Transcription-Factor-based Biosensor Engineering for Applications in Synthetic Biology

Ding, Nana; Zhou, Shenghu; Deng, Yu

doi:10.1021/acssynbio.0c00252

Cited by 74 publications

(70 citation statements)

References 92 publications

(202 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An increased understanding of regulatory components opens the door to protein and DNA engineering to optimise the specificity, sensitivity, dynamic range, detection range and response time of these systems for use as biosensors ( Ding et al, 2021 ). The flexibility of regulatory proteins in detecting multiple inducers can be seen as a double-edged sword ( Diplock et al, 2010 ); this may be useful in nature for a bacterium to respond to multiple possible carbon sources, but may not be ideal for biosensing of specific analytes.…”

Section: Development and Optimisation Of Hydrocarbon Biosensorsmentioning

confidence: 99%

“…The flexibility of regulatory proteins in detecting multiple inducers can be seen as a double-edged sword ( Diplock et al, 2010 ); this may be useful in nature for a bacterium to respond to multiple possible carbon sources, but may not be ideal for biosensing of specific analytes. Factors targeted for optimisation include host strain, promoter sequence, replication origin, ribosome binding site, protein-promoter binding sites, and the sequence of the regulatory protein; the latter may also involve addition of degradation tags to reduce the metabolic burden on the cell ( Ding et al, 2021 ).…”

Section: Development and Optimisation Of Hydrocarbon Biosensorsmentioning

confidence: 99%

“…Challenges at the proof-of-concept stage are often due to issues with robustness, shelf-life, and applicability to different real-world environments ( Hicks et al, 2020 ) e.g., how to safely immobilise the cells while maintaining their function. Investigation into the localisation of wild type regulatory proteins could also be valuable, as it can influence the response time of the biosensor ( Ding et al, 2021 ).…”

Section: Future Research Priorities and Conclusionmentioning

confidence: 99%

See 2 more Smart Citations

Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Moratti

Scott

Coleman

2022

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

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.

show abstract

Section: Development and Optimisation Of Hydrocarbon Biosensorsmentioning

confidence: 99%

Section: Development and Optimisation Of Hydrocarbon Biosensorsmentioning

confidence: 99%

Section: Future Research Priorities and Conclusionmentioning

confidence: 99%

See 1 more Smart Citation

Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Moratti

Scott

Coleman

2022

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

show abstract

“…Overall, TFs seem a particularly useful target for intelligent host engineering (e.g. [432][433][434], including in biosensors [435][436][437][438][439][440][441][442][443][444]).…”

Section: Transcription Factor Engineeringmentioning

confidence: 99%

Intelligent host engineering for metabolic flux optimisation in biotechnology

Munro

Kell

2021

Biochemical Journal

View full text Add to dashboard Cite

Optimising the function of a protein of length N amino acids by directed evolution involves navigating a ‘search space’ of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is ‘making such biology predictable’. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.

show abstract

“… 6 − 8 Compared with traditional high-end analytical techniques, bacterial biosensors are cost-effective, easy to integrate, portable, and easily applied for high-throughput testing. 9 , 10 The development of sensitive whole-cell sensors requires sophisticated sensing and signal transduction elements. Nevertheless, whole-cell sensors based on natural sensing systems have certain shortcomings, such as high leakage, low induced fold change, and poor sensitivity.…”

mentioning

confidence: 99%

De Novo Design of the ArsR Regulated P_ars Promoter Enables a Highly Sensitive Whole-Cell Biosensor for Arsenic Contamination

Chen

Zhang

et al. 2022

Anal. Chem.

View full text Add to dashboard Cite

Whole-cell biosensors for arsenic contamination are typically designed based on natural bacterial sensing systems, which are often limited by their poor performance for precisely tuning the genetic response to environmental stimuli. Promoter design remains one of the most important approaches to address such issues. Here, we use the arsenic-responsive ArsR-P ars regulation system from Escherichia coli MG1655 as the sensing element and coupled gfp or lacZ as the reporter gene to construct the genetic circuit for characterizing the refactored promoters. We first analyzed the ArsR binding site and a library of RNA polymerase binding sites to mine potential promoter sequences. A set of tightly regulated P ars promoters by ArsR was designed by placing the ArsR binding sites into the promoter’s core region, and a novel promoter with maximal repression efficiency and optimal fold change was obtained. The fluorescence sensor P lacV -P arsOC2 constructed with the optimized P arsOC2 promoter showed a fold change of up to 63.80-fold (with green fluorescence visible to the naked eye) at 9.38 ppb arsenic, and the limit of detection was as low as 0.24 ppb. Further, the optimized colorimetric sensor P lacV -P arsOC2 - lacZ with a linear response between 0 and 5 ppb was used to perform colorimetric reactions in 24-well plates combined with a smartphone application for the quantification of the arsenic level in groundwater. This study offers a new approach to improve the performance of bacterial sensing promoters and will facilitate the on-site application of arsenic whole-cell biosensors.

show abstract

Transcription-Factor-based Biosensor Engineering for Applications in Synthetic Biology

Cited by 74 publications

References 92 publications

Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Intelligent host engineering for metabolic flux optimisation in biotechnology

De Novo Design of the ArsR Regulated P_ars Promoter Enables a Highly Sensitive Whole-Cell Biosensor for Arsenic Contamination

Contact Info

Product

Resources

About

Transcription-Factor-based Biosensor Engineering for Applications in Synthetic Biology

Cited by 74 publications

References 92 publications

Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Intelligent host engineering for metabolic flux optimisation in biotechnology

De Novo Design of the ArsR Regulated Pars Promoter Enables a Highly Sensitive Whole-Cell Biosensor for Arsenic Contamination

Contact Info

Product

Resources

About

De Novo Design of the ArsR Regulated P_ars Promoter Enables a Highly Sensitive Whole-Cell Biosensor for Arsenic Contamination