Sequence and structural evolution of the KsgA/Dim1 methyltransferase family
BMC Research Notes
Short Report Sequence and structural evolution of the KsgA/Dim1 methyltransferase family
Heather C O'Farrell 1
Zhili Xu 0
Gloria M Culver 0
Jason P Rife 1
0 Department of Biology, University of Rochester , Rochester, New York 14627 , USA
1 Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University , Richmond, Virginia 23219 , USA
Background: One of the 60 or so genes conserved in all domains of life is the ksgA/dim1 orthologous group. Enzymes from this family perform the same post-transcriptional nucleotide modification in ribosome biogenesis, irrespective of organism. Despite this common function, divergence has enabled some family members to adopt new and sometimes radically different functions. For example, in S. cerevisiae Dim1 performs two distinct functions in ribosome biogenesis, while human mtTFB is not only an rRNA methyltransferase in the mitochondria but also a mitochondrial transcription factor. Thus, these proteins offer an unprecedented opportunity to study evolutionary aspects of structure/function relationships, especially with respect to our recently published work on the binding mode of a KsgA family member to its 30S subunit substrate. Here we compare and contrast KsgA orthologs from bacteria, eukaryotes, and mitochondria as well as the paralogous ErmC enzyme. Results: By using structure and sequence comparisons in concert with a unified ribosome binding model, we have identified regions of the orthologs that are likely related to gains of function beyond the common methyltransferase function. There are core regions common to the entire enzyme class that are associated with ribosome binding, an event required in rRNA methylation activity, and regions that are conserved in subgroups that are presumably related to non-methyltransferase functions. Conclusion: The ancient protein KsgA/Dim1 has adapted to cellular roles beyond that of merely an rRNA methyltransferase. These results provide a structural foundation for analysis of multiple aspects of ribosome biogenesis and mitochondrial transcription.
Findings
Ribosome biogenesis is a fundamental process in all cells,
requiring the consumption of large quantities of cellular
resources under the control of an extraordinary level of
regulation. In comparing prokaryotic and eukaryotic
ribosome biogenesis pathways, the conservation of the
KsgA/Dim1 family is unique. The presence and function
of this enzyme has been maintained in every evolutionary
lineage, including eukaryotic organelles.
KsgA catalyzes the conversion of two adjacent adenosines
in the small subunit rRNA (A1518 and A1519 of 16S
rRNA, E. coli numbering) to N6,N6-dimethyladenosines
[
1
]. The KsgA family carries out this core
methyltransferase function in all domains of life, including
organelles, but has also added new roles as cellular
organization became more complex. In eukaryotes, the KsgA
ortholog Dim1 is essential for proper processing of the
pre-18S small subunit rRNA [
2
], and Dim1 knockout is
lethal. Pfc1, which is the KsgA ortholog found in
chloroplasts of Arabidopsis thaliana, is important for chloroplast
formation under chilling conditions [
3
].
A distinct eukaryotic ortholog, mtTFB, is transported into
the mitochondria where, in addition to methylating the
small subunit rRNA, it has adopted the ribosomally
unrelated function of serving as a mitochondrial transcription
factor [
4,5
]. In some mitochondria, there are two separate
mtTFB proteins, mtTFB1 and mtTFB2, which are proposed
to have arisen from a gene duplication event [5]. There is
evidence that mtTFB1 has retained stronger
methyltransferase activity, while mtTFB2 is more active as a
transcription factor [
5,6
]. The fungi have only a single mtTFB,
suggesting either loss of one of the paralogs in this
lineage, or that the duplication occurred later in evolution. In
at least one case, S. cerevisiae, the single mtTFB protein
(scmtTFB) serves as a transcription factor but has lost its
methyltransferase activity entirely [7]. sc-mtTFB lacks
significant sequence homology to any of the KsgA/Dim1
enzymes; yeast mtTFBs are generally poorly conserved and
difficult to identify via sequence homology [
8
].
Another important offshoot of the KsgA lineage is the Erm
family of methyltransferases, which confer antibiotic
resistance by methylating A2058 of the 23S rRNA [
9
]. The
present-day Erm family almost certainly resulted from one
or more gene duplications of a KsgA gene and subsequent
evolution to permit recognition of a distinct target base
[
10
].
KsgA's remarkable degree of conservation, coupled with
the adaptation of new cellular functions, give us a unique
opportunity to look at structural/function evolution of a
single protein lineage. Previous studies have established
the structural similarity between some rRNA adenosine
dimethyltransferases [
11,12
]. Based on recent work in our
groups we can now make pre (...truncated)