Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA - PubMed (original) (raw)

Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA

Lakshminarayan M Iyer et al. Nucleic Acids Res. 2013 Sep.

Abstract

Discovery of the TET/JBP family of dioxygenases that modify bases in DNA has sparked considerable interest in novel DNA base modifications and their biological roles. Using sensitive sequence and structure analyses combined with contextual information from comparative genomics, we computationally characterize over 12 novel biochemical systems for DNA modifications. We predict previously unidentified enzymes, such as the kinetoplastid J-base generating glycosyltransferase (and its homolog GREB1), the catalytic specificity of bacteriophage TET/JBP proteins and their role in complex DNA base modifications. We also predict the enzymes involved in synthesis of hypermodified bases such as alpha-glutamylthymine and alpha-putrescinylthymine that have remained enigmatic for several decades. Moreover, the current analysis suggests that bacteriophages and certain nucleo-cytoplasmic large DNA viruses contain an unexpectedly diverse range of DNA modification systems, in addition to those using previously characterized enzymes such as Dam, Dcm, TET/JBP, pyrimidine hydroxymethylases, Mom and glycosyltransferases. These include enzymes generating modified bases such as deazaguanines related to queuine and archaeosine, pyrimidines comparable with lysidine, those derived using modified S-adenosyl methionine derivatives and those using TET/JBP-generated hydroxymethyl pyrimidines as biosynthetic starting points. We present evidence that some of these modification systems are also widely dispersed across prokaryotes and certain eukaryotes such as basidiomycetes, chlorophyte and stramenopile alga, where they could serve as novel epigenetic marks for regulation or discrimination of self from non-self DNA. Our study extends the role of the PUA-like fold domains in recognition of modified nucleic acids and predicts versions of the ASCH and EVE domains to be novel 'readers' of modified bases in DNA. These results open opportunities for the investigation of the biology of these systems and their use in biotechnology.

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Figures

Figure 1.

Figure 1.

Pathways are numbered in the order of discussion in the ‘Results and Discussion’ section. Names of enzymes are given above reaction arrows. Location of the reaction in DNA or free bases is indicated in parentheses below reaction arrows. Chemical groups added during a step are highlighted in red in the ensuing product. Green labels indicate entry points for pathway intermediates and products into non-base modification pathways. The orange dot indicates a compound and the purple dot a DNA-modification enzyme predicted here for the first time.

Figure 2.

Figure 2.

Previously described and well-supported eukaryotic clades of TET/JBP proteins are collapsed. Nodes supported by bootstrap >75% are shown. Relevant domain architectures and operons of TET/JBP and TAGT families are shown between or below the trees. Proteins are either denoted by a species abbreviation (eukaryotes and bacteria) or by the complete name (phages/viruses) followed by GenBank GIs. Branch coloring: Phage sequences- blue, bacteria- pink, kinetoplastid- red and _C. subellipsoidea_- green. See

Supplementary Data

for species abbreviations.

Figure 3.

Figure 3.

Multiple sequence alignment of the DNA base glycosyltransferases (A) and the aG/P-T-pyrophosphorylases (B). Protein sequences are labeled by gene names followed by species abbreviation and Genbank GIs. Phage protein names are colored blue, bacterial ones in pink, archaea in orange and eukaryotes in black. Predicted catalytic residues for both TAGT and aG/PT-PPlase are indicated by asterisks, with secondary structure assignments shown above the alignment. Alignment columns are colored based on the 80% conservation consensus. Topology of the glycosyltransferase domain is adjacent to the alignment. See

Supplementary Data

for species abbreviations.

Figure 4.

Figure 4.

Gene neighborhoods and contextual information network of domains involved in DNA modification. Genes are shown as arrows pointing from the 5′ to the 3′ end. Representative gene-neighborhoods are labeled with taxonomic lineage and species name of origin and an anchor GI number of the gene marked with an asterisk. Operons are grouped by the type of predicted DNA modification they catalyze and also by Roman numerals to match corresponding nodes in the network. Domain architectures are shown as insets. In the network, gray edges connect neighboring genes (5′–>3′), and magenta-colored edges connect neighboring domains (N–>C terminus). Nodes are clustered either by their common function or by the predicted DNA modifications they catalyze. Thickness of edges reflects the frequency of associations between two nodes. The graph was calculated from 1751 gene neighborhoods, including 101 nodes, 377 pairwise connections and 5922 genes.

Figure 5.

Figure 5.

Structures, domain architectures and operons of representative members of the PUA-like fold. (A) Structures are centered on the conserved binding cleft with regions contributing to it colored in green. Family-specific inserts are colored in orange. The EVE structure was crystallized with a 3[N-morpholino]propane sulfonic acid molecule in the predicted binding site. (B). Genes in operons are represented and labeled as described in Figure 4. Fusions of the EVE-like domain are shown to the left.

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