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Mitra S, Oikawa H, Rajendran D, Kowada T, Mizukami S, Naganathan AN, Takahashi S. Flexible Target Recognition of the Intrinsically Disordered DNA-Binding Domain of CytR Monitored by Single-Molecule Fluorescence Spectroscopy. J Phys Chem B 2022; 126:6136-6147. [PMID: 35969476 PMCID: PMC9422980 DOI: 10.1021/acs.jpcb.2c02791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/03/2022] [Indexed: 11/29/2022]
Abstract
The intrinsically disordered DNA-binding domain of cytidine repressor (CytR-DBD) folds in the presence of target DNA and regulates the expression of multiple genes in E. coli. To explore the conformational rearrangements in the unbound state and the target recognition mechanisms of CytR-DBD, we carried out single-molecule Förster resonance energy transfer (smFRET) measurements. The smFRET data of CytR-DBD in the absence of DNA show one major and one minor population assignable to an expanded unfolded state and a compact folded state, respectively. The population of the folded state increases and decreases upon titration with salt and denaturant, respectively, in an apparent two-state manner. The peak FRET efficiencies of both the unfolded and folded states change continuously with denaturant concentration, demonstrating the intrinsic flexibility of the DNA-binding domain and the deviation from a strict two-state transition. Remarkably, the CytR-DBD exhibits a compact structure when bound to both the specific and nonspecific DNA; however, the peak FRET efficiencies of the two structures are slightly but consistently different. The observed conformational heterogeneity highlights the potential structural changes required for CytR to bind variably spaced operator sequences.
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Affiliation(s)
- Shrutarshi Mitra
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Hiroyuki Oikawa
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Divya Rajendran
- Department
of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Toshiyuki Kowada
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Shin Mizukami
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Athi N. Naganathan
- Department
of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Satoshi Takahashi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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Wang Q, Wang X, Zhang W, Li X, Zhou Y, Li D, Wang Y, Tian J, Jiang W, Zhang Z, Peng Y, Wang L, Li Y, Li J. Physiological characteristics of Magnetospirillum gryphiswaldense MSR-1 that control cell growth under high-iron and low-oxygen conditions. Sci Rep 2017; 7:2800. [PMID: 28584275 PMCID: PMC5459824 DOI: 10.1038/s41598-017-03012-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/21/2017] [Indexed: 11/17/2022] Open
Abstract
Magnetosome formation by Magnetospirillum gryphiswaldense MSR-1 is dependent on iron and oxygen levels. We used transcriptome to evaluate transcriptional profiles of magnetic and non-magnetic MSR-1 cells cultured under high-iron and low-iron conditions. A total of 80 differentially expressed genes (DEGs) were identified, including 53 upregulated and 27 downregulated under high-iron condition. These DEGs belonged to the functional categories of biological regulation, oxidation-reduction process, and ion binding and transport, and were involved in sulfur metabolism and cysteine/methionine metabolism. Comparison with our previous results from transcriptome data under oxygen-controlled conditions indicated that transcription of mam or mms was not regulated by oxygen or iron signals. 17 common DEGs in iron- and oxygen-transcriptomes were involved in energy production, iron transport, and iron metabolism. Some unknown-function DEGs participate in iron transport and metabolism, and some are potential biomarkers for identification of Magnetospirillum strains. IrrA and IrrB regulate iron transport in response to low-oxygen and high-iron signals, respectively. Six transcription factors were predicted to regulate DEGs. Fur and Crp particularly co-regulate DEGs in response to changes in iron or oxygen levels, in a proposed joint regulatory network of DEGs. Our findings provide new insights into biomineralization processes under high- vs. low-iron conditions in magnetotactic bacteria.
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Affiliation(s)
- Qing Wang
- State Key Laboratories for Agro-biotechnology, China Agricultural University, Beijing, 100193, P.R. China.,France-China Bio-mineralization and Nano-structure Laboratory, Beijing, 100193, P.R. China
| | - Xu Wang
- State Key Laboratories for Agro-biotechnology, China Agricultural University, Beijing, 100193, P.R. China.,France-China Bio-mineralization and Nano-structure Laboratory, Beijing, 100193, P.R. China
| | - Weijia Zhang
- Institute of Deep-sea Science and Engineering, China Academy of Sciences, Sanya, 572000, P.R. China.,France-China Bio-mineralization and Nano-structure Laboratory, Beijing, 100193, P.R. China
| | - Xianyu Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, P.R. China
| | - Yuan Zhou
- State Key Laboratories for Agro-biotechnology, China Agricultural University, Beijing, 100193, P.R. China
| | - Dan Li
- State Key Laboratories for Agro-biotechnology, China Agricultural University, Beijing, 100193, P.R. China
| | - Yinjia Wang
- Tianjin Biochip Corporation, Tianjin, 300457, P.R. China
| | - Jiesheng Tian
- State Key Laboratories for Agro-biotechnology, China Agricultural University, Beijing, 100193, P.R. China.,France-China Bio-mineralization and Nano-structure Laboratory, Beijing, 100193, P.R. China
| | - Wei Jiang
- State Key Laboratories for Agro-biotechnology, China Agricultural University, Beijing, 100193, P.R. China.,France-China Bio-mineralization and Nano-structure Laboratory, Beijing, 100193, P.R. China
| | - Ziding Zhang
- State Key Laboratories for Agro-biotechnology, China Agricultural University, Beijing, 100193, P.R. China
| | - Youliang Peng
- State Key Laboratories for Agro-biotechnology, China Agricultural University, Beijing, 100193, P.R. China
| | - Lei Wang
- Tianjin Biochip Corporation, Tianjin, 300457, P.R. China
| | - Ying Li
- State Key Laboratories for Agro-biotechnology, China Agricultural University, Beijing, 100193, P.R. China. .,France-China Bio-mineralization and Nano-structure Laboratory, Beijing, 100193, P.R. China.
| | - Jilun Li
- State Key Laboratories for Agro-biotechnology, China Agricultural University, Beijing, 100193, P.R. China.,France-China Bio-mineralization and Nano-structure Laboratory, Beijing, 100193, P.R. China
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Nakano M, Ogasawara H, Shimada T, Yamamoto K, Ishihama A. Involvement of cAMP-CRP in transcription activation and repression of the pck gene encoding PEP carboxykinase, the key enzyme of gluconeogenesis. FEMS Microbiol Lett 2014; 355:93-9. [PMID: 24814025 DOI: 10.1111/1574-6968.12466] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 05/08/2014] [Accepted: 05/08/2014] [Indexed: 11/30/2022] Open
Abstract
cAMP receptor protein (CRP) is the best characterized global regulator of Escherichia coli. After genomic SELEX screening, a total of minimum 378 promoters have been identified as its regulation targets on the E. coli genome. Among a number of promoters carrying two CRP-binding sites, several promoters carry two CRP-binding sites, one upstream but another downstream of transcription initiation sites. The regulatory role of downstream CRP site remains unsolved. Using the pck gene encoding phosphoenolpyruvate carboxykinase as a model promoter, we analyzed the role of CRP-associated downstream of the transcription initiation site. Gel shift assay and AFM observation indicate that CRP binds to both the promoter-distal site (CRP box-1) at -90.5 and the site (CRP box-2) at +13.5 downstream of transcription initiation site. The binding affinity is higher for CRP box-1. Roles of two CRP sites were examined using in vitro transcription assay and in vivo reporter assay. In both cases, transcription repression was observed in the presence of high concentrations of CRP. Taken together, we propose that cAMP-CRP associated at downstream CRP box-2 plays as a repressor for pck transcription only in the presence of high levels of cAMP-CRP.
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Affiliation(s)
- Masahiro Nakano
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
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