Engineered bacteria to report gut function: technologies and implementation

Tanna, Tanmay; Ramachanderan, Raghavendra; Platt, Randall J.

doi:10.1016/j.mib.2020.07.014

Cited by 29 publications

(23 citation statements)

References 62 publications

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“…Some strains colonize the gut without disrupting the microbiome, and others could generate serious side effects. 177 We expect that future advances in synthetic biology greatly expand the use of stimuliresponsive ELMs that could be effective in the detection and quantification of complex, highly specific molecules for healthcare applications.…”

Section: Biosensing Technologies For Molecule Detection and Diagnosticsmentioning

confidence: 99%

Stimuli-responsive engineered living materials

2021

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Section: Biosensing Technologies For Molecule Detection and Diagnosticsmentioning

confidence: 99%

Stimuli-responsive engineered living materials

2021

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“… 2017 ), thanks to the ability of systems of this type to store highly transcribed regions potentially containing the information of interest. Moreover, these systems could be used as highly scalable bacterial biosensors to report on gut function (Tanna, Ramachanderan and Platt 2021 ). In addition, the characterization of singular RTs linked to CRISPR-Cas systems could provide useful tools, such as groups of RTs fused to a putative primase (AEP) domain that might not require priming for cDNA reactions.…”

Section: Introductionmentioning

confidence: 99%

Prokaryotic reverse transcriptases: from retroelements to specialized defense systems

González-Delgado

Mestre

Martı́nez-Abarca

et al. 2021

FEMS Microbiology Reviews

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Reverse transcriptases (RTs) catalyze the polymerization of DNA from an RNA template. These enzymes were first discovered in RNA tumor viruses in 1970, but it was not until 1989 that they were found in prokaryotes as a key component of retrons. Apart from RTs encoded by the “selfish” mobile retroelements known as group II introns, prokaryotic RTs are extraordinarily diverse, but their function has remained elusive. However, recent studies have revealed that different lineages of prokaryotic RTs, including retrons, those associated with CRISPR-Cas systems, Abi-like RTs, and other yet uncharacterized RTs, are key components of different lines of defense against phages and other mobile genetic elements. Prokaryotic RTs participate in various antiviral strategies, including abortive infection (Abi), in which the infected cell is induced to commit suicide to protect the host population, adaptive immunity, in which a memory of previous infection is used to build an efficient defense, and other as yet unidentified mechanisms. These prokaryotic enzymes are attracting considerable attention, both for use in cutting-edge technologies, such as genome editing, and as an emerging research topic. In this review, we discuss what is known about prokaryotic RTs, and the exciting evidence for their domestication from retroelements to create specialized defense systems.

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“… What are the design principles of sensor HKs? How sensor HKs may be efficiently employed in the generation of new molecular biology tools, including artificial sensors [ 16 , 17 , 18 ] and reporters [ 15 , 22 ]? …”

Section: Discussionmentioning

confidence: 99%

“…Since many of them are important for bacterial survival and pathogenicity, TCS constitute promising targets for antimicrobial treatments [ 12 , 13 , 14 ]. TCS receptors are also often used in synthetic biology, in engineered proteins and cellular networks [ 15 , 16 , 17 , 18 , 19 ], as well as whole cell biosensors [ 20 , 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity

Gushchin

Aleksenko

Orekhov

et al. 2021

IJMS

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Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.

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Engineered bacteria to report gut function: technologies and implementation

Cited by 29 publications

References 62 publications

Stimuli-responsive engineered living materials

Stimuli-responsive engineered living materials

Prokaryotic reverse transcriptases: from retroelements to specialized defense systems

Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity

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