Clearing up of toxic pollutants using a bacterial protein

A science communication commentary on a recently published paper

Most pollutants are introduced in our environment in the form of herbicides, pesticides, and industrial effluents. The aromatic phenolic compounds, produced by a variety of industries, including phenol-formaldehyde resin, petrochemical plants, coal conversion, and leather processing make up for a major percentage of these pollutants. Improper treatment of these toxic pollutants can lead to heavily contaminated soil and groundwater.

Microorganisms particularly the bacterial species termed as Pseudomonas sp. have been used for a long time to clean up phenol from water in treatment plants. One such (methyl) phenol-degrading strain Pseudomonas putida KCTC 1452 has been studied with respect to its metabolic pathways involved in biodegradation.  The bacterium uses a protein called as DmpR, an acronym for di-methyl phenol regulator, for phenol degradation. While DmpR protein has been used in biosensors for detection of  pollutants in environment, the exact mechanism of DmpR activation has puzzled researchers for many years.

A recent study made a breakthrough by solving the molecular structure of the protein, DmpR when bound to phenol. The challenge was overcome by an international team of researchers from three different countries. Scientists from the Korea Research Institute of Bioscience and Biotechnology (KRIBB), South Korea worked together with scientists from the Kavli Institute of Nanoscience Delft, Netherlands and the Department of Molecular Biology, Umea University, Sweden to understand the mechanism of DmpR by solving its phenol-bound crystal structure. This study published in Nature Communications, provides valuable insights into the oligomerization and the signal transduction mechanism of DmpR, which eventually results in degradation of phenolic pollutants.

The team led by Dr. Eui Jeon Woo at the Disease Target Structure Research Center, KRIBB and  Dr. Chirlmin Joo at the Department of Bionanoscience, at the Kavli Institute pioneered the DmpR structural studies advancing the DmpR biosensor technology field. Their discovery of the tetrameric oligomerization state, in contrast to previously thought hexameric state, of the protein helped in understanding its binding to signal transduction factors. The researchers also discovered that protein itself does not utilize energy from hydrolysis of ATP, the cellular currency, to attain oligomeric state but rather directs the energy towards signal transduction and transcriptional activation of proteins involved in the (methyl)phenol-degradative system. With a better understanding of this protein structure and function, highly sensitive whole-cell biosensors can be engineered which can sense and degrade these toxic pollutants. Such sensors can help to prevent accumulation of toxic chemicals that could otherwise cause serious ecological damage as well as contaminate food supplies.  Similarly, DmpR related proteins could also be developed as biosensors that can be used to test different pollutant levels present in the water bodies for protection of the aquatic flora and fauna, thus helping towards preserving ecological niches.

Citation: Park, K., Kim, S., Lee, S. et al. Tetrameric architecture of an active phenol-bound form of the AAA+ transcriptional regulator DmpR. Nat Commun 11, 2728 (2020).

Arti Dumbrepatil is a science writer. She did her postdoctoral work at the University of Michigan, Ann Arbor, MI, USA. During her tenure at the University of Michigan, she has worked as a Science Communication Fellow (at the Natural History Museum, UMICH) and as a Science Communication Writer (LSA, UMICH). Arti continues to write as a contributing science writer to American Society for Biochemistry and Molecular Biology (ASBMB),Microbiome Digest,Bio Voice News.

Twitter @rtisciwrites

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