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][SW|Categories] containing this gene/protein
[SW|biofilm formation], [SW|sporulation/ other]Gene
Coordinates on the chromosome (coding sequence)
1,768,941 -> 1,769,735
Phenotypes of a mutant
strong overexpression of ''[protein|search|hag]'' [Pubmed|21856853]defective in [SW|biofilm formation] [Pubmed|21856853,22113911]the phenotypes of the ''ymdB'' mutant can be suppressed by overexpression of ''[protein|search|slrR]'' [Pubmed|21856853]inactivation of ''[protein|search|ymdB]'' restores beta-lactam resistance in a ''[protein|search|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 ''[SW|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]Structure
[PDB|4B2O] [Pubmed|24163345][SW|Interactions]
forms tetramers [Pubmed|24163345]Expression and Regulation
Operon
''[protein|search|rny]-[protein|search|ymdB]'' (weak readthrough transcription) [Pubmed|21856853]Regulation
constitutiveAdditional information
there is a terminator between ''[SW|rny]'' and ''[SW|ymdB]'', most transcripts terminate there [PubMed|21856853]the [SW|transcription] terminator between ''[SW|rny]'' and ''[SW|ymdB]'' is strong and [SW|NusA]-independent [http://www.nature.com/articles/nmicrobiol20157 Reference]Biological materials
Mutant
GP583 (spc), available in [SW|Jörg Stülke]'s lab [Pubmed|21856853]GP922 (cat), available in [SW|Jörg Stülke]'s lab [Pubmed|21856853]GP921 (spc) NCIB3610 derivate, available in [SW|Jörg Stülke]'s lab [Pubmed|21856853]GP969 (''[protein|search|ymdB]''(E39Q)-cat) inactive enzyme, available in [SW|Jörg Stülke]'s lab [Pubmed|24163345]GP1558 (aphA3; cassette w/o terminator), available in [SW|Jörg Stülke]'s labGP1573 (aphA3), available in [SW|Jörg Stülke]'s labGP1848 (replacement of ''[SW|ymdB]-[SW|spoVS]'' by a ''spc'' cassette), available in [SW|Jörg Stülke]'s labExpression vector
for 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 (''[protein|search|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 working on this gene/protein
[SW|Jörg Stülke], University of Göttingen, Germany[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]References
Reviews
Original Publications
21856853,22211522,22113911,24163345,26904951,26906740,26735940 Functional and structural analysis of orthologs in other organisms
