Fig 1.
Hypothesized catabolic pathway of DTDB by R. erythropolis MI2.
DTDB is cleaved into two molecules 4MB by Nox using NADH. Then, a putative oxygenase converts 4MB into 4-oxo-4-sulfanylbutyric acid, which could most probably be desulfhydrated yielding succinic acid, thereby releasing the sulfur as H2S. Intermediates and the enzyme emphasized in boxes have been identified in previous studies [9, 10].
Table 1.
Genomes, number of genes, GC content, number of plasmids and Bioproject number of available completely sequenced R. erythropolis strains.
Fig 2.
Alignment of R. erythropolis strains proteomes applying BLAST (TBLASTN) [44] and BLAST Ring Image Generator (BRIG) [37].
Strain MI2 (circle 1, orange) compared to that of strain BG43 (circle 2, green), strain CCM2595 (circle 3, blue) and strain PR4 (circle 4, red), Similarity of the proteins is symbolized by colored blocks. The more intense the color—the higher the similarity. Circles 5 and 6 represent the GC skew and GC content, respectively. Strain MI2-specific regions are highlighted by black frames labeled with roman numerals (I–IV).
Fig 3.
Duel channel images of both exponential and stationary phase.
Dual channel images were generated applying the software Delta 2D 4.2 showing differences in the proteome of R. erythropolis MI2 cells cultivated with DTDB or succinate as revealed by 2D PAGE. In total, 1.5 mg protein was loaded onto 17 cm IPG strips with a pH range of 4–7. A) Cells of R. erythropolis MI2 grown with succinate (blue spots) or DTDB (orange spots), both from the exponential growth phase. B) Cells of R. erythropolis MI2 grown with succinate (blue spots) or DTDB (orange spots), both from the stationary phase. Black spots in A and B represent equally expressed proteins. Spots with significantly increased expression during the growth with DTDB by a factor ≥ 3 and successfully identified by MALDI-TOF-MS/MS are represented by arrows with locus tags.
Table 2.
Proteins exhibiting significantly increased expression of ≥ 3 during exponential growth phase in cells of R. erythropolis strain MI2 cultivated with DTDB (D) in comparison to cells cultivated with succinate (S).
Table 3.
Proteins exhibiting significantly increased expression of ≥ 3 during stationary growth phase in cells of R. erythropolis strain MI2 cultivated with DTDB (D) in comparison to cells cultivated with succinate (S).
Fig 4.
Organization of genes putatively involved in the degradation of DTDB.
Genes encoding the remarkable proteins identified during proteome analysis are marked in gray. A) Cluster coding for (locus tags left to right): RERY_05600, superoxide dismutase; RERY_05640, putative luciferase-like monooxygenase F420-dependent enzyme. B) Cluster coding for (locus tags from left to right): RERY_02650, putative OsmC-like protein; RERY_02670, putative flavin amine oxidase; RERY_02710, putative sulfide: quinone oxidoreductase; RERY_02720, putative Zn metallo-beta lactamase/putative rhodanese domain-containing protein; RERY_02740, putative rhodanese-related sulfurtransferase. C) Cluster coding for (locus tags left to right): RERY_66330, putative acyl-CoA dehydrogenase; RERY_66340, alpha/beta hydrolase domain-containing protein.
Fig 5.
Updated degradation pathway of DTDB in R. erythropolis MI2.
Nox, using NADH, cleaves DTDB into two molecules 4MB. Then, a putative oxygenase converts 4MB into 4-oxo-4-sulfanylbutyric acid. A) Desulfurization of 4-oxo-4-sulfanylbutyric acid by either the action of SQR or the putative desulfhydrase. B) Hypothesized alternative sulfur oxidation process. Abbreviations: NoxMI2, NADH:flavin oxidoreductase, LLM, luciferase-like monooxygenase; SQR, sulfide:quinone oxidoreductase; OsmC-like, osmotically induced protein; SodAMI2, superoxide dismutase.