A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum

Abstract

In the present study, we compared the proteome response of Allochromatium vinosum when growing photoautotrophically in the presence of sulfide, thiosulfate, and elemental sulfur with the proteome response when the organism was growing photoheterotrophically on malate. Applying tandem mass tag analysis as well as two-dimensional (2D) PAGE, we detected 1,955 of the 3,302 predicted proteins by identification of at least two peptides (59.2%) and quantified 1,848 of the identified proteins. Altered relative protein amounts (≥1.5-fold) were observed for 385 proteins, corresponding to 20.8% of the quantified A. vinosum proteome. A significant number of the proteins exhibiting strongly enhanced relative protein levels in the presence of reduced sulfur compounds are well documented essential players during oxidative sulfur metabolism, e.g., the dissimilatory sulfite reductase DsrAB. Changes in protein levels generally matched those observed for the respective relative mRNA levels in a previous study and allowed identification of new genes/proteins participating in oxidative sulfur metabolism. One gene cluster (hyd; Alvin_2036-Alvin_2040) and one hypothetical protein (Alvin_2107) exhibiting strong responses on both the transcriptome and proteome levels were chosen for gene inactivation and phenotypic analyses of the respective mutant strains, which verified the importance of the so-called Isp hydrogenase supercomplex for efficient oxidation of sulfide and a crucial role of Alvin_2107 for the oxidation of sulfur stored in sulfur globules to sulfite. In addition, we analyzed the sulfur globule proteome and identified a new sulfur globule protein (SgpD; Alvin_2515).

FIG 1

2D display of soluble proteins of Allochromatium vinosum cells grown on 22 mM malate (A) or 4 mM sulfide (B). Highly abundant proteins (circles) and proteins exhibiting especially conspicuous changes in spot intensities (squares) are highlighted.

FIG 2

Pathway of assimilatory sulfate reduction in Allochromatium vinosum. The proteomic profiles (circles) and transcriptomic profiles (boxes) are depicted next to the respective proteins. Relative fold changes in mRNA levels above 2 (green) were considered significant enhancement. Relative changes smaller than 0.5 (red) were considered to indicate significant decreases in mRNA levels. Relative fold changes between 0.5 and 2 (yellow) indicated unchanged mRNA levels. The same color coding is applied to changes at the protein level. Here, values above 1.5 (green) and below 0.67 (red) were considered significant. Those cases where transcriptomic data were not available or the respective protein was not detected in the proteomic approach are indicated by white squares or circles. Sulfur compounds added, from left to right, are sulfide, thiosulfate, elemental sulfur, and sulfite. Changes on sulfite were not determined on the proteome level. APS, adenosine-5′-phosphosulfate; OAS, O-acetylserine; NAS, N-acetylserine.

FIG 3

Current model of sulfur oxidation in Allochromatium vinosum. The proteomic profiles (circles) and transcriptomic profiles (boxes) are depicted next to the respective proteins. Relative fold changes in mRNA levels above 2 (green) were considered significant enhancement. Relative changes smaller than 0.5 (red) were considered to indicate significant decreases in mRNA levels. Relative fold changes between 0.5 and 2 (yellow) indicated unchanged mRNA levels. The same color coding is applied to changes on the protein level. Here, values above 1.5 (green) and below 0.67 (red) were considered significant. Those cases where transcriptomic data were not available or the respective protein was not detected in the proteomic approach are indicated by white squares or circles. Sulfur compounds added, from left to right, are sulfide, thiosulfate, elemental sulfur, and sulfite. Changes on sulfite were not determined on the proteome level.