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Identification of the Proteins Required for
Biosynthesis of Diphthamide, the Target of
Bacterial ADP-Ribosylating Toxins on
Translation Elongation Factor 2
Shihui Liu, G. Todd Milne, Jeffrey G. Kuremsky, Gerald R. Fink, Stephen H. Leppla
Molecular and Cellular Biology, Nov 2004: 9487-9497
Diphthamide
Random Yeast Mutagenesis
Grow 6 generations
Spheroblasts
Incubate with diphtheria fragment
Isolate resistant yeast
Ethyl methane
sulfonate
-Mutated yeasts isolated and sporolated, analyzed for
ADPR-EF2 production (as opposed to other survival
factors)
-Isolates crossed with Toxin-sensitive mating strain
-Genetic crossing analysis performed
- Resistance segregated genetically as if single-copy
- Over 31 sets crossed pair-wise
- All fell into one of 5 complimentation sets
- dph1, dph2, dph3, dph4, dph5
Dph5
-enzymatic action identified as late process
-Dph5 mutant produced EF2 can be converted to ADPRTable
EF2 using dph5 based lysate
-Dph5 determined later to be responsible for the trimethylation
-Gene identified: 300 residue
-AdoMet transferase conserved function
Dph2
• Gene identified 534 residue
• No conserved domains, function suggestion
CHO-Cells
-Similar work done previously with CHO cells and mutants
-4 complimenting strains identified as toxin-resistant
-CG-1, CG-2, CG-3, CG-4
-CG-2 recently identified 82 residue protein, with a functional
homolog in yeast responsible for zymocin toxin sensitivity
This research..
• Borrowed the dph# yeast mutants from Bodley
• Borrowed the CG-# CHO strains
• Created a large series of mating strains for
crossing
• Created strains using recently identified putative
genes as cross-testing candidates
Mutagenesis
-Cell lines mutagenized by transformation of transposonmutagenized genomic library
-Also used a pool of spontaneous mutations
-Cells transfected to express DT catalytic fragment on
demand, to screen for resistivity and sensitivity
-Complimentation crossings done with dph# strains
-Of 484 recessive mutants identified, all were one of dpn1,
dph2, dph4 or dph5 -- none in dpn3
Dph1/dph4 discovery
-Given that dph5 and dph2 genes had been previously identified,
focus was on the unidentified genes
-Genetic-crossing tests consistant with single-gene mutations
-Transposon marker always followed the DTR marker
-Transposon insertion sites were sequenced
-Genes identified, and deletion-mutant strains prepared for each
Dph1: YIL103w ORF
Dph4: YJR097w ORF
Dph3
-Not obtained from transposon-based mutagenesis method
-Screened only from DT-expression/selection of 10^8 cells
-363 recessive DTR mutants divided into one of all 5 dph groups
-Very elaborate screening to isolate dph3 mutant strains
-Overlapping genetic-fragment analysis used to identify gene
-Deletion mutant of dph3 created
Dph3: YBL071w-A ORF
CHO-Genes
-CHO based mutants made by fusion analysis
-This mutation system revealed a new CG-4 compliment group
-CG-2 mutation previously identified: DESR1
- is a homolog of TBL071w-A (dph3)
-CG-genes identified by sequence-similarity to yeast genes
-Corresponding mouse genes put into protein expression system
-Transformed into the various CG strains
-Reversal of DTR to confirm gene function
Dph1/2
-These genes have 16% identity between each other
-Previously, human dph1 has been called dph2L due to
misidentification because of homology
-yeast/mammalian sequences:
Dph1 – 49% identity
(CG-4)
Dph2 – 22% identity
(CG-3)
-Non-interchangible products, they ARE functionally distinct
Biosynthetic Intermediates
-EF2 products and ribosylated products run on nondenaturing PAGE
-Net 0 charge – HIS precursor, “intermediate” and diphthine
-Net +1 charge – diphthamide
-Net –1 charge – ADPR-diphthamide
-Different bands observed on gels, but ALL could run as ADPR-Dip when cells
transfected with missing gene
-dph1, dph2 involved first-step approximately equally
-dph5 later (known)
Dph1/dph2 Interact
-Dph1, dph2 AND dph3 appear to be involved in early steps
-Similarity of dph1 and dph2, and small (82 res) size dph3 suggests the
possibility of a catalytic complex
-All gene products produced with his/myc tags
- Each product restores activity in defective organism (no tag probs)
-Various combinations of constructs transfected into CHO cells
-immunoprecipitation of dph1 brings out dph2, and vice-versa
-dph5 expressed at high levels, but no cross-precipitation
-dph3 not expressed at detectable levels for precipitations
-Two-hybrid studies elsewhere of dph1/2 locate interaction regions,
- These two proteins likely form a heterodimer/multimer
Details – dph1
Yeast 425 residue, 49% identity with mouse dph1
Identified in CG-4 cells
Previously identified as OVCA1, dphl1
-dphl1: identified as tumor suppressor gene in humans
-Located in highly conserved region on Ch17 which shows loss of
heterozygosity in ovarian/breast cancer cells
-Knockout single dph1 in mice  Increased tumerogenesis
-Knockout both dph1 in mice  embroyonic lethality
-Forced expression suppressed cell proliferation in ovarian cell line
Details – dph2
Yeast 534 residue protein, 22% indentity to mouse gene
16% identity to dph1, identified as CG-3
Interacts with dph1, likely heterodimer
Mutation in either 1 or 2  no synthesis, thus functionally
different from dph1 despite similarities
Like dph1 gene product, dph2 gene product is localized in the
cytoplasm (where dip-synthesis expected)
Details – dph3
Yeast 82 residue protein, small in others too
Previously identified DESR1 gene
High percentage of negatively charged residues
Highly conserved in residues 1-60, differing C-termini
Conserved region: CSL Zinc-finger domain (cys-chelating)
*An identified allele sequence results in subbing tyr for cys
Dph3 localized in both cytoplasm and nucleus
continued….
Details – dph3
Dph3 previously identified as KTI11 zymocin resistance in Yeast
KTI11shown to associate with dph1, dph2 and EF2 via tandem-purifications.
Also associates with Elongator core complex, Elp1, Elp2, Elp3
Dph1 AND dph2 mutants are slightly resistant to zymocin, suggesting a large
complex is involved at some stage
*While link appears between dip-synthesis and elongator-complex, its not
reciprocal: mutants of elp1, elp2, elp3 are not defective in dipthamide
biosynthesis
•dph3 is the only dph# mutant which doesn’t have subtle phenotype changes
• posess pleiotropic growth defects
• primarily slow growth and drug / temperature hypersensitivity
Details – dph4
Yeast YJR097w gene, encodes DNAJ-like protein, 172 residues
Has no corresponding CHO compliment mutant set
First half of gene= typical J-domain
- DnaJ-like proteins cochaperones for HSP70 proteins
- assist in folding of newly synthesized proteins
•May ensure proper folding required for other dph genes?
•Second half of gene = typical CSL zinc-finger domain
•Mammalian homologs show same arrangement as yeast
•Mouse homolog shown to be expressed ubiquitously, is a cochaperone, and
stimulates ATPase activity of several HSP70 proteins
•Localized in both cytoplasm and nucleus
Details – dph5
Previously identified 300-residue SAM-methyltransferase
Highly homologous to mammalian homologs (50% to 55%)
Belong to larger class of SAM-methyltransferases
No functional redundancy found elsewhere in yeast or CHO
* Unique methylation step
Dph5 protein localized in cytoplasm
Biosynthesis of Diphthamide
1) Dph1, 2 and 3 = multimer complex to stick on carbon chain
2) Dph4 stabilizes the complex
3) Dph5 Unique methylation step
** Unknown, does it do the first one, or all of them
4) Unidentified product ATP-driven amidation
Role of Diphthamide?
Targeted by two externally produced bacterial toxins
Found in eukaryotes in all environments, as well as the extremeophile
archeabacteria (volcanic caves, acid pools, thermal vents, metallic brines)
Produced by multiple enzymes, multiple enzyme steps – important!
Likely it plays a STRUCTURAL or REGULATORY role
His699all 19 other aas, non of them adp-ribosylatable
13 of them expressed temperature sensitive growth
6 of them were non-functional
* Strongly indicative of a STRUCTURAL role
Role of Diphthamide?
However, the ADP-Ribosylation of diphthamide suggests regulatory role
Mono-ADPRT in bacterial systems as posttranslational regulation mechanism
Similar possibilities for many monoADPRTs in other eukaryotic systems
•There most likely does appear to exist an intrinsic ADPRTase for EF2
Take-home power-observation linker:
Dph1 gene is previously identified having a role as a tumor
suppressor and thus suggests Diphthamide might have a role in
cell growth regulation