A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases - PubMed (original) (raw)

Comparative Study

Lakshminarayan M Iyer et al. Biol Direct. 2008.

Abstract

Using sequence profile methods and structural comparisons we characterize a previously unknown family of nucleic acid polymerases in a group of mobile elements from genomes of diverse bacteria, an algal plastid and certain DNA viruses, including the recently reported Sputnik virus. Using contextual information from domain architectures and gene-neighborhoods we present evidence that they are likely to possess both primase and DNA polymerase activity, comparable to the previously reported prim-pol proteins. These newly identified polymerases help in defining the minimal functional core of superfamily A DNA polymerases and related RNA polymerases. Thus, they provide a framework to understand the emergence of both DNA and RNA polymerization activity in this class of enzymes. They also provide evidence that enigmatic DNA viruses, such as Sputnik, might have emerged from mobile elements coding these polymerases.

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Figures

Figure 1

Figure 1

Contextual information graph, domain architectures, gene neighborhoods, cartoon and topology diagrams. A) Contextual information was derived from gene neighborhoods, domain architectures and functional associations (see methods used to obtain contextual information [Additional file 1]). Black arrows represent domain architectures with the arrow head pointing to the C-terminal domain. Red arrows represent gene neighborhoods, with the arrow head pointing from the 5' to 3' direction of the coding sequence. Blue edges represent physical associations and the green edge depicts domain insertion. Domain architectures of TV-Pol proteins are shown at the bottom. Gene neighborhoods (predicted operons) of TV-Pol proteins are shown to the right. Genes are represented as pointing from the 5' to the 3' end of the coding sequence. Below each gene-neighborhood cartoon is the representative TV-Pol gene name, it species abbreviation and gi. The "D5 Helicase" module includes both the core AAA+ ATPase domain and the unique D5N domain of these proteins. Likewise in the AEP module the PRICT1/2 domains are included. B) Cartoon representation of the Taq DNA polymerase (pdb: 1BGX) showing key structural units shared by TV-Pols and superfamily A polymerases. The HTH is shown in blue and the thumb domain in faded yellow. Active site and other key conserved residues are highlighted as ball and stick and labeled. C) Topology diagram of the core catalytic domain of these polymerases with key conserved features and residues. Cylinders represent helices and green arrows strands. D) Cartoon representation of various HTH domains in comparison with that seen in superfamily A DNA polymerases. Species abbreviations are in the legend to Fig. 2.

Figure 2

Figure 2

Multiple sequence alignment of the TV-Pol domain. Secondary structure is shown above the alignment helices shown as cylinders and strands as arrows (See additional file 1 [Additional file 1] for details on alignment and secondary structure prediction methods). The 80% consensus shown below the alignment was derived using the following classes of amino acids: the aliphatic (l: LIV, yellow shading); hydrophobic (h: ACFILMVWY, yellow shading); small (s: ACDGNPSTV, green); tiny (u: GAS, green); big (b:KMILEWRYFQ); polar (p: CDEHKNQRST, blue); charged (c: DEHKR, pink); basic (+: HKR, pink). Strongly conserved amino acids are shaded red. Sequences are denoted by their gene name followed by species abbreviation and GenBank Identifier separated by underscores. In addition to the TV-Pols some of the key superfamily A polymerases and T7-like RNA polymerases detected with significant e-values are also shown in the alignment. The species abbreviations are: Amac: Alteromonas macleodii; Apro: alpha proteobacterium; BPMa-LMM01: Microcystis phage Ma-LMM01; BPT7: Enterobacteria phage T7; BPvirophage: Sputnik virophage; Bmel: Brucella melitensis; Bsui: Brucella suis; Chut: Cytophaga hutchinsonii; Dole: Desulfococcus oleovorans; Ecol: Escherichia coli; Fbac: Flavobacteriales bacterium; Gbem: Geobacter bemidjiensis; Gobs: Gemmata obscuriglobus; Gpro: gamma proteobacterium; Gste: Geobacillus stearothermophilus; Lves: Loktanella vestfoldensis; Mgam: marine gamma proteobacterium HTCC2143; Mmet: marine metagenome; Mnod: Methylobacterium nodulans; Mpop: Methylobacterium populi; Noli: Nephroselmis olivacea; Oind: Oceanibulbus indolifex; Pden: Paracoccus denitrificans; Pdok: Polaribacter dokdonensis; Ptor: Psychroflexus torquis; Rbac: Rhodobacterales bacterium; Rbal: Rhodopirellula baltica; Rnub: Roseovarius nubinhibens; Rpal: Rhodopseudomonas palustris; Rsp.: Reinekea sp.; Rsp.: Roseobacter sp.; Saur: Staphylococcus aureus; Shae: Staphylococcus haemolyticus; Ssp.: Sulfitobacter sp.; Taqu: Thermus aquaticus; Tsp.: Thauera sp.; Vsp.: Vibrio sp.

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