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Qian J, Wang Y, Hu Z, Shi T, Wang Y, Ye C, Huang H. Bacillus sp. as a microbial cell factory: Advancements and future prospects. Biotechnol Adv 2023; 69:108278. [PMID: 37898328 DOI: 10.1016/j.biotechadv.2023.108278] [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: 07/07/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Bacillus sp. is one of the most distinctive gram-positive bacteria, able to grow efficiently using cheap carbon sources and secrete a variety of useful substances, which are widely used in food, pharmaceutical, agricultural and environmental industries. At the same time, Bacillus sp. is also recognized as a safe genus with a relatively clear genetic background, which is conducive to the industrial production of target metabolites. In this review, we discuss the reasons why Bacillus sp. has been so extensively studied and summarize its advances in systems and synthetic biology, engineering strategies to improve microbial cell properties, and industrial applications in several metabolic engineering applications. Finally, we present the current challenges and possible solutions to provide a reliable basis for Bacillus sp. as a microbial cell factory.
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Affiliation(s)
- Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Yuzhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Zijian Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
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2
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Zhang K, Yin M, Lei S, Zhang H, Yin X, Niu Q. Bacillus sp. YC7 from intestines of Lasioderma serricorne degrades nicotine due to nicotine dehydrogenase. AMB Express 2023; 13:87. [PMID: 37603100 PMCID: PMC10441963 DOI: 10.1186/s13568-023-01593-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
A large number of nicotine-containing wastes produced during the tobacco manufacturing process are seriously harmful to the environment and human health. The degradation and transformation of nicotine-containing environmental contaminants to harmless substances has become an urgent requirement. Lasioderma serricorne can grow and reproduce in nicotine-rich sources, and their intestinal microbiota show promising potential to degrade and utilize nicotine. The purpose of this study is to screen and identify nicotine-degrading bacteria from the intestines of L. serricorne and explore their degradation characteristics. A dominant strain, YC7, with significant nicotine degradation capabilities was isolated from the intestines of L. serricorne. The strain was identified as Bacillus using a polyphasic approach. The test results showed it can produce multiple enzymes that include β-glucosidase, cellulase, proteases, and amylases. The nicotine-degrading bacteria were functionally annotated using databases. Nicotine dehydrogenase (NDH) was found by combining an activity tracking test and protein mass spectrometry analysis. The YC-7 NDH in the pathway was molecularly docked and functionally verified via the gene knockdown method. The binding ability of nicotine to nicotine-degrading enzymes was investigated using molecular docking. A high-efficiency nicotine-degrading bacteria, YC-7, was isolated and screened from tobacco, and the gene functions related to degradation were verified. This investigation provides a new hypothesis for screening nicotine-degrading bacteria and increases our knowledge of potential nicotine-degrading microbial sources.
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Affiliation(s)
- Ke Zhang
- College of Environmental Engineering and Chemistry, Luoyang Institute of Science and Technology, 90 Wangcheng Road, Luoyang, 471023, Henan, China
| | - Mingshen Yin
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Shengwei Lei
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Hongxin Zhang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Xiaoyan Yin
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Qiuhong Niu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
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Niu Q, Liu S, Yin M, Lei S, Rezzonico F, Zhang L. Phytobacter diazotrophicus from Intestine of Caenorhabditis elegans Confers Colonization-Resistance against Bacillus nematocida Using Flagellin (FliC) as an Inhibition Factor. Pathogens 2022; 11:pathogens11010082. [PMID: 35056030 PMCID: PMC8778419 DOI: 10.3390/pathogens11010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 12/04/2022] Open
Abstract
Symbiotic microorganisms in the intestinal tract can influence the general fitness of their hosts and contribute to protecting them against invading pathogens. In this study, we obtained isolate Phytobacter diazotrophicus SCO41 from the gut of free-living nematode Caenorhabditis elegans that displayed strong colonization-resistance against invading biocontrol bacterium Bacillus nematocida B16. The colonization-resistance phenotype was found to be mediated by a 37-kDa extracellular protein that was identified as flagellin (FliC). With the help of genome information, the fliC gene was cloned and heterologously expressed in E. coli. It could be shown that the B. nematocida B16 grows in chains rather than in planktonic form in the presence of FliC. Scanning Electronic Microscopy results showed that protein FliC-treated B16 bacterial cells are thinner and longer than normal cells. Localization experiments confirmed that the protein FliC is localized in both the cytoplasm and the cell membrane of B16 strain, in the latter especially at the position of cell division. ZDOCK analysis showed that FliC could bind with serine/threonine protein kinase, membrane protein insertase YidC and redox membrane protein CydB. It was inferred that FliC interferes with cell division of B. nematocidal B16, therefore inhibiting its colonization of C. elegans intestines in vivo. The isolation of P. diazotrophicus as part of the gut microbiome of C. elegans not only provides interesting insights about the lifestyle of this nitrogen-fixing bacterium, but also reveals how the composition of the natural gut microbiota of nematodes can affect biological control efforts by protecting the host from its natural enemies.
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Affiliation(s)
- Qiuhong Niu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Suyao Liu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Mingshen Yin
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Shengwei Lei
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland
| | - Lin Zhang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
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Han R, Wang Y, Deng Y, Zhang Y, Zhang L, Niu Q. Stenotrophomonas strain CPCC 101271, an intestinal lifespan-prolonging bacterium for Caenorhabditis elegans that assists in host resistance to "Bacillus nematocida" colonization. Arch Microbiol 2021; 203:4951-4960. [PMID: 34258643 PMCID: PMC8502144 DOI: 10.1007/s00203-021-02467-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/25/2022]
Abstract
The soil-dwelling, opportunistic pathogenic bacterium "Bacillus nematocida" B16 exhibits strong killing activities against a variety of pathogenic nematodes via a “Trojan horse” mechanism that can kill worm species like Caenorhabditis elegans. The bacterial strain CPCC 101271 was previously isolated from the intestines of C. elegans that were recovered from natural habitats and can serve as a probiotic for C. elegans, while also assisting in resistance to infection by the pathogenic strain B16. In this study, the lifespan of C. elegans fed with strain CPCC 101271 cells was extended by approximately 40% compared with that of worms fed with Escherichia coli OP50 cells. In addition, the colonization of C. elegans by the pathogenic bacterium "B. nematocida" B16 was inhibited when pre-fed with strain CPCC 101271. Metagenomic sequence analysis of intestinal microbiota of C. elegans fed with strain CPCC 101271 and infected with B16 revealed that pre-feeding worms with CPCC 101271 improved the diversity of the intestinal bacteria. Moreover, community structure significantly varied in coordination with Stenotrophomonas spp. and Bacillus spp. abundances when competition between strains CPCC 101271 and B16 was evaluated. In conclusion, the nematode microbiota strain CPCC 101271 assisted in its host resistance to colonization by the pathogen "Bacillus nematocida" and can also promote life span-prolongation in C. elegans. These results underscore that understanding the interactions between C. elegans microbiota and pathogens can provide new insights into achieving effective biological control of agricultural pests.
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Affiliation(s)
- Rui Han
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Yu Wang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Lin Zhang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
| | - Qiuhong Niu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
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Zhang L, Wei Y, Tao Y, Zhao S, Wei X, Yin X, Liu S, Niu Q. Molecular mechanism of the smart attack of pathogenic bacteria on nematodes. Microb Biotechnol 2020; 13:683-705. [PMID: 31730281 PMCID: PMC7111092 DOI: 10.1111/1751-7915.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/16/2019] [Accepted: 10/20/2019] [Indexed: 11/28/2022] Open
Abstract
Nematode-bacterial associations are far-reaching subjects in view of their impact on ecosystems, economies, agriculture and human health. There is still no conclusion regarding which pathogenic bacteria sense nematodes. Here, we found that the pathogenic bacterium Bacillus nematocida B16 was sensitive to C. elegans and could launch smart attacks to kill the nematodes. Further analysis revealed that the spores of B. nematocida B16 are essential virulence factors. Once gaseous molecules (morpholine) produced from C. elegans were sensed, the sporulation of B16 was greatly accelerated. Then, B16 showed maximum attraction to C. elegans during the spore-forming process but had no attraction until all the spores were formed. The disruption of either the spore formation gene spo0A or the germination gene gerD impaired colonization and attenuated infection in B16. In contrast, complementation with the intact genes restored most of the above-mentioned deficient phenotypes, which indicated that the spo0A gene was a key factor in the smart attack of B16 on C. elegans. Further, transcriptome, molecular simulations and quantitative PCR analysis showed that morpholine from C. elegans could promote sporulation and initiate infection by increasing the transcription of the spo0A gene by decreasing the transcription of the rapA and spo0E genes. The overexpression of rapA or spo0E decreased the induced sporulation effect, and morpholine directly reduced the level of phosphorylation of purified recombinant RapA and Spo0E compared to that of Spo0A. Collectively, these findings further support a 'Trojan horse-like' infection model. The significance of our paper is that we showed that the soil-dwelling bacterium B. nematocida B16 has the ability to actively detect, attract and attack their host C. elegans. These studies are the first report on the behaviours, signalling molecules and mechanism of the smart attack of B16 on nematodes and also reveal new insights into microbe-host interactions.
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Affiliation(s)
- Lin Zhang
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
- State Key Laboratory of Cotton BiologyHenan Key Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifengHenan475001China
| | - Yuping Wei
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Ye Tao
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Suya Zhao
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Xuyang Wei
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Xiaoyan Yin
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Suyao Liu
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Qiuhong Niu
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
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Mahipant G, Kato J, Kataoka N, Vangnai AS. An alternative genome-integrated method for undomesticated Bacillus subtilis and related species. J GEN APPL MICROBIOL 2019; 65:96-105. [PMID: 30487367 DOI: 10.2323/jgam.2018.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Given their applicability in genetic engineering, undomesticated Bacillus strains are extensively used as non-natural hosts for chemical production due to their high tolerance of toxic substrates or products. However, they are difficult to genomically modify due to their low transformation efficiencies. In this study, the Bacillus-E. coli shuttle vector pHY300PLK, which is widely used in gram-positive bacteria, was adopted for genome integration in organic solvent-tolerant Bacillus isolates. The Bacillus-replicative vector was used to deliver homologous recombinant DNA and propagate itself inside the host cell, increasing the likelihood of genome integration of the recombinant DNA. Then, the unintegrated vectors were cured by cell cultivation in antibiotic-free medium with facilitation of nickel ions. The developed protocol was successfully demonstrated and validated by the disruption of amyE gene in B. subtilis 168. With an improved clonal selection protocol, the probability of clonal selection of the amyE::cat genome-integrated mutants was increased up to 42.0 ± 10.2%. Genome integration in undomesticated, organic solvent tolerant Bacillus strains was also successfully demonstrated with amyE as well as proB gene creating the gene-disrupted mutants with the corresponding phenotype and genotype. Not only was this technique effectively applied to several strains of undomesticated B. subtilis, but it was also successfully applied to B. cereus. This study validates the possibility of the application of Bacillus-replicative vector as well as the developed protocol in a variety of genome modification of undomesticated Bacillus species.
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Affiliation(s)
- Gumpanat Mahipant
- Biological Sciences Program, Faculty of Science, Chulalongkorn University.,Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University
| | - Junichi Kato
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University
| | - Naoya Kataoka
- Division of Agricultural Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University
| | - Alisa S Vangnai
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University.,Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University
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Wang B, Huang B, Chen J, Li W, Yang L, Yao L, Niu Q. Whole-genome analysis of the colonization-resistant bacterium Phytobacter sp. SCO41 T isolated from Bacillus nematocida B16-fed adult Caenorhabditis elegans. Mol Biol Rep 2019; 46:1563-1575. [PMID: 30879274 DOI: 10.1007/s11033-018-04574-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Colonization resistance is an important attribute for bacterial interactions with hosts, but the mechanism is still not completely clear. In this study, we found that Phytobacter sp. SCO41T can effectively inhibit the in vivo colonization of Bacillus nematocida B16 in Caenorhabditis elegans, and we revealed the colonization resistance mechanism. Three strains of colonization-resistant bacteria, SCO41T, BX15, and BC7, were isolated from the intestines of the free-living nematode C. elegans derived from rotten fruit and soil. The primary characteristics and genome map of one of the three isolates was investigated to explore the underlying mechanism of colonization resistance in C. elegans. In addition, we performed exogenous iron supplementation and gene cluster knockout experiments to validate the sequencing results. The results showed that relationship was close among the three strains, which was identified as belonging to the genus Phytobacter. The type strain is SCO41T (= CICC 24103T = KCTC 52362T). Whole genome analysis showed that csgA, csgB, csgC, csgE, csgF, and csgG were involved in the curli adhesive process and that fepA, fepB, fepC, fepD, and fepG played important roles in SCO41T against the colonization of B. nematocida B16 in C. elegans by competing for iron. Exogenous iron supplementation showed that exogenous iron can increase the colonization of B. nematocida B16, which was additionally confirmed by a deletion mutant strain. The csg gene family contributes to the colonization of SCO41T in C. elegans. Curli potentially contribute to the colonization of SCO41T in C. elegans, and enterobactin has a key role in SCO41T to resist the colonization of B. nematocida B16 by competing for iron.
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Affiliation(s)
- Bowen Wang
- Department of Life Science and Biotechnology, Nanyang Normal University, Nanyang, 473000, People's Republic of China
| | - Bingfen Huang
- Department of Life Science and Biotechnology, Nanyang Normal University, Nanyang, 473000, People's Republic of China
| | - Junmei Chen
- Department of Life Science and Biotechnology, Nanyang Normal University, Nanyang, 473000, People's Republic of China
| | - Wenpeng Li
- Department of Life Science and Biotechnology, Nanyang Normal University, Nanyang, 473000, People's Republic of China
| | - Ling Yang
- Nanyang Academy of Agricultural Sciences, Nanyang, 473083, Henan, People's Republic of China
| | - Lunguang Yao
- Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang, People's Republic of China.
| | - Qiuhong Niu
- Department of Life Science and Biotechnology, Nanyang Normal University, Nanyang, 473000, People's Republic of China. .,China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, 473000, People's Republic of China.
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