Comparative Genomics of a Bovine Mycobacterium tuberculosis Isolate and Other Strains Reveals Its Potential Mechanism of Bovine Adaptation
The Mycobacterium tuberculosis complex causes tuberculosis (TB) in humans and other animal species, but Mycobacterium tuberculosis has a distinct host preference to humans. The present study aimed to determine whether a bovine M. tb strain 1458 has evolved some genetic properties in their genome tha...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2017-12-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2017.02500/full |
| _version_ | 1828760483050553344 |
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| author | Xuekai Xiong Xuekai Xiong Rui Wang Dachuan Deng Dachuan Deng Yingyu Chen Yingyu Chen Han Liu Han Liu Tianqi Wang Tianqi Wang Jieru Wang Jieru Wang Xiaojie Zhu Xiaojie Zhu Xifang Zhu Xifang Zhu Yongqiang Zhu Xinyan Lu Huanchun Chen Huanchun Chen Huajun Zheng Aizhen Guo Aizhen Guo |
| author_facet | Xuekai Xiong Xuekai Xiong Rui Wang Dachuan Deng Dachuan Deng Yingyu Chen Yingyu Chen Han Liu Han Liu Tianqi Wang Tianqi Wang Jieru Wang Jieru Wang Xiaojie Zhu Xiaojie Zhu Xifang Zhu Xifang Zhu Yongqiang Zhu Xinyan Lu Huanchun Chen Huanchun Chen Huajun Zheng Aizhen Guo Aizhen Guo |
| author_sort | Xuekai Xiong |
| collection | DOAJ |
| description | The Mycobacterium tuberculosis complex causes tuberculosis (TB) in humans and other animal species, but Mycobacterium tuberculosis has a distinct host preference to humans. The present study aimed to determine whether a bovine M. tb strain 1458 has evolved some genetic properties in their genome that might be associated with their bovine adaptation. The genome of the M. tb strain 1458 was sequenced and subjected to an extensive comparative genomic analysis. A phylogenetic analysis showed that strain 1458 is most closely related to a Chinese M. tb strain, CCDC5079, of the same Beijing family. Compared with three human M. tb Beijing family strains, the strain 1458 has the fewest unique genes. However, there are most (21) IS6110 insertion sequences in the strain 1458 genome at either intragenic or intergenic sites, resulting in the interruption of 11 genes including three PPE family-encoding genes (PPE16, PPE38, and PPE59). Only the strain 1458 genome has the upstream insertion in esxS and phoP genes. PCR confirmed four upstream insertions and qPCR determined that transcription of esxS, phoP, dnaN, and ctpD genes differed significantly between M. tb strain 1458 and H37Rv or M. bovis. A Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that the genes affected by non-synonymous SNPs are enriched in RNA polymerase. Moreover, 127 of the 133 unique SNPs in strain 1458 are either different to those in the M. bovis genome. In conclusion, some critical genes responsible for bacterial virulence and immunogenicity were interrupted in the genome of bovine M. tb strain 1458 by IS insertions and non-synonymous SNPs, which might contribute to its bovine adaptation, and the modification of its virulence and immunogenicity in cattle. |
| first_indexed | 2024-12-11T01:14:39Z |
| format | Article |
| id | doaj.art-7ff50f15309348dc8c7750c105c45780 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-11T01:14:39Z |
| publishDate | 2017-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-7ff50f15309348dc8c7750c105c457802022-12-22T01:25:56ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2017-12-01810.3389/fmicb.2017.02500305984Comparative Genomics of a Bovine Mycobacterium tuberculosis Isolate and Other Strains Reveals Its Potential Mechanism of Bovine AdaptationXuekai Xiong0Xuekai Xiong1Rui Wang2Dachuan Deng3Dachuan Deng4Yingyu Chen5Yingyu Chen6Han Liu7Han Liu8Tianqi Wang9Tianqi Wang10Jieru Wang11Jieru Wang12Xiaojie Zhu13Xiaojie Zhu14Xifang Zhu15Xifang Zhu16Yongqiang Zhu17Xinyan Lu18Huanchun Chen19Huanchun Chen20Huajun Zheng21Aizhen Guo22Aizhen Guo23National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaCollege of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaShanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, ChinaNational Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaCollege of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaCollege of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaCollege of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaCollege of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaCollege of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaCollege of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaNational Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaCollege of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaShanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, ChinaShanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, ChinaNational Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaCollege of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaShanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, ChinaNational Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, ChinaCollege of Veterinary Medicine, Huazhong Agricultural University, Wuhan, ChinaThe Mycobacterium tuberculosis complex causes tuberculosis (TB) in humans and other animal species, but Mycobacterium tuberculosis has a distinct host preference to humans. The present study aimed to determine whether a bovine M. tb strain 1458 has evolved some genetic properties in their genome that might be associated with their bovine adaptation. The genome of the M. tb strain 1458 was sequenced and subjected to an extensive comparative genomic analysis. A phylogenetic analysis showed that strain 1458 is most closely related to a Chinese M. tb strain, CCDC5079, of the same Beijing family. Compared with three human M. tb Beijing family strains, the strain 1458 has the fewest unique genes. However, there are most (21) IS6110 insertion sequences in the strain 1458 genome at either intragenic or intergenic sites, resulting in the interruption of 11 genes including three PPE family-encoding genes (PPE16, PPE38, and PPE59). Only the strain 1458 genome has the upstream insertion in esxS and phoP genes. PCR confirmed four upstream insertions and qPCR determined that transcription of esxS, phoP, dnaN, and ctpD genes differed significantly between M. tb strain 1458 and H37Rv or M. bovis. A Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that the genes affected by non-synonymous SNPs are enriched in RNA polymerase. Moreover, 127 of the 133 unique SNPs in strain 1458 are either different to those in the M. bovis genome. In conclusion, some critical genes responsible for bacterial virulence and immunogenicity were interrupted in the genome of bovine M. tb strain 1458 by IS insertions and non-synonymous SNPs, which might contribute to its bovine adaptation, and the modification of its virulence and immunogenicity in cattle.http://journal.frontiersin.org/article/10.3389/fmicb.2017.02500/fullMycobacterium tuberculosisgenomesequencingcattlezoonosistuberculosis |
| spellingShingle | Xuekai Xiong Xuekai Xiong Rui Wang Dachuan Deng Dachuan Deng Yingyu Chen Yingyu Chen Han Liu Han Liu Tianqi Wang Tianqi Wang Jieru Wang Jieru Wang Xiaojie Zhu Xiaojie Zhu Xifang Zhu Xifang Zhu Yongqiang Zhu Xinyan Lu Huanchun Chen Huanchun Chen Huajun Zheng Aizhen Guo Aizhen Guo Comparative Genomics of a Bovine Mycobacterium tuberculosis Isolate and Other Strains Reveals Its Potential Mechanism of Bovine Adaptation Frontiers in Microbiology Mycobacterium tuberculosis genome sequencing cattle zoonosis tuberculosis |
| title | Comparative Genomics of a Bovine Mycobacterium tuberculosis Isolate and Other Strains Reveals Its Potential Mechanism of Bovine Adaptation |
| title_full | Comparative Genomics of a Bovine Mycobacterium tuberculosis Isolate and Other Strains Reveals Its Potential Mechanism of Bovine Adaptation |
| title_fullStr | Comparative Genomics of a Bovine Mycobacterium tuberculosis Isolate and Other Strains Reveals Its Potential Mechanism of Bovine Adaptation |
| title_full_unstemmed | Comparative Genomics of a Bovine Mycobacterium tuberculosis Isolate and Other Strains Reveals Its Potential Mechanism of Bovine Adaptation |
| title_short | Comparative Genomics of a Bovine Mycobacterium tuberculosis Isolate and Other Strains Reveals Its Potential Mechanism of Bovine Adaptation |
| title_sort | comparative genomics of a bovine mycobacterium tuberculosis isolate and other strains reveals its potential mechanism of bovine adaptation |
| topic | Mycobacterium tuberculosis genome sequencing cattle zoonosis tuberculosis |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2017.02500/full |
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