The global distribution and evolutionary history of the pT26-2 archaeal plasmid family

Abstract

Although plasmids play an important role in biological evolution, the number of plasmid families well-characterized in terms of geographical distribution and evolution remains limited, especially in archaea. Here, we describe the first systematic study of an archaeal plasmid family, the pT26-2 plasmid family. The in-depth analysis of the distribution, biogeography and host-plasmid co-evolution patterns of 26 integrated and 3 extrachromosomal plasmids of this plasmid family shows that they are widespread in Thermococcales and Methanococcales isolated from around the globe but are restricted to these two orders. All members of the family share seven core genes but employ different integration and replication strategies. Phylogenetic analysis of the core genes and CRISPR spacer distribution suggests that plasmids of the pT26-2 family evolved with their hosts independently in Thermococcales and Methanococcales, despite these hosts exhibiting similar geographic distribution. Remarkably, core genes are conserved even in integrated plasmids that have lost replication genes and/or replication origins suggesting that they may be beneficial for their hosts. We hypothesize that the core proteins encode for a novel type of DNA/protein transfer mechanism, explaining the widespread oceanic distribution of the pT26-2 plasmid family.

Figure 1

Biogeography of the Thermococcales and Methanococcales isolation sites of the NCBI available genomes. A. Barplot indicating the number of Methanococcales and Thermococcales isolates. For both orders, we also indicate the number of isolate containing a spacer against a plasmids of the pT26‐2 family, or containing a plasmids of the pT26‐2 family t or containing both. B. The isolation sites corresponding to Methanococcales and Thermococcales are indicated on the world map by red and blue dots respectively. Six major regions have been also indicated by different cloud on the world map East Pacific Ocean Ridge, Gulf of Mexico, North Atlantic Ridge, Vulcano island, North West Pacific Ocean Ridges and Oceania. For each region, the number of isolate is indicated with a pie chart and the presence of plasmids of the pT26‐2 family or a spacer against theses are indicated using the same colour code than in the a panel. [Color figure can be viewed at http://wileyonlinelibrary.com]

Figure 2

Network view of plasmids of the pT26‐2 family conservation. Results of Bidirectional best‐hit are represented as a network. The line thickness is related to the number of conserved genes between two elements. In addition for plasmids of the pT26‐2 family, they are coloured depending of their host genera in several kind of green for Methanococcales and two kind of blue for Thermococcales. This network analysis suggests that pT26‐2 and related elements are not transferred between the two orders and have co‐evolved with theirs host. This network show that some plasmids of the pT26‐2 family shared genes with archaeal viruses or other unknown kind of archaeal MGEs. [Color figure can be viewed at http://wileyonlinelibrary.com]

Figure 3

Comparison of Thermococcales plasmids of the pT26‐2 family. In this schematic representation, the CORE genes and the integrase genes are indicated in green and orange respectively. The different genes encoding for putative replication protein are indicated with different shade of purple. The result of conservation between two plasmids of the pT26‐2 family by tblastx is indicated with several shade of blue based on the protein identity percentage. The schematic phylogenetic tree in the left corresponds to a part of the phylogenetic tree obtained with the concatenation of the core proteins in Fig. 5. [Color figure can be viewed at http://wileyonlinelibrary.com]

Figure 4

Comparison of Methanococcales plasmids of the pT26‐2 family. In this schematic representation, the CORE genes and the integrase genes are indicated in green and orange respectively. The location of the putative replication origin is indicated on the plasmid with a purple circle. The different genes encoding for putative replication protein are indicated with different shade of purple. The result of conservation between two plasmids of the pT26‐2 family by tblastx is indicated with several shade of blue based on the protein identity percentage. The schematic phylogenetic tree in the left corresponds to a part of the phylogenetic tree obtained with the concatenation of the core proteins in Fig. 5. [Color figure can be viewed at http://wileyonlinelibrary.com]

Figure 5

Maximum likelihood tree of the concatenated CORE proteins. The isolation region is indicated by a coloured square. The scale‐bars represent the average number of substitutions per site. Values at nodes represent support calculated by nonparametric bootstrap (out of 100). [Color figure can be viewed at http://wileyonlinelibrary.com]

Figure 6

att site variability. A. The att sites correspond to the 3′ terminus of the tRNA genes. On the alignment, the anti‐codon is framed. The consensus sequences among Thermococcales and among Methanococcales att sites are highlighted in colour. Long sequences were only partially presented. B and C. The att sites are displayed on the structure of the targeted tRNA for Thermococcales and Methanococcales respectively. Circles represent tRNA nucleotides. Red circles correspond to the anti‐codon. Squares represent att sites nucleotides downstream of the tRNA gene. Black nucleotides are present in all att sites, darker grey in more than 77% and lighter grey in more than 33%. [Color figure can be viewed at http://wileyonlinelibrary.com]

Figure 7

The evolutive model of the pT26‐2 family. In this schematic representation, the core module and the integrase module are indicated in green and orange respectively. The different replication modules are indicated with different shade of purple. [Color figure can be viewed at http://wileyonlinelibrary.com]