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Comparative genomics and transcriptomics analyses provide insights into the high yield and regulatory mechanism of Norvancomycin biosynthesis in Amycolatopsis orientalis NCPC 2-48
Bin Hong
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6244-8298
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This work is licensed under a CC BY 4.0 License. Read Full License
Background Norvancomycin has been widely used in clinic to treat against MRSA (Methicillin-resistant Staphylococcus aureus) and MRSE (Methicillin-resistant Staphylococcus epidermidis) infections in China. Amycolatopsis orientalis NCPC 2-48, a high yield strain derived from A. orientalis CPCC 200066, has been applied in industrial large-scale production of norvancomycin by North China Pharmaceutical Group. However, the potential high-yield and regulatory mechanism involved in norvancomycin biosynthetic pathway has not yet been addressed.
Results Here we sequenced and compared the genomes and transcriptomes of A. orientalis CPCC 200066 and NCPC 2-48. These two genomes are extremely similar with an identity of more than 99.9%, and no duplication and structural variation was found in the norvancomycin biosynthetic gene cluster. Comparative transcriptomic analysis indicated that biosynthetic genes of norvancomycin, as well as some primary metabolite pathways for the biosynthetic precursors of norvancomycin were generally upregulated. AoStrR1 and AoLuxR1, two cluster-situated regulatory genes in norvancomycin cluster, were 23.3-fold and 5.8-fold upregulated in the high yield strain at 48 h, respectively. Over-expression of AoStrR1 and AoLuxR1 in CPCC 200066 resulted in an increase of norvancomycin production, indicating their positive roles in norvancomycin biosynthesis. Furthermore, AoStrR1 can regulate the production of norvancomycin by directly interacting with at least 8 promoters of norvancomycin biosynthetic genes or operons.
Conclusion Our results suggested that the high yield of NCPC 2-48 can be ascribed to increased expression level of norvancomycin biosynthetic genes in its cluster as well as the genes responsible for the supply of its precursors. The norvancomycin biosynthetic genes are presumably regulated by AoStrR1 and AoLuxR1, of them AoStrR1 is possibly the ultimate pathway-specific regulator for the norvancomycin production. These results are helpful for further clarification of the holistic and pathway-specific regulatory mechanism of norvancomycin biosynthesis in the industrial production strain.
Keywords
Norvancomycin, Amycolatopsis orientalis, Comparative transcriptomics, Biosynthetic gene cluster, Transcriptional regulation
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CURRENT STATUS: Under Revision
Version 2
Posted 12 Jan, 2021
No community comments so far
Editorial decision: Minor Revision
On 07 Jan, 2021
Review #1 received
Received 06 Jan, 2021
Review #2 received
Received 06 Jan, 2021
Reviewer #2 agreed
On 31 Dec, 2020
Reviewer #1 agreed
On 29 Dec, 2020
Editor assigned
On 28 Dec, 2020
Reviewers invited
Invitations sent on 28 Dec, 2020
Submission checks complete
On 28 Dec, 2020
Editor invited
On 28 Dec, 2020
No comments provided
Review #2 received
Received 28 Sep, 2020
Editorial decision: Major Revision
On 28 Sep, 2020
Review #1 received
Received 10 Sep, 2020
Reviewer #2 agreed
On 07 Sep, 2020
Reviewer #1 agreed
On 26 Aug, 2020
Reviewers invited
Invitations sent on 25 Aug, 2020
Editor invited
On 20 Jul, 2020
Editor assigned
On 20 Jul, 2020
Submission checks complete
On 19 Jul, 2020
First submitted
On 13 Jul, 2020
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Subject Areas
Applied & Industrial Microbiology
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This preprint is under consideration at Microbial Cell Factories. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research
Comparative genomics and transcriptomics analyses provide insights into the high yield and regulatory mechanism of Norvancomycin biosynthesis in Amycolatopsis orientalis NCPC 2-48
Bin Hong
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6244-8298
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Revision
Version 2
Posted 12 Jan, 2021
No community comments so far
Editorial decision: Minor Revision
On 07 Jan, 2021
Review #1 received
Received 06 Jan, 2021
Review #2 received
Received 06 Jan, 2021
Reviewer #2 agreed
On 31 Dec, 2020
Reviewer #1 agreed
On 29 Dec, 2020
Editor assigned
On 28 Dec, 2020
Reviewers invited
Invitations sent on 28 Dec, 2020
Submission checks complete
On 28 Dec, 2020
Editor invited
On 28 Dec, 2020
No comments provided
Review #2 received
Received 28 Sep, 2020
Editorial decision: Major Revision
On 28 Sep, 2020
Review #1 received
Received 10 Sep, 2020
Reviewer #2 agreed
On 07 Sep, 2020
Reviewer #1 agreed
On 26 Aug, 2020
Reviewers invited
Invitations sent on 25 Aug, 2020
Editor invited
On 20 Jul, 2020
Editor assigned
On 20 Jul, 2020
Submission checks complete
On 19 Jul, 2020
First submitted
On 13 Jul, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Applied & Industrial Microbiology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background Norvancomycin has been widely used in clinic to treat against MRSA (Methicillin-resistant Staphylococcus aureus) and MRSE (Methicillin-resistant Staphylococcus epidermidis) infections in China. Amycolatopsis orientalis NCPC 2-48, a high yield strain derived from A. orientalis CPCC 200066, has been applied in industrial large-scale production of norvancomycin by North China Pharmaceutical Group. However, the potential high-yield and regulatory mechanism involved in norvancomycin biosynthetic pathway has not yet been addressed.
Results Here we sequenced and compared the genomes and transcriptomes of A. orientalis CPCC 200066 and NCPC 2-48. These two genomes are extremely similar with an identity of more than 99.9%, and no duplication and structural variation was found in the norvancomycin biosynthetic gene cluster. Comparative transcriptomic analysis indicated that biosynthetic genes of norvancomycin, as well as some primary metabolite pathways for the biosynthetic precursors of norvancomycin were generally upregulated. AoStrR1 and AoLuxR1, two cluster-situated regulatory genes in norvancomycin cluster, were 23.3-fold and 5.8-fold upregulated in the high yield strain at 48 h, respectively. Over-expression of AoStrR1 and AoLuxR1 in CPCC 200066 resulted in an increase of norvancomycin production, indicating their positive roles in norvancomycin biosynthesis. Furthermore, AoStrR1 can regulate the production of norvancomycin by directly interacting with at least 8 promoters of norvancomycin biosynthetic genes or operons.
Conclusion Our results suggested that the high yield of NCPC 2-48 can be ascribed to increased expression level of norvancomycin biosynthetic genes in its cluster as well as the genes responsible for the supply of its precursors. The norvancomycin biosynthetic genes are presumably regulated by AoStrR1 and AoLuxR1, of them AoStrR1 is possibly the ultimate pathway-specific regulator for the norvancomycin production. These results are helpful for further clarification of the holistic and pathway-specific regulatory mechanism of norvancomycin biosynthesis in the industrial production strain.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5