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Feng R, Zhao J, Zhang Q, Zhu Z, Zhang J, Liu C, Zheng X, Wang F, Su J, Ma X, Mi X, Guo L, Yan X, Liu Y, Li H, Chen X, Deng Y, Wang G, Zhang Y, Liu X, Liu J. Generation of Anti-Mastitis Gene-Edited Dairy Goats with Enhancing Lysozyme Expression by Inflammatory Regulatory Sequence using ISDra2-TnpB System. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404408. [PMID: 39099401 DOI: 10.1002/advs.202404408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/29/2024] [Indexed: 08/06/2024]
Abstract
Gene-editing technology has become a transformative tool for the precise manipulation of biological genomes and holds great significance in the field of animal disease-resistant breeding. Mastitis, a prevalent disease in animal husbandry, imposes a substantial economic burden on the global dairy industry. In this study, a regulatory sequence gene editing breeding strategy for the successful creation of a gene-edited dairy (GED) goats with enhanced mastitis resistance using the ISDra2-TnpB system and dairy goats as the model animal is proposed. This included the targeted integration of an innate inflammatory regulatory sequence (IRS) into the promoter region of the lysozyme (LYZ) gene. Upon Escherichia Coli (E. coli) mammary gland infection, GED goats exhibited increased LYZ expression, showing robust anti-mastitis capabilities, mitigating PANoptosis activation, and alleviating blood-milk-barrier (BMB) damage. Notably, LYZ is highly expressed only in E. coli infection. This study marks the advent of anti-mastitis gene-edited animals with exogenous-free gene expression and demonstrates the feasibility of the gene-editing strategy proposed in this study. In addition, it provides a novel gene-editing blueprint for developing disease-resistant strains, focusing on disease specificity and biosafety while providing a research basis for the widespread application of the ISDra2-TnpB system.
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Affiliation(s)
- Rui Feng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Jianglin Zhao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Qian Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Zhenliang Zhu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Junyu Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Chengyuan Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xiaoman Zheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Fan Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Jie Su
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xianghai Ma
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xiaoyu Mi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Lin Guo
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xiaoxue Yan
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Yayi Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Huijia Li
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xu Chen
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Yi Deng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Guoyan Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xu Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
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Nahar A, Baker AL, Nichols DS, Bowman JP, Britz ML. Benchmarking DNA Extraction Methods for Phylogenomic Analysis of Sub-Antarctic Rhodococcus and Williamsia Species. Microorganisms 2021; 9:microorganisms9061253. [PMID: 34207615 PMCID: PMC8227252 DOI: 10.3390/microorganisms9061253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
Bacteria containing mycolic acids in their cell envelope are often recalcitrant to cell lysis, so extracting DNA of sufficient quality for third-generation sequencing and high-fidelity genome assembly requires optimization, even when using commercial kits with protocols for hard-to-lyse bacteria. We benchmarked three spin-column-based kits against a classical DNA extraction method employing lysozyme, proteinase K and SDS for six lysozyme-resistant, sub-Antarctic strains of Corynebaceriales. Prior cultivation in broths containing glycine at highly growth-inhibitory concentrations (4.0–4.5%) improved cell lysis using both classical and kit methods. The classical method produced DNA with average fragment sizes of 27–59 Kbp and tight fragment size ranges, meeting quality standards for genome sequencing, assembly and phylogenomic analyses. By 16S rRNA gene sequencing, we classified two strains as Williamsia and four strains as Rhodococcus species. Pairwise comparison of average nucleotide identity (ANI) and alignment fraction (AF), plus genome clustering analysis, confirmed Rhodococcus sp. 1163 and 1168 and Williamsia sp. 1135 and 1138 as novel species. Phylogenetic, lipidomic and biochemical analyses classified psychrotrophic strains 1139 and 1159 as R. qingshengii and R. erythropolis, respectively, using ANI similarity of >98% and AF >60% for species delineation. On this basis, some members of the R. erythropolis genome cluster groups, including strains currently named as R. enclensis, R. baikonurensis, R. opacus and R. rhodochrous, would be reclassified either as R. erythropolis or R. qingshengii.
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Affiliation(s)
- Akhikun Nahar
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
- Correspondence: (A.N.); (M.L.B.)
| | - Anthony L. Baker
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
| | - David S. Nichols
- Central Science Laboratory, Division of Research, University of Tasmania, Hobart, TAS 7005, Australia;
| | - John P. Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
| | - Margaret L. Britz
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
- Correspondence: (A.N.); (M.L.B.)
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