Reprogramming Metabolic Networks and Manipulating Circadian Clocks for Biotechnological Applications

Wang, Bo; Young, Jamey D.; Xu, Yao

doi:10.1007/978-3-030-72158-9_14

Cited by 3 publications

(3 citation statements)

References 208 publications

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“…On the other hand, the cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis ) has long been a model organism for photosynthesis research and biotechnological applications ( Nixon et al, 1992 ; Pakrasi & Vermaas, 1992 ; Shen et al, 1993 ; Ikeuchi & Tabata, 2001 ; Jagannathan & Golbeck, 2009 ; Santos-Merino et al, 2019 ; Wang et al, 2021b ) partially due to the early discovery of its natural competence for genetic transformation ( Grigorieva & Shestakov, 1982 ). For example, Synechocystis has served as a model platform for the structural and functional characterization of photosynthetic mechanisms, especially of photosystem II ( Nixon et al, 1992 ; Pakrasi & Vermaas, 1992 ; Larom et al, 2010 ).…”

Section: Introductionmentioning

confidence: 99%

“…As a result of this genomic data, research productivity involving this strain dramatically accelerated. In particular, Synechocystis -derived strains were explored as microbial cell factories to produce a variety of fuels and chemicals ( Wang, et al, 2021b ), including precursors to (biodegradable) plastics, such as poly-3-hydroxybutyrate ( Wu et al, 2001 ; Agarwal et al, 2022 ), 3-hydroxybutyrate ( Wang et al, 2018b ), 3-hydroxypropionate ( Wang Y. et al, 2016 ), lactate ( Varman et al, 2013 ; Angermayr et al, 2014 ), and ethylene ( Ungerer et al, 2012 ; Zhu et al, 2015 ; Wang et al, 2021a ).…”

Section: Introductionmentioning

confidence: 99%

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Synechocystis: A model system for expanding the study of cyanobacterial circadian rhythms

Zhao

Wang

et al. 2023

Front. Physiol.

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The study of circadian rhythms in bacteria was transformed by studies of the cyanobacterium Synechococcus elongatus. However, in a number of respects S. elongatus is atypical, and while those unusual characteristics were helpful for rapid progress in the past, another commonly used cyanobacterial species, Synechocystis sp. PCC 6803, may be more representative and therefore more productive for future insights into bacterial clock mechanisms. In the past, circadian studies of Synechocystis have suffered from not having an excellent reporter of circadian gene expression, but we introduce here a new luminescence reporter that rivals the reporters that have been used so successfully in S. elongatus. Using this new system, we generate for the first time in Synechocystis circadian period mutants resulting from point mutations. The temperature compensation and dark-pulse resetting that mediates entrainment to the environment is characterized. Moreover, we analyse the complex organization of clock genes in Synechocystis and identify which genes are essential for circadian rhythmicity and adaptive fitness for entrainment and optimal phase alignment to environmental cycles (and which genes are not). These developments will provide impetus for new approaches towards understanding daily timekeeping mechanisms in bacteria.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Synechocystis: A model system for expanding the study of cyanobacterial circadian rhythms

Zhao

Wang

et al. 2023

Front. Physiol.

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“…The cold‐adapted strain CRUB 1823 was isolated from the axial side of the leaves, marking not only the discovery of a yeast‐like fungus with a functional circadian oscillator, but the first experimental evidence of a circadian clock operating at temperatures as low as 10–20°C (Franco et al, 2017). Given the growing interest in circadian control systems in organisms with high plasticity (Wang et al, 2021), our laboratory identified homologous clock genes in the reference strain of A. pullulans . However, CRUB 1823 still requires comprehensive genomic characterization and annotation to promote a full understanding of the system.…”

Section: Introductionmentioning

confidence: 99%

Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation

Parra

Libkind

Hittinger

et al. 2023

Yeast

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Aureobasidium pullulans is a yeast‐like fungus with remarkable phenotypic plasticity widely studied for its importance for the pharmaceutical and food industries. So far, genomic studies with strains from all over the world suggest they constitute a genetically unstructured population, with no association by habitat. However, the mechanisms by which this genome supports so many phenotypic permutations are still poorly understood. Recent works have shown the importance of sequencing yeast genomes from extreme environments to increase the repertoire of phenotypic diversity of unconventional yeasts. In this study, we present the genomic draft of A. pullulans strain from a Patagonian yeast diversity hotspot, re‐evaluate its taxonomic classification based on taxogenomic approaches, and annotate its genome with high‐depth transcriptomic data. Our analysis suggests this isolate could be considered a novel variant at an early stage of the speciation process. The discovery of divergent strains in a genomically homogeneous group, such as A. pullulans, can be valuable in understanding the evolution of the species. The identification and characterization of new variants will not only allow finding unique traits of biotechnological importance, but also optimize the choice of strains whose phenotypes will be characterized, providing new elements to explore questions about plasticity and adaptation.

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Clocking out and letting go to unleash green biotech applications in a photosynthetic host

Xu,

Jabbur,

Mori

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

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Cyanobacteria are photosynthetic bacteria whose gene expression patterns are globally regulated by their circadian (daily) clocks. Due to their ability to use sunlight as their energy source, they are also attractive hosts for “green” production of pharmaceuticals, renewable fuels, and chemicals. However, despite the application of traditional genetic tools such as the identification of strong promoters to enhance the expression of heterologous genes, cyanobacteria have lagged behind other microorganisms such as Escherichia coli and yeast as economically efficient cell factories. The previous approaches have ignored large-scale constraints within cyanobacterial metabolic networks on transcription, predominantly the pervasive control of gene expression by the circadian (daily) clock. Here, we show that reprogramming gene expression by releasing circadian repressor elements in the transcriptional regulatory pathways coupled with inactivation of the central oscillating mechanism enables a dramatic enhancement of expression in cyanobacteria of heterologous genes encoding both catalytically active enzymes and polypeptides of biomedical significance.

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Reprogramming Metabolic Networks and Manipulating Circadian Clocks for Biotechnological Applications

Cited by 3 publications

References 208 publications

Synechocystis: A model system for expanding the study of cyanobacterial circadian rhythms

Synechocystis: A model system for expanding the study of cyanobacterial circadian rhythms

Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation

Clocking out and letting go to unleash green biotech applications in a photosynthetic host

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