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Liu J, He C, Tan W, Zheng JH. Path to bacteriotherapy: From bacterial engineering to therapeutic perspectives. Life Sci 2024:122897. [PMID: 38971366 DOI: 10.1016/j.lfs.2024.122897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/30/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
The major reason for the failure of conventional therapies is the heterogeneity and complexity of tumor microenvironments (TMEs). Many malignant tumors reprogram their surface antigens to evade the immune surveillance, leading to reduced antigen-presenting cells and hindered T-cell activation. Bacteria-mediated cancer immunotherapy has been extensively investigated in recent years. Scientists have ingeniously modified bacteria using synthetic biology and nanotechnology to enhance their biosafety with high tumor specificity, resulting in robust anticancer immune responses. To enhance the antitumor efficacy, therapeutic proteins, cytokines, nanoparticles, and chemotherapeutic drugs have been efficiently delivered using engineered bacteria. This review provides a comprehensive understanding of oncolytic bacterial therapies, covering bacterial design and the intricate interactions within TMEs. Additionally, it offers an in-depth comparison of the current techniques used for bacterial modification, both internally and externally, to maximize their therapeutic effectiveness. Finally, we outlined the challenges and opportunities ahead in the clinical application of oncolytic bacterial therapies.
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Affiliation(s)
- Jinling Liu
- The Affiliated Xiangtan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, China; College of Biology, Hunan University, Changsha 410082, China
| | - Chongsheng He
- College of Biology, Hunan University, Changsha 410082, China
| | - Wenzhi Tan
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, Hunan 410114, China.
| | - Jin Hai Zheng
- The Affiliated Xiangtan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, China.
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2
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Zhao J, Sun H, Wang G, Wang Q, Wang Y, Li Q, Bi S, Qi Q, Wang Q. Engineering Chimeric Chemoreceptors and Two-Component Systems for Orthogonal and Leakless Biosensing of Extracellular γ-Aminobutyric Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14216-14228. [PMID: 38860925 DOI: 10.1021/acs.jafc.4c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Two-component systems (TCSs) sensing and responding to various stimuli outside and inside cells are valuable resources for developing biosensors with synthetic biology applications. However, the use of TCS-based biosensors suffers from a limited effector spectrum, hypersensitivity, low dynamic range, and unwanted signal crosstalk. Here, we developed a tailor-made Escherichia coli whole-cell γ-aminobutyric acid (GABA) biosensor by engineering a chimeric GABA chemoreceptor PctC and TCS. By testing different TCSs, the chimeric PctC/PhoQ showed the response to GABA. Chimera-directed evolution and introduction of the insulated chimeric pair PctC/PhoQ*PhoP* produced biosensors with up to 3.50-fold dynamic range and good orthogonality. To further enhance the dynamic range and lower the basal leakage, three strategies, engineering of PhoP DNA binding sites, fine-tuning reporter expression by optimizing transcription/translation components, and a tobacco etch virus protease-controlled protein degradation, were integrated. This chimeric biosensor displayed a low basal leakage, a large dynamic range (15.8-fold), and a high threshold level (22.7 g L-1). Finally, the optimized biosensor was successfully applied in the high-throughput microdroplet screening of GABA-overproducing Corynebacterium glutamicum, demonstrating its desired properties for extracellular signal biosensing.
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Affiliation(s)
- Jingyu Zhao
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Huanhuan Sun
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Gege Wang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Qi Wang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Yipeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qingbin Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qian Wang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
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Jiang G, Wang C, Wang Y, Wang J, Xue Y, Lin Y, Hu X, Lv Y. Exogenous putrescine plays a switch-like influence on the pH stress adaptability of biofilm-based activated sludge. Appl Environ Microbiol 2024:e0056924. [PMID: 38916292 DOI: 10.1128/aem.00569-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/04/2024] [Indexed: 06/26/2024] Open
Abstract
Microbial community adaptability to pH stress plays a crucial role in biofilm formation. This study aims to investigate the regulatory mechanisms of exogenous putrescine on pH stress, as well as enhance understanding and application for the technical measures and molecular mechanisms of biofilm regulation. Findings demonstrated that exogenous putrescine acted as a switch-like distributor affecting microorganism pH stress, thus promoting biofilm formation under acid conditions while inhibiting it under alkaline conditions. As pH decreases, the protonation degree of putrescine increases, making putrescine more readily adsorbed. Protonated exogenous putrescine could increase cell membrane permeability, facilitating its entry into the cell. Subsequently, putrescine consumed intracellular H+ by enhancing the glutamate-based acid resistance strategy and the γ-aminobutyric acid metabolic pathway to reduce acid stress on cells. Furthermore, putrescine stimulated ATPase expression, allowing for better utilization of energy in H+ transmembrane transport and enhancing oxidative phosphorylation activity. However, putrescine protonation was limited under alkaline conditions, and the intracellular H+ consumption further exacerbated alkali stress and inhibits cellular metabolic activity. Exogenous putrescine promoted the proportion of fungi and acidophilic bacteria under acidic stress and alkaliphilic bacteria under alkali stress while having a limited impact on fungi in alkaline biofilms. Increasing Bdellovibrio under alkali conditions with putrescine further aggravated the biofilm decomposition. This research shed light on the unclear relationship between exogenous putrescine, environmental pH, and pH stress adaptability of biofilm. By judiciously employing putrescine, biofilm formation could be controlled to meet the needs of engineering applications with different characteristics.IMPORTANCEThe objective of this study is to unravel the regulatory mechanism by which exogenous putrescine influences biofilm pH stress adaptability and understand the role of environmental pH in this intricate process. Our findings revealed that exogenous putrescine functioned as a switch-like distributor affecting the pH stress adaptability of biofilm-based activated sludge, which promoted energy utilization for growth and reproduction processes under acidic conditions while limiting biofilm development to conserve energy under alkaline conditions. This study not only clarified the previously ambiguous relationship between exogenous putrescine, environmental pH, and biofilm pH stress adaptability but also offered fresh insights into enhancing biofilm stability within extreme environments. Through the modulation of energy utilization, exerting control over biofilm growth and achieving more effective engineering goals could be possible.
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Affiliation(s)
- Guanyu Jiang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Can Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Yongchao Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Jiayi Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Yimei Xue
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Yuting Lin
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Xurui Hu
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
| | - Yahui Lv
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, China
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Sharma D, Chetri PB, Ranga V, Sen S, Sarmah BK, Barooah M. Genomic analysis of acid tolerance genes and deciphering the function of ydaG gene in mitigating acid tolerance in Priestia megaterium. Front Microbiol 2024; 15:1414777. [PMID: 38966390 PMCID: PMC11222612 DOI: 10.3389/fmicb.2024.1414777] [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: 04/09/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
Adverse environmental conditions, such as acid stress, induce bacteria to employ several strategies to overcome these stressors. These strategies include forming biofilms and activating specific molecular pathways, such as the general stress response (GSR). The genome of Priestia megaterium strain G18 was sequenced using the Illumina NextSeq 500 system, resulting in a de novo assembly of 80 scaffolds. The scaffolded genome comprises 5,367,956 bp with a GC content of 37.89%, and was compared to related strains using the MiGA web server, revealing high similarity to P. megaterium NBRC 15308 and P. aryabhattai B8W22 with ANI scores of 95.4%. Phylogenetic and ribosomal multilocus sequence typing (rMLST) analyses, based on the 16S rRNA and ribosomal protein-encoding alleles, confirmed close relationships within the P. megaterium species. Functional annotation identified 5,484 protein-coding genes, with 72.31% classified into 22 COG categories, highlighting roles in amino acid transport, transcription, carbohydrate metabolism, and ribosomal structure. An in-depth genome analysis of P. megaterium G18 revealed several key genes associated with acid tolerance. Targeted inactivation of the ydaG gene from SigB regulon, a general stress response gene, significantly reduced growth under acidic conditions compared to the wild type. qRT-PCR analysis showed increased ydaG expression in acidic conditions, further supporting its role in acid stress response. Microscopic analysis revealed no morphological differences between wild-type and mutant cells, suggesting that ydaG is not involved in maintaining cellular morphology but in facilitating acid tolerance through stress protein production. This research contributes to understanding the molecular mechanisms underlying acid tolerance in soil bacteria, P. megaterium, shedding light on potential applications in agriculture and industry.
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Affiliation(s)
- Darshana Sharma
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Purna Bahadur Chetri
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Vipin Ranga
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Subhajit Sen
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Bidyut Kumar Sarmah
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Madhumita Barooah
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
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Allen ME, Kamilova E, Monck C, Ceroni F, Hu Y, Yetisen AK, Elani Y. Engineered Bacteria as Living Biosensors in Dermal Tattoos. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2309509. [PMID: 38884139 DOI: 10.1002/advs.202309509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/02/2024] [Indexed: 06/18/2024]
Abstract
Dermal tattoo biosensors are promising platforms for real-time monitoring of biomarkers, with skin used as a diagnostic interface. Traditional tattoo sensors have utilized small molecules as biosensing elements. However, the rise of synthetic biology has enabled the potential employment of engineered bacteria as living analytical tools. Exploiting engineered bacterial sensors will allow for potentially more sensitive detection across a broad biomarker range, with advanced processing and sense/response functionalities using genetic circuits. Here, the interfacing of bacterial biosensors as living analytics in tattoos is shown. Engineered bacteria are encapsulated into micron-scale hydrogel beads prepared through scalable microfluidics. These biosensors can sense both biochemical cues (model biomarkers) and biophysical cues (temperature changes, using RNA thermometers), with fluorescent readouts. By tattooing beads into skin models and confirming sensor activity post-tattooing, our study establishes a foundation for integrating bacteria as living biosensing entities in tattoos.
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Affiliation(s)
- Matthew E Allen
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ, UK
- Institute of Chemical Biology, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ, UK
- Department of Chemical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
- fabriCELL, Imperial College London and King's College London, London, W12 0BZ, UK
| | - Elina Kamilova
- Department of Chemical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Carolina Monck
- Department of Chemical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Yubing Hu
- Department of Chemical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Ali K Yetisen
- Department of Chemical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Yuval Elani
- Institute of Chemical Biology, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ, UK
- Department of Chemical Engineering, Imperial College London, South Kensington, London, SW7 2AZ, UK
- fabriCELL, Imperial College London and King's College London, London, W12 0BZ, UK
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Jiang B, Liu J, Wang J, Zhao G, Zhao Z. Adaptive Evolution for the Efficient Production of High-Quality d-Lactic Acid Using Engineered Klebsiella pneumoniae. Microorganisms 2024; 12:1167. [PMID: 38930549 PMCID: PMC11205318 DOI: 10.3390/microorganisms12061167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
d-Lactic acid serves as a pivotal platform chemical in the production of poly d-lactic acid (PDLA) and other value-added products. This compound can be synthesized by certain bacteria, including Klebsiella pneumoniae. However, industrial-scale lactic acid production in Klebsiella pneumoniae faces challenges due to growth inhibition caused by lactic acid stress, which acts as a bottleneck in commercial microbial fermentation processes. To address this, we employed a combination of evolutionary and genetic engineering approaches to create an improved Klebsiella pneumoniae strain with enhanced lactic acid tolerance and production. In flask fermentation experiments, the engineered strain achieved an impressive accumulation of 19.56 g/L d-lactic acid, representing the highest production yield observed in Klebsiella pneumoniae to date. Consequently, this strain holds significant promise for applications in industrial bioprocessing. Notably, our genome sequencing and experimental analyses revealed a novel correlation between UTP-glucose-1-phosphate uridylyltransferase GalU and lactic acid resistance in Klebsiella pneumoniae. Further research is warranted to explore the potential of targeting GalU for enhancing d-lactic acid production.
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Affiliation(s)
- Bo Jiang
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (B.J.); (J.L.); (J.W.)
| | - Jiezheng Liu
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (B.J.); (J.L.); (J.W.)
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingnan Wang
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (B.J.); (J.L.); (J.W.)
| | - Guang Zhao
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (B.J.); (J.L.); (J.W.)
| | - Zhe Zhao
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (B.J.); (J.L.); (J.W.)
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Tan Q, Gou L, Fan TP, Cai Y. Enzymatic properties of ornithine decarboxylase from Clostridium aceticum DSM1496. Biotechnol Appl Biochem 2024; 71:525-535. [PMID: 38225812 DOI: 10.1002/bab.2556] [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: 07/21/2023] [Accepted: 12/31/2023] [Indexed: 01/17/2024]
Abstract
Clostridium aceticum DSM1496 is an acid-resistant strain in which ornithine decarboxylase (ODC) plays a crucial role in acid resistance. In this study, we expressed ODC derived from C. aceticum DSM1496 in Escherichia coli BL21 (DE3) and thoroughly examined its enzymatic properties. The enzyme has a molecular weight of 55.27 kDa and uses pyridoxal-5'-phosphate (PLP) as a coenzyme with a Km = 0.31 mM. ODC exhibits optimal activity at pH 7.5, and it maintains high stability even at pH 4.5. The peak reaction temperature for ODC is 30°C. Besides, it can be influenced by certain metal ions such as Mn2+. Although l-ornithine serves as the preferred substrate for ODC, the enzyme also decarboxylates l-arginine and l-lysine simultaneously. The results indicate that ODC derived from C. aceticum DSM1496 exhibits the ability to produce putrescine, cadaverine, and agmatine through decarboxylation. These polyamines have the potential to neutralize acid in an acidic environment, facilitating the growth of microorganisms. These significant findings provide a strong basis for further investigation into the acid-resistant mechanisms contributed by ODC.
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Affiliation(s)
- Qian Tan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Linbo Gou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Layla A, Syed QA, Zahoor T, Shahid M. Investigating the role of Lactiplantibacillus plantarum vs. spontaneous fermentation in improving nutritional and consumer safety of the fermented white cabbage sprouts. Int Microbiol 2024; 27:753-764. [PMID: 37700156 DOI: 10.1007/s10123-023-00426-1] [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: 06/22/2023] [Revised: 08/15/2023] [Accepted: 08/25/2023] [Indexed: 09/14/2023]
Abstract
Brassicaceae sprouts are promising candidates for functional food because of their unique phytochemistry and high nutrient density compared to their seeds and matured vegetables. Despite being admired for their health-promoting properties, white cabbage sprouts have been least explored for their nutritional significance and behavior to lactic acid fermentation. This study aimed to investigate the role of lactic acid fermentation, i.e., inoculum vs. spontaneous, in reducing intrinsic toxicants load and improving nutrients delivering potential of the white cabbage sprouts. White cabbage sprouts with a 5-7 cm average size were processed as raw, blanched, Lactiplantibacillus plantarum-inoculated fermentation, and spontaneous fermentation. Plant material was dehydrated at 40 °C and evaluated for microbiological quality, macronutrients, minerals, and anti-nutrient contents. The results indicate L. plantarum inoculum fermentation of blanched cabbage sprouts (IF-BCS) to increase lactic acid bacteria count of the sprouts from 0.97 to 8.47 log CFU/g. Compared with the raw cabbage sprouts (RCS), inoculum fermented-raw cabbage sprouts (IF-RCS), and spontaneous fermented-raw cabbage sprouts (SF-RCS), the highest content of Ca (447 mg/100 g d.w.), Mg (204 mg/100 g d.w.), Fe (9.3 mg/100 g d.w.), Zn (5 mg/100 g d.w.), and Cu (0.5 mg/100 g d.w.) were recorded in IF-BCS. L. plantarum-led fermentation of BCS demonstrated a reduction in phytates, tannins, and oxalates contents at a rate of 42%, 66%, and 53%, respectively, while standalone lactic acid fermentation of the raw sprouts reduced the burden of anti-nutrients in a range between 32 and 56%. The results suggest L. plantarum-led lactic acid fermentation coupled with sprout blanching is the most promising way to improve the nutritional quality and safety of the white cabbage sprouts.
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Affiliation(s)
- Anam Layla
- National Institute of Food Science & Technology, University of Agriculture, Faisalabad, Pakistan
| | - Qamar Abbas Syed
- National Institute of Food Science & Technology, University of Agriculture, Faisalabad, Pakistan.
| | - Tahir Zahoor
- National Institute of Food Science & Technology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Shahid
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
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Ma K, Chinelo OR, Gu M, Kong F, Jiang Y, Wang H, Xue T. Role of ArcA in the regulation of antibiotic sensitivity in avian pathogenic Escherichia coli. Poult Sci 2024; 103:103686. [PMID: 38574461 PMCID: PMC11004985 DOI: 10.1016/j.psj.2024.103686] [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: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is one of the common extraintestinal infectious disease pathogens in chickens, geese, and other birds, inducing serious impediments to the development of the poultry industry. Hence, investigating how bacteria regulate themselves amidst different challenging conditions is immense essential in prevention and treatment for bacterial pathogen infections. The ArcA regulatory factor has been reported to regulate oxygen availability in strains, but its role in regulation of antibiotics resistance in APEC is unclear. This study delved into understanding how ArcA regulates antibiotic resistance in APEC. An E. coli APEC40 arcA knockout strain was constructed, and the regulatory mechanism of arcA on APEC antibiotic susceptibility was identified by drug sensitivity test, colony counting assay, real-time quantitative PCR, β-galactosidase assays and electrophoretic mobility shift assay (EMSA). The results showed that ArcA directly binds to the promoter region of the outer membrane protein OmpC/OmpW and regulates bacterial susceptibility to kanamycin and penicillin G. At the same time, the double knockout of ompW and ompW/arcA resulted in an increase in resistance to kanamycin compared to the deletion of the arcA gene. This outcome provided experimental proof suggesting that the outer membrane protein OmpW could serve as a crucial pathway for the ingress of kanamycin into cells. These results confirmed the important regulatory role of ArcA transcription factors under APEC antibiotic stress.
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Affiliation(s)
- Kai Ma
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Okoro Ruth Chinelo
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Mantian Gu
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Fanwenqing Kong
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ying Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Hui Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Ting Xue
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China.
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10
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Wang Y, Ling N, Jiao R, Zhang X, Ren Y, Zhao W, Chen H, Ye Y. A universal mechanism on desiccation tolerance of Cronobacter based on intracellular trehalose accumulation regulated by EnvZ/OmpR. Food Microbiol 2024; 119:104455. [PMID: 38225055 DOI: 10.1016/j.fm.2023.104455] [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: 06/13/2023] [Revised: 12/04/2023] [Accepted: 12/20/2023] [Indexed: 01/17/2024]
Abstract
Cronobacter (seven species) can survive in dry powdered infant formula for a long time, but the thorough molecular mechanism of resistance to desiccation remains elusive. Here we examine the regulation mechanism of Cronobacter's tolerance to desiccation by the typical two-component system (TCS) EnvZ/OmpR. When exposed to desiccation conditions, Cronobacter showed higher survival than other pathogens, as well as significantly up-regulated expression of ompR and otsAB genes with markedly decreased survival of their mutants, suggesting their relationship with desiccation tolerance. OmpR directly binds to the promoter of trehalose biosynthesis operon otsBA, significantly enhancing their expression, and boosting the trehalose levels. The ompR-deletion in other six species further confirmed its positive regulation in desiccation tolerance. Our data present a hypothesis that EnvZ/OmpR increases intracellular trehalose levels against damage to the cells, which prompts Cronobacter to survive in desiccation conditions. This study reveals a universal molecular mechanism for desiccation resistance in Cronobacter species.
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Affiliation(s)
- Yang Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Na Ling
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Rui Jiao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Xiyan Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Yuwei Ren
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Wenhua Zhao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Hanfang Chen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Yingwang Ye
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China; State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China.
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11
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Dong M, Holle MJ, Miller MJ, Banerjee P, Feng H. Fates of attached E. coli o157:h7 on intact leaf surfaces revealed leafy green susceptibility. Food Microbiol 2024; 119:104432. [PMID: 38225040 DOI: 10.1016/j.fm.2023.104432] [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: 09/06/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 01/17/2024]
Abstract
Leafy greens, especially lettuce, are repeatedly linked to foodborne outbreaks. This paper studied the susceptibility of different leafy greens to human pathogens. Five commonly consumed leafy greens, including romaine lettuce, green-leaf lettuce, baby spinach, kale, and collard, were selected by their outbreak frequencies. The behavior of E. coli O157:H7 87-23 on intact leaf surfaces and in their lysates was investigated. Bacterial attachment was positively correlated with leaf surface roughness and affected by the epicuticular wax composition. At room temperature, E. coli O157:H7 had the best growth potentials on romaine and green-leaf lettuce surfaces. The bacterial growth was positively correlated with stomata size and affected by epicuticular wax compositions. At 37 °C, E. coli O157:H7 87-23 was largely inhibited by spinach and collard lysates, and it became undetectable in kale lysate after 24 h of incubation. Kale and collard lysates also delayed or partially inhibited the bacterial growth in TSB and lettuce lysate at 37 °C, and they sharply reduced the E. coli O157:H7 population on green leaf lettuce at 4 °C. In summary, the susceptibility of leafy greens to E. coli O157:H7 is determined by a produce-specific combination of physiochemical properties and temperature.
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Affiliation(s)
- Mengyi Dong
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Maxwell J Holle
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Michael J Miller
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Pratik Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Hao Feng
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
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12
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Li K, Fang S, Zhang X, Wei X, Wu P, Zheng R, Liu L, Zhang H. Effects of Environmental Stresses on Synthesis of 2-Phenylethanol and IAA by Enterobacter sp. CGMCC 5087. Microorganisms 2024; 12:663. [PMID: 38674607 PMCID: PMC11052032 DOI: 10.3390/microorganisms12040663] [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: 02/13/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
2-Phenylethanol (2-PE) and indole-3-acetic acid (IAA) are important secondary metabolites produced by microorganisms, and their production are closely linked to the growth state of microorganisms and environmental factors. Enterobacter CGMCC 5087 can produce both 2-PE and IAA depending on α-ketoacid decarboxylase KDC4427. This study aimed to investigate the effects of different environment factors including osmotic pressure, temperature, and pH on the synthesis of 2-PE and IAA in Enterobacter sp. CGMCC 5087. The bacteria exhibited an enhanced capacity for 2-PE synthesis while not affecting IAA synthesis under 5% NaCl and pH 4.5 stress conditions. In an environment with pH 9.5, the synthesis capacity of 2-PE remained unchanged while the synthesis capacity of IAA decreased. The synthesis ability of 2-PE was enhanced with an increase in temperature within the range of 25 °C to 37 °C, while the synthesis capacity of IAA was not affected significantly. Additionally, the expression of KDC4427 varied under stress conditions. Under 5% NaCl stress and decreased temperature, expression of the KDC4427 gene was increased. However, altering pH did not result in significant differences in gene expression levels, while elevated temperature caused a decrease in gene expression. Furthermore, molecular docking and molecular dynamics simulations suggested that these conditions may induce fluctuation in the geometry shape of binding cavity, binding energy, and especially the dαC-C- value, which played key roles in affecting the enzyme activity. These results provide insights and strategies for the synthesis of metabolic products 2-PE and IAA in bacterial fermentation, even under unfavorable conditions.
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Affiliation(s)
- Ke Li
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot 010022, China; (K.L.); (X.W.); (P.W.)
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.F.); (X.Z.); (H.Z.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Senbiao Fang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.F.); (X.Z.); (H.Z.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiao Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.F.); (X.Z.); (H.Z.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiaodi Wei
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot 010022, China; (K.L.); (X.W.); (P.W.)
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.F.); (X.Z.); (H.Z.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Pingle Wu
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot 010022, China; (K.L.); (X.W.); (P.W.)
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.F.); (X.Z.); (H.Z.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Rong Zheng
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot 010022, China; (K.L.); (X.W.); (P.W.)
| | - Lijuan Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.F.); (X.Z.); (H.Z.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Haibo Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (S.F.); (X.Z.); (H.Z.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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13
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Lee TH, Charchar P, Separovic F, Reid GE, Yarovsky I, Aguilar MI. The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes. Chem Sci 2024; 15:3408-3427. [PMID: 38455013 PMCID: PMC10915831 DOI: 10.1039/d3sc04523d] [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: 08/27/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
It is now evident that the cell manipulates lipid composition to regulate different processes such as membrane protein insertion, assembly and function. Moreover, changes in membrane structure and properties, lipid homeostasis during growth and differentiation with associated changes in cell size and shape, and responses to external stress have been related to drug resistance across mammalian species and a range of microorganisms. While it is well known that the biomembrane is a fluid self-assembled nanostructure, the link between the lipid components and the structural properties of the lipid bilayer are not well understood. This perspective aims to address this topic with a view to a more detailed understanding of the factors that regulate bilayer structure and flexibility. We describe a selection of recent studies that address the dynamic nature of bacterial lipid diversity and membrane properties in response to stress conditions. This emerging area has important implications for a broad range of cellular processes and may open new avenues of drug design for selective cell targeting.
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Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
| | - Patrick Charchar
- School of Engineering, RMIT University Melbourne Victoria 3001 Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne VIC 3010 Australia
| | - Gavin E Reid
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne VIC 3010 Australia
- Department of Biochemistry and Pharmacology, University of Melbourne Parkville VIC 3010 Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University Melbourne Victoria 3001 Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
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14
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Yoon JH, Bae YM, Shin Y, Lee SY. Escherichia coli O157:H7 had a high degree of acid resistance in the presence of osmolytes (glycerol, glycine or fructose) by altering its lipid membrane composition. Food Microbiol 2024; 117:104388. [PMID: 37919012 DOI: 10.1016/j.fm.2023.104388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/12/2023] [Accepted: 09/17/2023] [Indexed: 11/04/2023]
Abstract
This study aims to investigate the resistance of E. coli O157:H7 to acetic acid (AA) or malic acid (MA) by adding osmolytes, such as glycerol, glycine, glucose, and fructose, in Luria-Bertani broth without NaCl (LBW/S) or phosphate buffer (PB) stored at 25 °C. In LBW/S, a significantly (p < 0.05) higher D-value of E. coli O157:H7 was observed when treated with AA and 20% glycine (D-value: 1.18-3.44) or 40% glucose (D-value: 1.05-2.52) compared to that of AA alone (D-value: 0.40-0.47). In contrast, the addition of osmolytes (i.e. 3-40% glucose, 3-40% fructose or 20% glycine) to LBW/S acidified by MA significantly decreased D-values of E. coli O157:H7, which was enumerated by using a selective medium. Furthermore, when E. coli O157:H7 was incubated in LBW/S containing AA and osmolytes at 25 °C for 3 d, this bacterium had an increased proportion of C16:0 and C17:0 cyclo (cyclopropane acid) compared to its AA-treated counterparts. Along with the altered shift in membrane phospholipids, the addition of osmolytes into a laboratory medium in the presence of nutritive substrates may increase the resistance of E. coli O157:H7 to AA.
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Affiliation(s)
- Jae-Hyun Yoon
- Department of Food and Nutrition, Sunchon National University, 235 Jungang-ro, Suncheon-si, Jeollanam-do, 57922, Republic of Korea
| | - Young-Min Bae
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodong-dearo, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Yooncheol Shin
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodong-dearo, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Sun-Young Lee
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodong-dearo, Anseong-si, Gyeonggi-do, 17546, Republic of Korea.
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15
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Melchionna M, Ganusova EE, Harmon N, Alexandre G. TrhA, a bacterial progestin and adiponectin receptor homolog, couples membrane energetics homeostasis and unsaturated fatty acid metabolism. J Bacteriol 2024; 206:e0039723. [PMID: 38054739 PMCID: PMC10810207 DOI: 10.1128/jb.00397-23] [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: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Members of the widely conserved progestin and adipoQ receptor (PAQR) family function to maintain membrane homeostasis: membrane fluidity and fatty acid composition in eukaryotes and membrane energetics and fatty acid composition in bacteria. All PAQRs consist of a core seven transmembrane domain structure and five conserved amino acids (three histidines, one serine, and one aspartic acid) predicted to form a hydrolase-like catalytic site. PAQR homologs in Bacteria (called TrhA, for transmembrane homeostasis protein A) maintain homeostasis of membrane charge gradients, like the membrane potential and proton gradient that comprise the proton motive force, but their molecular mechanisms are not yet understood. Here, we show that TrhA in Escherichia coli has a periplasmic C-terminus, which places the five conserved residues shared by all PAQRs at the cytoplasmic interface of the membrane. Here, we characterize several conserved residues predicted to form an active site by site-directed mutagenesis. We also identify a specific role for TrhA in modulating unsaturated fatty acid biosynthesis with conserved residues required to either promote or reduce the abundance of unsaturated fatty acids. We also identify distinct roles for the conserved residues in supporting TrhA's role in maintaining membrane energetics homeostasis that suggest that both functions are intertwined and probably partly dependent on one another. An analysis of domain architecture of TrhA-like domains in Bacteria further supports a function of TrhA linking membrane energetics homeostasis with biosynthesis of unsaturated fatty acid in the membrane. IMPORTANCE Progestin and adipoQ receptor (PAQR) family proteins are evolutionary conserved regulators of membrane homeostasis and have been best characterized in eukaryotes. Bacterial PAQR homologs, named TrhA (transmembrane homeostasis protein A), regulate membrane energetics homeostasis through an unknown mechanism. Here, we present evidence linking TrhA to both membrane energetics homeostasis and unsaturated fatty acid biosynthesis. Analysis of domain architecture together with experimental evidence suggests a model where TrhA activity on unsaturated fatty acid biosynthesis is regulated by changes in membrane energetics to dynamically adjust membrane homeostasis.
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Affiliation(s)
- Maddison Melchionna
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Elena E. Ganusova
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Neyland Harmon
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Gladys Alexandre
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
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16
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Tian J, Deng W, Zhang Z, Xu J, Yang G, Zhao G, Yang S, Jiang W, Gu Y. Discovery and remodeling of Vibrio natriegens as a microbial platform for efficient formic acid biorefinery. Nat Commun 2023; 14:7758. [PMID: 38012202 PMCID: PMC10682008 DOI: 10.1038/s41467-023-43631-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
Formic acid (FA) has emerged as a promising one-carbon feedstock for biorefinery. However, developing efficient microbial hosts for economically competitive FA utilization remains a grand challenge. Here, we discover that the bacterium Vibrio natriegens has exceptional FA tolerance and metabolic capacity natively. This bacterium is remodeled by rewiring the serine cycle and the TCA cycle, resulting in a non-native closed loop (S-TCA) which as a powerful metabolic sink, in combination with laboratory evolution, enables rapid emergence of synthetic strains with significantly improved FA-utilizing ability. Further introduction of a foreign indigoidine-forming pathway into the synthetic V. natriegens strain leads to the production of 29.0 g · L-1 indigoidine and consumption of 165.3 g · L-1 formate within 72 h, achieving a formate consumption rate of 2.3 g · L-1 · h-1. This work provides an important microbial chassis as well as design rules to develop industrially viable microorganisms for FA biorefinery.
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Affiliation(s)
- Jinzhong Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- Xianghu Laboratory, Hangzhou, 311231, China.
| | - Wangshuying Deng
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziwen Zhang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Xu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311215, China
| | | | - Guoping Zhao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sheng Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weihong Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yang Gu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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17
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Totsline N, Kniel KE, Bais HP. Microgravity and evasion of plant innate immunity by human bacterial pathogens. NPJ Microgravity 2023; 9:71. [PMID: 37679341 PMCID: PMC10485020 DOI: 10.1038/s41526-023-00323-x] [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: 02/20/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
Spaceflight microgravity and modeled-microgravity analogs (MMA) broadly alter gene expression and physiology in both pathogens and plants. Research elucidating plant and bacterial responses to normal gravity or microgravity has shown the involvement of both physiological and molecular mechanisms. Under true and simulated microgravity, plants display differential expression of pathogen-defense genes while human bacterial pathogens exhibit increased virulence, antibiotic resistance, stress tolerance, and reduced LD50 in animal hosts. Human bacterial pathogens including Salmonella enterica and E. coli act as cross-kingdom foodborne pathogens by evading and suppressing the innate immunity of plants for colonization of intracellular spaces. It is unknown if evasion and colonization of plants by human pathogens occurs under microgravity and if there is increased infection capability as demonstrated using animal hosts. Understanding the relationship between microgravity, plant immunity, and human pathogens could prevent potentially deadly outbreaks of foodborne disease during spaceflight. This review will summarize (1) alterations to the virulency of human pathogens under microgravity and MMA, (2) alterations to plant physiology and gene expression under microgravity and MMA, (3) suppression and evasion of plant immunity by human pathogens under normal gravity, (4) studies of plant-microbe interactions under microgravity and MMA. A conclusion suggests future study of interactions between plants and human pathogens under microgravity is beneficial to human safety, and an investment in humanity's long and short-term space travel goals.
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Affiliation(s)
- Noah Totsline
- Department of Plant and Soil Sciences, AP Biopharma, University of Delaware, Newark, DE, USA.
| | - Kalmia E Kniel
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, USA
| | - Harsh P Bais
- Department of Plant and Soil Sciences, AP Biopharma, University of Delaware, Newark, DE, USA
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18
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Frantz R, Gwozdzinski K, Gisch N, Doijad SP, Hudel M, Wille M, Abu Mraheil M, Schwudke D, Imirzalioglu C, Falgenhauer L, Ehrmann M, Chakraborty T. A Single Residue within the MCR-1 Protein Confers Anticipatory Resilience. Microbiol Spectr 2023; 11:e0359222. [PMID: 37071007 PMCID: PMC10269488 DOI: 10.1128/spectrum.03592-22] [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: 09/12/2022] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Abstract
The envelope stress response (ESR) of Gram-negative enteric bacteria senses fluctuations in nutrient availability and environmental changes to avert damage and promote survival. It has a protective role toward antimicrobials, but direct interactions between ESR components and antibiotic resistance genes have not been demonstrated. Here, we report interactions between a central regulator of ESR viz., the two-component signal transduction system CpxRA (conjugative pilus expression), and the recently described mobile colistin resistance protein (MCR-1). Purified MCR-1 is specifically cleaved within its highly conserved periplasmic bridge element, which links its N-terminal transmembrane domain with the C-terminal active-site periplasmic domain, by the CpxRA-regulated serine endoprotease DegP. Recombinant strains harboring cleavage site mutations in MCR-1 are either protease resistant or degradation susceptible, with widely differing consequences for colistin resistance. Transfer of the gene encoding a degradation-susceptible mutant to strains that lack either DegP or its regulator CpxRA restores expression and colistin resistance. MCR-1 production in Escherichia coli imposes growth restriction in strains lacking either DegP or CpxRA, effects that are reversed by transactive expression of DegP. Excipient allosteric activation of the DegP protease specifically inhibits growth of isolates carrying mcr-1 plasmids. As CpxRA directly senses acidification, growth of strains at moderately low pH dramatically increases both MCR-1-dependent phosphoethanolamine (PEA) modification of lipid A and colistin resistance levels. Strains expressing MCR-1 are also more resistant to antimicrobial peptides and bile acids. Thus, a single residue external to its active site induces ESR activity to confer resilience in MCR-1-expressing strains to commonly encountered environmental stimuli, such as changes in acidity and antimicrobial peptides. Targeted activation of the nonessential protease DegP can lead to the elimination of transferable colistin resistance in Gram-negative bacteria. IMPORTANCE The global presence of transferable mcr genes in a wide range of Gram-negative bacteria from clinical, veterinary, food, and aquaculture environments is disconcerting. Its success as a transmissible resistance factor remains enigmatic, because its expression imposes fitness costs and imparts only moderate levels of colistin resistance. Here, we show that MCR-1 triggers regulatory components of the envelope stress response, a system that senses fluctuations in nutrient availability and environmental changes, to promote bacterial survival in low pH environments. We identify a single residue within a highly conserved structural element of mcr-1 distal to its catalytic site that modulates resistance activity and triggers the ESR. Using mutational analysis, quantitative lipid A profiling and biochemical assays, we determined that growth in low pH environments dramatically increases colistin resistance levels and promotes resistance to bile acids and antimicrobial peptides. We exploited these findings to develop a targeted approach that eliminates mcr-1 and its plasmid carriers.
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Affiliation(s)
- Renate Frantz
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Konrad Gwozdzinski
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Swapnil Prakash Doijad
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Martina Hudel
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Maria Wille
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Mobarak Abu Mraheil
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site: Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Airway Research Center North, Partner Site: Research Center Borstel, Borstel, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
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19
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Doranga S, Conway T. OmpC-Dependent Bile Tolerance Contributes to E. coli Colonization of the Mammalian Intestine. Microbiol Spectr 2023; 11:e0524122. [PMID: 37014216 PMCID: PMC10269588 DOI: 10.1128/spectrum.05241-22] [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: 12/22/2022] [Accepted: 03/09/2023] [Indexed: 04/05/2023] Open
Abstract
Escherichia coli persistently colonizes the mammalian intestine by mechanisms that are not fully understood. Previously, we found when streptomycin-treated mice were fed E. coli MG1655, the intestine selected for envZ missense mutants that outcompeted the wild type. The better-colonizing envZ mutants had a higher level of OmpC and reduced OmpF. This suggested the EnvZ/OmpR two-component system and outer membrane proteins play a role in colonization. In this study, we show that wild-type E. coli MG1655 outcompetes an envZ-ompR knockout mutant. Moreover, ompA and ompC knockout mutants are outcompeted by the wild type, while an ompF knockout mutant colonizes better than the wild type. Outer membrane protein gels show the ompF mutant overproduces OmpC. An ompC mutant is more sensitive to bile salts than the wild type and ompF mutant. The ompC mutant initiates colonization slowly because it is sensitive to physiological concentrations of bile salts in the intestine. Overexpression of ompC under the control of a constitutive promoter confers a colonization advantage only when ompF is deleted. These results indicate that fine-tuning of OmpC and OmpF levels is needed to maximize competitive fitness in the intestine. RNA sequencing reveals the EnvZ/OmpR two-component system is active in the intestine: ompC is upregulated and ompF is downregulated. While other factors could also contribute to the advantage provided by OmpC, we provide evidence that OmpC is important for E. coli to colonize the intestine because its smaller pore size excludes bile salts or other unknown toxic substances, while OmpF is deleterious because its larger pore size allows bile salts or other unknown toxic substances to enter the periplasm. IMPORTANCE Every mammalian intestine is colonized with Escherichia coli. Although E. coli is one of the most studied model organisms, how it colonizes the intestine is not fully understood. Here, we investigated the role of the EnvZ/OmpR two-component system and outer membrane proteins in colonization of the mouse intestine by E. coli. We report that an ompC mutant is a poor colonizer, while an ompF mutant, which overproduces OmpC, outcompetes the wild type. OmpF has a larger pore size that allows toxic bile salts or other toxic compounds into the cell and is deleterious for colonization of the intestine. OmpC has a smaller pore size and excludes bile salts. Our findings provide insights into why E. coli fine-tunes the levels of OmpC and OmpF during colonization via the EnvZ/OmpR two-component system.
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Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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20
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Zhou S, Zhang Y, Wei Z, Park S. Recent advances in metabolic engineering of microorganisms for the production of monomeric C3 and C4 chemical compounds. BIORESOURCE TECHNOLOGY 2023; 377:128973. [PMID: 36972803 DOI: 10.1016/j.biortech.2023.128973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 06/18/2023]
Abstract
Bio-based C3 and C4 bi-functional chemicals are useful monomers in biopolymer production. This review describes recent progresses in the biosynthesis of four such monomers as a hydroxy-carboxylic acid (3-hydroxypropionic acid), a dicarboxylic acid (succinic acid), and two diols (1,3-propanediol and 1,4-butanediol). The use of cheap carbon sources and the development of strains and processes for better product titer, rate and yield are presented. Challenges and future perspectives for (more) economical commercial production of these chemicals are also briefly discussed.
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Affiliation(s)
- Shengfang Zhou
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yingli Zhang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zhiwen Wei
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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21
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The role of PhoP/PhoQ system in regulating stress adaptation response in Escherichia coli O157:H7. Food Microbiol 2023; 112:104244. [PMID: 36906298 DOI: 10.1016/j.fm.2023.104244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/19/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
The development of acid tolerance response (ATR) as a result of low pH in Escherichia coli O157:H7 (E. coli O157:H7) contaminating beef during processing is considered a major food safety concern. Thus, in order to explore the formation and molecular mechanisms of the tolerance response of E. coli O157:H7 in a simulated beef processing environment, the resistance of a wild-type (WT) strain and its corresponding ΔphoP mutant to acid, heat, and osmotic pressure was evaluated. Strains were pre-adapted under different conditions of pH (5.4 and 7.0), temperature (37 °C and 10 °C), and culture medium (meat extract and Luria-Bertani broth media). In addition, the expression of genes related to stress response and virulence was also investigated among WT and ΔphoP strains under the tested conditions. Pre-acid adaptation increased the resistance of E. coli O157:H7 to acid and heat treatment while resistance to osmotic pressure decreased. Moreover, acid adaptation in meat extract medium simulating slaughter environment increased ATR, whereas pre-adaptation at 10 °C reduced the ATR. Furthermore, it was shown that mildly acidic conditions (pH = 5.4) and the PhoP/PhoQ two-component system (TCS) acted synergistically to enhance acid and heat tolerance in E. coli O157:H7. Additionally, the expression of genes related to arginine and lysine metabolism, heat shock, and invasiveness was up-regulated, which revealed that the mechanism of acid resistance and cross-protection under mildly acidic conditions was mediated by the PhoP/PhoQ TCS. Both acid adaptation and phoP gene knockout reduced the relative expression of stx1 and stx2 genes which were considered as critical pathogenic factors. Collectively, the current findings indicated that ATR could occur in E. coli O157:H7 during beef processing. Thus, there is an increased food safety risk due to the persistence of tolerance response in the following processing conditions. The present study provides a more comprehensive basis for the effective application of hurdle technology in beef processing.
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Pino AFS, Espinosa ZYD, Cabrera EVR. Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau. BMC PLANT BIOLOGY 2023; 23:217. [PMID: 37098489 PMCID: PMC10127060 DOI: 10.1186/s12870-023-04182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The microbial biodiversity and the role of microorganisms in the fermentation of washed coffee in Colombia were investigated using the Bourbon and Castillo coffee varieties. DNA sequencing was used to evaluate the soil microbial biota and their contribution to fermentation. The potential benefits of these microorganisms were analyzed, including increased productivity and the need to understand the rhizospheric bacterial species to optimize these benefits. METHODS This study used coffee beans for DNA extraction and 16 S rRNA sequencing. The beans were pulped, samples were stored at 4ºC, and the fermentation process was at 19.5ºC and 24ºC. The fermented mucilage and root-soil samples were collected in duplicate at 0, 12, and 24 h. DNA was extracted from the samples at a concentration of 20 ng/µl per sample, and the data obtained were analyzed using the Mothur platform. RESULTS The study demonstrates that the coffee rhizosphere is a diverse ecosystem composed primarily of microorganisms that cannot be cultured in the laboratory. This suggests that the microbial community may vary depending on the coffee variety and play an essential role in fermentation and overall coffee quality. CONCLUSIONS The study highlights the importance of understanding and optimizing the microbial diversity in coffee production, which could have implications for the sustainability and success of coffee production. DNA sequencing techniques can help characterize the structure of the soil microbial biota and evaluate its contribution to coffee fermentation. Finally, further research is needed to fully understand the biodiversity of coffee rhizospheric bacteria and their role.
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Affiliation(s)
- Andrés Felipe Solis Pino
- Corporación Universitaria Comfacauca - Unicomfacauca, Cl. 4 N. 8-30, Popayán, Cauca, 190001, Colombia.
| | | | - Efren Venancio Ramos Cabrera
- Corporación Universitaria Comfacauca - Unicomfacauca, Cl. 4 N. 8-30, Popayán, Cauca, 190001, Colombia
- Universidad Nacional Abierta y a Distancia - UNAD, Calle 5 # 46N -67, Popayán, Cauca, 190001, Colombia
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De A, Roychowdhury P, Bhuyan NR, Ko YT, Singh SK, Dua K, Kuppusamy G. Folic Acid Functionalized Diallyl Trisulfide-Solid Lipid Nanoparticles for Targeting Triple Negative Breast Cancer. Molecules 2023; 28:molecules28031393. [PMID: 36771058 PMCID: PMC9921651 DOI: 10.3390/molecules28031393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
DATS (diallyl trisulfide), an anti-oxidant and cytotoxic chemical derived from the plant garlic, has been found to have potential therapeutic activity against triple-negative breast cancer (TNBC). Its hydrophobicity, short half-life, lack of target selectivity, and limited bioavailability at the tumor site limit its efficacy in treating TNBC. Overexpression of the Folate receptor on the surface of TNBC is a well-known target receptor for overcoming off-targeting, and lipid nanoparticles solve the limitations of limited bioavailability and short half-life. In order to overcome these constraints, we developed folic acid (FA)-conjugated DATS-SLNs in this research. The design of experiment (DoE) method was employed to optimize the FA-DATS-SLNs' nanoformulation, which resulted in a particle size of 168.2 ± 3.78 nm and a DATS entrapment of 71.91 ± 6.27%. The similarity index between MCF-7 and MDA-MB-231 cell lines demonstrates that FA-DATS-SLNs are more therapeutically efficacious in the treatment of aggravating TNBC. Higher cellular internalization and efficient Bcl2 protein downregulation support the hypothesis that functionalization of the FA on the surface of DATS-SLNs improves anticancer efficacy when compared with DATS and DATS-SLNs. FA-functionalized DATS-SLNs have demonstrated to be a promising therapeutic strategy for TNBC management.
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Affiliation(s)
- Anindita De
- College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon 21936, Republic of Korea
- Correspondence: (A.D.); (G.K.); Tel.: +82-1098218750 (A.D.); +91-9443089812 (G.K.)
| | - Parikshit Roychowdhury
- Department of Pharmaceutical Chemistry, Himalayan Pharmacy Institute, Majitar 737136, East Sikkim, India
| | - Nihar Ranjan Bhuyan
- Department of Pharmaceutical Chemistry, Himalayan Pharmacy Institute, Majitar 737136, East Sikkim, India
| | - Young Tag Ko
- College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon 21936, Republic of Korea
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary & Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Gowthamarajan Kuppusamy
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty 643001, Tamil Nadu, India
- Correspondence: (A.D.); (G.K.); Tel.: +82-1098218750 (A.D.); +91-9443089812 (G.K.)
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An G, Yan R, Fu Z, Chen Z, Guo Y, Yang J, Zhou Y. Adaptation of anammox consortia in microbial fuel cell to low temperature: Microbial community and predictive functional profiling. BIORESOURCE TECHNOLOGY 2023; 370:128565. [PMID: 36596367 DOI: 10.1016/j.biortech.2022.128565] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
The purpose of this study was to explore the tolerance mechanism of anammox consortia in microbial fuel cell (MFC) system at low temperature. Data showed that nearly 80 % total nitrogen removal was achieved after the temperature decreased from 30 °C to 15 °C. The nitrogenremovalrate (NRR) of the system was decreased by 26.3 %, from 0.441 kgN·m-3·d-1 at 30 °C to 0.325 kgN·m-3·d-1 at 15 °C. Isotope experiment in 15NH4+-containing reactor found that much more 29N2 were produced than 30N2, confirming that anammox was the main 15NH4+ removal pathway and electrochemical oxidation participate in this process. High throughput sequencing analysis indicated the low temperature stimulated the enrichment of heterotrophic bacteria, such as Comamonadaceae and Rhodobacteraceae. While the relative abundance of Candidatus Brocadia, typical anammox bacteria, decreased significantly. Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis showed that the low temperature induced a more efficient expression in synthesis of unsaturated fatty acids (UFAs) and ABC membrane transports. This study indicates that anammox consortia are likely to maintain high nitrogen removal performance of MFC system by changing the proportion of membrane composition and EPS exportation.
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Affiliation(s)
- Geer An
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Rong Yan
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China; Inner Mongolia Lvchuang Environmental Protection Technology Co., Ltd., Hohhot 010051, China
| | - Zhimin Fu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China.
| | - Zepeng Chen
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Yaru Guo
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Jun Yang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
| | - Yongheng Zhou
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia, Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot 010040, China
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Hu W, Tong Y, Liu J, Chen P, Yang H, Feng S. Improving acid resistance of Escherichia coli base on the CfaS-mediated membrane engineering strategy derived from extreme acidophile. Front Bioeng Biotechnol 2023; 11:1158931. [PMID: 37025359 PMCID: PMC10070827 DOI: 10.3389/fbioe.2023.1158931] [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: 02/04/2023] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
Industrial microorganisms used for the production of organic acids often face challenges such as inhibited cell growth and reduced production efficiency due to the accumulation of acidic metabolites. One promising way for improving the acid resistance of microbial cells is to reconstruct their membranes. Herein, the overexpression of cfa2 from extreme acidophile endowed E. coli with high-performance on resistance to the acid stress. The engineered strain M1-93-Accfa2, constructed by CRISPR/Cas9-mediated chromosome integration, also exhibited a significantly higher resistance to severe acid stress. The analysis of fatty acid profiles indicated that the proportion of Cy-19:0 in the cell membrane of M1-93-Accfa2 increased by 5.26 times compared with the control, while the proportion of C18:1w9c decreased by 5.81 times. Correspondingly, the permeability and fluidity of the membrane decreased significantly. HPLC analysis demonstrated that the contents of intracellular glutamic acid, arginine, methionine and aspartic acid of M1-93-Accfa2 were 2.59, 2.04, 22.07 and 2.65 times that of the control after environmental acidification, respectively. Meanwhile, transmission electron microscopy observation indicated that M1-93-Accfa2 could maintain a plumper cell morphology after acid stimulation. M1-93-Accfa2 also exhibited higher-performance on the resistance to organic acids, especially succinic acid stress. These results together demonstrated the great potential of M1-93-Accfa2 constructed here in the production of organic acids.
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Affiliation(s)
- Wenbo Hu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yanjun Tong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Junjie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Panyan Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, Jiangnan University, Wuxi, China
| | - Hailin Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, Jiangnan University, Wuxi, China
- *Correspondence: Hailin Yang, ; Shoushuai Feng,
| | - Shoushuai Feng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, Jiangnan University, Wuxi, China
- *Correspondence: Hailin Yang, ; Shoushuai Feng,
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Spoto M, Riera Puma JP, Fleming E, Guan C, Ondouah Nzutchi Y, Kim D, Oh J. Large-Scale CRISPRi and Transcriptomics of Staphylococcus epidermidis Identify Genetic Factors Implicated in Lifestyle Versatility. mBio 2022; 13:e0263222. [PMID: 36409086 PMCID: PMC9765180 DOI: 10.1128/mbio.02632-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus epidermidis is a ubiquitous human commensal skin bacterium that is also one of the most prevalent nosocomial pathogens. The genetic factors underlying this remarkable lifestyle plasticity are incompletely understood, mainly due to the difficulties of genetic manipulation, precluding high-throughput functional profiling of this species. To probe the versatility of S. epidermidis to survive across a diversity of environmental conditions, we developed a large-scale CRISPR interference (CRISPRi) screen complemented by transcriptional profiling (RNA sequencing) across 24 diverse conditions and piloted a droplet-based CRISPRi approach to enhance throughput and sensitivity. We identified putative essential genes, importantly revealing amino acid metabolism as crucial to survival across diverse environments, and demonstrated the importance of trace metal uptake for survival under multiple stress conditions. We identified pathways significantly enriched and repressed across our range of stress and nutrient-limited conditions, demonstrating the considerable plasticity of S. epidermidis in responding to environmental stressors. Additionally, we postulate a mechanism by which nitrogen metabolism is linked to lifestyle versatility in response to hyperosmotic challenges, such as those encountered on human skin. Finally, we examined the survival of S. epidermidis under acid stress and hypothesize a role for cell wall modification as a vital component of the survival response under acidic conditions. Taken together, this study integrates large-scale CRISPRi and transcriptomics data across multiple environments to provide insights into a keystone member of the human skin microbiome. Our results additionally provide a valuable benchmarking analysis for CRISPRi screens and are a rich resource for other staphylococcal researchers. IMPORTANCE Staphylococcus epidermidis is a bacteria that broadly inhabits healthy human skin, yet it is also a common cause of skin infections and bloodstream infections associated with implanted medical devices. Because human skin has many different types of S. epidermidis, each containing different genes, our goal is to determine how these different genes allow S. epidermidis to switch from healthy growth in the skin to being an infectious pathogen. Understanding this switch is critical to developing new strategies to prevent and treat S. epidermidis infections.
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Affiliation(s)
- Michelle Spoto
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
- The University of Connecticut Health Center, Farmington, Connecticut, USA
| | | | - Elizabeth Fleming
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Changhui Guan
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | | | - Dean Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Gold A, Chen L, Zhu J. More than Meets the Eye: Untargeted Metabolomics and Lipidomics Reveal Complex Pathways Spurred by Activation of Acid Resistance Mechanisms in Escherichia coli. J Proteome Res 2022; 21:2958-2968. [PMID: 36322795 PMCID: PMC10317704 DOI: 10.1021/acs.jproteome.2c00459] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Escherichia coli is a ubiquitous group of bacteria that can be either commensal gut microbes or enterohemorrhagic food-borne pathogens. Regardless, both forms must survive acidic environments in the stomach and intestines to reach and colonize the gut, a process that partially relies on amino acid-dependent acid resistance (AR) mechanisms and modifications to membrane phospholipids. However, only the basic tenets of these mechanisms have been elucidated. In this paper, we aim to conduct a full-scale metabolic and lipidomic characterization of E. coli's adaptations to acid stress. We hypothesized that the use of untargeted metabolomics and lipidomics would reveal mechanisms downstream of AR processes that provide novel contributions to acid stress survival. We detected significant differences in the extracellular metabolome and the lipidome induced by amino acid supplementation (glutamine, arginine, or lysine) and contextualized these results using real-time quantitative polymerase chain reaction (RT-qPCR). We additionally identified several metabolic pathways as well as a significant alteration in phospholipid synthetic pathways induced by differential amino acid supplementation. These results demonstrate that AR may extend beyond canonical mechanisms to a coordinated metabolic phenotype. Future studies may benefit from our analysis to further elucidate distinct targets for prebiotic supplements to cultivate commensal strains or therapies to combat pathogenic ones.
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Affiliation(s)
- Andrew Gold
- Human Nutrition Program & James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Li Chen
- Human Nutrition Program & James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Jiangjiang Zhu
- Human Nutrition Program & James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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In Vitro and In Vivo Evaluation of Lacticaseibacillus rhamnosus GG and Bifidobacterium lactis Bb12 Against Avian Pathogenic Escherichia coli and Identification of Novel Probiotic-Derived Bioactive Peptides. Probiotics Antimicrob Proteins 2022; 14:1012-1028. [PMID: 34458959 DOI: 10.1007/s12602-021-09840-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 12/24/2022]
Abstract
Avian pathogenic E. coli (APEC), an extra-intestinal pathogenic E. coli (ExPEC), causes colibacillosis in poultry and is also a potential foodborne zoonotic pathogen. Currently, APEC infections in poultry are controlled by antibiotic medication; however, the emergence of multi-drug-resistant APEC strains and increased restrictions on the use of antibiotics in food-producing animals necessitate the development of new antibiotic alternative therapies. Here, we tested the anti-APEC activity of multiple commensal and probiotic bacteria in an agar-well diffusion assay and identified Lacticaseibacillus rhamnosus GG and Bifidobacterium lactis Bb12 producing strong zone of inhibition against APEC. In co-culture assay, L. rhamnosus GG and B. lactis Bb12 completely inhibited the APEC growth by 24 h. Further investigation revealed that antibacterial product(s) in the culture supernatants of L. rhamnosus GG and B. lactis Bb12 were responsible for the anti-APEC activity. The analysis of culture supernatants using LC-MS/MS identified multiple novel bioactive peptides (VQAAQAGDTKPIEV, AFDNTDTSLDSTFKSA, VTDTSGKAGTTKISNV, and AESSDTNLVNAKAA) in addition to the production of lactic acid. The oral administration (108 CFU/chicken) of L. rhamnosus GG significantly (P < 0.001) reduced the colonization (~ 1.6 logs) of APEC in the cecum of chickens. Cecal microbiota analysis revealed that L. rhamnosus GG moderated the APEC-induced alterations of the microbial community in the cecum of chickens. Further, L. rhamnosus GG decreased (P < 0.05) the abundance of phylum Proteobacteria, particularly those belonging to Enterobacteriaceae (Escherichia-Shigella) family. These studies indicate that L. rhamnosus GG is a promising probiotic to control APEC infections in chickens. Further studies are needed to optimize the delivery of L. rhamnosus GG in feed or water and in conditions simulating the field to facilitate its development for commercial applications.
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Abstract
The two-component system CpxRA can sense environmental stresses and regulate transcription of a wide range of genes for the purpose of adaptation. Despite extensive research on this system, the identification of the CpxR regulon is not systematic or comprehensive. Herein, genome-wide screening was performed using a position-specific scoring matrix, resulting in the discovery of more than 10,000 putative CpxR binding sites, which provides an extensive and selective set of targets based on sequence. More than half of the candidate genes ultimately selected (73/97) were experimentally confirmed to be CpxR-regulated genes through experimental analysis. These genes are involved in various physiological functions, indicating that the CpxRA system regulates complex cellular processes. The study also found for the first time that the CpxR-regulated genes ydeE, xylE, alx, and galP contribute to Escherichia coli resistance to acid stress, whereas prlF, alx, casA, yacH, ydeE, sbmA, and ampH contribute to E. coli resistance to cationic antimicrobial peptide stress. Among these CpxR-regulated genes, ydeE and alx responded to both stressors. In a similar way, a cationic antimicrobial peptide is capable of directly activating the periplasmic domain of CpxA kinase in vitro, which is consistent with the CpxA response to acid stress. These results greatly expand our understanding of the CpxRA-dependent stress response network in E. coli. IMPORTANCE CpxRA system is found in many pathogens and plays an essential role in sensing environmental signals and transducing information inside cells for adaptation. It usually regulates expression of specific genes in response to different environmental stresses and is important for bacterial pathogenesis. However, systematically identifying CpxRA-regulated genes and elucidating the regulative role of CpxRA in bacteria responding to environmental stress remains challenging. This study discovered more than 10,000 putative CpxR binding sites based on sequence. This bioinformatics approach, combined with experimental assays, allowed the identification of many previously unknown CpxR-regulated genes. Among the novel 73 CpxRA-regulated genes identified in this study, the role of nine of them in contributing to E. coli resistance to acid or cationic antimicrobial peptide stress was studied. The potential correlation between these two environmental stress responses provides insight into the CpxRA-dependent stress response network. This also improves our understanding of environment-bacterium interaction and Gram-negative pathogenesis.
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Kammel M, Pinske C, Sawers RG. FocA and its central role in fine-tuning pH homeostasis of enterobacterial formate metabolism. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36197793 DOI: 10.1099/mic.0.001253] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
During enterobacterial mixed-acid fermentation, formate is generated from pyruvate by the glycyl-radical enzyme pyruvate formate-lyase (PflB). In Escherichia coli, especially at low pH, formate is then disproportionated to CO2 and H2 by the cytoplasmically oriented, membrane-associated formate hydrogenlyase (FHL) complex. If electron acceptors are available, however, formate is oxidized by periplasmically oriented, respiratory formate dehydrogenases. Formate translocation across the cytoplasmic membrane is controlled by the formate channel, FocA, a member of the formate-nitrite transporter (FNT) family of homopentameric anion channels. This review highlights recent advances in our understanding of how FocA helps to maintain intracellular formate and pH homeostasis during fermentation. Efflux and influx of formate/formic acid are distinct processes performed by FocA and both are controlled through protein interaction between FocA's N-terminal domain with PflB. Formic acid efflux by FocA helps to maintain cytoplasmic pH balance during exponential-phase growth. Uptake of formate against the electrochemical gradient (inside negative) is energetically and mechanistically challenging for a fermenting bacterium unless coupled with proton/cation symport. Translocation of formate/formic acid into the cytoplasm necessitates an active FHL complex, whose synthesis also depends on formate. Thus, FocA, FHL and PflB function together to govern formate homeostasis. We explain how FocA achieves efflux of formic acid and propose mechanisms for pH-dependent uptake of formate both with and without proton symport. We propose that FocA displays both channel- and transporter-like behaviour. Whether this translocation behaviour is shared by other members of the FNT family is also discussed.
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Affiliation(s)
- Michelle Kammel
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Constanze Pinske
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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An international comprehensive benchmarking analysis of synthetic biology in China from 2015 to 2020. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2021.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Discovery of a novel acrylic acid formation pathway in Gluconobacter oxydans and its application in biosynthesis of acrylic acid from glycerol. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.04.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Wu L, Bao F, Li L, Yin X, Hua Z. Bacterially mediated drug delivery and therapeutics: Strategies and advancements. Adv Drug Deliv Rev 2022; 187:114363. [PMID: 35649449 DOI: 10.1016/j.addr.2022.114363] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 12/12/2022]
Abstract
It was already clinically apparent 150 years ago that bacterial therapy could alleviate diseases. Recently, a burgeoning number of researchers have been using bacterial regimens filled with microbial therapeutic leads to diagnose and treat a wide range of disorders and diseases, including cancers, inflammatory diseases, metabolic disorders and viral infections. Some bacteria that were designed to have low toxicity and high efficiency in drug delivery have been used to treat diseases successfully, especially in tumor therapy in animal models or clinical trials, thanks to the progress of genetic engineering and synthetic bioengineering. Therefore, genetically engineered bacteria can serve as efficient drug delivery vehicles, carrying nucleic acids or genetic circuits that encode and regulate therapeutic payloads. In this review, we summarize the development and applications of this approach. Strategies for genetically modifying strains are described in detail, along with their objectives. We also describe some controlled strategies for drug delivery and release using these modified strains as carriers. Furthermore, we discuss treatment methods for various types of diseases using engineered bacteria. Tumors are discussed as the most representative example, and other diseases are also briefly described. Finally, we discuss the challenges and prospects of drug delivery systems based on these bacteria.
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Loss of β-Ketoacyl Acyl Carrier Protein Synthase III Activity Restores Multidrug-Resistant Escherichia coli Sensitivity to Previously Ineffective Antibiotics. mSphere 2022; 7:e0011722. [PMID: 35574679 PMCID: PMC9241538 DOI: 10.1128/msphere.00117-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gram-negative pathogens are a major concern for global public health due to increasing rates of antibiotic resistance and the lack of new drugs. A major contributing factor toward antibiotic resistance in Gram-negative bacteria is their formidable outer membrane, which acts as a permeability barrier preventing many biologically active antimicrobials from reaching the intracellular targets and thus limiting their efficacy.
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Xue M, Fu D, Hu J, Shao Y, Tu J, Song X, Qi K. The Transcription Regulator YgeK Affects Biofilm Formation and Environmental Stress Resistance in Avian Pathogenic Escherichia coli. Animals (Basel) 2022; 12:ani12091160. [PMID: 35565586 PMCID: PMC9100123 DOI: 10.3390/ani12091160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 01/25/2023] Open
Abstract
Simple Summary Avian pathogenic Escherichia coli (APEC) is the pathogen responsible for colibacillosis in poultry. Transcriptional regulator ygeK has been shown to decrease APEC’s flagellar formation ability, bacterial motility ability, serum sensitivity, and adhesion ability. However, we did not study the effects of ygeK on biofilm formation and environmental stress resistance in APEC. In this study, we investigated ygeK in APEC biofilm formation and bacterial resistance to different environmental stresses. We also analyzed the multi-level regulation of ygeK in APEC and investigated associations between differentially expressed proteins and key ygeK targets. This work provides a basis for further analysis of APEC pathogenesis mechanisms. Abstract Avian pathogenic Escherichia coli (APEC) is one of the most common pathogens in poultry and a potential gene source of human extraintestinal pathogenic E. coli (ExPEC), leading to serious economic losses in the poultry industry and public health concerns. Exploring the pathogenic mechanisms underpinning APEC and the identification of new targets for disease prevention and treatment are warranted. YgeK is a transcriptional regulator in APEC and is localized to the type III secretion system 2 of E. coli. In our previous work, the transcription factor ygeK significantly affected APEC flagella formation, bacterial motility, serum sensitivity, adhesion, and virulence. To further explore ygeK functions, we evaluated its influence on APEC biofilm formation and resistance to environmental stress. Our results showed that ygeK inactivation decreased biofilm formation and reduced bacterial resistance to environmental stresses, including acid and oxidative stress. In addition, the multi-level regulation of ygeK in APEC was analyzed using proteomics, and associations between differentially expressed proteins and the key targets of ygeK were investigated. Overall, we identified ygeK’s new function in APEC. These have led us to better understand the transcriptional regulatory ygeK and provide new clues about the pathogenicity of APEC.
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Affiliation(s)
- Mei Xue
- Jinling Institute of Technology, College of Animal Science and Food Engineering, Nanjing 211169, China;
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei 230036, China; (D.F.); (J.H.); (Y.S.); (J.T.)
| | - Dandan Fu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei 230036, China; (D.F.); (J.H.); (Y.S.); (J.T.)
| | - Jiangang Hu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei 230036, China; (D.F.); (J.H.); (Y.S.); (J.T.)
| | - Ying Shao
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei 230036, China; (D.F.); (J.H.); (Y.S.); (J.T.)
| | - Jian Tu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei 230036, China; (D.F.); (J.H.); (Y.S.); (J.T.)
| | - Xiangjun Song
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei 230036, China; (D.F.); (J.H.); (Y.S.); (J.T.)
- Correspondence: (X.S.); (K.Q.); Tel.: +86-551-6578-5310 (K.Q.)
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei 230036, China; (D.F.); (J.H.); (Y.S.); (J.T.)
- Correspondence: (X.S.); (K.Q.); Tel.: +86-551-6578-5310 (K.Q.)
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Firrman J, Liu L, Mahalak K, Tanes C, Bittinger K, Tu V, Bobokalonov J, Mattei L, Zhang H, Van den Abbeele P. The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production. FEMS Microbiol Ecol 2022; 98:6564177. [PMID: 35383853 DOI: 10.1093/femsec/fiac038] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/17/2022] [Accepted: 04/01/2022] [Indexed: 11/12/2022] Open
Abstract
Environmental pH is a critical parameter for maintenance of the gut microbiota. Here, the impact of pH on the gut microbiota luminal and mucosal community structure and short chain fatty acid (SCFA) production was evaluated in vitro, and data compiled to reveal a donor-independent response to an increase or decrease in environmental pH. The results found that raising environmental pH significantly increased luminal community richness and decreased mucosal community evenness. This corresponded with an increased abundance of Ruminococcaceae Ruminococcus, and Erysipelotrichaceae Erysipelatoclostridium, and a decreased abundance of Coriobacteriaceae Collinsella, and Enterobacteriaceae Shigella for both the luminal and mucosal communities. Total SCFA levels were significantly higher, primarily due to an increase in acetic and 2-methylbutanoic acids. Lowering pH decreased luminal community evenness and decreased mucosal community evenness and richness. This corresponded with an increased abundance of Lachnospiraceae Enterocloster, Veillonellaceae Megasphaera, Veillonellaceae Sporomusa, Erysipelotrichaceae Eubacterium, and Alcaligenaceae Sutterella, and decreased abundance of Odoribacteraceae Butyricimonas, Fusobacteriaceae Fusobacterium, Veillonellaceae Phascolarctobacterium, and multiple Enterobacteriaceae species for both the luminal and mucosal communities. Total SCFA levels were significantly lower, with an observed drop in acetic and propionic acids, and increased butyric and valeric acids. Taken together, these results indicate that alterations to environmental pH can modulate the gut microbiota community structure and function, and some changes may occur in a donor-independent manner.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States of America
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States of America
| | - Karley Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States of America
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Vincent Tu
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Jamshed Bobokalonov
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States of America
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Huanjia Zhang
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
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Bacterial Homologs of Progestin and AdipoQ Receptors (PAQRs) Affect Membrane Energetics Homeostasis but Not Fluidity. J Bacteriol 2022; 204:e0058321. [PMID: 35285724 PMCID: PMC9017321 DOI: 10.1128/jb.00583-21] [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] [Indexed: 11/20/2022] Open
Abstract
Membrane potential homeostasis is essential for cell survival. Defects in membrane potential lead to pleiotropic phenotypes, consistent with the central role of membrane energetics in cell physiology. Homologs of the progestin and AdipoQ receptors (PAQRs) are conserved in multiple phyla of Bacteria and Eukarya. In eukaryotes, PAQRs are proposed to modulate membrane fluidity and fatty acid (FA) metabolism. The role of bacterial homologs has not been elucidated. Here, we use Escherichia coli and Bacillus subtilis to show that bacterial PAQR homologs, which we name “TrhA,” have a role in membrane energetics homeostasis. Using transcriptional fusions, we show that E. coli TrhA (encoded by yqfA) is part of the unsaturated fatty acid biosynthesis regulon. Fatty acid analyses and physiological assays show that a lack of TrhA in both E. coli and B. subtilis (encoded by yplQ) provokes subtle but consistent changes in membrane fatty acid profiles that do not translate to control of membrane fluidity. Instead, membrane proteomics in E. coli suggested a disrupted energy metabolism and dysregulated membrane energetics in the mutant, though it grew similarly to its parent. These changes translated into a disturbed membrane potential in the mutant relative to its parent under various growth conditions. Similar dysregulation of membrane energetics was observed in a different E. coli strain and in the distantly related B. subtilis. Together, our findings are consistent with a role for TrhA in membrane energetics homeostasis, through a mechanism that remains to be elucidated. IMPORTANCE Eukaryotic homologs of the progestin and AdipoQ receptor family (PAQR) have been shown to regulate membrane fluidity by affecting, through unknown mechanisms, unsaturated fatty acid (FA) metabolism. The bacterial homologs studied here mediate small and consistent changes in unsaturated FA metabolism that do not seem to impact membrane fluidity but, rather, alter membrane energetics homeostasis. Together, the findings here suggest that bacterial and eukaryotic PAQRs share functions in maintaining membrane homeostasis (fluidity in eukaryotes and energetics for bacteria with TrhA homologs).
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Corsini PM, Wang S, Rehman S, Fenn K, Sagar A, Sirovica S, Cleaver L, Edwards-Gayle CJC, Mastroianni G, Dorgan B, Sewell LM, Lynham S, Iuga D, Franks WT, Jarvis J, Carpenter GH, Curtis MA, Bernadó P, Darbari VC, Garnett JA. Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation. NPJ Biofilms Microbiomes 2022; 8:9. [PMID: 35217675 PMCID: PMC8881592 DOI: 10.1038/s41522-022-00272-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
Escherichia coli is a Gram-negative bacterium that colonises the human intestine and virulent strains can cause severe diarrhoeal and extraintestinal diseases. The protein SslE is secreted by a range of pathogenic and commensal E. coli strains. It can degrade mucins in the intestine, promotes biofilm maturation and it is a major determinant of infection in virulent strains, although how it carries out these functions is not well understood. Here, we examine SslE from the commensal E. coli Waksman and BL21 (DE3) strains and the enterotoxigenic H10407 and enteropathogenic E2348/69 strains. We reveal that SslE has a unique and dynamic structure in solution and in response to acidification within mature biofilms it can form a unique aggregate with amyloid-like properties. Furthermore, we show that both SslE monomers and aggregates bind DNA in vitro and co-localise with extracellular DNA (eDNA) in mature biofilms, and SslE aggregates may also associate with cellulose under certain conditions. Our results suggest that interactions between SslE and eDNA are important for biofilm maturation in many E. coli strains and SslE may also be a factor that drives biofilm formation in other SslE-secreting bacteria.
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Affiliation(s)
- Paula M Corsini
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sunjun Wang
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Katherine Fenn
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Amin Sagar
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Slobodan Sirovica
- Centre for Oral Bioengineering, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | | | - Giulia Mastroianni
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ben Dorgan
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Lee M Sewell
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, King's College London, London, UK
| | - Dinu Iuga
- Department of Physics, University of Warwick, Coventry, UK
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry, UK
| | - James Jarvis
- Randall Division of Cell and Molecular Biophysics and Centre for Biomolecular Spectroscopy, King's College London, London, UK
| | - Guy H Carpenter
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Michael A Curtis
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Pau Bernadó
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Vidya C Darbari
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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Multi-Omic Analysis to Characterize Metabolic Adaptation of the E. coli Lipidome in Response to Environmental Stress. Metabolites 2022; 12:metabo12020171. [PMID: 35208246 PMCID: PMC8880424 DOI: 10.3390/metabo12020171] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/17/2022] Open
Abstract
As an adaptive survival response to exogenous stress, bacteria undergo dynamic remodelling of their lipid metabolism pathways to alter the composition of their cellular membranes. Here, using Escherichia coli as a well characterised model system, we report the development and application of a ‘multi-omics’ strategy for comprehensive quantitative analysis of the temporal changes in the lipidome and proteome profiles that occur under exponential growth phase versus stationary growth phase conditions i.e., nutrient depletion stress. Lipidome analysis performed using ‘shotgun’ direct infusion-based ultra-high resolution accurate mass spectrometry revealed a quantitative decrease in total lipid content under stationary growth phase conditions, along with a significant increase in the mol% composition of total cardiolipin, and an increase in ‘odd-numbered’ acyl-chain length containing glycerophospholipids. The inclusion of field asymmetry ion mobility spectrometry was shown to enable the enrichment and improved depth of coverage of low-abundance cardiolipins, while ultraviolet photodissociation-tandem mass spectrometry facilitated more complete lipid structural characterisation compared with conventional collision-induced dissociation, including unambiguous assignment of the odd-numbered acyl-chains as containing cyclopropyl modifications. Proteome analysis using data-dependent acquisition nano-liquid chromatography mass spectrometry and tandem mass spectrometry analysis identified 83% of the predicted E. coli lipid metabolism enzymes, which enabled the temporal dependence associated with the expression of key enzymes responsible for the observed adaptive lipid metabolism to be determined, including those involved in phospholipid metabolism (e.g., ClsB and Cfa), fatty acid synthesis (e.g., FabH) and degradation (e.g., FadA/B,D,E,I,J and M), and proteins involved in the oxidative stress response resulting from the generation of reactive oxygen species during β-oxidation or lipid degradation.
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40
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Liu S, Xu JZ, Zhang WG. Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production. World J Microbiol Biotechnol 2022; 38:22. [PMID: 34989926 DOI: 10.1007/s11274-021-03212-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
As an important raw material for pharmaceutical, food and feed industry, highly efficient production of L-tryptophan by Escherichia coli has attracted a considerable attention. However, there are complicated and multiple layers of regulation networks in L-tryptophan biosynthetic pathway and thus have difficulty to rewrite the biosynthetic pathway for producing L-tryptophan with high efficiency in E. coli. This review summarizes the biosynthetic pathway of L-tryptophan and highlights the main regulatory mechanisms in E. coli. In addition, we discussed the latest metabolic engineering strategies achieved in E. coli to reconstruct the L-tryptophan biosynthetic pathway. Moreover, we also review a few strategies that can be used in E. coli to improve robustness and streamline of L-tryptophan high-producing strains. Lastly, we also propose the potential strategies to further increase L-tryptophan production by systematic metabolic engineering and synthetic biology techniques.
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Affiliation(s)
- Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
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41
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De Marchi S, García-Lojo D, Bodelón G, Pérez-Juste J, Pastoriza-Santos I. Plasmonic Au@Ag@mSiO 2 Nanorattles for In Situ Imaging of Bacterial Metabolism by Surface-Enhanced Raman Scattering Spectroscopy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:61587-61597. [PMID: 34927427 PMCID: PMC8719315 DOI: 10.1021/acsami.1c21812] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
It is well known that microbial populations and their interactions are largely influenced by their secreted metabolites. Noninvasive and spatiotemporal monitoring and imaging of such extracellular metabolic byproducts can be correlated with biological phenotypes of interest and provide new insights into the structure and development of microbial communities. Herein, we report a surface-enhanced Raman scattering (SERS) hybrid substrate consisting of plasmonic Au@Ag@mSiO2 nanorattles for optophysiological monitoring of extracellular metabolism in microbial populations. A key element of the SERS substrate is the mesoporous silica shell encapsulating single plasmonic nanoparticles, which furnishes colloidal stability and molecular sieving capabilities to the engineered nanostructures, thereby realizing robust, sensitive, and reliable measurements. The reported SERS-based approach may be used as a powerful tool for deciphering the role of extracellular metabolites and physicochemical factors in microbial community dynamics and interactions.
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Affiliation(s)
- Sarah De Marchi
- CINBIO,
Universidade de Vigo, Departamento de Química Física, Campus Universitario As Lagoas, Marcosende, 36310 Vigo, Spain
- Galicia
Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
| | - Daniel García-Lojo
- CINBIO,
Universidade de Vigo, Departamento de Química Física, Campus Universitario As Lagoas, Marcosende, 36310 Vigo, Spain
- Galicia
Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
| | - Gustavo Bodelón
- CINBIO,
Universidade de Vigo, Departamento de Química Física, Campus Universitario As Lagoas, Marcosende, 36310 Vigo, Spain
- Galicia
Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
| | - Jorge Pérez-Juste
- CINBIO,
Universidade de Vigo, Departamento de Química Física, Campus Universitario As Lagoas, Marcosende, 36310 Vigo, Spain
- Galicia
Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
| | - Isabel Pastoriza-Santos
- CINBIO,
Universidade de Vigo, Departamento de Química Física, Campus Universitario As Lagoas, Marcosende, 36310 Vigo, Spain
- Galicia
Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
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Chang D, Islam ZU, Zheng J, Zhao J, Cui X, Yu Z. Inhibitor tolerance and bioethanol fermentability of levoglucosan-utilizing Escherichia coli were enhanced by overexpression of stress-responsive gene ycfR: The proteomics-guided metabolic engineering. Synth Syst Biotechnol 2021; 6:384-395. [PMID: 34853817 PMCID: PMC8605246 DOI: 10.1016/j.synbio.2021.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/28/2021] [Accepted: 11/08/2021] [Indexed: 01/06/2023] Open
Abstract
Pretreatment of lignocellulosic biomass is crucial for the release of biofermentable sugars for biofuels production, which could greatly alleviate the burgeoning environment and energy crisis caused by the massive usage of traditional fossil fuels. Pyrolysis is a cost-saving pretreatment process that can readily decompose biomass into levoglucosan, a promising anhydrosugar; however, many undesired toxic compounds inhibitory to downstream microbial fermentation are also generated during the pyrolysis, immensely impeding the bioconversion of levoglucosan-containing pyrolysate. Here, we took the first insight into the proteomic responses of a levoglucosan-utilizing and ethanol-producing Escherichia coli to three representative biomass-derived inhibitors, identifying large amounts of differentially expressed proteins (DEPs) that could guide the downstream metabolic engineering for the development of inhibitor-resistant strains. Fifteen up- and eight down-regulated DEPs were further identified as the biomarker stress-responsive proteins candidate for cellular tolerance to multiple inhibitors. Among these biomarker proteins, YcfR exhibiting the highest expression fold-change level was chosen as the target of overexpression to validate proteomics results and develop robust strains with enhanced inhibitor tolerance and fermentation performance. Finally, based on four plasmid-borne genes encoding the levoglucosan kinase, pyruvate decarboxylase, alcohol dehydrogenase, and protein YcfR, a new recombinant strain E. coli LGE-ycfR was successfully created, showing much higher acetic acid-, furfural-, and phenol-tolerance levels compared to the control without overexpression of ycfR. The specific growth rate, final cell density, ethanol concentration, ethanol productivity, and levoglucosan consumption rate of the recombinant were also remarkably improved. From the proteomics-guided metabolic engineering and phenotypic observations, we for the first time corroborated that YcfR is a stress-induced protein responsive to multiple biomass-derived inhibitors, and also developed an inhibitors-resistant strain that could produce bioethanol from levoglucosan in the presence of inhibitors of relatively high concentration. The newly developed E. coli LGE-ycfR strain that could eliminate the commonly-used costly detoxicification processes, is of great potential for the in situ cost-effective bioethanol production from the biomass-derived pyrolytic substrates.
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Affiliation(s)
- Dongdong Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zia Ul Islam
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Junfang Zheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, PR China
| | - Jie Zhao
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiaoyong Cui
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, No. 380 Huaibei Town, Huairou District, Beijing, 101408, PR China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, 100085, PR China
- Corresponding author. College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China.
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43
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Kucukyildirim S, Miller SF, Lynch M. Low base-substitution mutation rate and predominance of insertion-deletion events in the acidophilic bacterium Acidobacterium capsulatum. Ecol Evol 2021; 11:17609-17614. [PMID: 35003627 PMCID: PMC8717266 DOI: 10.1002/ece3.8429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/07/2022] Open
Abstract
Analyses of spontaneous mutation have shown that total genome-wide mutation rates are quantitatively similar for most prokaryotic organisms. However, this view is mainly based on organisms that grow best around neutral pH values (6.0-8.0). In particular, the whole-genome mutation rate has not been determined for an acidophilic organism. Here, we have determined the genome-wide rate of spontaneous mutation in the acidophilic Acidobacterium capsulatum using a direct and unbiased method: a mutation-accumulation experiment followed by whole-genome sequencing. Evaluation of 69 mutation accumulation lines of A. capsulatum after an average of ~2900 cell divisions yielded a base-substitution mutation rate of 1.22 × 10-10 per site per generation or 4 × 10-4 per genome per generation, which is significantly lower than the consensus value (2.5-4.6 × 10-3) of mesothermophilic (~15-40°C) and neutrophilic (pH 6-8) prokaryotic organisms. However, the insertion-deletion rate (0.43 × 10-10 per site per generation) is high relative to the base-substitution mutation rate. Organisms with a similar effective population size and a similar expected effect of genetic drift should have similar mutation rates. Because selection operates on the total mutation rate, it is suggested that the relatively high insertion-deletion rate may be balanced by a low base-substitution rate in A. capsulatum, with selection operating on the total mutation rate.
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Affiliation(s)
- Sibel Kucukyildirim
- Department of BiologyHacettepe UniversityAnkaraTurkey
- Department of BiologyIndiana UniversityBloomingtonINUSA
| | - Samuel F. Miller
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeArizonaUSA
| | - Michael Lynch
- Biodesign Center for Mechanisms of EvolutionArizona State UniversityTempeArizonaUSA
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Sawant N, Singh H, Appukuttan D. Overview of the Cellular Stress Responses Involved in Fatty Acid Overproduction in E. coli. Mol Biotechnol 2021; 64:373-387. [PMID: 34796451 DOI: 10.1007/s12033-021-00426-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/10/2021] [Indexed: 12/29/2022]
Abstract
Research on microbial fatty acid metabolism started in the late 1960s, and till date, various developments have aided in elucidating the fatty acid metabolism in great depth. Over the years, synthesis of microbial fatty acid has drawn industrial attention due to its diverse applications. However, fatty acid overproduction imparts various stresses on its metabolic pathways causing a bottleneck to further increase the fatty acid yields. Numerous strategies to increase fatty acid titres in Escherichia coli by pathway modulation have already been published, but the stress generated during fatty acid overproduction is relatively less studied. Stresses like pH, osmolarity and oxidative stress, not only lower fatty acid titres, but also alter the cell membrane composition, protein expression and membrane fluidity. This review discusses an overview of fatty acid synthesis pathway and presents a panoramic view of various stresses caused due to fatty acid overproduction in E. coli. It also addresses how certain stresses like high temperature and nitrogen limitation can boost fatty acid production. This review paper also highlights the interconnections that exist between these stresses.
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Affiliation(s)
- Neha Sawant
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Vile Parle (West), Mumbai, 400056, India
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Vile Parle (West), Mumbai, 400056, India.
| | - Deepti Appukuttan
- Biosystems Engineering Lab, Department of Chemical Engineering, IIT Bombay, Powai, Mumbai, 400076, India.
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Chang D, Wang C, Ndayisenga F, Yu Z. Mutations in adaptively evolved Escherichia coli LGE2 facilitated the cost-effective upgrading of undetoxified bio-oil to bioethanol fuel. BIORESOUR BIOPROCESS 2021; 8:105. [PMID: 38650237 PMCID: PMC10991953 DOI: 10.1186/s40643-021-00459-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Levoglucosan is a promising sugar present in the lignocellulose pyrolysis bio-oil, which is a renewable and environment-friendly source for various value-added productions. Although many microbial catalysts have been engineered to produce biofuels and chemicals from levoglucosan, the demerits that these biocatalysts can only utilize pure levoglucosan while inhibited by the inhibitors co-existing with levoglucosan in the bio-oil have greatly limited the industrial-scale application of these biocatalysts in lignocellulose biorefinery. In this study, the previously engineered Escherichia coli LGE2 was evolved for enhanced inhibitor tolerance using long-term adaptive evolution under the stress of multiple inhibitors and finally, a stable mutant E. coli-H was obtained after ~ 374 generations' evolution. In the bio-oil media with an extremely acidic pH of 3.1, E. coli-H with high inhibitor tolerance exhibited remarkable levoglucosan consumption and ethanol production abilities comparable to the control, while the growth of the non-evolved strain was completely blocked even when the pH was adjusted to 7.0. Finally, 8.4 g/L ethanol was achieved by E. coli-H in the undetoxified bio-oil media with ~ 2.0% (w/v) levoglucosan, reaching 82% of the theoretical yield. Whole-genome re-sequencing to monitor the acquisition of mutations identified 4 new mutations within the globally regulatory genes rssB, yqhA, and basR, and the - 10 box of the putative promoter of yqhD-dgkA operon. Especially, yqhA was the first time to be revealed as a gene responsible for inhibitor tolerance. The mutations were all responsible for improved fitness, while basR mutation greatly contributed to the fitness improvement of E. coli-H. This study, for the first time, generated an inhibitor-tolerant levoglucosan-utilizing strain that could produce cost-effective bioethanol from the toxic bio-oil without detoxification process, and provided important experimental evidence and valuable genetic/proteinic information for the development of other robust microbial platforms involved in lignocellulose biorefining processes.
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Affiliation(s)
- Dongdong Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Cong Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
- RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, 100085, People's Republic of China.
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46
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The challenges and prospects of Escherichia coli as an organic acid production host under acid stress. Appl Microbiol Biotechnol 2021; 105:8091-8107. [PMID: 34617140 DOI: 10.1007/s00253-021-11577-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Organic acids have a wide range of applications and have attracted the attention of many industries, and their large-scale applications have led fermentation production to low-cost development. Among them, the microbial fermentation method, especially using Escherichia coli as the production host, has the advantages of fast growth and low energy consumption, and has gradually shown better advantages and prospects in organic acid fermentation production. IMPORTANCE However, when the opportunity comes, the acidified environment caused by the acid products accumulated during the fermentation process also challenges E. coli. The acid sensitivity of E. coli is a core problem that needs to be solved urgently. The addition of neutralizers in traditional operations led to the emergence of osmotic stress inadvertently, the addition of strong acid substances to recover products in the salt state not only increases production costs, but the discharged sewage is also harmful to the environment. ELABORATION This article summarizes the current status of the application of E. coli in the production of organic acids, and based on the impact of acid stress on the physiological state of cells and the impact of industrial production profits, put forward some new conjectures that can make up for the deficiencies in existing research and application. IMPLICATION At this point, the diversified transformation of E. coli has become a chassis microbe that is more suitable for industrial fermentation, enhancing industrial application value. KEY POINTS • E. coli is a potential host for high value-added organic acids production. • Classify the damage mechanism and coping strategies of E. coli when stimulated by acid molecules. • Multi-dimensional expansion tools are needed to create acid-resistant E. coli chassis.
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Wang H, Shang F, Shen J, Xu J, Chen X, Ni J, Yu L, Xue T. LsrR, the effector of AI-2 quorum sensing, is vital for the H 2O 2 stress response in mammary pathogenic Escherichia coli. Vet Res 2021; 52:127. [PMID: 34600565 PMCID: PMC8487509 DOI: 10.1186/s13567-021-00998-8] [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: 05/16/2021] [Accepted: 09/11/2021] [Indexed: 12/12/2022] Open
Abstract
Mammary pathogenic Escherichia coli (MPEC) is an important causative agent of mastitis in dairy cows that results in reduced milk quality and production, and is responsible for severe economic losses in the dairy industry worldwide. Oxidative stress, as an imbalance between reactive oxygen species (ROS) and antioxidants, is a stress factor that is common in most bacterial habitats. The presence of ROS can damage cellular sites, including iron-sulfur clusters, cysteine and methionine protein residues, and DNA, and may cause bacterial cell death. Previous studies have reported that Autoinducer 2 (AI-2) can regulate E. coli antibiotic resistance and pathogenicity by mediating the intracellular receptor protein LsrR. This study explored the regulatory mechanism of LsrR on the H2O2 stress response in MPEC, showing that the transcript levels of lsrR significantly decreased under H2O2 stress conditions. The survival cell count of lsrR mutant XW10/pSTV28 was increased about 3080-fold when compared with that of the wild-type WT/pSTV28 in the presence of H2O2 and overexpression of lsrR (XW10/pUClsrR) resulted in a decrease in bacterial survival rates under these conditions. The β-galactosidase reporter assays showed that mutation of lsrR led to a remarkable increase in expression of the promoters of ahpCF, katG and oxyR, while lsrR-overexpressing significantly reduced the expression of ahpCF and katG. The electrophoretic mobility shift assays confirmed that LsrR could directly bind to the promoter regions of ahpCF and katG. These results revealed the important role played by LsrR in the oxidative stress response of MPEC.
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Affiliation(s)
- Hui Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Fei Shang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jiawei Shen
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jingyi Xu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xiaolin Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jingtian Ni
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Lumin Yu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China. .,Institute of Microbe and Host Health, Linyi University, Linyi, 276005, Shandong, China.
| | - Ting Xue
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, Anhui, China.
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48
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Patel V, Matange N. Adaptation and compensation in a bacterial gene regulatory network evolving under antibiotic selection. eLife 2021; 10:70931. [PMID: 34591012 PMCID: PMC8483737 DOI: 10.7554/elife.70931] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/22/2021] [Indexed: 12/28/2022] Open
Abstract
Gene regulatory networks allow organisms to generate coordinated responses to environmental challenges. In bacteria, regulatory networks are re-wired and re-purposed during evolution, though the relationship between selection pressures and evolutionary change is poorly understood. In this study, we discover that the early evolutionary response of Escherichia coli to the antibiotic trimethoprim involves derepression of PhoPQ signaling, an Mg2+-sensitive two-component system, by inactivation of the MgrB feedback-regulatory protein. We report that derepression of PhoPQ confers trimethoprim-tolerance to E. coli by hitherto unrecognized transcriptional upregulation of dihydrofolate reductase (DHFR), target of trimethoprim. As a result, mutations in mgrB precede and facilitate the evolution of drug resistance. Using laboratory evolution, genome sequencing, and mutation re-construction, we show that populations of E. coli challenged with trimethoprim are faced with the evolutionary ‘choice’ of transitioning from tolerant to resistant by mutations in DHFR, or compensating for the fitness costs of PhoPQ derepression by inactivating the RpoS sigma factor, itself a PhoPQ-target. Outcomes at this evolutionary branch-point are determined by the strength of antibiotic selection, such that high pressures favor resistance, while low pressures favor cost compensation. Our results relate evolutionary changes in bacterial gene regulatory networks to strength of selection and provide mechanistic evidence to substantiate this link.
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Affiliation(s)
- Vishwa Patel
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, The Maharaja Sayajirao University of Baroda, Vadodara, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Nishad Matange
- Indian Institute of Science Education and Research (IISER), Pune, India
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49
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Tran VG, Zhao H. Engineering robust microorganisms for organic acid production. J Ind Microbiol Biotechnol 2021; 49:6373449. [PMID: 34549297 PMCID: PMC9118992 DOI: 10.1093/jimb/kuab067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/11/2021] [Indexed: 11/24/2022]
Abstract
Organic acids are an important class of compounds that can be produced by microbial conversion of renewable feedstocks and have huge demands and broad applications in food, chemical, and pharmaceutical industries. An economically viable fermentation process for production of organic acids requires robust microbial cell factories with excellent tolerance to low pH conditions, high concentrations of organic acids, and lignocellulosic inhibitors. In this review, we summarize various strategies to engineer robust microorganisms for organic acid production and highlight their applications in a few recent examples.
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Affiliation(s)
- Vinh G Tran
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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50
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Du C, Huo X, Gu H, Wu D, Hu Y. Acid resistance system CadBA is implicated in acid tolerance and biofilm formation and is identified as a new virulence factor of Edwardsiella tarda. Vet Res 2021; 52:117. [PMID: 34521475 PMCID: PMC8438976 DOI: 10.1186/s13567-021-00987-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/27/2021] [Indexed: 11/10/2022] Open
Abstract
Edwardsiella tarda is a facultative intracellular pathogen in humans and animals. The Gram-negative bacterium is widely considered a potentially important bacterial pathogen. Adaptation to acid stress is important for the transmission of intestinal microbes, so the acid-resistance (AR) system is essential. However, the AR systems of E. tarda are totally unknown. In this study, a lysine-dependent acid resistance (LDAR) system in E. tarda, CadBA, was characterized and identified. CadB is a membrane protein and shares high homology with the lysine/cadaverine antiporter. CadA contains a PLP-binding core domain and a pyridoxal phosphate-binding motif. It shares high homology with lysine decarboxylase. cadB and cadA are co-transcribed under one operon. To study the function of the cadBA operon, isogenic cadA, cadB and cadBA deletion mutant strains TX01ΔcadA, TX01ΔcadB and TX01ΔcadBA were constructed. When cultured under normal conditions, the wild type strain and three mutants exhibited the same growth performance. However, when cultured under acid conditions, the growth of three mutants, especially TX01ΔcadA, were obviously retarded, compared to the wild strain TX01, which indicates the important involvement of the cadBA operon in acid resistance. The deletion of cadB or cadA, especially cadBA, significantly attenuated bacterial activity of lysine decarboxylase, suggesting the vital participation of cadBA operon in lysine metabolism, which is closely related to acid resistance. The mutations of cadBA operon enhanced bacterial biofilm formation, especially under acid conditions. The deletions of the cadBA operon reduced bacterial adhesion and invasion to Hela cells. Consistently, the deficiency of cadBA operon abated bacterial survival and replication in macrophages, and decreased bacterial dissemination in fish tissues. Our results also show that the expression of cadBA operon and regulator cadC were up-regulated upon acid stress, and CadC rigorously regulated the expression of cadBA operon, especially under acid conditions. These findings demonstrate that the AR CadBA system was a requisite for the resistance of E. tarda against acid stress, and played a critical role in bacterial infection of host cells and in host tissues. This is the first study about the acid resistance system of E. tarda and provides new insights into the acid-resistance mechanism and pathogenesis of E. tarda.
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Affiliation(s)
- Chunmei Du
- College of Basic Medicine, Jiamusi University, 154007, Jiamusi, China.,Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, 571101, Haikou, China.,College of Life Science, Jiamusi University, 154007, Jiamusi, China
| | - Xiaoping Huo
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, 571101, Haikou, China.,College of Life Science, Jiamusi University, 154007, Jiamusi, China
| | - Hanjie Gu
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, 571101, Haikou, China.,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, 571101, Haikou, China
| | - Dongmei Wu
- College of Basic Medicine, Jiamusi University, 154007, Jiamusi, China. .,Heilongjiang Provincial Key Laboratory of New Drug Development and Evaluation of the Efficacy of Toxicology, 154007, Jiamusi, China.
| | - Yonghua Hu
- Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, 571101, Haikou, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), 266071, Qingdao, China. .,College of Life Science, Jiamusi University, 154007, Jiamusi, China. .,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, 571101, Haikou, China.
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