Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Abstract

Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature's own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases have been identified, yet the regulation of only a few of these have been investigated in detail. A wealth of genetic and functional diversity of regulatory enzymes and promoter elements still remains unexplored and unexploited, both in published genome sequences and in yet-to-be-cultured bacteria. In this review we examine in detail the current state of research on monooxygenase gene regulation, and on the development of transcription-factor-based microbial biosensors for detection of alkanes and alkenes. A new framework for the systematic characterisation of the underlying genetic components and for further development of biosensors is presented, and we identify focus areas that should be targeted to enable progression of more biosensor candidates to commercialisation and deployment in industry and in the environment.

Keywords: alkane; alkene; bacteria; biosensor; hydrocarbon; monooxygenase; regulation; transcription factor.

FIGURE 1

Gene regulation via repressor protein (A) or activator protein (B).

FIGURE 2

Representative monooxygenase gene clusters showing relative arrangements of metabolic genes (orange) and regulatory genes (black).

FIGURE 3

Alkene monooxygenase gene cluster configurations in Xanthobacter Py2, Rhodococcus B-276 and Nocardioides JS614. Colours indicate type of gene in monooxygenase to aid with comparison between clusters. Yellow = beta subunit; green = coupling protein; red = alpha subunit; blue = rubredoxin; white fill = all other genes. % identity also presented.

FIGURE 4

Organisation of seven representative monooxygenase gene clusters from M. chubuense NBB4. Orange arrows represent monooxygenase subunits, black arrows represent putative regulator genes, and light grey arrows show other genes in the region.

FIGURE 5

Status of development of octane (A), medium-chain alkane (B), and alkene biosensors (C), with priority research areas yielding maximum impacts indicated by the dark outlined arrows.