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      Nitric oxide sensor NsrR is the key direct regulator of magnetosome formation and nitrogen metabolism in Magnetospirillum

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      Nucleic Acids Research
      Oxford University Press

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          Abstract

          Nitric oxide (NO) plays an essential role as signaling molecule in regulation of eukaryotic biomineralization, but its role in prokaryotic biomineralization is unknown. Magnetospirillum gryphiswaldense MSR-1, a model strain for studies of prokaryotic biomineralization, has the unique ability to form magnetosomes (magnetic organelles). We demonstrate here that magnetosome biomineralization in MSR-1 requires the presence of NsrR Mg (an NO sensor) and a certain level of NO. MSR-1 synthesizes endogenous NO via nitrification-denitrification pathway to activate magnetosome formation. NsrR Mg was identified as a global transcriptional regulator that acts as a direct activator of magnetosome gene cluster (MGC) and nitrification genes but as a repressor of denitrification genes. Specific levels of NO modulate DNA-binding ability of NsrR Mg to various target promoters, leading to enhancing expression of MGC genes, derepressing denitrification genes, and repressing nitrification genes. These regulatory functions help maintain appropriate endogenous NO level. This study identifies for the first time the key transcriptional regulator of major MGC genes, clarifies the molecular mechanisms underlying NsrR-mediated NO signal transduction in magnetosome formation, and provides a basis for a proposed model of the role of NO in the evolutionary origin of prokaryotic biomineralization processes.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            The rise of oxygen in Earth's early ocean and atmosphere.

            The rapid increase of carbon dioxide concentration in Earth's modern atmosphere is a matter of major concern. But for the atmosphere of roughly two-and-half billion years ago, interest centres on a different gas: free oxygen (O2) spawned by early biological production. The initial increase of O2 in the atmosphere, its delayed build-up in the ocean, its increase to near-modern levels in the sea and air two billion years later, and its cause-and-effect relationship with life are among the most compelling stories in Earth's history.
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                Author and article information

                Contributors
                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                12 April 2024
                09 January 2024
                09 January 2024
                : 52
                : 6
                : 2924-2941
                Affiliations
                State Key Laboratory of Animal Biotech Breeding and College of Biological Sciences, China Agricultural University , Beijing 100193, China
                State Key Laboratory of Animal Biotech Breeding and College of Biological Sciences, China Agricultural University , Beijing 100193, China
                State Key Laboratory of Animal Biotech Breeding and College of Biological Sciences, China Agricultural University , Beijing 100193, China
                State Key Laboratory of Animal Biotech Breeding and College of Biological Sciences, China Agricultural University , Beijing 100193, China
                State Key Laboratory of Animal Biotech Breeding and College of Biological Sciences, China Agricultural University , Beijing 100193, China
                Author notes
                To whom correspondence should be addressed. Tel: +86 10 62733751; Email: tianhome@ 123456cau.edu.cn
                Correspondence may also be addressed to Ying Wen. Tel: +86 10 62732715; Email: wen@ 123456cau.edu.cn
                Author information
                https://orcid.org/0000-0003-2924-2428
                Article
                gkad1230
                10.1093/nar/gkad1230
                11014258
                38197240
                62f77a38-741a-4957-81e9-3461c537f380
                © The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 14 December 2023
                : 07 December 2023
                : 01 June 2023
                Page count
                Pages: 18
                Funding
                Funded by: Inter-Governmental International Scientific and Technological Innovation Cooperation;
                Award ID: 2019YFE0115800
                Funded by: Ministry of Science and Technology of the People's Republic of China, DOI 10.13039/501100002855;
                Categories
                AcademicSubjects/SCI00010
                Gene regulation, Chromatin and Epigenetics

                Genetics
                Genetics

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