Global Transcriptomic and Proteomic Responses of Dehalococcoides ethenogenes Strain 195 to Fixed Nitrogen Limitation

Abstract

Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systemslevel approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing cells of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation (FNL), as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (nif) genes were differentially upregulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), the product of which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and is implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly upregulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally downregulated in response to FNL, and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition, while others were associated with general stress responses. A number of genes related to the functions of nucleotide synthesis, replication, transcription, translation, and posttranslational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number of genes coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate environmental cellular nitrogen status. Bacteria of the genus Dehalococcoides play a key role in the bioremediation of the carcinogenic and toxic chlorinated ethenes because of their ability to reductively dechlorinate tetrachloroethene (PCE) and its daughter products to the innocuous product ethene (9,10,29,36,49). While bacteria from diverse genera can dechlorinate PCE and trichloroethene (TCE) to isomers of dichloroethene (DCE), to date, dechlorination beyond DCE to vinyl chloride (VC) and ethene has been observed only for strains of Dehalococcoides (47). Through transcriptional and protein analyses, the reductive dehalogenase (RDase)-and hydrogenase-encoding genes for energy generation in Dehalococcoides isolates and enrichments have been studied extensively (6,16,19,23,27,28,34,36,39,40,55). However, other aspects of the physiology of Dehalococcoides are not as well understood.Currently, the genomes of four Dehalococcoides strains have been sequenced, annotated, and published (20,30,45). A nitrogenase-encoding operon (nif) for the reduction of atmospheric dinitrogen to ammonia is present in the genome annotation of Dehalococcoides ethenogenes strain 195 (45) ...

Inferring Gene Networks for Strains of Dehalococcoides Highlights Conserved Relationships between Genes Encoding Core Catabolic and Cell-Wall Structural Proteins

“…A previous microarray study also displayed a tight correlation (R 2 = 0.997) between the S-layer and tceA transcripts in a batch culture study of D2 [13]. This conserved relationship is notable because the S-Layer and major RDase proteins are among the most abundant proteins detected in proteomic assays for Dhc samples across cultures [17, 36–38]. As the major components of the cell wall and membrane-associated respiration processes, the expression of these transcripts may be tightly linked in both cultures because of their requirement for biomass growth.…”

“…Previous investigations have utilized various techniques, such as differential expression analyses and gene clustering, to relate transcript abundance to an experimental condition and to predict the function of the enzymes encoded on the expressed transcripts in Dhc . These studies include investigations of Dhc as the organism transitions from exponential growth to stationary phase [13], biosynthesizes molecules through the central carbon metabolism pathway [14], acquires and modifies key cobalamin cofactors required for growth [15], fixes nitrogen [16], or grows under nitrogen limitation [17]. These transcriptomic and proteomic studies have shown success in producing, testing, and supporting hypotheses.…”

The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics

“…This genus, although phylogenetically distant to Dehalobacter, inhabits similar ecological niches, and is exclusively dependent on OHR metabolism with H 2 as electron donor. These studies have used both transcriptomics using full genome microarrays and proteomics to identify key components of the metabolism of OHRB under different growth conditions or growth phases [23][24][25][26][27][28][29].…”

Genomic insights into organohalide respiration

“…Many such studies in Dehalococcoides have been conducted recently. These include studies focused on: regulation of functional genes and cell cycle genes [47,48], fixed nitrogen limitation [60,61], chemical stressors such as acid and oxygen [56], corrinoid limitation [62], coculture growth with Desulfovibrio and Methanobacterium [63], exogenous amino acid provision [64], carbon metabolism [65], and elucidation of a novel citrate synthase [66 ]. Outside the Dehalococcoides, two studies have characterized genome-wide expression patterns as a function of electron acceptors and donors provided: one in Desulfitobacterium strain Y51 [67] and the other in Desulfitobacterium strain TCE1 [68].…”