This webpage was developed as a component of a course offered at the University of Washington:
FISH 507a Applied Bioinformatics for Fishery and Aquatic Sciences

A. Baxter MY FAVORITE GENE

Updated Oct 22, 2007 

The pathogenic microorganism =

Vibrio parahaemolyticus

The electron microscopic image was taken by T. Iida



The_Gene:_scrG
Conserved Domains
Blink
Structure
Function
References

Vibrio parahaemolyticus is a naturally occuring estuarine bacteria that can cause acute gastroenteritis in humans when it is ingested in significant quantities, usually via raw or undercooked seafood, typically oysters.  The mean incubation period for V. parahaemolyticus infection is 15 h (range, 4 to 96 h).  Virulence mechanisms utilized by V. parahaemolyticus are not fully understood but outbreaks tend to be concentrated along coastal regions during the summer and early fall when higher water temperatures favor higher levels of bacteria....

 


"scr" for swarming and capsular polysaccharide regulation


Swarming is important for:   -group migration over survaces and through viscous environments

                                        -growth within biofilm communities

                                        -formation of cohesive pellicles at air-liquid interfaces



Circular representation of the V. parahaemolyticus chromosome 1 and 2

The two chromosomes, large (Chr. 1) and small (Chr. 2), are depicted. From the outside inward: the first and second circles show predicted protein-coding regions on the plus and minus strands. Colors correspond to the main classes of genes. Black denotes hypothetical proteins including both conserved and non-conserved in other bacteria. The third circle shows transposon-related (black), phage-related (blue), super-integron (pink), flagella-related (green) and pathogenesis-related (including pili and adhesins)(red) genes. The fourth circle shows GC skew. The fifth circle shows percentage G+C in relation to mean G+C for the chromosome. The sixth and seventh circles are rRNA and tRNA, respectively.

Image courtesy of :  Genome Information Research Center 2002

The Gene:   scrG

Contains the Diguanylate-cyclase (DGC) or GGDEF domain


Nucleotide sequence FASTA format, GenBank Accession number: AY216910


    >gi|28975361:4415-6121 Vibrio parahaemolyticus scr locus, complete sequence
CTATGAATTCAATGAATATCGGCTAGCACTTGCGACAGATAAGGGTTTTGAGAACCAGTAACCTTGTAAA
TAGTCGACGCCCATCTGAGTAAAGAAGTCGCACATCTTCGCATCCTCAATGCCTTCAATCACTACCTCAA
TATTGTTCTCGTGGCACATTGCAATCAAAAACTTTAGGTACTCTCGCGAAGAGTGGTTTGTCAGCGTTTT
CCAAGCCATCGATTTATCGATTTTTATCTGCGTCATCGGTAAATCAAAGAAGCAGTTTAAAGAACTGTAC
CCGGAACCAAAGTCATCCAAAGACAACGCAAAACCCAACTCACGAAGCGTGTTTAAGGGGGCCATAGCCG
TTTGGTTGTTATCCAAAATGAATGTTTCGGTGAGCTCTAGCACGATAGACTGAGGTGCGACGCCAGCCTC
GTCAGCCATGGCTTTGATTCTTGAGGGAAACTCACCATTCATAAGCTGCAGAACGGAGACGTTTACGTTC
ACTCTTACTTCATTTTGGTAGCGTTCACGGTATTGTTTTATGAACTGACAAGCTTTCGCGAACACTTGAT
AGCCTAGCTCGACGATCAAGCCTTTGTTCTCGGCTACGGGAATAAACTCATCGGGATAAATTTCGCCAAA
CTCTTTGCTACGCCAACGAACGAGAGATTCAAAACTCACCACTTCGGAGCTTTTTGCATTAATGATTGGT
TGAAACTTCACACTCAAGGTTTGCTTTTCTAGTGCGCTTTTCAAACCTTGTTCGATAAAAAAGTAACGAT
CTACCGCGTGTTGAGTGCGTTGGCTGTAAATGGCAATCCTATCTTTATTTTGTTCACTGGCGTATTGGCA
TGTTCTTGCAGCTTTACGCAAAATTTCATCAGCAGAGTGAGCAGGGTCGATACAAGGGTACAAGCCAATG
CTGATGTTACTGCCAAGATACTGGCCTTCTTCTACAACGGCTTCGTGATAGGTTTGTTTTATCGTCTCGG
CATAAGCTTGAAGCGTGTCTATTGAGCAATCGTCCTGAATTAAAATTGCGAAATCGTCATCATGTACGCG
ATACACTGAGCAGTTGGGGGATGGCAGATGACTGAGCGTTTGCAGCAGCTTTTCCACCAAACCATTGACC
AGTTCATTGCCGTACTGGTTCAGATAGGATTTGATCTCATTGATTTGGATGTAGCAAATCGACGTTGGCG
TGTCTGTCGAACAGACGTGTTCTTCAATATCAAGCAACAAATGCGCGCGGTTTGCCATACCTGAGGCGTT
ATCATGGAACGCGACTTGATGAATGTAGCTTTCCATTAATTTACGTTCAGAAATGTCGCGATGGCTACCC
ACCATATAATGGCCATGCTCAGTTTCTTTGGTCATCGCAACGCCTTCAATCCAAACGTATTGCCCGTTGG
GTTTACGCAGGCGGTAAGTGGTTGTGACGCGCGTATTGTCGGTATTAATGTGGGCATCGACGCGCTTGGA
CAGTCTTTCCCTATCCAACGGATGCACTAAATCCAACCAGCGATCTAGGTTGATGCGTCCAGCATTGATT
CCAAGTTGCTCATAAAATCCCTGATTGTAGAAAACCATCGTCCCGAACTCGTCCATGTAGAAGAGGCCTT
CGTTGAACACATCAAAGATATGAATAAAGCGTTCTTCGACGATCTTGAGAAACTCGCGATCATTGTCTGA
GGCCTGTTGATCAAAAATGGTGGTCAA

Protein Sequence FASTA format: AAO61794.1

>gi|149750160:1-568 ScrG [Vibrio parahaemolyticus AQ3810]
MTTIFDQQASDNDREFLKIVEERFIHIFDVFNEGLFYMDEFGTMVFYNQGFYEQLGINAGRINLDRWLDL
VHPLDRERLSKRVDAHINTDNKRVTTTYRLRKPNGQYVWIEGVAMTKETEHGHYMVGSHRDISERKLMES
YIHQVAFHDNASGMANRAHLLLDIEEHVCSTDTPTSICYIQINEIKSYLNQYGNELVNGLVEKLLQTLSH
LPSPNCSVYRVHDDDFAILIQDDCSIDTLQAYAETIKQTYHEAVVEEGQYLGSNISIGLYPCIDPAHSAD
EILRKAARTCQYASEQNKDRIAIYSQRTQHAVDRYFFIEQGLKSALEKQTLSVKFQPIINAKSSEVVSFE
SLVRWRSKEFGEIYPDEFIPVAEKKGLIVELGYQVFAKTCQFIKQYRERYQNEVRVNVNVSVLQLMNGEF
PSRIKAMADEAGVAPQSIVLELTETFILDNNQTAMSPLNTLRELGFALSLDDFGSGYSSLNCFFDLPMTQ
IKIDKSMAWKTLTNHSSREYLKFLIAMCHENNIEVVIEGIEDAKMCDFFTQMGVDYLQGYWFSKPLSVAS
ASRYSLNS



Structure: GGDEF domain indicated by the arrow A site. 




This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain [1] and has diguanylate cyclase activity [4]. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate.


NCBINCBI Structure Group logo



ScrG [Vibrio parahaemolyticus]


Descriptions

TitlePssmIdMulti-DomE-value
cd01948, EAL, EAL domain. This domain is found in diverse bacterial signaling proteins...30163No1e-60
cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a co...30164No3e-13
cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probab...29035Yes7e-07
pfam08447, PAS_3, PAS fold. The PAS fold corresponds to the structural domain that has...71876Yes2e-13
CD Search Reference:
Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.

GGDEF conserved domain tree
BLink : Organisms with similar genes
Blink



Function:

ScrG primarily acts as a phospodiesterase.  Mutants with defects in scrG show altered swarming, lateral flagellin production and colony morphology (but not swimming motility).

Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as domain of unknown function 1 (DUF1). It is widely present in bacteria and often links to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain has been suggested to be homologous to the adenylyl cyclase catalytic domain. This prediction correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesiveness in bacteria.

Cyclic diguanosine monophosphate serves as a specific allosteric activator of cellulose synthesis.

 
Full textProc Natl Acad Sci U S A 101:17084-17089 (2004)
PubMed id: 15569936  
 
 
Structural basis of activity and allosteric control of diguanylate cyclase.
C.Chan, R.Paul, D.Samoray, N.C.Amiot, B.Giese, U.Jenal, T.Schirmer.
 
  ABSTRACT  
 
Recent discoveries suggest that a novel second messenger, bis-(3'-->5')-cyclic di-GMP (c-diGMP), is extensively used by bacteria to control multicellular behavior. Condensation of two GTP to the dinucleotide is catalyzed by the widely distributed diguanylate cyclase (DGC or GGDEF) domain that occurs in various combinations with sensory and/or regulatory modules. The crystal structure of the unorthodox response regulator PleD from Caulobacter crescentus, which consists of two CheY-like receiver domains and a DGC domain, has been solved in complex with the product c-diGMP. PleD forms a dimer with the CheY-like domains (the stem) mediating weak monomer-monomer interactions. The fold of the DGC domain is similar to adenylate cyclase, but the nucleotide-binding mode is substantially different. The guanine base is H-bonded to Asn-335 and Asp-344, whereas the ribosyl and alpha-phosphate moieties extend over the beta2-beta3-hairpin that carries the GGEEF signature motif. In the crystal, c-diGMP molecules are crosslinking active sites of adjacent dimers. It is inferred that, in solution, the two DGC domains of a dimer align in a two-fold symmetric way to catalyze c-diGMP synthesis. Two mutually intercalated c-diGMP molecules are found tightly bound at the stem-DGC interface. This allosteric site explains the observed noncompetitive product inhibition. We propose that product inhibition is due to domain immobilization and sets an upper limit for the concentration of this second messenger in the cell.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Product binding to the allosteric inhibitory I-site. (a) A close-up view of the two mutually intercalated c-diGMP molecules (khaki and gray carbon atoms) bound at the D2 (yellow)-DGC (green) interface. The omit map of the ligand is contoured at 4 .(b) The ligand is tightly bound to both domains [carbons are colored in magenta (D2) and cyan (DGC)] by a multitude of specific interactions, including a recurrent arginine-guanine-binding motif. Figures were generated by DINO (A. Philippsen, www.dino3d.org). 		Figure 4.
Fig. 4. Mechanistic model of PleD regulation. The catalytic DGC domain (green) is tethered via a flexible linker peptide to the D1/D2 stem. The DGC domain is postulated to be mobile with respect to the stem, as indicated by the curved broken arrow. (Upper) PleD is activated by phosphorylation at the D1 domain, which induces dimerization mediated by the stems and allows the two substrate-binding sites (with bound GTP substrate in yellow) to approach each other and the condensation reaction (2 GTP c-diGMP + 2 PPi) to occur. (Lower) Allosteric product inhibition occurs by binding of (c-diGMP)[2] to the I-site at the stem-DGC interface, whereby the DGC domain is immobilized with respect to the stem and barred from approaching its counterpart in the dimer.
 
  Figures were selected by an automated process.  


Literature references