Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

Abstract

Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the microbial cell. In addition, leaching of Cu from pipelines results in elevated Cu concentration in the environment, which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to grow in toxic levels of Cu. However, reports on Cu toxicity towards SRB have primarily focused on the degree of toxicity and subsequent elimination. Here, Cu(II) stress-related effects on a model SRB, Desulfovibrio alaskensis G20, is reported. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5 µM and 15 µM). In the pairwise comparison of control vs. 5 µM Cu(II), 61.43% of genes were downregulated, and 38.57% were upregulated. In control vs. 15 µM Cu(II), 49.51% of genes were downregulated, and 50.5% were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in the expression of critical biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentrations. These results will help us better understand the Cu(II) stress-response mechanism and provide avenues for future research.

Comparative transcriptome and coexpression network analysis reveals key pathways and hub candidate genes associated with sunflower (Helianthus annuus L.) drought tolerance

“…This is in agreement with the findings obtained in studies on Auricularia fibrillifera [ 78 ]. Tripathi et al suggested that the translation process is energy-consuming, and the downregulation of translation under drought stress saves energy [ 79 ]. However, the response mechanism of genes in the ribosomal pathway under drought stress is still unclear, and further investigation is needed to elucidate the underlying mechanism involved.…”

Molecular regulation of conditioning film formation and quorum quenching in sulfate reducing bacteria

“…Several studies have demonstrated the toxic nature of Cu toward the SRB (Zampieri et al, 2022). Copper metal completely inhibits SRB mixed culture at a concentration ~ 4 mg/L (Hao et al, 1994), and ~50% reduction in total cell protein was reported at a concentration of 15 μM of Cu(II) for Oleidesulfovibrio alaskensis G20 (Tripathi et al, 2022). In the case of O. alaskensis G20 growth rate decreased from 0.17 to 0.10 h −1 when the concentration of Cu(II) was increased upto 15 μM.…”

“…Repressed energy conversion is a commonly observed phenomenon in SRB during Cu stress. A total of five genes (DVU3132, DVU3133, DVU2091, DVU2348, and DVU1081) in D. vulgaris Hildenborough (Chen et al, 2019) and lactate dehydrogenase (Dde_3239) in D. alaskensis G20 (Tripathi et al, 2022) involved in lactate oxidation were downregulated. Furthermore, the gene encoding for the 30 and 50s ribosomal protein was downregulated by ~90% in D. alaskensis G20.…”

“…vulgaris Hildenborough ( Chen et al, 2019 ) and lactate dehydrogenase (Dde_3239) in D . alaskensis G20 ( Tripathi et al, 2022 ) involved in lactate oxidation were downregulated. Furthermore, the gene encoding for the 30 and 50s ribosomal protein was downregulated by ~90% in D .…”

Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T

“…The study of the genome-wide transcriptional adjustments during silver stress may link genomic data to biological processes and molecular networks. This approach can potentially unveil crucial gene regulatory targets that play significant roles in promoting heavy metal tolerance [ 14 ].…”