Present address: Department of Chemistry and Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, 103 Chemistry Research Building, Bozeman, MT 59717, USA.
A thermophilic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase
Version of Record online: 3 NOV 2010
© 2010 Society for Applied Microbiology and Blackwell Publishing Ltd
Volume 12, Issue 11, pages 2904–2917, November 2010
How to Cite
Barkay, T., Kritee, K., Boyd, E. and Geesey, G. (2010), A thermophilic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase. Environmental Microbiology, 12: 2904–2917. doi: 10.1111/j.1462-2920.2010.02260.x
- Issue online: 3 NOV 2010
- Version of Record online: 3 NOV 2010
- Received 17 November, 2009; accepted 15 April, 2010.
Fig. S1. A neighbour-Joining phylogeny of MerA from the Gammaproteobacteria. Names in blue signify marine bacteria, open and full triangles depict core and full MerA respectively; all other MerA included in the analysis are full MerA; ? for S. fridgimarina NCIMB 400 indicates that the presence of NmerA is questionable as the 60 amino acids N-terminus extension contains a GMSCPSSV rather than the consensus GMTCXXC motif; bar indicates 0.05 substitutions per 10 positions. The 87 gammaproteobacterial MerA sequences (see Table S1) were aligned using Clustal X (Thompson et al., 1997), using default program settings, followed by verification by eye which included the removal of most sequences with > 98% similarity to other sequences in the alignment. The remaining 48 sequences were then used to build the tree using the NJ and distance functions of PAUP* version 4.0 beta 10 (Sinaur and Associates, Sunderland, MA). MerA of S. solfataricus P2 served as outgroup for the tree.
Fig. S2. Eh-pH diagrams for mercury and sulfur speciation at sea water salinities and high (A) and low (B) sulfur concentrations. A. Speciation with [Hg]total at 10 pM, [Cl–] at 10−0.55 M and [S]total at 1 mM. B. Speciation with [Hg]total at 10 pM, [Cl–] at 10−0.55 M and [S]total at 1 µM. All diagrams modelled at 25°C and total pressure of 1 atm. The area between the two solid black lines defines the redox potential limits of water stability above which water is oxidized to gaseous oxygen and below which it is reduced to gaseous hydrogen. The solid red lines and dashed blue lines represent the boundaries that mark the transition between different Hg and S species respectively. Areas shaded in light yellow are regions in the diagram where solid and insoluble Hg species (i.e. HgS) dominate.
Fig. S3. Phylogenetic reconstruction of MerP and NmerA deduced amino acid sequences. Sequences labelled as NmerA represent only the N-terminal extension of full MerA sequences. The scale bar represents eight substitutions per 10 positions. MerP sequences were compiled in March of 2009 by tblastx searches of the Entrez Nucleotide database (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide) and the complete microbial genomes database (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi) using the MerP sequence of Tn501 (accession number CAA7732) as a query. All MerP sequences were aligned with all full MerA sequences (see section on the methodology of phylogenetic analysis of MerA) with the ClustalX (ver. 2.0) (Larkin et al., 2007) using the Gonnet substitution matrix and default settings. Core MerA sequences were then trimmed, leaving just the NmerA extension and MerP in the alignments. The remaining sequences (70 amino acid positions) were realigned as described above and the resulting alignment was subjected to evolutionary model prediction using ProtTest (Abascal et al., 2005). The phylogenetic position of MerP and NmerA was evaluated using PhyML employing the JTT substitution model with gamma-distributed rate variation across sites. Phylograms were projected from 100 bootstrap replicate trees using FigTree (ver. 1.2.2) (http://tree.bio.ed.ac.uk/software/figtree/). Bootstrap support for the consensus tree topology was low due to the few informative or variable positions in the alignment. Manual inspection of the 100 replicate trees indicated similar topologies, with differences primarily in the branching order of taxa within the indicated lobes. Given these observations, only taxa with MerP or NmerA that do not cluster within the MerP or NmerA lobes are indicated.
Table S1 MerA sequences included in this study.
Table S2 Characteristics of Archaea whose genomes contain merA homologs.
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