• Journal of Microbiology and Biotechnology
• /
• 제33권10호
• /
• pp.1257-1267
• /
• 2023

Although rational genetic engineering is nowadays the favored method for microbial strain improvement, building up mutant libraries based on directed evolution for improvement is still in many cases the better option. In this regard, the demand for precise and efficient screening methods for mutants with high performance has stimulated the development of biosensor-based high-throughput screening strategies. Genetically encoded biosensors provide powerful tools to couple the desired phenotype to a detectable signal, such as fluorescence and growth rate. Herein, we review recent advances in engineering several classes of biosensors and their applications in directed evolution. Furthermore, we compare and discuss the screening advantages and limitations of two-component biosensors, transcription-factor-based biosensors, and RNA-based biosensors. Engineering these biosensors has focused mainly on modifying the expression level or structure of the biosensor components to optimize the dynamic range, specificity, and detection range. Finally, the applications of biosensors in the evolution of proteins, metabolic pathways, and genome-scale metabolic networks are described. This review provides potential guidance in the design of biosensors and their applications in improving the bioproduction of microbial cell factories through directed evolution.

• Journal of Microbiology and Biotechnology
• /
• 제33권4호
• /
• pp.552-558
• /
• 2023

Levulinic acid (LA) is a valuable chemical used in fuel additives, fragrances, and polymers. In this study, we proposed possible biosynthetic pathways for LA production from lignin and poly(ethylene terephthalate). We also created a genetically encoded biosensor responsive to LA, which can be used for screening and evolving the LA biosynthesis pathway genes, by employing an LvaR transcriptional regulator of Pseudomonas putida KT2440 to express a fluorescent reporter gene. The LvaR regulator senses LA as a cognate ligand. The LA biosensor was first examined in an Escherichia coli strain and was found to be non-functional. When the host of the LA biosensor was switched from E. coli to P. putida KT2440, the LA biosensor showed a linear correlation between fluorescence intensity and LA concentration in the range of 0.156-10 mM LA. In addition, we determined that 0.156 mM LA was the limit of LA detection in P. putida KT2440 harboring an LA-responsive biosensor. The maximal fluorescence increase was 12.3-fold in the presence of 10 mM LA compared to that in the absence of LA. The individual cell responses to LA concentrations reflected the population-averaged responses, which enabled high-throughput screening of enzymes and metabolic pathways involved in LA biosynthesis and sustainable production of LA in engineered microbes.

• Molecules and Cells
• /
• 제39권1호
• /
• pp.46-52
• /
• 2016

It is increasingly apparent that nature evolved peroxiredoxins not only as $H_2O_2$ scavengers but also as highly sensitive $H_2O_2$ sensors and signal transducers. Here we ask whether the $H_2O_2$ sensing role of Prx can be exploited to develop probes that allow to monitor intracellular $H_2O_2$ levels with unprecedented sensitivity. Indeed, simple gel shift assays visualizing the oxidation of endogenous 2-Cys peroxiredoxins have already been used to detect subtle changes in intracellular $H_2O_2$ concentration. The challenge however is to create a genetically encoded probe that offers real-time measurements of $H_2O_2$ levels in intact cells via the Prx oxidation state. We discuss potential design strategies for Prx-based probes based on either the redoxsensitive fluorophore roGFP or the conformation-sensitive fluorophore cpYFP. Furthermore, we outline the structural and chemical complexities which need to be addressed when using Prx as a sensing moiety for $H_2O_2$ probes. We suggest experimental strategies to investigate the influence of these complexities on probe behavior. In doing so, we hope to stimulate the development of Prx-based probes which may spearhead the further study of cellular $H_2O_2$ homeostasis and Prx signaling.

• Molecules and Cells
• /
• 제41권9호
• /
• pp.809-817
• /
• 2018

Discovery of the naturally evolved fluorescent proteins and their genetically engineered biosensors have enormously contributed to current bio-imaging techniques. These reporters to trace dynamic changes of intracellular protein activities have continuously transformed according to the various demands in biological studies. Along with that, light-inducible optogenetic technologies have offered scientists to perturb, control and analyze the function of intracellular machineries in spatiotemporal manner. In this review, we present an overview of the molecular strategies that have been exploited for producing genetically encoded protein reporters and various optogenetic modules. Finally, in particular, we discuss the current efforts for combined use of these reporters and optogenetic modules as a powerful tactic for the control and imaging of signaling events in cells and tissues.

• International Journal of Oral Biology
• /
• 제38권4호
• /
• pp.169-173
• /
• 2013

HyPer is the genetically encoded biosensor of intracellular hydrogen peroxide ($H_2O_2$), the most stable of the reactive oxygen species (ROS) generated by living cells. HyPer has a high sensitivity and specificity for detecting intracellular $H_2O_2$ by confocal laser microscopy. However, it was not known whether high speed ratiometric imaging of $H_2O_2$ by HyPer is possible. We thus investigated the sensitivity of HyPer in detecting changes to the intracellular $H_2O_2$ levels in HEK293 and PC12 cells using a microfluorometer imaging system. Increase in the HyPer ratio were clearly evident on stimulations of more than $100{\mu}M$ $H_2O_2$ and fast changes in the HyPer ratio were observed on ratiometric fluorescent images after $H_2O_2$ treatment. These results suggest that HyPer is a potent biosensor of the fast temporal production of intracellular $H_2O_2$.

• 생명과학회지
• /
• 제33권2호
• /
• pp.191-198
• /
• 2023

세포막의 국소 접착부 복합체에 있는 한 구성원으로써 Src은 비수용체 타이로신 인산화효소 중 하나로 세포부착과 세포 이동성을 조절한다. 그러나 extracellular matrix (ECM)의 구성에 따라 세포막 미세영역에서 어떻게 Src 활성이 조절되는지는 여전히 잘 알려져 있지 않다. 본 연구는 유전적으로 암호화된 FRET 기반 세포막 하위 도메인 표적 Src 바이오센서를 이용해서 3개의 각기 다른 대표적 ECM 단백질인 제1형 콜라겐, 피브로넥틴, 라미닌에 따른 Src의 활성도를 비교 및 조사하였다. FRET 기반 바이오센서는 살아있는 세포에서 단백질의 활성을 시공간적 고해상력을 토대로 실시간으로 분석할 수 있게 해준다. 결과적으로 모든 ECM 조건에서 지질유동섬(Lipid raft)에서 높은 Src 활성을 보였고 ECM 조건에 따라 큰 차이를 보이지 않았다. 반면에 비-지질유동섬(non-Lipid raft)에선 낮은 Src 활성을 보였다. 게다가 같은 ECM 조건일 때 지질유동섬에서 비-지질유동섬보다 높은 Src 활성을 보였다. 따라서 본 연구는 Src 활성이 지질유동섬과 비-지질유동섬에 따라 다르게 조절된다는 것을 보여주었다.

• 생명과학회지
• /
• 제32권2호
• /
• pp.148-154
• /
• 2022

국소접착인산화효소(FAK)는 국소접착부에서 세포부착, 세포이동, 세포역학적 신호전달 등에 관여한다고 알려져 있다. 그러나 세포 외 기질(ECM)과 상호작용하는 인테그린 막단백질과 함께 위치하는 세포막 미세영역(membrane microdomain)의 종류와 ECM 구성에 따른 FAK 활성은 여전히 불분명하다. 형광 공명 에너지 전달(FRET)을 기반으로 유전적으로 인코딩 된 바이오센서는 세포 내 FAK 신호를 높은 시공간 해상도로 제공할 수 있다. 본 연구에서는 유리, 제1형 콜라겐, 피브로넥틴, 라미닌의 ECM 조건에서 FRET 기반 막 표적 FAK 바이오센서를 사용하여 지질유동섬(Lipid raft) 및 비-지질유동섬(non-Lipid raft)에서 FAK의 활성을 분석하고 시각화 하였다. 흥미롭게도, 지질유동섬에서 라미닌 조건 하의 FAK 활성은 다른 ECM 조건보다 낮았고, 비-지질유동섬에서 FAK 활성은 다른 ECM 조건보다 낮았다. 동일한 ECM 조건 상의 비교에서는 피브로넥틴 조건일 때 지질유동섬에서 비-지질유동섬 보다 높은 FAK 활성이 관측되었다. 따라서 이번 연구는 FAK 활성도가 ECM 유형 및 세포막 미세영역에 따라 특이적으로 조절되는 것을 시각적, 정량적으로 보여준다.