phosphodiesterase, controls bistable gene expression, required for nanotube formation
function
control of bistable gene expression
product
phosphodiesterase
Genomic Context
categories
[category|SW 4|Lifestyles] → [category|SW 4.1|Exponential and early post-exponential lifestyles] → [category|SW 4.1.2|Biofilm formation][category|SW 4|Lifestyles] → [category|SW 4.1|Exponential and early post-exponential lifestyles] → [category|SW 4.1.2|Biofilm formation] → [category|SW 4.1.2.4|Regulation]Gene
Coordinates
1,768,941 1,769,735
Phenotypes of a mutant
strong overexpression of ''[gene|E0BB77C8F1220E931D16A1FA6B75AE8907C76FDB|hag]'' [Pubmed|21856853]defective in [SW|biofilm formation] [Pubmed|21856853,22113911]selective pressure for the inactivation of the [gene|5A6FBAE6553343092862CB79E150F934978C32A9|sinR] gene to allow [SW|biofilm formation] [pubmed|30181249]the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[gene|920F91E748EE079FF864011D9052B073567C41E4|slrR]'' [Pubmed|21856853]inactivation of ''[gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]'' restores beta-lactam resistance in a ''[gene|081DF3EE9FA56209D648C7677188C61CE3AA8E41|sigM]'' mutant [Pubmed|22211522]increased expression of genes encoding small acid-soluble proteins [Pubmed|24163345]increased intracellular levels of cyclic AMP [Pubmed|26904951]abberant colony development, reduced colony size [Pubmed|26904951]reduced formation of nanotubes [Pubmed|26906740]inactivation of ''[gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]'' reduces sporulation efficiency to 11.4% that of wild type cells [Pubmed|26735940]The protein
Catalyzed reaction/ biological activity
phosphodiesterase activity toward 2',3'-cAMP [Pubmed|24163345]nucleoside 2',3'-cyclic phosphate + H2O --> nucleoside 3'-phosphate + H+ (according to UniProt)Structure
[PDB|4B2O] [Pubmed|24163345]Expression and Regulation
Operons
genes
[gene|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|rny]-[gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]
description
[Pubmed|21856853]
regulation
constitutiveadditional information
the [SW|transcription] terminator between ''[SW|rny]'' and ''[SW|ymdB]'' is strong and [SW|NusA]-independent [http://www.nature.com/articles/nmicrobiol20157 Reference]view in new tabBiological materials
Mutant
MGNA-B070 (ymdB::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/1069 NBRP B. subtilis, Japan]GP583 ([gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]::spc), available in [SW|Jörg Stülke]'s lab [Pubmed|21856853]GP922 ([gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]::cat), available in [SW|Jörg Stülke]'s lab [Pubmed|21856853]GP921 ([gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]::spc) NCIB3610 derivative, available in [SW|Jörg Stülke]'s lab [Pubmed|21856853]GP969 (''[gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]''(E39Q)-cat) inactive enzyme, available in [SW|Jörg Stülke]'s lab [Pubmed|24163345]GP1558 ([gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]::aphA3; cassette w/o terminator), available in [SW|Jörg Stülke]'s labGP1573 ([gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]::aphA3), available in [SW|Jörg Stülke]'s labGP1848 ([gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]-[gene|384D4D4C58FCBEB46B762E01478F4081FC6FAE4A|spoVS]::''spc'' cassette), available in [SW|Jörg Stülke]'s labBKE16970 ([gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE16970 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATTTTGTAAATCCTTTCTT, downstream forward: _UP4_TAGTTGAACATATGGTTATTBKK16970 ([gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK16970 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATTTTGTAAATCCTTTCTT, downstream forward: _UP4_TAGTTGAACATATGGTTATTExpression vectors
for expression/ purification from ''B. subtilis'', in [SW|pBQ200]: pGP1039, available in [SW|Jörg Stülke]'s labfor expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [SW|SPINE], in [SW|pGP380]: pGP1041, available in [SW|Jörg Stülke]'s labfor expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [SW|SPINE], in [SW|pGP382]: pGP1919, available in [SW|Jörg Stülke]'s labfor expression/ purification from ''E. coli'' with N-terminal His-tag, in [SW|pWH844]: pGP1040, available in [SW|Jörg Stülke]'s labfor expression/ purification from ''E. coli'' with N-terminal Strep-tag, in [SW|pGP172]: pGP1917, available in [SW|Jörg Stülke]'s lab [Pubmed|24163345]GP970 (''[gene|154862E3FFA7CEBA5725BAD08E09D0E1C6B7F946|ymdB]''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [SW|SPINE], available in [SW|Jörg Stülke]'s labtwo-hybrid system
B. pertussis adenylate cyclase-based bacterial two hybrid system ([SW|BACTH]), available in [SW|Jörg Stülke]'s labFLAG-tag construct
GP1018 (spc, based on [SW|pGP1331]), available in [SW|Jörg Stülke]'s lablabs
[SW|Jörg Stülke], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]References
Reviews
25837850,28961452,30218468,30482826 Original Publications
21856853,22211522,22113911,24163345,26904951,26906740,26735940,28827522,30181249 Functional and structural analysis of orthologs in other organisms