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BMC Research Notes

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August 2014


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.


© 2008 Rife et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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VCU Medicinal Chemistry Publications

1756-0500-1-108-s1.pdf (279 kB)
Sequence alignment of KsgA orthologs. Archaeal, eukaryotic, and mitochondrial KsgA orthologues were identified by performing a genomic BLAST search using the E. coli protein sequence (accession number P06992) as the query sequence. Organisms were chosen to represent a broad evolutionary diversity of species. The structure-based sequence alignment was perfomed using the program Expresso [18]. Structures used for the alignment were 1QYR[12], 1ZQ9 (A. Dong, H. Wu, H. Zeng, P. Loppnau, M. Sundstrom, C. Arrowsmith, A. Edwards, A. Bochkarev and A. Plotnikov, unpublished data), and 2H1R[13]. Organisms represented are as follows. Eukaryotes: Arabidopsis thaliana (at), Dictyostelium discoideum (dd), Leishmania brazilensis (lb), Giardia lamblia (gl), Plasmodium vivax (pv), Homo sapiens (hs), Saccharomyces cerevisiae (sc), Drosophila melanogaster (dm), and Caenorhabditis elegans (ce). Archaea: Methanopyrus kandleri (mk), Methanosaeta thermophila (mth), Haloquadratum walsbyi (hw), Methanoculleus marisnigri (mma), Methanocaldococcus jannaschii (mj), Pyrococcus horikoshii (ph), Methanosphaera stadtmanae (ms), Picrophilus torridus (pt), Archaeoglobus fulgidus (af), Aeropyrum pernix (ap), Sulfolobus solfataricus (ss), Pyrobaculum aerophilum (pa), and Cenarchaeum symbiosum (cs). Bacteria: Synechococcus elongatus (se), Bacillus subtilis (bs), Mycobacterium tuberculosis (mtu), Thermus thermophilus (tt), Bacteroides fragilis (bf), Chlamydia trachomatis (ct), Borrelia burgdorferi (bb), and Escherichia coli (ec). Accession numbers for each sequence are found in Additional file 4.

1756-0500-1-108-s2.pdf (354 kB)
Sequence alignment of mtTFB, mtTFB1, and mtTFB2 proteins. The structure-based sequence alignment was perfomed using the program Expresso [18]. The structure 1I4W[11] was used for the alignment. Organisms represented are Caenorhabditis elegans (ce), Homo sapiens (hs), Drosophila melanogaster (dm), Anopheles gambiae (ag), Apis mellifera (am), Xenopus laevis (xl), Takifugu rubripes (tr), Ciona intestinalis (ci), Rattus norvegicus (rn), Pan troglodytes (pt), Mus musculus (mmu), Bos taurus (bt), Tetraodon nigroviridis (tn), Saccharomyces cerevisiae (sc), Schizosaccharomyces pombe (sp), Kluyveromyces lactis (kl), Eremothecium gossypii (eg), Candida albicans (ca), Dictyostelium discoideum (dd), Trypanosoma brucei (tb), and Leishmania major (lm). Accession numbers for each sequence are found in Additional file 4.

1756-0500-1-108-s3.pdf (230 kB)
Sequence alignment of Erm enzymes. Erm enzymes were identified using the Nomenclature Center for MLS Genes, maintained by Dr. Marilyn C. Roberst [28]. One member of each class was chosen, with two exceptions. ErmI was not used because a corresponding sequence could not be found. Erm32 was not used because this enzyme methylates G748 rather than A2058 [29]. The structure based sequence alignment was performed with Expresso [18]. Structures used for the alignment were 1QAM[23] and 1YUB[24]. Organisms represented are Staphylococcus aureus, Enterococcus faecalis, Bacillus subtilis, Bacillus licheniformis, Saccharopolyspora erythraea, Bacteroides fragilis, Lysinibacillus sphaericus, Streptomyces thermotolerans, Streptomyces fradiae, Streptomyces coelicolor, Clostridium perfringens, Aeromicrobium erythreum, Lactobacillus reuteri, Streptomyces lincolnensis, Streptomyces viridochromogenes, Micromonospora griseorubida, Corynebacterium jeikeium, Streptomyces ambofaciens, Streptomyces venezuelae, Staphylococcus sciuri, Bacillus clausii, Bacteroides coprosuis, Micrococcus luteus, Mycobacterium tuberculosis, Mycobacterium smegmatis, Mycobacterium fortuitum, Mycobacterium mageritense, and Mycobacterium abscessus, Accession numbers are found in Additional file 4.

1756-0500-1-108-s4.pdf (87 kB)
Sequences used in protein alignments. Sequences were compiled from NCBI and Ensembl; organisms and accession numbers are indicated.