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

Abstract

The interpretation of high-throughput gene expression data for non-model microorganisms remains obscured because of the high fraction of hypothetical genes and the limited number of methods for the robust inference of gene networks. Therefore, to elucidate gene-gene and gene-condition linkages in the bioremediation-important genus Dehalococcoides, we applied a Bayesian inference strategy called Reverse Engineering/Forward Simulation (REFS™) on transcriptomic data collected from two organohalide-respiring communities containing different Dehalococcoides mccartyi strains: the Cornell University mixed community D2 and the commercially available KB-1® bioaugmentation culture. In total, 49 and 24 microarray datasets were included in the REFS™ analysis to generate an ensemble of 1,000 networks for the Dehalococcoides population in the Cornell D2 and KB-1® culture, respectively. Considering only linkages that appeared in the consensus network for each culture (exceeding the determined frequency cutoff of ≥ 60%), the resulting Cornell D2 and KB-1® consensus networks maintained 1,105 nodes (genes or conditions) with 974 edges and 1,714 nodes with 1,455 edges, respectively. These consensus networks captured multiple strong and biologically informative relationships. One of the main highlighted relationships shared between these two cultures was a direct edge between the transcript encoding for the major reductive dehalogenase (tceA (D2) or vcrA (KB-1®)) and the transcript for the putative S-layer cell wall protein (DET1407 (D2) or KB1_1396 (KB-1®)). Additionally, transcripts for two key oxidoreductases (a [Ni Fe] hydrogenase, Hup, and a protein with similarity to a formate dehydrogenase, “Fdh”) were strongly linked, generalizing a strong relationship noted previously for Dehalococcoides mccartyi strain 195 to multiple strains of Dehalococcoides. Notably, the pangenome array utilized when monitoring the KB-1® culture was capable of resolving signals from multiple strains, and the network inference engine was able to reconstruct gene networks in the distinct strain populations.

Structural dynamics and transcriptomic analysis of Dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor

“…Although the exact function of the Fdh-like oxidoreductase in D. mccartyi remains unknown, protein analysis of D. mccartyi strain CBDB1 suggested it is involved in the enzyme complexes that are critical to the electron transport chain of the D. mccartyi species (Kublik, et al 2016;Türkowsky et al 2018). In our study, the expression levels of fdh (DET0186-DET 0187) in both ANAS and CANAS were found to be at similar levels to the hydrogenases hup, hym, and vhu (Supplemental material Table S4), consistent with the previous findings (Mansfeldt et al 2014, Mansfeldt et al 2016, Heavner et al 2018.…”

“…However, a recent transcriptomic study revealed that DET0187 was expressed at similar levels to the Hup subunit (DET 0112) in multiple D.mccartyi strains (Mansfeldt et al 2014). The Fdh-like oxidoreductase (DET0187) was shown to be associated with the Fdh-like protein DET0112 from the hup operon (Mansfeldt et al 2014) and a recent transcriptomic study of D. mccartyi-containing microbial communities indicated the expression pattern of the Hup and the Fdh-like oxidoreductase are strongly linked (Mansfeldt et al 2016). Although the exact function of the Fdh-like oxidoreductase in D. mccartyi remains unknown, protein analysis of D. mccartyi strain CBDB1 suggested it is involved in the enzyme complexes that are critical to the electron transport chain of the D. mccartyi species (Kublik, et al 2016;Türkowsky et al 2018).…”

Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM

“…Additionally there was strong evidence for expression of the formate-dehydrogenase like (“Fdh”-like) oxidoreductase (NSAF = 4.62 × 10 −3 for the alpha subunit). Although the exact function of “Fdh” in DMC remains unknown, this oxidoreductase is proposed to be involved in enzyme complexes critical to DMC’s electron transport chain [ 29 , 37 ]. With respect to the high expression levels of respiratory enzymes in DMC these protein abundance findings agreed with previously published omics datasets [ 28 , 47 ].…”

“…Continuous TCE feed experiments were conducted as 100 mL subcultures of undiluted KB-1 TM culture with 60 mL of anaerobic headspace in 160 mL, anaerobic serum bottles as described previously [ 22 , 37 ]. Parameters for the experiments are presented in Table S1 .…”

“…Microarray analysis including preparation of cDNA, hybridization conditions, and data normalization were performed as previously published [ 37 , 40 ]. The data for this study is freely available at the NCBI Gene Expression Omnibus under the experimental series GSE42136 for the experiments GSM1033361-66.…”