Whole-Genome Transcriptional Analysis of Chemolithoautotrophic Thiosulfate Oxidation by Thiobacillus denitrificans under Aerobic versus Denitrifying Conditions

Abstract

Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur compound oxidation and CO 2 fixation) under aerobic versus denitrifying conditions, we conducted wholegenome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately 10% of the genome) as differentially expressed using RMA (robust multiarray average) statistical analysis and a twofold cutoff. Genes upregulated (ca. 6-to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb 3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4-to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated, respectively, with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription-quantitative PCR analysis was used to validate these trends.Thiobacillus denitrificans is an obligately chemolithoautotrophic bacterium characterized by its ability to conserve energy from the oxidation of inorganic sulfur compounds under either aerobic or denitrifying conditions (5). As a facultative anaerobe, T. denitrificans may benefit from modulating key components of its energy metabolism, such as sulfur compound oxidation or carbon dioxide fixation, according to whether oxygen or nitrate is the terminal electron acceptor. For example, T. denitrificans can express both form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which have different relative affinities for CO 2 and the competing substrate O 2 and therefore may differ in CO 2 fixation efficiency under aerobic versus denitrifying conditions. Also, among its large complement of genes associated with sulfur compound oxidation, T. denitrificans shares some genes with aerobic, chemolithotrophic sulfur-oxidizing bacteria and some with anaerobic, phototrophic sulfur bacteria (5). There is very little information on how (or whether) T. denitrificans modulates the expression of these sulfur-oxidizing genes as a function of the prevailing terminal electron acceptor. The recent availability of the complete genome sequence of T. ...

Transcriptome Dynamics during the Transition from Anaerobic Photosynthesis to Aerobic Respiration in Rhodobacter sphaeroides 2.4.1

“…This observation might also lead to the temporary high iron demand after the shift. Such responses have been observed in many bacteria, including R. sphaeroides, under oxidative-stress conditions (8,62,86). Other genes for a siderophore-mediated ferric iron transport system (RSP1437-RSP1440, RSP3056, RSP3221-RSP3224, and RSP3678) were also found in class III-4.…”

“…Iron homeostasis during the transition. The aerobic upregulation of iron transport genes usually occurs in bacteria (5,8). Iron is present in the soluble ferrous form under anaerobic conditions, but it is oxidized to the insoluble ferric form in the presence of oxygen.…”

Stability of the cbb 3 -Type Cytochrome Oxidase Requires Specific CcoQ-CcoP Interactions

“…Also, many pathogenic bacteria, such as Brucella suis (22) or Campylobacter jejuni (54), use cbb 3 -Cox mainly at low oxygen concentrations. On the other hand, in Thiobacillus denitrificans cbb 3 -Cox is highly upregulated under aerobic conditions (2). In contrast to R. sphaeroides, R. capsulatus lacks aa 3 -Cox (13) but instead contains in addition to cbb 3 -Cox a less-well-characterized CydAB-type quinol oxidase (23).…”

Influence of Fe3+ Ions on Nitrate Removal by Autotrophic Denitrification Using Thiobacillus denitrificans

“…Firstly, there was an adaptation phase of the bacterial cells to the environment (lag phase), and secondly, some portion of oxygen still remained in the system, and oxygen has precedence over nitrate and nitrite ions as a terminal electron acceptor in the energy metabolism of T. denitrificans. 20 The values of dissolved oxygen concentration higher than 0.5 mg L -1 were determined in the initial phase of the process (see Fig. 1), indicating a considerable contribution of the latter mechanism.…”