Survey for g‐proteins in the prokaryotic genomes: Prediction of functional roles based on classification

Pandit, Shashi Bhushan; Srinivasan, N.

doi:10.1002/prot.10420

Cited by 25 publications

(30 citation statements)

References 87 publications

(105 reference statements)

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“…The replacement of Asp by Glu in NKXD motif in some proteins (Fig. 6) might not affect the specificity for the guanine nucleotide and is also seen in other G-proteins (26). Based on this analysis, we conclude that the MeaI domain of IcmF, like MeaB, belongs to the SIMIBI subclass of G-proteins because two key aspartate residues at the N terminus of the Walker B motif and in the Mg 2ϩ -binding motif are present (Fig.…”

Section: Bioinformatics Analysis Of Icmfmentioning

confidence: 65%

IcmF Is a Fusion between the Radical B12 Enzyme Isobutyryl-CoA Mutase and Its G-protein Chaperone

Cracan

Padovani²,

Banerjee

2010

Journal of Biological Chemistry

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Coenzyme B 12 is used by two highly similar radical enzymes, which catalyze carbon skeleton rearrangements, methylmalonyl-CoA mutase and isobutyryl-CoA mutase (ICM). ICM catalyzes the reversible interconversion of isobutyryl-CoA and n-butyryl-CoA and exists as a heterotetramer. In this study, we have identified >70 bacterial proteins, which represent fusions between the subunits of ICM and a P-loop GTPase and are currently misannotated as methylmalonyl-CoA mutases. We designate this fusion protein as IcmF (isobutyryl-CoA mutase fused). All IcmFs are composed of the following three domains: the N-terminal 5-deoxyadenosylcobalamin binding region that is homologous to the small subunit of ICM (IcmB), a middle P-loop GTPase domain, and a C-terminal part that is homologous to the large subunit of ICM (IcmA). The P-loop GTPase domain has very high sequence similarity to the Methylobacterium extorquens MeaB, which is a chaperone for methylmalonyl-CoA mutase. We have demonstrated that IcmF is an active ICM by cloning, expressing, and purifying the IcmFs from Geobacillus kaustophilus, Nocardia farcinica, and Burkholderia xenovorans. This finding expands the known distribution of ICM activity well beyond the genus Streptomyces, where it is involved in polyketides biosynthesis, and suggests a role for this enzyme in novel bacterial pathways for amino acid degradation, myxalamid biosynthesis, and acetyl-CoA assimilation.

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Section: Bioinformatics Analysis Of Icmfmentioning

confidence: 65%

IcmF Is a Fusion between the Radical B12 Enzyme Isobutyryl-CoA Mutase and Its G-protein Chaperone

Cracan

Padovani²,

Banerjee

2010

Journal of Biological Chemistry

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“…This implies not only homology of the core factors of these two systems but also that the ER is topologically derived from the prokaryotic plasma membrane, a point nearly universally included in theories of the origins of the eukaryotic trafficking system. More generally, ␤-propeller and ␣-solenoid domains, as well as small GTPases, are all crucial building blocks of the eukaryotic membrane-trafficking machinery: proteins containing these domains are present in both bacteria and archaea (Devos et al, 2004;Pandit and Srinivasan, 2003).…”

Section: Introductionmentioning

confidence: 99%

Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode

Dacks

Field

2007

Journal of Cell Science

250

241

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The emergence of an endomembrane system was a crucial stage in the prokaryote-to-eukaryote evolutionary transition. Recent genomic and molecular evolutionary analyses have provided insight into how this critical system arrived at its modern configuration. The apparent relative absence of prokaryotic antecedents for the endomembrane machinery contrasts with the situation for mitochondria, plastids and the nucleus. Overall, the evidence suggests an autogenous origin for the eukaryotic membrane-trafficking machinery. The emerging picture is that early eukaryotic ancestors had a complex endomembrane system, which implies that this cellular system evolved relatively rapidly after the proto-eukaryote diverged away from the other prokaryotic lines. Many of the components of the trafficking system are the result of gene duplications that have produced proteins that have similar functions but differ in their subcellular location. A proto-eukaryote possessing a very simple trafficking system could thus have evolved to near modern complexity in the last common eukaryotic ancestor (LCEA) via paralogous gene family expansion of the proteins encoding organelle identity. The descendents of this common ancestor have undergone further modification of the trafficking machinery; unicellular simplicity and multicellular complexity are the prevailing trend, but there are some remarkable counter-examples.

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“…GTPases are found in all three kingdoms of life (9,13,50,63) and can be broadly classified into four large subfamilies according to their cellular roles and molecular weights: small GTP-binding proteins involved in cell proliferation, translational GTPases, ␣-subunits of heterotrimeric G proteins involved in cell signaling, and large GTP-binding proteins (50). In eukaryotes, all these families are present, and the last two decades have witnessed a tremendous increase in our understanding of the structures and functions of many of their members (9,63,67,70,71).…”

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confidence: 99%

Interactions of an EssentialBacillus subtilisGTPase, YsxC, with Ribosomes

et al. 2008

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YsxC is a small GTPase of Bacillus subtilis with essential but still unknown function, although recent works have suggested that it might be involved in ribosome biogenesis. Here, purified YsxC overexpressed in Escherichia coli was found to be partly associated with high-molecular-weight material, most likely rRNA, and thus eluted from gel filtration as a large complex. In addition, purification of ribosomes from an E. coli strain overexpressing YsxC allowed the copurification of the YsxC protein. Purified YsxC was shown to bind preferentially to the 50S subunit of B. subtilis ribosomes; this interaction was modulated by nucleotides and was stronger in the presence of a nonhydrolyzable GTP analogue than with GTP. Far-Western blotting analysis performed with His 6 -YsxC and ribosomal proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that YsxC interacted with at least four ribosomal proteins from the 50S subunit. Two of these putative protein partners were identified by mass spectrometry as L1 and L3, while the third reactive band in the one-dimensional gel contained L6 and L10. The fourth band that reacted with YsxC contained a mixture of three proteins, L7/L12, L23, and L27, suggesting that at least one of them binds to YsxC. Coimmobilization assays confirmed that L1, L6, and L7/L12 interact with YsxC. Together, these results suggest that YsxC plays a role in ribosome assembly.

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Survey for g‐proteins in the prokaryotic genomes: Prediction of functional roles based on classification

Cited by 25 publications

References 87 publications

IcmF Is a Fusion between the Radical B12 Enzyme Isobutyryl-CoA Mutase and Its G-protein Chaperone

IcmF Is a Fusion between the Radical B12 Enzyme Isobutyryl-CoA Mutase and Its G-protein Chaperone

Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode

Interactions of an EssentialBacillus subtilisGTPase, YsxC, with Ribosomes

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