darB

168

c-di-AMP binding protein, stimulates (p)ppGpp accumulation under conditions of potassium starvation

locus: BSU_14130

Molecular weight: 16.49 kDa

pI: 5.16

Protein length: 147 aa

Gene length: 444 bp

function: control of [protein|CEE73284EFC0DBE8870CE0B474922DED79475A57|rel] activity, trigger of the stringent response under conditions of potassium starvation

product: c-di-AMP binding protein

essential: no

synonyms: darB, ykuL

List of homologs in different organisms

Gene

Coordinates: 1,485,453  1,485,896

Phenotypes of a mutant

• inactivation of [gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB] facilitates the adaptation of a strain lacking c-di-AMP to growth on complex medium [pubmed|33481774]

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The protein

Catalyzed reaction/ biological activity

• apo-[protein|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB] (under conditions of potassium starvation) binds to [protein|CEE73284EFC0DBE8870CE0B474922DED79475A57|rel] to trigger (p)ppGpp accumulation [pubmed|33619274]

[wiki|Domains]

• [wiki|CBS domain] (aa 18-78) (according to UniProt)

Structure

• [PDB|6YJ8] (Apo-DarB) [pubmed|35714772]
• [PDB|6YJA] (complex with c-di-AMP) [pubmed|35714772]
• [PDB|8ACU] (the [protein|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]₂-[protein|CEE73284EFC0DBE8870CE0B474922DED79475A57|rel]^NTD₂ complex) [pubmed|36652515]
• [AF|O31698]

Effectors of protein activity

• binds c-di-AMP [pubmed|33619274,31061098], this prevents binding to [protein|CEE73284EFC0DBE8870CE0B474922DED79475A57|rel] [pubmed|33619274]

Expression and Regulation

Operons

• genes: [gene|A26502ADAC214D45A8F7F394587B0BDFBE7AF28E|ykuJ]-[gene|7FD784C885605F7FD27898BC9E83C28F21BE0E9D|ykuK]-[gene|899FF5BEE5D3F01778A0175E293EDBBDEB25717D|abbA]-[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]-[gene|FE15A41A58A8177280817CA3825764C39185021A|ccpC]

  description: [Pubmed|16395550]

  regulation

  • expressed under conditions that trigger sporulation ([wiki|Spo0A]) [Pubmed|14651647]

  regulatory mechanism

  • [protein|2C54FE2ADC82FF414D732018C90649D477A925AD|spo0A]: activation, by [protein|2C54FE2ADC82FF414D732018C90649D477A925AD|spo0A]~P [Pubmed|18840696,14651647], in [regulon|protein:2C54FE2ADC82FF414D732018C90649D477A925AD|spo0A regulon]
  • [protein|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|ccpA]: repression, [Pubmed|16395550,12850135], in [regulon|protein:E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|ccpA regulon]

Biological materials

Mutant

• MGNA-A773 (darB::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/773 NBRP B. subtilis, Japan]
• GP2769 (Δ[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]::erm) available in [wiki|Jörg Stülke]'s lab
• GP3409(Δ[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]::cat) available in [wiki|Jörg Stülke]'s lab
• BKE14130 (''darB''::''erm  trpC2'') available in the Bacillus Genetic Stock Center and in [wiki|Jörg Stülke]'s lab [pubmed|28189581]
• GP214 (deletion of [gene|A26502ADAC214D45A8F7F394587B0BDFBE7AF28E|ykuJ]-[gene|7FD784C885605F7FD27898BC9E83C28F21BE0E9D|ykuK]-[gene|899FF5BEE5D3F01778A0175E293EDBBDEB25717D|abbA]-[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB], replaced by ''kan''), available in [wiki|Jörg Stülke]'s lab
• BKE14130 ([gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]::erm  trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKE14130 BGSC],  [Pubmed|28189581], upstream reverse: _UP1_CATGTTTTCGACCCCTTTTC,  downstream forward: _UP4_TAGGCTGTACGGTCCTATTT
• BKK14130 ([gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]::kan  trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKK14130 BGSC],  [Pubmed|28189581], upstream reverse: _UP1_CATGTTTTCGACCCCTTTTC,  downstream forward: _UP4_TAGGCTGTACGGTCCTATTT
• GP2800 (Δ[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]-[gene|FE15A41A58A8177280817CA3825764C39185021A|ccpC]::phleo), available in [wiki|Jörg Stülke]'s lab

Expression vectors

• pGP2929 (N-terminal 6xHis-tag, purification from E. coli, in [wiki|pWH844]), available in [wiki|Jörg Stülke]'s lab
• pGP2972 (N-terminal 6xHis-SUMO-tag, purification from E. coli, in pET-SUMO), available in [wiki|Jörg Stülke]'s lab
• pGP635: expression of Strep-[gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB] by [wiki|pGP380] in B. subtilis suitable for [wiki|SPINE], available in [wiki|Jörg Stülke]'s lab
• pGP767: expression of [gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]-Strep by [wiki|pGP382] in B. subtilis suitable for [wiki|SPINE], available in [wiki|Jörg Stülke]'s lab
• pGP3306: expression of [gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB] by [wiki|pBQ200] in B. subtilis, available in [wiki|Jörg Stülke]'s lab

two-hybrid system

• B. pertussis adenylate cyclase-based bacterial two hybrid system ([wiki|BACTH]), available in [wiki|Jörg Stülke]'s lab

FLAG-tag construct

• GP2810 [gene|90AFF93D6E7BC993B2773C12EE400C80A87A4831|darB]-3xFLAG spc (based on [wiki|pGP1331]), available in [wiki|Jörg Stülke]'s lab

labs

• [wiki|Jörg Stülke], University of Göttingen, Germany [http://genmibio.uni-goettingen.de Homepage]

References

Reviews

• 32603625,37954098

Original Publications

• 14651647,16395550,31061098,25215494,33481774,33619274,35130724,35714772,36629470,36652515