 7:182-196, 2004). Under these conditions, strain CRX2 efficiently consumed xylose and produced predominantly lactic and succinic acids without growth. Moreover, in mineral medium containing a sugar mixture of 5% glucose and 2.5% xylose, oxygen-deprived strain CRX2 cells simultaneously consumed both sugars, demonstrating the absence of diauxic phenomena relative to the new xylA-xylB construct, albeit glucose-mediated regulation still exerted a measurable influence on xylose consumption kinetics.
Collapse
Affiliation(s)
- Hideo Kawaguchi
- Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizu-cho, Soraku-gun, Kyoto 619-0292, Japan
| | | | | | | | | |
Collapse
|
48
|
Raposo MP, Inácio JM, Mota LJ, de Sá-Nogueira I. Transcriptional regulation of genes encoding arabinan-degrading enzymes in Bacillus subtilis. J Bacteriol 2004; 186:1287-96. [PMID: 14973026 PMCID: PMC344415 DOI: 10.1128/jb.186.5.1287-1296.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis produces hemicellulases capable of releasing arabinosyl oligomers and arabinose from plant cell walls. In this work, we characterize the transcriptional regulation of three genes encoding arabinan-degrading enzymes that are clustered with genes encoding enzymes that further catabolize arabinose. The abfA gene comprised in the metabolic operon araABDLMNPQ-abfA and the xsa gene located 23 kb downstream most probably encode alpha-L-arabinofuranosidases (EC 3.2.1.55). Here, we show that the abnA gene, positioned immediately upstream from the metabolic operon, encodes an endo-alpha-1,5-arabinanase (EC 3.2.1.99). Furthermore, by in vivo RNA studies, we inferred that abnA and xsa are monocistronic and are transcribed from sigma(A)-like promoters. Transcriptional fusion analysis revealed that the expression of the three arabinases is induced by arabinose and arabinan and is repressed by glucose. The levels of induction by arabinose and arabinan are higher during early postexponential growth, suggesting a temporal regulation. Moreover, the induction mechanism of these genes is mediated through negative control by the key regulator of arabinose metabolism, AraR. Thus, we analyzed AraR-DNA interactions by in vitro quantitative DNase I footprinting and in vivo analysis of single-base-pair substitutions within the promoter regions of xsa and abnA. The results indicate that transcriptional repression of the abfA and xsa genes is achieved by a tightly controlled mechanism but that the regulation of abnA is more flexible. We suggest that the expression of genes encoding extracellular degrading enzymes of arabinose-containing polysaccharides, transport systems, and intracellular enzymes involved in further catabolism is regulated by a coordinate mechanism triggered by arabinose via AraR.
Collapse
Affiliation(s)
- Maria Paiva Raposo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
| | | | | | | |
Collapse
|
49
|
Bayer EA, Belaich JP, Shoham Y, Lamed R. The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol 2004; 58:521-54. [PMID: 15487947 DOI: 10.1146/annurev.micro.57.030502.091022] [Citation(s) in RCA: 597] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discrete multicomponent, multienzyme cellulosome complex of anaerobic cellulolytic bacteria provides enhanced synergistic activity among the different resident enzymes to efficiently hydrolyze intractable cellulosic and hemicellulosic substrates of the plant cell wall. A pivotal noncatalytic subunit called scaffoldin secures the various enzymatic subunits into the complex via the cohesin-dockerin interaction. The specificity characteristics and tenacious binding between the scaffoldin-based cohesin modules and the enzyme-borne dockerin domains dictate the supramolecular architecture of the cellulosome. The diversity in cellulosome architecture among the known cellulosome-producing bacteria is manifest in the arrangement of their genes in either multiple-scaffoldin or enzyme-linked clusters on the genome. The recently described three-dimensional crystal structure of the cohesin-dockerin heterodimer sheds light on the critical amino acids that contribute to this high-affinity protein-protein interaction. In addition, new information regarding the regulation of cellulosome-related genes, budding genetic tools, and emerging genomics of cellulosome-producing bacteria promises new insight into the assembly and consequences of the multienzyme complex.
Collapse
Affiliation(s)
- Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
| | | | | | | |
Collapse
|
50
|
Inácio JM, Costa C, de Sá-Nogueira I. Distinct molecular mechanisms involved in carbon catabolite repression of the arabinose regulon in Bacillus subtilis. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2345-2355. [PMID: 12949161 DOI: 10.1099/mic.0.26326-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Bacillus subtilis proteins involved in the utilization of L-arabinose are encoded by the araABDLMNPQ-abfA metabolic operon and by the araE/araR divergent unit. Transcription from the ara operon, araE transport gene and araR regulatory gene is induced by L-arabinose and negatively controlled by AraR. Additionally, expression of both the ara operon and the araE gene is regulated at the transcriptional level by glucose repression. Here, by transcriptional fusion analysis in different mutant backgrounds, it is shown that CcpA most probably complexed with HPr-Ser46-P plays the major role in carbon catabolite repression of the ara regulon by glucose and glycerol. Site-directed mutagenesis and deletion analysis indicate that two catabolite responsive elements (cres) present in the ara operon (cre araA and cre araB) and one cre in the araE gene (cre araE) are implicated in this mechanism. Furthermore, cre araA located between the promoter region of the ara operon and the araA gene, and cre araB placed 2 kb downstream within the araB gene are independently functional and both contribute to glucose repression. In Northern blot analysis, in the presence of glucose, a CcpA-dependent transcript consistent with a message stopping at cre araB was detected, suggesting that transcription 'roadblocking' of RNA polymerase elongation is the most likely mechanism operating in this system. Glucose exerts an additional repression of the ara regulon, which requires a functional araR.
Collapse
Affiliation(s)
- José Manuel Inácio
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida de República, Apartado 127, 2781-901 Oeiras, Portugal
| | - Carla Costa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida de República, Apartado 127, 2781-901 Oeiras, Portugal
| | - Isabel de Sá-Nogueira
- Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida de República, Apartado 127, 2781-901 Oeiras, Portugal
| |
Collapse
|