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Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform from Bacillus thuringiensis .

التفاصيل البيبلوغرافية
العنوان: Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform from Bacillus thuringiensis .
المؤلفون: Liu L; National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China., Luo D; National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China., Zhang Y; National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China., Liu D; National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China., Yin K; National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China., Tang Q; National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China., Chou S-H; National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China., He J; National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.
المصدر: Microbiology spectrum [Microbiol Spectr] 2024 Jul 02; Vol. 12 (7), pp. e0045024. Date of Electronic Publication: 2024 May 31.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: ASM Press Country of Publication: United States NLM ID: 101634614 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2165-0497 (Electronic) Linking ISSN: 21650497 NLM ISO Abbreviation: Microbiol Spectr Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Washington, DC : ASM Press, 2013-
مواضيع طبية MeSH: Riboswitch*/genetics , Cyclic GMP*/analogs & derivatives , Cyclic GMP*/metabolism , Cyclic GMP*/genetics , Gene Expression Regulation, Bacterial* , Bacillus thuringiensis*/genetics , Bacillus thuringiensis*/metabolism, Nucleic Acid Conformation ; Transcription, Genetic ; Terminator Regions, Genetic/genetics ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism
مستخلص: A riboswitch generally regulates the expression of its downstream genes through conformational change in its expression platform (EP) upon ligand binding. The cyclic diguanosine monophosphate (c-di-GMP) class I riboswitch Bc1 is widespread and conserved among Bacillus cereus group species. In this study, we revealed that Bc1 has a long EP with two typical ρ-independent terminator sequences 28 bp apart. The upstream terminator T1 is dominant in vitro , while downstream terminator T2 is more efficient in vivo . Through mutation analysis, we elucidated that Bc1 exerts a rare and incoherent "transcription-translation" dual regulation with T2 playing a crucial role. However, we found that Bc1 did not respond to c-di-GMP under in vitro transcription conditions, and the expressions of downstream genes did not change with fluctuation in intracellular c-di-GMP concentration. To explore this puzzle, we conducted SHAPE-MaP and confirmed the interaction of Bc1 with c-di-GMP. This shows that as c-di-GMP concentration increases, T1 unfolds but T2 remains almost intact and functional. The presence of T2 masks the effect of T1 unwinding, resulting in no response of Bc1 to c-di-GMP. The high Shannon entropy values of EP region imply the potential alternative structures of Bc1. We also found that zinc uptake regulator can specifically bind to the dual terminator coding sequence and slightly trigger the response of Bc1 to c-di-GMP. This work will shed light on the dual-regulation riboswitch and enrich our understanding of the RNA world.IMPORTANCEIn nature, riboswitches are involved in a variety of metabolic regulation, most of which preferentially regulate transcription termination or translation initiation of downstream genes in specific ways. Alternatively, the same or different riboswitches can exist in tandem to enhance regulatory effects or respond to multiple ligands. However, many putative conserved riboswitches have not yet been experimentally validated. Here, we found that the c-di-GMP riboswitch Bc1 with a long EP could form a dual terminator and exhibit non-canonical and incoherent "transcription-translation" dual regulation. Besides, zinc uptake regulator specifically bound to the coding sequence of the Bc1 EP and slightly mediated the action of Bc1. The application of SHAPE-MaP to the dual regulation mechanism of Bc1 may establish the foundation for future studies of such complex untranslated regions in other bacterial genomes.
Competing Interests: The authors declare no conflict of interest.
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معلومات مُعتمدة: 31770087 MOST | National Natural Science Foundation of China (NSFC); 31970074 MOST | National Natural Science Foundation of China (NSFC); 32171424 MOST | National Natural Science Foundation of China (NSFC)
فهرسة مساهمة: Keywords: Bacillus cereus group; SHAPE-MaP; Zur (zinc uptake regulator); cyclic di-GMP riboswitch; dual regulation; dual terminator
المشرفين على المادة: 0 (Riboswitch)
H2D2X058MU (Cyclic GMP)
61093-23-0 (bis(3',5')-cyclic diguanylic acid)
0 (Bacterial Proteins)
0 (RNA, Bacterial)
تواريخ الأحداث: Date Created: 20240531 Date Completed: 20240702 Latest Revision: 20240711
رمز التحديث: 20240711
مُعرف محوري في PubMed: PMC11218506
DOI: 10.1128/spectrum.00450-24
PMID: 38819160
قاعدة البيانات: MEDLINE
الوصف
تدمد:2165-0497
DOI:10.1128/spectrum.00450-24