Metabolic engineering strategies have been developed in systems level for the development of metabolically engineered microorganisms as host strains in biorefinery processes to produce bio-based fuels [31–35], chemicals [36–41] and polymers [42–47] from renewable resources. Also, engineered strains that have high levels of growth and tolerance in the presence of high concentrations of sugars and inhibitors are extensively being developed to utilize biomass-derived renewable resources [48–53]. Therefore, it is important to develop a high-throughput screening method to identify the high-producing strains. High-producing strains can be screened using a riboselector, which is composed of a riboswitch that can detect the target compound and a selection module such as tetA, which will enable favorable growth of a lysine-accumulating cell in the presence of selection pressure (NiCl2) . Likewise, chimeric TCRS can be potentially used in screening for high-producing strains (Fig. 3). DcuSZ is an EnvZ/OmpR-based chimeric TCRS that was constructed by fusing the DcuS HK sensory domain with the cytoplasmic domain of EnvZ. The chimeric DcuSZ is highly specific to fumarate in such a way that the expression of the gfp gene under the control of the ompR-regulated ompC promoter is proportional to different fumarate concentrations in the medium . Other chimeric TCRSs based on EnvZ/OmpR were constructed by fusing the HK sensory domain of MalK and AauS to the EnvZ catalytic domain to detect high malate- and aspartate-producing strains, respectively [56, 57].Fig. 3Application of TCRSs in bioremediation and microbial biorefinery. TCRSs serve as a regulatory system for the expression of genes encoding enzymes for the degradation of the detected target pollutant compound or for genes encoding enzymes for the production of the target chemical product