1
|
Lim SJ, Noor NDM, Sabri S, Ali MSM, Salleh AB, Oslan SN. Extracellular BSA-degrading SAPs in the rare pathogen Meyerozyma guilliermondii strain SO as potential virulence factors in candidiasis. Microb Pathog 2024; 193:106773. [PMID: 38960213 DOI: 10.1016/j.micpath.2024.106773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 05/08/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
Meyerozyma guilliermondii (Candida guilliermondii) is one of the Candida species associated with invasive candidiasis. With the potential for expressing industrially important enzymes, M. guilliermondii strain SO possessed 99 % proteome similarity with the clinical ATCC 6260 isolate and showed pathogenicity towards zebrafish embryos. Recently, three secreted aspartyl proteinases (SAPs) were computationally identified as potential virulence factors in this strain without in vitro verification of SAP activity. The quantification of Candida SAPs activity in liquid broth were also scarcely reported. Thus, this study aimed to characterize M. guilliermondii strain SO's ability to produce SAPs (MgSAPs) in different conditions (morphology and medium) besides analyzing its growth profile. MgSAPs' capability to cleave bovine serum albumin (BSA) was also determined to propose that MgSAPs as the potential virulence factors compared to the avirulent Saccharomyces cerevisiae. M. guilliermondii strain SO produced more SAPs (higher activity) in yeast nitrogen base-BSA-dextrose broth compared to yeast extract-BSA-dextrose broth despite insignificantly different SAP activity in both planktonic and biofilm cells. FeCl3 supplementation significantly increased the specific protein activity (∼40 %). The BSA cleavage by MgSAPs at an acidic pH was proven through semi-quantitative SDS-PAGE, sharing similar profile with HIV-1 retropepsin. The presented work highlighted the MgSAPs on fungal cell wall and extracellular milieu during host infection could be corroborated to the quantitative production in different growth modes presented herein besides shedding lights on the potential usage of retropepsin's inhibitors in treating candidiasis. Molecular and expression analyses of MgSAPs and their deletion should be further explored to attribute their respective virulence effects.
Collapse
Affiliation(s)
- Si Jie Lim
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Suriana Sabri
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Siti Nurbaya Oslan
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| |
Collapse
|
2
|
Ding Y, He W, Dai W, Xie X, Pan Y, Tang X, Zheng R, Zhou X. Quality and flavor development of solid-state fermented surimi with Actinomucor elegans: A perspective on the impacts of carbon and nitrogen sources. Food Chem 2024; 447:139053. [PMID: 38518616 DOI: 10.1016/j.foodchem.2024.139053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/22/2024] [Accepted: 03/14/2024] [Indexed: 03/24/2024]
Abstract
The influence of four carbon and nitrogen substrates on the quality and flavor of a novel surimi-based product fermented with Actinomucor elegans (A. elegans) was investigated, with a focus on carbon and nitrogen catabolite repression. The results showed that the substrate significantly affected mycelial growth, enzyme activities, and the metabolites of A. elegans. Although glucose significantly promoted A. elegans growth by 116.69%, it decreased enzyme secretion by 69.79% for α-amylase and 59.80% for protease, most likely by triggering the carbon catabolite repression pathway. Starch, soy protein, and wheat gluten substantially affected the textural properties of the fermented surimi. Furthermore, wheat gluten significantly promoted the protease activity (102.70%) and increased protein degradation during surimi fermentation. The fishy odor of surimi was alleviated through fermentation, and a correlation between the volatile compounds and A. elegans metabolism was observed. These results explore fermentation substrates in filamentous fungi metabolism from a catabolite repression perspective.
Collapse
Affiliation(s)
- Yicheng Ding
- Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, PR China; College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Wenjia He
- Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, PR China; College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Wangli Dai
- Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, PR China; College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xiaoben Xie
- Shaoxing Xianheng Food Co., Ltd, Shaoxing 312000, PR China
| | - Yibiao Pan
- Shaoxing Xianheng Food Co., Ltd, Shaoxing 312000, PR China
| | - Xiaoling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Renchao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China.
| | - Xuxia Zhou
- Zhejiang Key Laboratory of Green, Low-carbon and Efficient Development of Marine Fishery Resources, Hangzhou 310014, PR China; College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, PR China.
| |
Collapse
|
3
|
Wang Y, Hu J, Gao X, Cao Y, Ye S, Chen C, Wang L, Xu H, Guo M, Zhang D, Zhou R, Hua Y, Zhao Y. cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans. mBio 2024; 15:e0114424. [PMID: 38916345 PMCID: PMC11253593 DOI: 10.1128/mbio.01144-24] [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: 04/14/2024] [Accepted: 05/30/2024] [Indexed: 06/26/2024] Open
Abstract
The cAMP receptor proteins (CRPs) play a critical role in bacterial environmental adaptation by regulating global gene expression levels via cAMP binding. Here, we report the structure of DdrI, a CRP family protein from Deinococcus radiodurans. Combined with biochemical, kinetic, and molecular dynamics simulations analyses, our results indicate that DdrI adopts a DNA-binding conformation in the absence of cAMP and can form stable complexes with the target DNA sequence of classical CRPs. Further analysis revealed that the high-affinity cAMP binding pocket of DdrI is partially filled with Tyr113-Arg55-Glu65 sidechains, mimicking the anti-cAMP-mediated allosteric transition. Moreover, the second syn-cAMP binding site of DdrI at the protein-DNA interface is more negatively charged compared to that of classical CRPs, and manganese ions can enhance its DNA binding affinity. DdrI can also bind to a target sequence that mimics another transcription factor, DdrO, suggesting potential cross-talk between these two transcription factors. These findings reveal a class of CRPs that are independent of cAMP activation and provide valuable insights into the environmental adaptation mechanisms of D. radiodurans.IMPORTANCEBacteria need to respond to environmental changes at the gene transcriptional level, which is critical for their evolution, virulence, and industrial applications. The cAMP receptor protein (CRP) of Escherichia coli (ecCRP) senses changes in intracellular cAMP levels and is a classic example of allosteric effects in textbooks. However, the structures and biochemical activities of CRPs are not generally conserved and there exist different mechanisms. In this study, we found that the proposed CRP from Deinococcus radiodurans, DdrI, exhibited DNA binding ability independent of cAMP binding and adopted an apo structure resembling the activated CRP. Manganese can enhance the DNA binding of DdrI while allowing some degree of freedom for its target sequence. These results suggest that CRPs can evolve to become a class of cAMP-independent global regulators, enabling bacteria to adapt to different environments according to their characteristics. The first-discovered CRP family member, ecCRP (or CAP) may well not be typical of the family and be very different to the ancestral CRP-family transcription factor.
Collapse
Affiliation(s)
- Yudong Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jing Hu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xufan Gao
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuchen Cao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shumai Ye
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Cheng Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Miao Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Dong Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ruhong Zhou
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
- Department of Chemistry, Columbia University, New York, New York, USA
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
4
|
Ma Q, Yi J, Tang Y, Geng Z, Zhang C, Sun W, Liu Z, Xiong W, Wu H, Xie X. Co-utilization of carbon sources in microorganisms for the bioproduction of chemicals. Biotechnol Adv 2024; 73:108380. [PMID: 38759845 DOI: 10.1016/j.biotechadv.2024.108380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/14/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Carbon source is crucial for the cell growth and metabolism in microorganisms, and its utilization significantly affects the synthesis efficiency of target products in microbial cell factories. Compared with a single carbon source, co-utilizing carbon sources provide an alternative approach to optimize the utilization of different carbon sources for efficient biosynthesis of many chemicals with higher titer/yield/productivity. However, the efficiency of bioproduction is significantly limited by the sequential utilization of a preferred carbon source and secondary carbon sources, attributed to carbon catabolite repression (CCR). This review aimed to introduce the mechanisms of CCR and further focus on the summary of the strategies for co-utilization of carbon sources, including alleviation of CCR, engineering of the transport and metabolism of secondary carbon sources, compulsive co-utilization in single culture, co-utilization of carbon sources via co-culture, and evolutionary approaches. The findings of representative studies with a significant improvement in the bioproduction of chemicals via the co-utilization of carbon sources were discussed in this review. It suggested that by combining rational metabolic engineering and irrational evolutionary approaches, co-utilizing carbon sources can significantly contribute to the bioproduction of chemicals.
Collapse
Affiliation(s)
- Qian Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jinhang Yi
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yulin Tang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zihao Geng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chunyue Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenchao Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhengkai Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenwen Xiong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Heyun Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China.
| |
Collapse
|
5
|
Tao C, Wang Q, Ji J, Zhou Z, Yue B, Zhang R, Jiang S, Yuan T. Utilization of carbon catabolite repression for efficiently biotransformation of anthraquinone O-glucuronides by Streptomyces coeruleorubidus DM. Front Microbiol 2024; 15:1393073. [PMID: 38690368 PMCID: PMC11058961 DOI: 10.3389/fmicb.2024.1393073] [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: 02/28/2024] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
Carbon catabolite repression (CCR) is a highly conserved mechanism that regulates carbon source utilization in Streptomyces. CCR has a negative impact on secondary metabolite fermentation, both in industrial and research settings. In this study, CCR was observed in the daunorubicin (DNR)-producing strain Streptomyces coeruleorubidus DM, which was cultivated in high concentration of carbohydrates. Unexpectedly, DM exhibited a high ability for anthraquinone glucuronidation biotransformation under CCR conditions with a maximum bioconversion rate of 95% achieved at pH 6, 30°C for 24 h. The co-utilization of glucose and sucrose resulted in the highest biotransformation rate compared to other carbon source combinations. Three novel anthraquinone glucuronides were obtained, with purpurin-O-glucuronide showing significantly improved water solubility, antioxidant activity, and antibacterial bioactivity. Comparative transcript analysis revealed that glucose and sucrose utilization were significantly upregulated as DM cultivated under CCR condition, which strongly enhance the biosynthetic pathway of the precursors Uridine diphosphate glucuronic acid (UDPGA). Meanwhile, the carbon metabolic flux has significantly enhanced the fatty acid biosynthesis, the exhaust of acetyl coenzyme A may lead to the complete repression of the biosynthesis of DNR, Additionally, the efflux transporter genes were simultaneously downregulated, which may contribute to the anthraquinones intracellular glucuronidation. Overall, our findings demonstrate that utilizing CCR can be a valuable strategy for enhancing the biotransformation efficiency of anthraquinone O-glucuronides by DM. This approach has the potential to improve the bioavailability and therapeutic potential of these compounds, opening up new possibilities for their pharmaceutical applications.
Collapse
Affiliation(s)
- Chen Tao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Quyi Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Junyang Ji
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ziyue Zhou
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bingjie Yue
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ran Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shu Jiang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medical Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tianjie Yuan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| |
Collapse
|
6
|
Xia L, Hou Z, Zhu F, Wen J. Enhancing surfactin production in Bacillus subtilis: Insights from proteomic analysis of nitrate-induced overproduction and strategies for combinatorial metabolic engineering. BIORESOURCE TECHNOLOGY 2024; 397:130499. [PMID: 38417461 DOI: 10.1016/j.biortech.2024.130499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Surfactin biosynthesis in Bacillus subtilis is intricately regulated by environmental conditions. In the present study, addition of nitrate, a nitrogen source, increased the production of surfactin in B. subtilis ATCC 21332, whereas its absence resulted in minimal or no surfactin production. Proteomics revealed the mechanism underlying nitrate-induced surfactin overproduction, identifying three key differential proteins (preprotein translocase subunit SecA, signal recognition particle receptor FtsY, and cell division adenosine triphosphate-binding protein FtsE) relevant to surfactin transport and regulation. Combinatorial metabolic engineering strategies (enhanced nitrate reduction, fatty acid hydroxylation, rational transporter engineering, and feeding) led to a 41.4-fold increase in surfactin production compared with the initial production in the wild-type strain. This study provides insights into the molecular mechanism of nitrate-induced surfactin overproduction and strategies to enhance the performance of surfactin-producing strains.
Collapse
Affiliation(s)
- Li Xia
- Key Laboratory of Systems Bioengineering of the Ministry of Education, Tianjin University, Tianjin, 300350, PR China; Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin 300350, PR China; Center for Chemical Science and Engineering, Tianjin University, 300350, PR China
| | - Zhengjie Hou
- Key Laboratory of Systems Bioengineering of the Ministry of Education, Tianjin University, Tianjin, 300350, PR China; Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin 300350, PR China
| | - Fuzhou Zhu
- Key Laboratory of Systems Bioengineering of the Ministry of Education, Tianjin University, Tianjin, 300350, PR China; Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin 300350, PR China; Center for Chemical Science and Engineering, Tianjin University, 300350, PR China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering of the Ministry of Education, Tianjin University, Tianjin, 300350, PR China; Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin 300350, PR China; Center for Chemical Science and Engineering, Tianjin University, 300350, PR China.
| |
Collapse
|
7
|
Zhu Z, Zou G, Chai S, Xiao M, Wang Y, Wang P, Zhou Z. The protein methyltransferase TrSAM inhibits cellulase gene expression by interacting with the negative regulator ACE1 in Trichoderma reesei. Commun Biol 2024; 7:375. [PMID: 38548869 PMCID: PMC10978942 DOI: 10.1038/s42003-024-06072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/19/2024] [Indexed: 04/01/2024] Open
Abstract
Protein methylation is a commonly posttranslational modification of transcriptional regulators to fine-tune protein function, however, whether this regulation strategy participates in the regulation of lignocellulase synthesis and secretion in Trichoderma reesei remains unexplored. Here, a putative protein methyltransferase (TrSAM) is screened from a T. reesei mutant with the ability to express heterologous β-glucosidase efficiently even under glucose repression. The deletion of its encoding gene trsam causes a significant increase of cellulase activities in all tested T. reesei strains, including transformants of expressing heterologous genes using cbh1 promotor. Further investigation confirms that TrSAM interacts with the cellulase negative regulator ACE1 via its amino acid residue Arg383, which causes a decrease in the ACE1-DNA binding affinity. The enzyme activity of a T. reesei strain harboring ACE1R383Q increases by 85.8%, whereas that of the strains with trsam or ace1 deletion increases by more than 100%. By contrast, the strain with ACE1R383K shows no difference to the parent strain. Taken together, our results demonstrate that TrSAM plays an important role in regulating the expression of cellulase and heterologous proteins initiated by cbh1 promotor through interacting with ACE1R383. Elimination and mutation of TrSAM and its downstream ACE1 alleviate the carbon catabolite repression (CCR) in expressing cellulase and heterologous protein in varying degrees. This provides a new solution for the exquisite modification of T. reesei chassis.
Collapse
Affiliation(s)
- Zhihua Zhu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gen Zou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Science, 1000 Jinqi Rd, Shanghai, 201403, China
| | - Shunxing Chai
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meili Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yinmei Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 FengLin Rd, Shanghai, 200032, China.
| |
Collapse
|
8
|
Abrashev R, Krumova E, Petrova P, Eneva R, Dishliyska V, Gocheva Y, Engibarov S, Miteva-Staleva J, Spasova B, Kolyovska V, Angelova M. Glucose Catabolite Repression Participates in the Regulation of Sialidase Biosynthesis by Antarctic Strain Penicillium griseofulvum P29. J Fungi (Basel) 2024; 10:241. [PMID: 38667912 PMCID: PMC11051313 DOI: 10.3390/jof10040241] [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: 02/28/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Sialidases (neuraminidases) catalyze the removal of terminal sialic acid residues from glycoproteins. Novel enzymes from non-clinical isolates are of increasing interest regarding their application in the food and pharmaceutical industry. The present study aimed to evaluate the participation of carbon catabolite repression (CCR) in the regulation of cold-active sialidase biosynthesis by the psychrotolerant fungal strain Penicillium griseofulvum P29, isolated from Antarctica. The presence of glucose inhibited sialidase activity in growing and non-growing fungal mycelia in a dose- and time-dependent manner. The same response was demonstrated with maltose and sucrose. The replacement of glucose with glucose-6-phosphate also exerted CCR. The addition of cAMP resulted in the partial de-repression of sialidase synthesis. The CCR in the psychrotolerant strain P. griseofulvum P29 did not depend on temperature. Sialidase might be subject to glucose repression by both at 10 and 25 °C. The fluorescent assay using 4MU-Neu5Ac for enzyme activity determination under increasing glucose concentrations evidenced that CCR may have a regulatory role in sialidase production. The real-time RT-PCR experiments revealed that the sialidase gene was subject to glucose repression. To our knowledge, this is the first report that has studied the effect of CCR on cold-active sialidase, produced by an Antarctic strain.
Collapse
Affiliation(s)
- Radoslav Abrashev
- Department of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria; (R.A.); (E.K.); (V.D.); (J.M.-S.); (B.S.)
| | - Ekaterina Krumova
- Department of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria; (R.A.); (E.K.); (V.D.); (J.M.-S.); (B.S.)
| | - Penka Petrova
- Department of General Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria; (P.P.); (R.E.); (Y.G.); (S.E.)
| | - Rumyana Eneva
- Department of General Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria; (P.P.); (R.E.); (Y.G.); (S.E.)
| | - Vladislava Dishliyska
- Department of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria; (R.A.); (E.K.); (V.D.); (J.M.-S.); (B.S.)
| | - Yana Gocheva
- Department of General Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria; (P.P.); (R.E.); (Y.G.); (S.E.)
| | - Stefan Engibarov
- Department of General Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria; (P.P.); (R.E.); (Y.G.); (S.E.)
| | - Jeny Miteva-Staleva
- Department of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria; (R.A.); (E.K.); (V.D.); (J.M.-S.); (B.S.)
| | - Boryana Spasova
- Department of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria; (R.A.); (E.K.); (V.D.); (J.M.-S.); (B.S.)
| | - Vera Kolyovska
- Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Academician G. Bonchev 25, 1113 Sofia, Bulgaria;
| | - Maria Angelova
- Department of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Academician G. Bonchev 26, 1113 Sofia, Bulgaria; (R.A.); (E.K.); (V.D.); (J.M.-S.); (B.S.)
| |
Collapse
|
9
|
Zeng D, Zhang Y, Ma X, Li J, Yin F, Li D, Bie W. Biosynthesis of poly(β-L-malic acid) from rubberwood enzymatic hydrolysates in co-fermentation by Aureobasidium pullulans. Int J Biol Macromol 2024; 257:128605. [PMID: 38061508 DOI: 10.1016/j.ijbiomac.2023.128605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/27/2023] [Accepted: 12/02/2023] [Indexed: 01/26/2024]
Abstract
Co-fermentation of multiple substrates has emerged as the most effective method to improve the yield of bioproducts. Herein, sustainable rubberwood enzymatic hydrolysates (RWH) were co-fermented by Aureobasidium pullulans to produce poly(β-L-malic acid) (PMA), and RWH + glucose/xylose was also investigated as co-substrates. Owing to low inhibitor concentration and abundant natural nitrogen source content of RWH, a high PMA yield of 0.45 g/g and a productivity of 0.32 g/L/h were obtained by RWH substrate fermentation. After optimization, PMA yields following the fermentation of RWH + glucose and RWH + xylose reached 59.92 g/L and 53.71 g/L, respectively, which were 52 % and 36 % higher than that after the fermentation of RWH. RWH + glucose more significantly affected the correlation between PMA yield and substrate concentration than RWH + xylose. The results demonstrated that the co-fermentation of RWH co-substrate is a promising method for the synthesis of bioproducts.
Collapse
Affiliation(s)
- Dongdong Zeng
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Yutian Zhang
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Xiaojun Ma
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, PR China.
| | - Jianing Li
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, PR China
| | - Fen Yin
- College of Mechanical Engineering, Qinghai University, Xining 810016, PR China
| | - Dongna Li
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Wenxuan Bie
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, PR China
| |
Collapse
|
10
|
Chen Y, Gao S, Zhou J, Zeng W. Chromatin regulator Eaf3p regulates nitrogen metabolism in Saccharomyces cerevisiae as a trans-acting factor. Appl Environ Microbiol 2023; 89:e0145723. [PMID: 38047643 PMCID: PMC10734424 DOI: 10.1128/aem.01457-23] [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: 08/24/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE In this study, the mechanism of chromatin regulator Eaf3p regulating nitrogen metabolism in S. cerevisiae was investigated. It provides theoretical support for epigenetic modifications of cells to alter the level of histone modifications, coordinate the expression of multiple genes, and make it more conducive to the co-metabolism of multiple nitrogen sources. Moreover, it provides new ideas for industrial brewing yeast strains to achieve nitrogen source metabolism balance, reduce the accumulation of harmful nitrogen metabolites, and improve fermentation efficiency. This study provides a reference for changing the performance of microbial strains and improving the quality of traditional fermentation products and provides a theoretical basis for studying epigenetic modification and nitrogen metabolism regulation. It has an important theoretical explanation and practical application value. In addition, this study also provides useful clues for the study.
Collapse
Affiliation(s)
- Yu Chen
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, China
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Song Gao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Weizhu Zeng
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| |
Collapse
|
11
|
Subramaniyan Y, Khan A, Fathima F, Rekha PD. Differential expression of urease genes and ureolytic activity of uropathogenic Escherichia coli and Pseudomonas aeruginosa isolates in different nutritional conditions. Arch Microbiol 2023; 205:383. [PMID: 37973630 DOI: 10.1007/s00203-023-03722-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
Uropathogens have adaptation strategies to survive in the host urinary tract by efficiently utilizing and tolerating the urinary metabolites. Many uropathogens harbour the enzyme urease for the breakdown of urea and the enzymatic breakdown of urea increases the pH and facilitate the struvite crystallization. In this study, the differential urease activity of uropathogenic Escherichia coli and Pseudomonas aeruginosa strains was investigated under different nutritional conditions. The experiments included measurement of growth, pH, urease activity, NH4-N generation and urease gene (ureC) expression among the bacterial strains under different conditions. Further, the implications of urea breakdown on the struvite crystallization in vitro and biofilm formation were also assessed. The study included urease positive isolates and for comparison urease negative isolates were included. Compared to the urease negative strains the urease positive strains formed higher biofilms and motility. The urease positive P. aeruginosa showed significantly higher (p < 0.01) pH and urease activity (A557-A630) compared to E. coli under experimental conditions. Further, supplementation of glucose to the growth media significantly increased the urease activity in P. aeruginosa and in contrast, it was significantly lower in E. coli. The expression profile of urease gene (ureC) was significantly higher (p < 0.001) in P. aeruginosa compared to E. coli and was consistent with the biochemical results of the urease activity under the nutritional conditions. The differential urease activity under two nutritional conditions influenced the biogenic struvite crystallization. It correlated with the urease activity showing higher crystallization rate in P. aeruginosa compared to E. coli. The results highlight the differential urease activity in two common uropathogens under different nutritional conditions that may have significant role on the regulation of virulence, pathogenicity and in the kidney stone disease.
Collapse
Affiliation(s)
- Yuvarajan Subramaniyan
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Altaf Khan
- Department of Urology, Yenepoya Medical College and Hospital, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Fida Fathima
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Punchappady Devasya Rekha
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangalore, 575018, India.
| |
Collapse
|
12
|
Ran Y, Yang Q, Zeng J, Li F, Cao Y, Xu Q, Qiao D, Xu H, Cao Y. Potential xylose transporters regulated by CreA improved lipid yield and furfural tolerance in oleaginous yeast Saitozyma podzolica zwy-2-3. BIORESOURCE TECHNOLOGY 2023; 386:129413. [PMID: 37390935 DOI: 10.1016/j.biortech.2023.129413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Lignocellulose's hydrolysate, a significant renewable source, contains xylose and furfural, making it challenging for industrial production of oleaginous yeast. On xylose fermentation with furfural treatment, OE::DN7263 and OE::DN7661 increased lipid yield and furfural tolerance versus WT, while, which of OE::CreA were decreased owing to CreA regulating DN7263 and DN7661 negatively. OE::CreA generated reactive oxygen species (ROS) causing oxidative damage. OE::DN7263, OE::DN7661, and ΔCreA reduced furfural via NADH; while ΔCreA produced less ROS and OE::DN7263, and OE::DN7661 scavenged ROS quickly, minimizing oxidative damage. Overall, CreA knockout increased DN7263 and DN7661 expression to facilitate xylose assimilation, enhancing NADH generation and ROS clearance. Finally, with mixed sugar fermentation, ΔCreA and OE::DN7263's biomass and lipid yield rose without furfural addition, while that of ΔCreA remained higher than WT after furfural treatment. These findings revealed how oleaginous yeast zwy-2-3 resisted furfural stress and indicated ΔCreA and OE::DN7263 might develop into robust industrial chassis strains.
Collapse
Affiliation(s)
- Yulu Ran
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Qingzhuoma Yang
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Jie Zeng
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Fazhi Li
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Yu Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Qingrui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Dairong Qiao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Hui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China.
| | - Yi Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China.
| |
Collapse
|
13
|
Tang R, Yuan X, Yang J. Problems and corresponding strategies for converting CO 2 into value-added products in Cupriavidus necator H16 cell factories. Biotechnol Adv 2023; 67:108183. [PMID: 37286176 DOI: 10.1016/j.biotechadv.2023.108183] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/17/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
Elevated CO2 emissions have substantially altered the worldwide climate, while the excessive reliance on fossil fuels has exacerbated the energy crisis. Therefore, the conversion of CO2 into fuel, petroleum-based derivatives, drug precursors, and other value-added products is expected. Cupriavidus necator H16 is the model organism of the "Knallgas" bacterium and is considered to be a microbial cell factory as it can convert CO2 into various value-added products. However, the development and application of C. necator H16 cell factories has several limitations, including low efficiency, high cost, and safety concerns arising from the autotrophic metabolic characteristics of the strains. In this review, we first considered the autotrophic metabolic characteristics of C. necator H16, and then categorized and summarized the resulting problems. We also provided a detailed discussion of some corresponding strategies concerning metabolic engineering, trophic models, and cultivation mode. Finally, we provided several suggestions for improving and combining them. This review might help in the research and application of the conversion of CO2 into value-added products in C. necator H16 cell factories.
Collapse
Affiliation(s)
- Ruohao Tang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong Province, People's Republic of China
| | - Xianzheng Yuan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong Province, People's Republic of China
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China.
| |
Collapse
|
14
|
Cao Q, Dong Y, Guo C, Ji S, Nie M, Liu G, Wan X, Lu C, Liu Y. luxS contributes to intramacrophage survival of Streptococcus agalactiae by positively affecting the expression of fruRKI operon. Vet Res 2023; 54:83. [PMID: 37759250 PMCID: PMC10536698 DOI: 10.1186/s13567-023-01210-9] [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: 06/01/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
The LuxS quorum sensing system is a widespread system employed by many bacteria for cell-to-cell communication. The luxS gene has been demonstrated to play a crucial role in intramacrophage survival of piscine Streptococcus agalactiae, but the underlying mechanism remains largely unknown. In this study, transcriptome analysis, followed by the luxS gene deletion and subsequent functional studies, confirmed that impaired bacterial survival inside macrophages due to the inactivation of luxS was associated with reduced transcription of the fruRKI operon, encoding the fructose-specific phosphotransferase system. Further, luxS was determined not to enhance the transcription of fruRKI operon by binding its promoter, but to upregulate the expression of this operon via affecting the binding ability of catabolite control protein A (CcpA) to the catabolite responsive element (cre) in the promoter of fruRKI. Collectively, our study identifies a novel and previously unappreciated role for luxS in bacterial intracellular survival, which may give a more thorough understanding of the immune evasion mechanism in S. agalactiae.
Collapse
Affiliation(s)
- Qing Cao
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yuhao Dong
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Changming Guo
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Shuting Ji
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Meng Nie
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Guangjin Liu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xihe Wan
- Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Chengping Lu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yongjie Liu
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| |
Collapse
|
15
|
Murakami R, Yoshida K, Sakanaka M, Urashima T, Xiao JZ, Katayama T, Odamaki T. Preferential sugar utilization by bifidobacterial species. MICROBIOME RESEARCH REPORTS 2023; 2:31. [PMID: 38045925 PMCID: PMC10688810 DOI: 10.20517/mrr.2023.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/28/2023] [Accepted: 08/16/2023] [Indexed: 12/05/2023]
Abstract
Aim: Bifidobacteria benefit host health and homeostasis by breaking down diet- and host-derived carbohydrates to produce organic acids in the intestine. However, the sugar utilization preference of bifidobacterial species is poorly understood. Thus, this study aimed to investigate the sugar utilization preference (i.e., glucose or lactose) of various bifidobacterial species. Methods: Strains belonging to 40 bifidobacterial species/subspecies were cultured on a modified MRS medium supplemented with glucose and/or lactose, and their preferential sugar utilization was assessed using high-performance thin-layer chromatography. Comparative genomic analysis was conducted with a focus on genes involved in lactose and glucose uptake and genes encoding for carbohydrate-active enzymes. Results: Strains that preferentially utilized glucose or lactose were identified. Almost all the lactose-preferring strains harbored the lactose symporter lacS gene. However, the comparative genomic analysis could not explain all their differences in sugar utilization preference. Analysis based on isolate source revealed that all 10 strains isolated from humans preferentially utilized lactose, whereas all four strains isolated from insects preferentially utilized glucose. In addition, bifidobacterial species isolated from hosts whose milk contained higher lactose amounts preferentially utilized lactose. Lactose was also detected in the feces of human infants, suggesting that lactose serves as a carbon source not only for infants but also for gut microbes in vivo. Conclusion: The different sugar preference phenotypes of Bifidobacterium species may be ascribed to the residential environment affected by the dietary habits of their host. This study is the first to systematically evaluate the sugar uptake preference of various bifidobacterial species.
Collapse
Affiliation(s)
- Ryuta Murakami
- Next Generation Science Institute, R&D Division, Morinaga Milk Industry Co., Ltd., Kanagawa 252-8583, Japan
| | - Keisuke Yoshida
- Next Generation Science Institute, R&D Division, Morinaga Milk Industry Co., Ltd., Kanagawa 252-8583, Japan
| | - Mikiyasu Sakanaka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Tadasu Urashima
- Department of Food and Life Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Jin-Zhong Xiao
- Next Generation Science Institute, R&D Division, Morinaga Milk Industry Co., Ltd., Kanagawa 252-8583, Japan
| | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Toshitaka Odamaki
- Next Generation Science Institute, R&D Division, Morinaga Milk Industry Co., Ltd., Kanagawa 252-8583, Japan
| |
Collapse
|
16
|
Ren X, Palmer LD. Acinetobacter Metabolism in Infection and Antimicrobial Resistance. Infect Immun 2023:e0043322. [PMID: 37191522 DOI: 10.1128/iai.00433-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Acinetobacter infections have high rates of mortality due to an increasing incidence of infections by multidrug-resistant (MDR) and extensively-drug-resistant (XDR) strains. Therefore, new therapeutic strategies for the treatment of Acinetobacter infections are urgently needed. Acinetobacter spp. are Gram-negative coccobacilli that are obligate aerobes and can utilize a wide variety of carbon sources. Acinetobacter baumannii is the main cause of Acinetobacter infections, and recent work has identified multiple strategies A. baumannii uses to acquire nutrients and replicate in the face of host nutrient restriction. Some host nutrient sources also serve antimicrobial and immunomodulatory functions. Hence, understanding Acinetobacter metabolism during infection may provide new insights into novel infection control measures. In this review, we focus on the role of metabolism during infection and in resistance to antibiotics and other antimicrobial agents and discuss the possibility that metabolism may be exploited to identify novel targets to treat Acinetobacter infections.
Collapse
Affiliation(s)
- Xiaomei Ren
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Lauren D Palmer
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| |
Collapse
|
17
|
Dresen M, Valentin-Weigand P, Berhanu Weldearegay Y. Role of Metabolic Adaptation of Streptococcus suis to Host Niches in Bacterial Fitness and Virulence. Pathogens 2023; 12:pathogens12040541. [PMID: 37111427 PMCID: PMC10144218 DOI: 10.3390/pathogens12040541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Streptococcus suis, both a common colonizer of the porcine upper respiratory tract and an invasive pig pathogen, successfully adapts to different host environments encountered during infection. Whereas the initial infection mainly occurs via the respiratory tract, in a second step, the pathogen can breach the epithelial barrier and disseminate within the whole body. Thereby, the pathogen reaches other organs such as the heart, the joints, or the brain. In this review, we focus on the role of S. suis metabolism for adaptation to these different in vivo host niches to encounter changes in nutrient availability, host defense mechanisms and competing microbiota. Furthermore, we highlight the close link between S. suis metabolism and virulence. Mutants deficient in metabolic regulators often show an attenuation in infection experiments possibly due to downregulation of virulence factors, reduced resistance to nutritive or oxidative stress and to phagocytic activity. Finally, metabolic pathways as potential targets for new therapeutic strategies are discussed. As antimicrobial resistance in S. suis isolates has increased over the last years, the development of new antibiotics is of utmost importance to successfully fight infections in the future.
Collapse
Affiliation(s)
- Muriel Dresen
- Institute for Microbiology, University of Veterinary Medicine Hannover, 30173 Hannover, Germany
| | - Peter Valentin-Weigand
- Institute for Microbiology, University of Veterinary Medicine Hannover, 30173 Hannover, Germany
| | | |
Collapse
|
18
|
Factors Influencing the Nitrogen-Source Dependent Flucytosine Resistance in Cryptococcus Species. mBio 2023; 14:e0345122. [PMID: 36656038 PMCID: PMC9973006 DOI: 10.1128/mbio.03451-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Flucytosine (5-FC) is an antifungal agent commonly used for treatment of cryptococcosis and several other systemic mycoses. In fungi, cytosine permease and cytosine deaminase are known major players in flucytosine resistance by regulating uptake and deamination of 5-FC, respectively. Cryptococcus species have three paralogs each of cytosine permease (FCY2, FCY3, and FCY4) and cytosine deaminase (FCY1, FCY5 and FCY6). As in other fungi, we found FCY1 and FCY2 to be the primary cytosine deaminase and permease gene, respectively, in C. neoformans H99 (VNI), C. gattii R265 (VGIIa) and WM276 (VGI). However, when various amino acids were used as the sole nitrogen source, C. neoformans and C. gattii diverged in the function of FCY3 and FCY6. Though there was some lineage-dependent variability, the two genes functioned as the secondary permease and deaminase, respectively, only in C. gattii when the nitrogen source was arginine, asparagine, or proline. Additionally, the expression of FCY genes, excluding FCY1, was under nitrogen catabolic repression in the presence of NH4. Functional analysis of GAT1 and CIR1 gene deletion constructs demonstrated that these two genes regulate the expression of each permease and deaminase genes individually. Furthermore, the expression levels of FCY3 and FCY6 under different amino acids corroborated the 5-FC susceptibility in fcy2Δ or fcy1Δ background. Thus, the mechanism of 5-FC resistance in C. gattii under diverse nitrogen conditions is orchestrated by two transcription factors of GATA family, cytosine permease and deaminase genes. IMPORTANCE 5-FC is a commonly used antifungal drug for treatment of cryptococcosis caused by Cryptococcus neoformans and C. gattii species complexes. When various amino acids were used as the sole nitrogen source for growth, we found lineage dependent differences in 5-FC susceptibility. Deletion of the classical cytosine permease (FCY2) and deaminase (FCY1) genes caused increased 5-FC resistance in all tested nitrogen sources in C. neoformans but not in C. gattii. Furthermore, we demonstrate that the two GATA family transcription factor genes GAT1 and CIR1 are involved in the nitrogen-source dependent 5-FC resistance by regulating the expression of the paralogs of cytosine permease and deaminase genes. Our study not only identifies the new function of paralogs of the cytosine permease and deaminase and the role of their regulatory transcription factors but also denotes the differences in the mechanism of 5-FC resistance among the two etiologic agents of cryptococcosis under different nitrogen sources.
Collapse
|
19
|
Martín-González D, Bordel S, Solis S, Gutierrez-Merino J, Santos-Beneit F. Characterization of Bacillus Strains from Natural Honeybee Products with High Keratinolytic Activity and Antimicrobial Potential. Microorganisms 2023; 11:microorganisms11020456. [PMID: 36838421 PMCID: PMC9959047 DOI: 10.3390/microorganisms11020456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Two efficient feather-degrading bacteria were isolated from honeybee samples and identified as Bacillus sonorensis and Bacillus licheniformis based on 16S rRNA and genome sequencing. The strains were able to grow on chicken feathers as the sole carbon and nitrogen sources and degraded the feathers in a few days. The highest keratinase activity was detected by the B. licheniformis CG1 strain (3800 U × mL-1), followed by B. sonorensis AB7 (1450 U × mL-1). Keratinase from B. licheniformis CG1 was shown to be active across a wide range of pH, potentially making this strain advantageous for further industrial applications. All isolates displayed antimicrobial activity against Micrococcus luteus; however, only B. licheniformis CG1 was able to inhibit the growth of Mycobacterium smegmatis. In silico analysis using BAGEL and antiSMASH identified gene clusters associated with the synthesis of non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKSs) and/or ribosomally synthesized and post-translationally modified peptides (RiPPs) in most of the Bacillus isolates. B. licheniformis CG1, the only strain that inhibited the growth of the mycobacterial strain, contained sequences with 100% similarity to lichenysin (also present in the other isolates) and lichenicidin (only present in the CG1 strain). Both compounds have been described to display antimicrobial activity against distinct bacteria. In summary, in this work, we have isolated a strain (B. licheniformis CG1) with promising potential for use in different industrial applications, including animal nutrition, leather processing, detergent formulation and feather degradation.
Collapse
Affiliation(s)
- Diego Martín-González
- Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Sergio Bordel
- Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Selvin Solis
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | | | - Fernando Santos-Beneit
- Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
- Correspondence:
| |
Collapse
|
20
|
Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway. J Mol Evol 2023; 91:46-59. [PMID: 36482210 PMCID: PMC9734637 DOI: 10.1007/s00239-022-10079-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022]
Abstract
Galactose is a secondary fermentable sugar that requires specific regulatory and structural genes for its assimilation, which are under catabolite repression by glucose. When glucose is absent, the catabolic repression is attenuated, and the structural GAL genes are fully activated. In Saccharomyces cerevisiae, the GAL pathway is under selection in environments where galactose is present. However, it is unclear the adaptive strategies in response to long-term propagation in galactose as a sole carbon source in laboratory evolution experiments. Here, we performed a 4,000-generation evolution experiment using 48 diploid Saccharomyces cerevisiae populations to study adaptation in galactose. We show that fitness gains were greater in the galactose-evolved population than in identically evolved populations with glucose as a sole carbon source. Whole-genome sequencing of 96 evolved clones revealed recurrent de novo single nucleotide mutations in candidate targets of selection, copy number variations, and ploidy changes. We find that most mutations that improve fitness in galactose lie outside of the canonical GAL pathway. Reconstruction of specific evolved alleles in candidate target of selection, SEC23 and IRA1, showed a significant increase in fitness in galactose compared to glucose. In addition, most of our evolved populations (28/46; 61%) fixed aneuploidies on Chromosome VIII, suggesting a parallel adaptive amplification. Finally, we show greater loss of extrachromosomal elements in our glucose-evolved lineages compared with previous glucose evolution. Broadly, these data further our understanding of the evolutionary pressures that drive adaptation to less-preferred carbon sources.
Collapse
|
21
|
Han X, Liu J, Tian S, Tao F, Xu P. Microbial cell factories for bio-based biodegradable plastics production. iScience 2022; 25:105462. [DOI: 10.1016/j.isci.2022.105462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
22
|
Chiu PC, Nakamura Y, Nishimura S, Tabuchi T, Yashiroda Y, Hirai G, Matsuyama A, Yoshida M. Ferrichrome, a fungal-type siderophore, confers high ammonium tolerance to fission yeast. Sci Rep 2022; 12:17411. [PMID: 36302945 PMCID: PMC9613971 DOI: 10.1038/s41598-022-22108-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/10/2022] [Indexed: 01/12/2023] Open
Abstract
Microorganisms and plants produce siderophores, which function to transport environmental iron into cells as well as participate in cellular iron use and deposition. Their biological functions are diverse although their role in primary metabolism is poorly understood. Ferrichrome is a fungal-type siderophore synthesized by nonribosomal peptide synthetase (NRPS). Herein we show that ferrichrome induces adaptive growth of fission yeast on high ammonium media. Ammonium is a preferred nitrogen source as it suppresses uptake and catabolism of less preferred nitrogen sources such as leucine through a mechanism called nitrogen catabolite repression (NCR). Therefore, the growth of fission yeast mutant cells with leucine auxotrophy is suppressed in the presence of high concentrations of ammonium. This growth suppression was canceled by ferrichrome in a manner dependent on the amino acid transporter Cat1. Additionally, growth retardation of wild-type cells by excess ammonium was exacerbated by deleting the NRPS gene sib1, which is responsible for the biosynthesis of ferrichrome, suggesting that intrinsically produced ferrichrome functions in suppressing the metabolic action of ammonium. Furthermore, ferrichrome facilitated the growth of both wild-type and sib1-deficient cells under low glucose conditions. These results suggest that intracellular iron regulates primary metabolism, including NCR, which is mediated by siderophores.
Collapse
Affiliation(s)
- Po-Chang Chiu
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Yuri Nakamura
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Shinichi Nishimura
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan ,grid.26999.3d0000 0001 2151 536XCollaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Toshitsugu Tabuchi
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Yoko Yashiroda
- grid.509461.f0000 0004 1757 8255RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198 Japan
| | - Go Hirai
- grid.509461.f0000 0004 1757 8255RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198 Japan ,grid.177174.30000 0001 2242 4849Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 Japan
| | - Akihisa Matsuyama
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan ,grid.509461.f0000 0004 1757 8255RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198 Japan
| | - Minoru Yoshida
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan ,grid.26999.3d0000 0001 2151 536XCollaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657 Japan ,grid.509461.f0000 0004 1757 8255RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198 Japan
| |
Collapse
|
23
|
Iwama R, Sasano Y, Hiramatsu T, Otake S, Suzuki E, Hasumi K. Amine-Regulated pri-SMTP Oxidation in SMTP Biosynthesis in Stachybotrys: Possible Implication in Nitrogen Acquisition. J Fungi (Basel) 2022; 8:jof8090975. [PMID: 36135700 PMCID: PMC9502257 DOI: 10.3390/jof8090975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/06/2022] [Accepted: 09/16/2022] [Indexed: 12/01/2022] Open
Abstract
SMTP (the name SMTP is derived from Stachybotrys microspora triprenyl phenol) is a family of triprenyl phenol secondary metabolites from a black mold, Stachybotrys microspora. Some SMTP congeners exhibit anti-inflammatory and profibrinolytic activities that, in combination, contribute to the treatment of ischemic stroke. The final step in the SMTP biosynthesis is a non-enzymatic amine conjugation with an o-phthalaldehyde moiety of the precursor pre-SMTP, which can form adducts with proteins and nucleic acids. Thus, pre-SMTP formation should be a precisely regulated, rate-limiting step in the SMTP biosynthesis. To address the mechanism backing this regulation, we purified a metabolite that rapidly disappeared following amine feeding, identifying a novel compound, pri-SMTP. Furthermore, an enzyme, designated as pri-SMTP oxidase, responsible for pri-SMTP conversion to pre-SMTP, was purified. The formation of pri-SMTP, which is regulated by nitrogen and carbon nutrients, occurred in particular septate mycelia. Although pri-SMTP oxidase was expressed constitutively, the consumption of pri-SMTP was accelerated only when a primary amine was fed. Thus, SMTP biosynthesis is regulated by at least three mechanisms: (i) pri-SMTP formation affected by nutrients, (ii) the compartmentalization of pri-SMTP formation/storage, and (iii) amine-regulated pri-SMTP oxidation. Amine-regulated SMTP formation (i.e., amine-capturing with pre-SMTP) may play a role in the nitrogen acquisition/assimilation strategy in S. microspora, since pri-SMTP synthesis occurs on non-preferred nitrogen.
Collapse
Affiliation(s)
- Ryota Iwama
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yu Sasano
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Taichi Hiramatsu
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Shinya Otake
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Eriko Suzuki
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Keiji Hasumi
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
- Department of Research and Development, TMS Co., Fuchu, Tokyo 183-0055, Japan
- Correspondence:
| |
Collapse
|
24
|
Sharma R, Jasrotia T, Umar A, Sharma M, Sharma S, Kumar R, Alkhanjaf AAM, Vats R, Beniwal V, Kumar R, Singh J. Effective removal of Pb(II) and Ni(II) ions by Bacillus cereus and Bacillus pumilus: An experimental and mechanistic approach. ENVIRONMENTAL RESEARCH 2022; 212:113337. [PMID: 35469857 DOI: 10.1016/j.envres.2022.113337] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 04/03/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Herein, we report a bacteria-based strategy as an efficient, reasonable, benign, and promising methodology for remediating heavy metals fed waterbodies. The contemporary study deals with isolating, screening, and characterizing heavy metal resistive bacteria from metal-rich sites. The transcriptome analysis reveals the identity of the isolated species as Bacillus pumilus and Bacillus cereus. Batch studies put forth the bioremoval results in designed conditions of different pH, concentration, dose, and time. The mechanistic actions are drawn using complementary techniques such as Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The theory of surface adsorption of lead (Pb(II)) and nickel (Ni(II)) is further fostered by the application of adsorption isotherms. The conducted studies establish the bacterial morphological stratagems and multifarious biochemical approaches for countering metallic ions of Pb(II) and Ni(II). The exhibition of significant removal results by the isolated bacterial strains in simulated water samples with remarkable proliferation rates has opened up its favorability for industrial platforms.
Collapse
Affiliation(s)
- Rohit Sharma
- Department of Biotechnology, Maharishi Markandeshwar Deemed to Be University, Mullana (Ambala), 133207, Haryana, India
| | - Teenu Jasrotia
- Department of Environment Studies, Panjab University, Chandigarh, 160014, India; Department of Chemistry and Centre of Advanced Studies, Panjab University, Chandigarh, 160014, India
| | - Ahmad Umar
- Department of Chemistry, Faculty of Science and Arts, Najran University, Najran, 11001, Saudi Arabia; Promising Centre for Sensors and Electronic Devices (PCSED), Najran University, Najran, 11001, Saudi Arabia.
| | - Monu Sharma
- Department of Biotechnology, Maharishi Markandeshwar Deemed to Be University, Mullana (Ambala), 133207, Haryana, India
| | - Sonu Sharma
- Department of Biotechnology, Maharishi Markandeshwar Deemed to Be University, Mullana (Ambala), 133207, Haryana, India
| | - Rajeev Kumar
- Department of Environment Studies, Panjab University, Chandigarh, 160014, India
| | - Abdulrab Ahmed M Alkhanjaf
- Molecular Diagnostics, Clinical Laboratory Sciences Department, College of Applied Medical Sciences, Najran University, Najran, 11001, Saudi Arabia
| | - Rajeev Vats
- Scientist E and Head, Northern Regional Laboratory, Bureau of Indian Standards, Mohali, Punjab, India
| | - Vikas Beniwal
- Department of Microbiology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, 123031, India
| | - Raman Kumar
- Department of Biotechnology, Maharishi Markandeshwar Deemed to Be University, Mullana (Ambala), 133207, Haryana, India.
| | - Joginder Singh
- Department of Chemistry¸ Maharishi Markandeshwar (Deemed to Be University), Mullana (Ambala), 133207, Haryana, India
| |
Collapse
|
25
|
Hitomi K, Weng J, Ying BW. Contribution of the genomic and nutritional differentiation to the spatial distribution of bacterial colonies. Front Microbiol 2022; 13:948657. [PMID: 36081803 PMCID: PMC9448356 DOI: 10.3389/fmicb.2022.948657] [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: 05/20/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Colony growth is a common phenomenon of structured populations dispersed in nature; nevertheless, studies on the spatial distribution of colonies are largely insufficient. Here, we performed a systematic survey to address the questions of whether and how the spatial distribution of colonies was influenced by the genome and environment. Six Escherichia coli strains carrying either the wild-type or reduced genomes and eight media of varied nutritional richness were used to evaluate the genomic and environmental impacts, respectively. The genome size and nutritional variation contributed to the mean size and total area but not the variation and shape of size distribution of the colonies formed within the identical space and of equivalent spatial density. The spatial analysis by means of the Voronoi diagram found that the Voronoi correlation remained nearly constant in common, in comparison to the Voronoi response decreasing in correlation to genome reduction and nutritional enrichment. Growth analysis at the single colony level revealed positive correlations of the relative growth rate to both the maximal colony size and the Voronoi area, regardless of the genomic and nutritional variety. This result indicated fast growth for the large space assigned and supported homeostasis in the Voronoi correlation. Taken together, the spatial distribution of colonies might benefit efficient clonal growth. Although the mechanisms remain unclear, the findings provide quantitative insights into the genomic and environmental contributions to the growth and distribution of spatially or geographically isolated populations.
Collapse
|
26
|
Mao Q, Jiang J, Wu X, Ma Y, Zhang Y, Zhao Y, Zhang Y, Wang Q. Bifunctional alcohol/aldehyde dehydrogenase AdhE controls phospho-transferase system sugar utilization and virulence gene expression by interacting PtsH in Edwardsiella piscicida. Microbiol Res 2022; 260:127018. [DOI: 10.1016/j.micres.2022.127018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/26/2022] [Accepted: 03/29/2022] [Indexed: 10/18/2022]
|
27
|
Lu H, Xu H, Yang P, Bilal M, Zhu S, Zhong M, Zhao L, Gu C, Liu S, Zhao Y, Geng C. Transcriptome Analysis of Bacillus amyloliquefaciens Reveals Fructose Addition Effects on Fengycin Synthesis. Genes (Basel) 2022; 13:genes13060984. [PMID: 35741746 PMCID: PMC9222730 DOI: 10.3390/genes13060984] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 02/05/2023] Open
Abstract
Fengycin is a lipopeptide produced by Bacillus that has a strong inhibitory effect on filamentous fungi; however, its use is restricted due to poor production and low yield. Previous studies have shown that fengycin biosynthesis in B. amyloliquefaciens was found to be significantly increased after fructose addition. This study investigated the effect of fructose on fengycin production and its regulation mechanism in B. amyloliquefaciens by transcriptome sequencing. According to the RNA sequencing data, 458 genes were upregulated and 879 genes were downregulated. Transcriptome analysis results showed that fructose changed the transcription of amino acid synthesis, fatty acid metabolism, and energy metabolism; alterations in these metabolic pathways contribute to the synthesis of fengycin. In an MLF medium (modified Landy medium with fructose), the expression level of the fengycin operon was two-times higher than in an ML medium (modified Landy medium). After fructose was added to B. amyloliquefaciens, the fengycin-synthesis-associated genes were activated in the process of fengycin synthesis.
Collapse
Affiliation(s)
- Hedong Lu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
- National Engineering Research Center for Functional Food, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hai Xu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
| | - Panping Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
| | - Shaohui Zhu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
| | - Mengyuan Zhong
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
| | - Li Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
| | - Chengyuan Gu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
| | - Shuai Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
| | - Chengxin Geng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China; (H.L.); (H.X.); (P.Y.); (M.B.); (S.Z.); (M.Z.); (L.Z.); (C.G.); (S.L.); (Y.Z.)
- Correspondence: ; Tel.: +86-517-83559107
| |
Collapse
|
28
|
Chen Y, Zeng W, Ma W, Ma W, Zhou J. Chromatin Regulators Ahc1p and Eaf3p Positively Influence Nitrogen Metabolism in Saccharomyces cerevisiae. Front Microbiol 2022; 13:883934. [PMID: 35620110 PMCID: PMC9127870 DOI: 10.3389/fmicb.2022.883934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
There is a complex regulatory network of nitrogen metabolism in Saccharomyces cerevisiae, and many details of this regulatory network have not been revealed. This study explored the global regulation of nitrogen metabolism in S. cerevisiae from an epigenetic perspective. Comparative transcriptome analysis of S. cerevisiae S288C treated with 30 nitrogen sources identified nine chromatin regulators (CRs) that responded significantly to different nitrogen sources. Functional analysis showed that among the CRs identified, Ahc1p and Eaf3p promoted the utilization of non-preferred nitrogen sources through global regulation of nitrogen metabolism. Ahc1p regulated nitrogen metabolism through amino acid transport, nitrogen catabolism repression (NCR), and the Ssy1p-Ptr3p-Ssy5p signaling sensor system. Eaf3p regulated nitrogen metabolism via amino acid transport and NCR. The regulatory mechanisms of the effects of Ahc1p and Eaf3p on nitrogen metabolism depended on the function of their histone acetyltransferase complex ADA and NuA4. These epigenetic findings provided new insights for a deeper understanding of the nitrogen metabolism regulatory network in S. cerevisiae.
Collapse
Affiliation(s)
- Yu Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Weizhu Zeng
- Science Center for Future Foods, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Wenjian Ma
- Science Center for Future Foods, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Wei Ma
- Science Center for Future Foods, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, China
| |
Collapse
|
29
|
Yan Q, Han L, Liu X, You C, Zhou S, Zhou Z. Development of an auto-inducible expression system by nitrogen sources switching based on the nitrogen catabolite repression regulation. Microb Cell Fact 2022; 21:73. [PMID: 35484589 PMCID: PMC9047365 DOI: 10.1186/s12934-022-01794-5] [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: 02/24/2022] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The construction of protein expression systems is mainly focused on carbon catabolite repression and quorum-sensing systems. However, each of these regulatory modes has an inherent flaw, which is difficult to overcome. Organisms also prioritize using different nitrogen sources, which is called nitrogen catabolite repression. To date, few gene regulatory systems based on nitrogen catabolite repression have been reported. RESULTS In this study, we constructed a nitrogen switching auto-inducible expression system (NSAES) based on nitrogen catabolite regulation and nitrogen utilization in Aspergillus nidulans. The PniaD promoter that is highly induced by nitrate and inhibition by ammonia was used as the promoter. Glucuronidase was the reporter protein. Glucuronidase expression occurred after ammonium was consumed in an ammonium and nitrate compounding medium, achieving stage auto-switching for cell growth and gene expression. This system maintained a balance between cell growth and protein production to maximize stress products. Expressions of glycosylated and secretory proteins were successfully achieved using this auto-inducible system. CONCLUSIONS We described an efficient auto-inducible protein expression system based on nitrogen catabolite regulation. The system could be useful for protein production in the laboratory and industrial applications. Simultaneously, NSAES provides a new auto-inducible expression regulation mode for other filamentous fungi.
Collapse
Affiliation(s)
- Qin Yan
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xinyue Liu
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Cuiping You
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| |
Collapse
|
30
|
Tang L, Zhou Y, Zhang Y, Sun H. The role of energy/substrate in microbial hormesis. CURRENT OPINION IN TOXICOLOGY 2022. [DOI: 10.1016/j.cotox.2021.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|