Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis

Abstract

The first step in the sulfate reduction pathway is the transport of sulfate across the cell membrane. This uptake has a major effect on sulfate reduction rates. Much of the information available on sulfate transport was obtained by studies on assimilatory sulfate reduction, where sulfate transporters were identified among several types of protein families. Despite our growing knowledge on the physiology of dissimilatory sulfate-reducing microorganisms (SRM) there are no studies identifying the proteins involved in sulfate uptake in members of this ecologically important group of anaerobes. We surveyed the complete genomes of 44 sulfate-reducing bacteria and archaea across six phyla and identified putative sulfate transporter encoding genes from four out of the five surveyed protein families based on homology. We did not find evidence that ABC-type transporters (SulT) are involved in the uptake of sulfate in SRM. We speculate that members of the CysP sulfate transporters could play a key role in the uptake of sulfate in thermophilic SRM. Putative CysZ-type sulfate transporters were present in all genomes examined suggesting that this overlooked group of sulfate transporters might play a role in sulfate transport in dissimilatory sulfate reducers alongside SulP. Our in silico analysis highlights several targets for further molecular studies in order to understand this key step in the metabolism of SRMs.

Keywords: CysP; CysZ; DASS; SulP; sulfate transporter; sulfate-reducing microorganisms.

FIGURE 1

Maximum likelihood phylogenetic tree of SulP protein sequences. The different protein clades are marked with different colored backgrounds and given a letter label (A–C), while separate protein groupings are denoted by subscript numbering (i, ii, etc.). Phylum level classification of the protein sequences is indicated by colored dots next to the accession number (see Supplementary Table 1 for organism information). Reference sequences: BicA, bicarbonate transporter (UniProt: Q14SY0), DauA_Salm, dicarboxylic acid transporter (ACY88617), Rv1739c, sulfate transporter (SulP_Mt), SulP_Pseudo, sulfate transporter (PA1647). Bootstrap values ≥ 50% are indicated by purple dots on each branch where the size of the dot is proportional to the value. The scale bar represents 1 substitution per amino acid position.

FIGURE 2

Alignment of putative SulP sulfate transporters. The transporter sequences were selected based on their phylogenetic relationship to the model SulP sequences (Figure 1). Invariant, conserved, and non-conserved residues are indicated by green, olive and red bar chart, respectively. Predicted transmembrane helices (TMH) for SulP_Mt (sulfate transporter) are shown by a gray bar above the sequence. Conserved residues are also highlighted within the alignment by gray shading, the darker the shading the higher conservation. Residues of interest are indicated by black arrows, while the PXYGLY motif is highlighted with a blue box.

FIGURE 3

Maximum likelihood phylogenetic tree of CysP protein sequences. The different protein clades are marked with different colored backgrounds and given a letter label (A,B), while separate protein groupings are denoted by subscript numbering (i, ii, etc.). Phylum level classification of the protein sequences is indicated by colored dots next to the accession number (see Supplementary Table 1 for organism information). Reference sequences: PitA, inorganic phosphate transporter (UniProt P0AFJ7), PitB, inorganic phosphate transporter (UniProt P43676), Cys_Pit, sulfate transporter (BSUA_01689). Bootstrap values ≥ 50% are indicated by purple dots on each branch where the size of the dot is proportional to the value. The scale bar represents 1 substitution per amino acid position.

FIGURE 4

Alignment of selected putative CysP sulfate transporters. The selected transporter sequences clustered with the model CysP sequence on the phylogenetic tree (Clade B, Figure 3). Invariant, conserved, and non-conserved residues are indicated by green, olive and red bar charts, respectively. Conserved residues are also highlighted within the alignment by gray shading, the darker the shading the higher conservation. Residues of interest are indicated by black arrows, while the GANDVANA motif is highlighted with a blue box.

FIGURE 5

Maximum likelihood phylogenetic tree of DASS protein sequences. The different protein clades are marked with different colored backgrounds and given a letter label (A–C), while separate protein groupings are denoted by subscript numbering (i, ii, etc.). Phylum level classification of the protein sequences is indicated by colored dots next to the accession number (see Supplementary Table 1 for organism information). Reference sequences: citT, citrate/succinate antiporter (UniProt P0AE74), YP_003577054 (DASS sulfate transporter in R. capsulatus), EFH95871 (SdcS, sodium-dependent dicarboxylate transporter), NP_417535 (ttdT, L-tartrate/succinate antiporter). Bootstrap values ≥ 50% are indicated by purple dots on each branch where the size of the dot is proportional to the value. The scale bar represents 1 substitution per amino acid position.

FIGURE 6

Alignment of putative DASS sulfate transporters. The transporter sequences were selected on their phylogenetic relationship to the model DASS sequences. Invariant, conserved, and non-conserved residues are indicated by green, olive and red bar chart, respectively. Residues of interest are indicated by black arrows.

FIGURE 7

Maximum likelihood phylogenetic tree of CysZ protein sequences. The different protein clades are marked with different colored backgrounds and given a letter label (A–C). Phylum level classification of the protein sequences is indicated by colored dots next to the accession number (see Supplementary Table 1 for organism information). Collapsed nodes are presented as gray circles, the number of collapsed leaves is indicated next to the circle. The E. coli CysZ sequence is indicated on the tree by a star. Reference sequences: DUF81, probable sulfite/organosulfonate exporter (UniProt Q0K020), CAF20834 (CysZ sulfate transporter in C. glutamicum), TauE, probable sulfite/organosulfonate exporter (UniProt K7WU96). Bootstrap values ≥ 50% are indicated by purple dots on each branch where the size of the dot is proportional to the value. The scale bar represents 1 substitution per amino acid position.

FIGURE 8

The location of selected putative sulfate transporter genes in relation to genes involved in the sulfate reduction pathway in the examined SRM genomes. Distance was calculated using the locus tag numbers and assumed to correspond to genes away from query. Frequency was calculated as the percentage of putative sulfate tranposrters of a given protein family located a certain number of genes away from the query. The selected putative sulfate genes clustered with the model family protein with at least 50% bootstrap clade support.

FIGURE 9

The genomic location of putative sulfate transporter genes and their proximity to genes involved in the sulfate reduction pathway. sat, sulfate adenylyltransferase; aprA, adenosine-5′-phosphosulfate reductase alpha subunit; aprB, adenosine-5′-phosphosulfate reductase beta subunit; dsrAB, dissimilatory sulfite reductase alpha or beta subunit; dsrC, dissimilatory sulfite reductase C subunit; qmoABC, quinone-modifying oxidoreductase subunit A, B, or C; other, unrelated to sulfate metabolism genes.