Table 2

Repertoire of SAM-binding proteins in the Last Universal Common Ancestor

COG

Phyletic pattern parsimony1

Tree topology2

Protein product name and function

Fold class


SAM-binding proteins in LUCA – best-supported COGs

COG0030

1/0

+

KsgA, Dimethyladenosine transferase (rRNA methylation)

Rossmann fold

COG0144

1/0

+

Sun, tRNA and rRNA cytosine-C5-methylases

Rossmann fold

COG0192

0/1 3

+ 3

MetK, S-adenosylmethionine synthetase (releases SAM as product)

SAM synthase

COG0421

1/0

+

SpeE, Spermidine synthase

Rossmann fold

COG0500

1/0

+

SmtA, SAM-dependent methyltransferases

Rossmann fold

COG0621

1/0

+

MiaB, 2-methylthioadenine synthetase

Rossmann fold

COG1180

0/1

+

PflA, Pyruvate-formate lyase-activating enzyme

SAM radical (TIM barrel)

COG1586

0/1 3

+ 3

SpeD, S-adenosylmethionine decarboxylase

SAM decarboxylase

COG2890

1/0

+

PrmC (HemK), Methylase of polypeptide chain release factors

Rossmann fold

SAM-binding proteins in LUCA – tentatively supported COGs

COG0007

1/0

?

CysG, Uroporphyrinogen-III methylase

SAM radical (TIM barrel)

COG0220

1/0

?

Predicted S-adenosylmethionine-dependent methyltransferase

Rossmann fold

COG0293

0/1

?

FtsJ, 23S rRNA methylase

Rossmann fold

COG0320

0/1

?

LipA, Lipoate synthase

SAM radical (TIM barrel)

COG0502

0/1

?

BioB, Biotin synthase and related enzymes

SAM radical (TIM barrel)

COG0565

0/1

?

LasT, rRNA methylases

SPOUT

COG0685

1/0

?

MetF, 5,10-methylenetetrahydrofolate reductase (binds SAM as inhibitor)

TIM barrel

COG1189

0/1

?

Predicted rRNA methylase

Rossmann fold

COG2226

1/0

?

UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis

Rossmann fold


1 Placement of COGs in LUCA based on weighted parsimony analysis of phyletic patterns [138]. 1/0 indicates that this gene has been tracked back to LUCA genome under all tested conditions; 0/1 indicates tentative placement of gene in LUCA under some but not all conditions.

2 Phylogenetic analysis of each COG. Plus sign indicates tree topology that is fully consistent with gene presence in LUCA, and the question mark indicates a tentative support for the LUCA hypothesis (see Materials and Methods)

3 The common ancestry and phylogeny of archaeal, bacterial, and eukaryotic homologs was established in this work (see text for details).

Kozbial and Mushegian BMC Structural Biology 2005 5:19   doi:10.1186/1472-6807-5-19

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