The dialkylglycine decarboxylase repressor DgdR. Functional aspects and relation to other LysR proteins
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1 11/29/ The dialkylglycine decarboxylase repressor DgdR. Functional aspects and relation to other LysR proteins 1. Dialkylglycine amino acids 2. In vivo and in vitro studies on the DgdR repressor protein 3. Phylogenetic analysis of DgdR and DgdA proteins 4. Recent x-ray crystal structures of tetrameric LysR proteins
2 11/29/2011 2, -Dialkylglycines: -aminoisobutyric acid (Aib) R- and S-isovaline (Iva) D(R)- and L(S)-alanine
3 11/29/ Aminoisobutyrate (Aib) and Isovaline (Iva) occurrence 1. Fungal peptaibol antibiotic peptides Alamethicin: Ac-Aib-Pro-Aib-Ala-Aib-Ala-Gln-Aib-Val-Aib-Gly-Leu-Aib-Pro-Val-Aib-Aib-Glu-Gln-PheOH Cephaibol A: Ac-Phe-Aib-Aib-Aib-Aib-Gly-Leu-(R) Iva-Aib-Pro-Gln--(R) Iva-Pro-Aib-Pro-PheOH Bunkoczi, G. et al., J. Pept. Sci (2003) 9: 745. Non-ribosomal peptide synthase. Biosynthesis route to Aib and Iva is unknown.
4 11/29/ Aminoisobutyrate (Aib) and Isovaline (Iva) occurrence 2. Meteorites and bolide impact zones. Jeff Bada, Scripps Glavin & Dworkin PNAS (2009) 106, 5487.
5 11/29/ Burkholderia cepacia and several other bacteria and fungi (but not E. coli) can utilize Aib as the sole N source. The dialkylglycine decarboxylase was first isolated, purified, and characterized in the 60s by Esmond Snell and others. Dgd genes were cloned and sequenced at UAF (J. Biol. Chem. (1990) 265: 5531). by inserting B. cepacia DNA into an E. coli plasmid, and screening the recombinants with Aib/glucose agar. dgdr, the dialkylglycine repressor structural gene dgda, the dialkylglycine decarboxylase structural gene
6 11/29/ Basis for commercial interest and U.S. patents to JK and UA: 1. Aib is actively transported into many cell types, is non-toxic, and there are no known eukaryotic dgd gene analogues. 2. The E. coli lac repressor-operator system is functional in mouse cells.
7 11/29/ The biological role of the dgd genes and gene products is still not entirely clear. Dialkylglycine decarboxylase can process several amino acids including Aib, R-isovaline, D(R)-alanine, and others. So which one is the natural substrate?
8 11/29/ The natural substrate would be a good substrate, and also induce expression of the decarboxylase structural gene. These genes would have evolved together to be turned on by, and process, an amino acid. pror pros none H H H CH 3 No decarboxylation H CH 2 CH 3 H CH 2 CH 2 CH 3 H CH(CH 3 ) 2 H CH(CH 3 )CH 2 CH 3 CH 3 H Decarb, but no induction CH 3 CH 2 H CH 3 CH 2 CH 2 H (CH 3 ) 2 CH H CH 3 CH 2 CH(CH 3 ) H Rapid decarboxylation V. Slow decarboxyl n CH 3 CH 3 CH 3 CH 2 CH 3 CH 3 CH 2 CH 2 CH 3 Decarb, but no induction CH 3 CH 2 CH 3 E. coli JM109/pGEM7Z14: 20 h growth in YT medium + 20 mm amino acid. CH 3 CH 2 CH 2 CH 3 V. Slow decarboxyl n -CH 2 CH 2 CH 2 CH 2 - Decarboxylase specific activity (u/mg)
9 11/29/ Conclusion: the dgd genes evolved to metabolize Aib S-isovaline induces dgda expression (but R-isovaline is the better substrate for the dialkylglycine decarboxylase).
10 11/29/ The dgdr gene was overexpressed in E. coli and purified by standard methods. As has been found for many LysR-type DNA binding proteins, the DgdR protein can be concentrated only in the presence of high-salt buffers.
11 11/29/ Intergenic region and 5 -ends of dgd genes dgda dgda transcript dgdr Bacterial RNA polymerase promoter Footprint of DgdR protein This section of DNA was used in gel shift assays to measure effects of various amino acid on DgdR-DNA binding.
12 11/29/ Gel shift assay of purified DgdR protein bp DNA including 5 -ends of dgda and dgdr genes. fast (f) slow (s) DNA is bent and more rigid. This half of the PAGE gel contains 10 mm Aib
13 11/29/ The same four amino acids induce dgda gene expression in vivo, and enhance the formation of slow-shifted protein-dna complexes in vitro. In vivo inducers Other amino acids have no effect on dgda gene expression, or on formation of slow-shifted protein- DNA complexes. In vivo non-inducers amino acid This is a structure-activity correlation that implicates the formation of the slow-moving (bent) DgdR-DNA complex as a necessary component in expression of the dgda gene.
14 11/29/ The DgdR experimental work was carried out by graduate students Lilly Allen and HongHong Sun, with help from undergraduates Susan Bray, Marcia O Brien, and Renee Stapleton.
15 11/29/ Sequence analysis of DgdR homologues
16 11/29/ DgdR DgdA All dgda homologue genes have upstream ORFs dgdr homologues- that that are strongly similar to the LysR family. tblastn using as a probe the B. cepacia DgdA protein sequence DgdA hits in genbank database Now look for open reading frames upstream of and divergent from the dgda gene homologues.
17 11/29/ top BLAST hits for B. cepacia DgdA decarboxylase protein Active site catalytic Gln, which differentiates authentic dialkylglycine decarboxylases from other vitamin B6- dependent enzymes. clustalx.2
18 11/29/ Clustal alignment of DgdR proteins encoded by genes adjacent to the same decarboxylase-encoding genes (part of) the regulatory domain expected to bind Aib
19 11/29/ The phylogenetic trees derived from sequence alignments of two Dgd protein groups are virtually identical. This suggests that each gene pair has remained together and undergone evolutionary change independent of other dgd gene pairs.
20 11/29/ Therefore, the dgd regulator-enzyme gene pairs have probably existed for millions of years, providing an essential biological or ecological function for various microorganisms. But what is that function??
21 11/29/ About 20% of bacterial regulatory genes and proteins are in the LysR family. About aa long. Contain a Winged helix-turn-helix DNA binding domain at the N-terminus A long linker helix connecting the DBD to the C-terminus An / regulatory, or effector binding, domain consisting of two halves linked by two beta strands. A C-terminal helix that may be required for DNA binding
22 11/29/ X-ray crystal structures Most are regulatory domain only (~20 in protein data bank) First was CysB with sulfate ion bound (Tyrrell, R et al Structure 5, ) Full-length: (November 2011) Vibrio cholerae virulence activator, AphB (3SZP.pdb) Arginine permease ArgP from Mycobacterium tuberculosis (3ISP.pdb) Toluenesulfonic acid LysR-type regulator TsaR from Comamonas testosteroni (3FXQ.pdb) CbnR
23 11/29/ Two (or three) domains: winged-helix-turn-helix; / regulatory domain, which includes the C-terminal helix.
24 11/29/ All structures show a dimer-of-dimers quaternary structure. The monomers in each dimer adopt two conformations: extended and compact. The difference is how the DBD is situated relative to the RD: the connecting helix is either long, or bent back onto the RD.
25 11/29/ CbnR Muraoka et al. J. Mol. Biol. 2003
26 11/29/ The N-terminal w-hth domains present a linear curved surface (to DNA?).
27 11/29/ CbnR Muraoka et al. J. Mol. Biol. 2003
28 11/29/ Hypothesis by Monferrer et al for conformation change ( Mol Micro 2010) Sliding dimer hypothesis by Porrúa et al (Mol. Micro. 2007)
29 11/29/ Un-induced CbnR Induced TsaR
30 11/29/ Clustal alignment of DgdR proteins encoded by genes adjacent to a decarboxylase-encoding gene Where do these conserved aa s map onto the known LysR regulatory domain structures? Adjacent to the effector binding site?
31 11/29/ The End
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