Subsystem: At2g25870

This subsystem's description is:

HYPOTHESIS: Arabidopsis At2g25870 protein and it's counterparts in other plants (e.g. GRMZM5G873594 in Maize) appear to be fusions of two domains, both of which have clear homologs in bacteria (including in E.coli and B.subtilis), namely YbeY (UPF0054) and YidA, which occur as stand alone proteins. They are currently annotated in this database as follows:

-- Metal-dependent hydrolase YbeY, involved in rRNA and/or ribosome maturation and assembly
-- Promiscuous sugar phosphatase YidA, haloacid dehalogenase-like phosphatase family

The YbeY (UPF0054) protein family was recently shown to be involved in rRNA maturation (PMID: 20807199). Deletion of the Escherichia coli homologue causes serious defects that affect ribosome activity, translational fidelity and ribosome assembly (PMID: 20807199, PMID:20639334). However, expression pattern of the Arabidopsis protein and fusion (and coexpression) partners of YbeY(UPF0054) in plants and Desulfobacterales (see green tab "Illustrations") seem to contradict this finding and possibly point to a putative role in metabolite repair, salvage or detoxification. Possibly - of some compounds of pyridoxine metabolism (just a hypothesis!)

OBSERVATIONS

1. In several species of Desulfobacterales YbeY(UPF0054) homologs are fused with Pyridoxine 5'-phosphate synthase (e.g. fig|177439.6.peg.1732, fig|589865.3.peg.1963)

2. In plants YbeY homolog is fused with a putative HAD-like phosphatase domain, homologous to bacterial YidA family. In EC YidA was shown to be a promiscuous sugar phosphatase with erythrose-4-phosphate being it's preferred substrate (Kuznetsova et al., 2006).

3. The YidA family is closely related to (but distinct from) the Cof phosphatase family. In EC Cof protein was identified as HMP-PP hydrolase // pyridoxal phosphatase. It was detected in a genetic screen for thiamin metabolic genes (PMID:15292217) and also analyzed by (Kuznetsova et al., 2006).

4. In Arabidopsis At2g25870 shows constant expression under nearly all conditions and development stages tested, with a notable exception of mature pollen, where the abundance of its mRNA is increased 5-fold. This is contrary to what could be expected for a protein required for optimal ribosome activity.

5. Gene co-expression in Arabidopsis -
Ribosomal proteins do NOT appear to be highly correlated in expression with At2g25870. Indeed, At2g40010 (60S acidic ribosomal protein RPP0A) and At1g07210 (30S ribosomal protein S18 family) are ranked as #53 and #109 respectively (out of ~300 co-expressed genes reported by ATTED). The following proteins are on top of this list:
0.72 At3g55400 OVA1 (OVULE ABORTION 1)
0.70 At3g25470 bacterial hemolysin-related
0.58 At2g30320 tRNA pseudouridine synthase family protein
0.59 At3g58830 haloacid dehalogenase (HAD) superfamily protein
0.54 At5g47435 formyltetrahydrofolate deformylase, putative
0.51 At2g30160 mitochondrial substrate carrier family protein

6. Experimentally confirmed targeting of the Arabidopsis protein to plastids does not contradict the proposed involvement of this [YbeY + YidA] fused protein in repair, salvage or detoxification of an unknown pyridoxine-related metabolite

For more information, please check out the description and the additional notes tabs, below

DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional Notes 
Group Alias
Abbrev.Functional RoleReactionsScenario ReactionsGOLiterature
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Taxonomy Pattern 
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YbeY(UPF0054)YidAPdxJCofYigLTEMP
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HYPOTHESIS: Arabidopsis At2g25870 protein and it's counterparts in other plants (e.g. GRMZM5G873594 in Maize) appear to be fusions of two domains, both of which have clear homologs in bacteria (including in E.coli and B.subtilis), namely YbeY (UPF0054) and YidA, which occur as stand alone proteins. They are currently annotated in this database as follows:

-- Metal-dependent hydrolase YbeY, involved in rRNA and/or ribosome maturation and assembly
-- Promiscuous sugar phosphatase YidA, haloacid dehalogenase-like phosphatase family

The YbeY (UPF0054) protein family was recently shown to be involved in rRNA maturation (PMID: 20807199). Deletion of the Escherichia coli homologue causes serious defects that affect ribosome activity, translational fidelity and ribosome assembly (PMID: 20807199, PMID:20639334). However, expression pattern of the Arabidopsis protein and fusion (and coexpression) partners of YbeY(UPF0054) in plants and Desulfobacterales (see green tab "Illustrations") seem to contradict this finding and possibly point to a putative role in metabolite repair, salvage or detoxification. Possibly - of some compounds of pyridoxine metabolism (just a hypothesis!)

OBSERVATIONS

1. In several species of Desulfobacterales YbeY(UPF0054) homologs are fused with Pyridoxine 5'-phosphate synthase (e.g. fig|177439.6.peg.1732, fig|589865.3.peg.1963)

2. In plants YbeY homolog is fused with a putative HAD-like phosphatase domain, homologous to bacterial YidA family. In EC YidA was shown to be a promiscuous sugar phosphatase with erythrose-4-phosphate being it's preferred substrate (Kuznetsova et al., 2006).

3. The YidA family is closely related to (but distinct from) the Cof phosphatase family. In EC Cof protein was identified as HMP-PP hydrolase // pyridoxal phosphatase. It was detected in a genetic screen for thiamin metabolic genes (PMID:15292217) and also analyzed by (Kuznetsova et al., 2006).

4. In Arabidopsis At2g25870 shows constant expression under nearly all conditions and development stages tested, with a notable exception of mature pollen, where the abundance of its mRNA is increased 5-fold. This is contrary to what could be expected for a protein required for optimal ribosome activity.

5. Gene co-expression in Arabidopsis -
Ribosomal proteins do NOT appear to be highly correlated in expression with At2g25870. Indeed, At2g40010 (60S acidic ribosomal protein RPP0A) and At1g07210 (30S ribosomal protein S18 family) are ranked as #53 and #109 respectively (out of ~300 co-expressed genes reported by ATTED). The following proteins are on top of this list:
0.72 At3g55400 OVA1 (OVULE ABORTION 1)
0.70 At3g25470 bacterial hemolysin-related
0.58 At2g30320 tRNA pseudouridine synthase family protein
0.59 At3g58830 haloacid dehalogenase (HAD) superfamily protein
0.54 At5g47435 formyltetrahydrofolate deformylase, putative
0.51 At2g30160 mitochondrial substrate carrier family protein

6. Experimentally confirmed targeting of the Arabidopsis protein to plastids does not contradict the proposed involvement of this [YbeY + YidA] fused protein in repair, salvage or detoxification of an unknown pyridoxine-related metabolite
REFERENCES

Mol Microbiol. 2010 Oct;78(2):506-18.
Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing.
Davies BW, Köhrer C, Jacob AI, Simmons LA, Zhu J, Aleman LM, Rajbhandary UL, Walker GC.

The UPF0054 protein family is highly conserved with homologues present in nearly every sequenced bacterium. In some bacteria, the respective gene is essential, while in others its loss results in a highly pleiotropic phenotype. Despite detailed structural studies, a cellular role for this protein family has remained unknown. We report here that deletion of the Escherichia coli homologue, YbeY, causes striking defects that affect ribosome activity, translational fidelity and ribosome assembly. Mapping of 16S, 23S and 5S rRNA termini reveals that YbeY influences the maturation of all three rRNAs, with a particularly strong effect on maturation at both the 5'- and 3'-ends of 16S rRNA as well as maturation of the 5'-termini of 23S and 5S rRNAs. Furthermore, we demonstrate strong genetic interactions between ybeY and rnc (encoding RNase III), ybeY and rnr (encoding RNase R), and ybeY and pnp (encoding PNPase), further suggesting a role for YbeY in rRNA maturation. Mutation of highly conserved amino acids in YbeY, allowed the identification of two residues (H114, R59) that were found to have a significant effect in vivo. We discuss the implications of these findings for rRNA maturation and ribosome assembly in bacteria. PMID: 20807199

J Bacteriol. 2010 Sep;192(18):4592-6. Epub 2010 Jul 16.
The heat shock protein YbeY is required for optimal activity of the 30S ribosomal subunit.
Rasouly A, Davidovich C, Ron EZ.

The highly conserved bacterial ybeY gene is a heat shock gene whose function is not fully understood. Previously, we showed that the YbeY protein is involved in protein synthesis, as Escherichia coli mutants with ybeY deleted exhibit severe translational defects in vivo. Here we show that the in vitro activity of the translation machinery of ybeY deletion mutants is significantly lower than that of the wild type. We also show that the lower efficiency of the translation machinery is due to impaired 30S small ribosomal subunits. PMID:20639334