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Hu W, Huo X, Bai H, Chen Z, Zhang J, Yang H, Feng S. Insights into the complementation potential of the extreme acidophile's orthologue in replacing Escherichia coli hfq gene-particularly in bacterial resistance to environmental stress. World J Microbiol Biotechnol 2024; 40:105. [PMID: 38386219 DOI: 10.1007/s11274-024-03924-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
Acidithiobacillus caldus is a typical extreme acidophile widely used in the biohydrometallurgical industry, which often experiences extreme environmental stress in its natural habitat. Hfq, an RNA-binding protein, typically functions as a global regulator involved in various cellular physiological processes. Yet, the biological functions of Hfq derived from such extreme acidophile have not been extensively investigated. In this study, the recombinant strain Δhfq/Achfq, constructed by CRISPR/Cas9-mediated chromosome integration, fully or partially restored the phenotypic defects caused by hfq deletion in Escherichia coli, including impaired growth performance, abnormal cell morphology, impaired swarming motility, decreased stress resistance, decreased intracellular ATP and free amino acid levels, and attenuated biofilm formation. Particularly noteworthy, the intracellular ATP level and biofilm production of the recombinant strain were increased by 12.2% and 7.0%, respectively, compared to the Δhfq mutant. Transcriptomic analysis revealed that even under heterologous expression, AcHfq exerted global regulatory effects on multiple cellular processes, including metabolism, environmental signal processing, and motility. Finally, we established a potential working model to illustrate the regulatory mechanism of AcHfq in bacterial resistance to environmental stress.
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Affiliation(s)
- Wenbo Hu
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xingyu Huo
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Haochen Bai
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Zongling Chen
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Jianxin Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Hailin Yang
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Shoushuai Feng
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
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Sepúlveda-Rebolledo P, González-Rosales C, Dopson M, Pérez-Rueda E, Holmes DS, Valdés JH. Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives. Res Microbiol 2024; 175:104135. [PMID: 37678513 DOI: 10.1016/j.resmic.2023.104135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Extreme acidophiles thrive in acidic environments, confront a multitude of challenges, and demonstrate remarkable adaptability in their metabolism to cope with the ever-changing environmental fluctuations, which encompass variations in temperature, pH levels, and the availability of electron acceptors and donors. The survival and proliferation of members within the Acidithiobacillia class rely on the deployment of transcriptional regulatory systems linked to essential physiological traits. The study of these transcriptional regulatory systems provides valuable insights into critical processes, such as energy metabolism and nutrient assimilation, and how they integrate into major genetic-metabolic circuits. In this study, we examined the transcriptional regulatory repertoires and potential interactions of forty-three Acidithiobacillia complete and draft genomes, encompassing nine species. To investigate the function and diversity of Transcription Factors (TFs) and their DNA Binding Sites (DBSs), we conducted a genome-wide comparative analysis, which allowed us to identify these regulatory elements in representatives of Acidithiobacillia. We classified TFs into gene families and compared their occurrence among all representatives, revealing conservation patterns across the class. The results identified conserved regulators for several pathways, including iron and sulfur oxidation, the main pathways for energy acquisition, providing new evidence for viable regulatory interactions and branch-specific conservation in Acidithiobacillia. The identification of TFs and DBSs not only corroborates existing experimental information for selected species, but also introduces novel candidates for experimental validation. Moreover, these promising candidates have the potential for further extension to new representatives within the class.
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Affiliation(s)
- Pedro Sepúlveda-Rebolledo
- Centro de Genómica y Bioinformática and PhD. Program on Integrative Genomics, Facultad de Ciencias, Universidad Mayor, Santiago (8580745), Chile.
| | - Carolina González-Rosales
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago (8580638), Chile; Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Yucatán, Mexico.
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago (8580638), Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago (7510156), Chile.
| | - Jorge H Valdés
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago (8370146), Chile.
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Jiang Z, Lu J, Tong Y, Yang H, Feng S. Enhancement of acid tolerance of Escherichia coli by introduction of molecule chaperone CbpA from extremophile. World J Microbiol Biotechnol 2023; 39:158. [PMID: 37046107 DOI: 10.1007/s11274-023-03613-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/08/2023] [Indexed: 04/14/2023]
Abstract
Molecular chaperone CbpA from extreme acidophile Acidithiobacillus caldus was applied to improve acid tolerance of Escherichia coli via CRISPR/Cas9. Cell growth and viability of plasmid complementary strain indicated the importance of cbpAAc for bacteria acid tolerance. With in situ gene replacement by CRISPR/Cas9 system, colony formation unit (CFU) of genome recombinant strain BL21-ΔcbpA/AccbpA showed 7.7 times higher cell viability than deficient strain BL21-ΔcbpA and 2.3 times higher than wild type. Cell morphology observation using Field Emission Scanning Electron Microscopy (FESEM) revealed cell breakage of BL21-ΔcbpA and significant recovery of BL21-ΔcbpA/AccbpA. The intracellular ATP level of all strains gradually decreased along with the increased stress time. Particularly, the value of recombinant strain was 56.0% lower than that of deficient strain after 5 h, indicating that the recombinant strain consumed a lot of energy to resist acid stress. The arginine concentration in BL21-ΔcbpA/AccbpA was double that of BL21-ΔcbpA, while the aspartate and glutamate contents were 14.8% and 6.2% higher, respectively, compared to that of wild type. Moreover, RNA-Seq analysis examined 93 genes down-regulated in BL21-ΔcbpA compared to wild type strain, while 123 genes were up-regulated in BL21-ΔcbpA/AccbpA compared to BL21-ΔcbpA, with an emphasis on energy metabolism, transport, and cell components. Finally, the working model in response to acid stress of cbpA from A. caldus was developed. This study constructed a recombinant strain resistant to acid stress and also provided a reference for enhancing microorganisms' robustness to various conditions.
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Affiliation(s)
- Zhenming Jiang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jie Lu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yanjun Tong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, China
| | - Hailin Yang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Shoushuai Feng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
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Castro M, Moya-Beltrán A, Covarrubias PC, Gonzalez M, Cardenas JP, Issotta F, Nuñez H, Acuña LG, Encina G, Holmes DS, Johnson DB, Quatrini R. Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366). Stand Genomic Sci 2017; 12:77. [PMID: 29255572 PMCID: PMC5731081 DOI: 10.1186/s40793-017-0282-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022] Open
Abstract
Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic sulfur-oxidizer, with potential importance in the bioleaching of sulfidic metal ores, first described in the 1980s. Here we present the draft genome sequence of Acidithiobacillus albertensis DSM 14366T, thereby both filling a long-standing gap in the genomics of the acidithiobacilli, and providing further insight into the understanding of the biology of the non iron-oxidizing members of the Acidithiobacillus genus. The assembled genome is 3,1 Mb, and contains 47 tRNAs, tmRNA gene and 2 rRNA operons, along with 3149 protein-coding predicted genes. The Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession MOAD00000000.
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Affiliation(s)
- Matías Castro
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
| | - Ana Moya-Beltrán
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
| | - Paulo C. Covarrubias
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
- Current Address: uBiome Chile, SpA, Santiago, Chile
| | - Mónica Gonzalez
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
| | - Juan Pablo Cardenas
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
- Current Address: uBiome Chile, SpA, Santiago, Chile
| | | | - Harold Nuñez
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
- Current Address: uBiome Chile, SpA, Santiago, Chile
| | - Lillian G. Acuña
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
| | | | - David S. Holmes
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | | | - Raquel Quatrini
- Fundación Ciencia & Vida, Av. Zañartu 1482, Santiago, 7780272 Chile
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