Crystal structure of the <scp>DNA</scp>‐binding domain of the LysR‐type transcriptional regulator CbnR in complex with a <scp>DNA</scp> fragment of the recognition‐binding site in the promoter region

Koentjoro, Maharani Pertiwi; Adachi, Naruhiko; Senda, Masuo; Ogawa, Naoto; Senda, Toshiya

doi:10.1111/febs.14380

Cited by 25 publications

(39 citation statements)

References 45 publications

(77 reference statements)

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“…Mutational analyses of CbnR was performed on the basis of its crystal structure (Moriuchi et al 2017). Furthermore, the crystal structure of the DBD of CbnR (hereafter CbnR(DBD)) in complex with promoter DNA has been determined (Koentjoro et al, 2018). The crystal structure of the CbnR(DBD)-DNA complex revealed the molecular mechanism of the sequence specificity of CbnR (Koentjoro et al, 2018).…”

Section: Cbnr: One Of the Representative Models For Lttrsmentioning

confidence: 99%

“…Furthermore, the crystal structure of the DBD of CbnR (hereafter CbnR(DBD)) in complex with promoter DNA has been determined (Koentjoro et al, 2018). The crystal structure of the CbnR(DBD)-DNA complex revealed the molecular mechanism of the sequence specificity of CbnR (Koentjoro et al, 2018). In this report, we frequently use the crystal structure of CbnR as a representative model of LTTRs.…”

Section: Cbnr: One Of the Representative Models For Lttrsmentioning

confidence: 99%

“…The 3 helix is referred to as the recognition helix because it recognizes specific DNA sequences by inserting into the major groove of the DNA. A deep cleft forms between the 1 and 3 helices, which is a favored structural feature to facilitate packing into DNA via hydrophobic interactions (Alanazi et al, 2013;Koentjoro et al, 2018). Two wHTH motifs from the DBD dimer bind to pseudo twofold symmetric DNA operator sequences such that each monomer recognizes a half site (Laishram and Gowrishankar, 2007;Alanazi et al, 2013;Koentjoro et al, 2018).…”

Section: Structure Of the Dna Binding Domain (Dbd)mentioning

confidence: 99%

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STRUCTURAL STUDIES OF TRANSCRIPTIONAL REGULATION BY LysR-TYPE TRANSCRIPTIONAL REGULATORS IN BACTERIA

Koentjoro

Ogawa

2018

RAS

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LysR-type transcriptional regulators (LTTRs) comprise one of the largest families of transcriptional regulators in bacteria andcontrol gene expression of various types of metabolic, virulence and physiological functions. LTTRs typically form homotetramers and require an inducer molecule(s) to activate the transcription of target genes. The N-terminal region of LTTRs contains a DNAbinding domain (DBD) with the winged helix-turn-helix motif that specifically binds the promoter region of target genes. The C-terminal region of LTTRs is connected to the DBD by a linker helix and forms the regulatory domain (RD) that contains a binding pocket for inducer molecules. Crystal structures of several LTTR family members together with their biochemical analyses have provided a potential mechanism for the initial process of transcriptional activation by LTTRs. First, helix 3 of the winged helix-turn-helix motif in DBD is supposed to distinguish the recognition binding site (RBS) in the promoter region, resulting in complex formation through interactions between two DBDs in the tetrameric LTTR and RBS. Formation of this complex seems to enable interactions between the other two DBDs in the LTTR tetramer and the activation binding site (ABS) in the promoter region.The binding of the tetrameric LTTR to both the RBS and ABS causes the promoter DNA to adopt a bent structure because the four DBDs in the tetrameric LTTR are arranged in a V-shaped manner at the bottom of the LTTR. Interaction of an inducer molecule(s) with the RD seems to cause a quaternary structural change of the LTTR that relaxes the bending angle of the promoter DNA with a concomitant shift of the bound DBDs at the ABS. These events facilitate recruitment of RNA polymerase to its binding site in the promoter region, which overlaps with the ABS for LTTR.

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Section: Cbnr: One Of the Representative Models For Lttrsmentioning

confidence: 99%

Section: Cbnr: One Of the Representative Models For Lttrsmentioning

confidence: 99%

Section: Structure Of the Dna Binding Domain (Dbd)mentioning

confidence: 99%

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STRUCTURAL STUDIES OF TRANSCRIPTIONAL REGULATION BY LysR-TYPE TRANSCRIPTIONAL REGULATORS IN BACTERIA

Koentjoro

Ogawa

2018

RAS

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“…S2). CbnR from Cupriavidus necator (formerly Alcaligenes eutrophus) utilizes a threonine residue in position 33 instead of serine to bind to the cbnA promoter (Koentjoro et al, 2018). This explains the observed differences in RBS binding by BenM and CbnR.…”

Section: Discussionmentioning

confidence: 99%

“…Nevertheless, no structures of full-length LTTRs bound to DNA or interacting with RNA polymerase are currently available. Only the structures of the DNA binding domains of BenM and CbnR with DNA were solved (Alanazi et al, 2013, Koentjoro et al, 2018. Consequently, the knowledge of the detailed structure/ function relationship of LTTRs and its dynamic can still be improved.…”

Section: Introductionmentioning

confidence: 99%

Functional definition of the two effector binding sites, the oligomerization and DNA binding domains of the Bacillus subtilis LysR‐type transcriptional regulator AlsR

Härtig

Frädrich

Behringer

et al. 2018

Molecular Microbiology

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The LysR-type transcriptional regulator (LTTR) AlsR from Bacillus subtilis activates the transcription of the alsSD operon encoding enzymes for acetoin formation in response to the presence of acetate. The structural basis for effector binding, oligomerization, DNA binding, higher ordered complex formation, DNA bending and transcriptional control by B. subtilis AlsR was functionally characterized. The binding of two molecules of acetate per molecule AlsR was determined. Acetate-dependent transcription complex formation was observed. A structural model of AlsR was used to identify the amino acid residues V98, S100, H147 of the binding site 1, which were experimentally verified. The second binding site formed by T193, V194, A196, T201 and L202 mediated high acetate responsive induction. Residues L124, E225 Q74, I79 and R111 contributed to dimerization of AlsR. A22, Q29, P30, S33, K37, L39, E46, R50 and R53 of the winged helix-turn-helix motif were important for promoter recognition. The DNA binding domain alone dimerized and effectively bound the promoter. The LTTR promoter elements RBS and ABS had to be localized on the same site of the DNA. Higher ordered complex formation resulted in bending of promoter DNA and transcriptional activation.

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A novel LysR‐type regulator negatively affects biosynthesis of the immunosuppressant brasilicardin

Wolański

Krawiec

Schwarz

et al. 2020

Engineering in Life Sciences

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Brasilicardin A (BraA) is a promising immunosuppressive compound produced naturally by the pathogenic bacterium Nocardia terpenica IFM 0406. Heterologous host expression of brasilicardin gene cluster showed to be efficient to bypass the safety issues, low production levels and lack of genetic tools related with the use of native producer. Further improvement of production yields requires better understanding of gene expression regulation within the BraA biosynthetic gene cluster (Bra‐BGC); however, the only so far known regulator of this gene cluster is Bra12. In this study, we discovered the protein LysRNt, a novel member of the LysR‐type transcriptional regulator family, as a regulator of the Bra‐BGC. Using in vitro approaches, we identified the gene promoters which are controlled by LysRNt within the Bra‐BGC. Corresponding genes encode enzymes involved in BraA biosynthesis as well as the key Bra‐BGC regulator Bra12. Importantly, we provide in vivo evidence that LysRNt negatively affects production of brasilicardin congeners in the heterologous host Amycolatopsis japonicum. Finally, we demonstrate that some of the pathway related metabolites, and their chemical analogs, can interact with LysRNt which in turn affects its DNA‐binding activity.

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Crystal structure of the DNA‐binding domain of the LysR‐type transcriptional regulator CbnR in complex with a DNA fragment of the recognition‐binding site in the promoter region

Abstract: Atomic coordinates and structure factors for the DNA-binding domain of Cupriavidus necatorNH9 CbnR in complex with RBS are available in the Protein Data Bank under the accession code 5XXP.

Cited by 25 publications

References 45 publications

STRUCTURAL STUDIES OF TRANSCRIPTIONAL REGULATION BY LysR-TYPE TRANSCRIPTIONAL REGULATORS IN BACTERIA

STRUCTURAL STUDIES OF TRANSCRIPTIONAL REGULATION BY LysR-TYPE TRANSCRIPTIONAL REGULATORS IN BACTERIA

Functional definition of the two effector binding sites, the oligomerization and DNA binding domains of the Bacillus subtilis LysR‐type transcriptional regulator AlsR

A novel LysR‐type regulator negatively affects biosynthesis of the immunosuppressant brasilicardin

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