The role of systems biology in developing non-model cyanobacteria as hosts for chemical production

Mukherjee, Bratati; Madhu, Swati; Wangikar, Pramod P.

doi:10.1016/j.copbio.2019.10.003

Cited by 25 publications

(18 citation statements)

References 49 publications

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“…Generating robust and accurate genome-scale models (GSMs) is an iterative process dependent on the expansion and updating of draft simulation models with available experimental data obtained after measurement of fluxes and metabolic pool sizes [80,86,87]. However, GSMs are largely based on gene function predicted "by sequence analogy" with genes characterized in other model organisms, which may behave differently in the studied organism [88].…”

Section: Danger Of Genome Annotation Based Only On Sequence Comparisonmentioning

confidence: 99%

“…Unfortunately, Synechococcus UTEX2973, Synechococcus PCC 11801, and Synechococcus PCC 11802 are very closely related to the freshwater model Synechococcus PCC 7942, in sharing, respectively, 99.8% and about 83% of genome identity with it [149][150][151]157]. Similarly, Synechococcus PCC 11901 shares 96.7% sequence identity with the marine model Synechococcus PCC 7002 [87,152]. Thus, future studies carried out with these new model strains will not significantly increase our understanding of the cyanobacterial biodiversity.…”

Section: A Few Cyanobacteria Are Currently Amenable To Gene Manipulatmentioning

confidence: 99%

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Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications

Cassier‐Chauvat

Blanc-Garin

Chauvat

2021

Genes

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Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive “omics” data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.

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Section: Danger Of Genome Annotation Based Only On Sequence Comparisonmentioning

confidence: 99%

Section: A Few Cyanobacteria Are Currently Amenable To Gene Manipulatmentioning

confidence: 99%

Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications

Cassier‐Chauvat

Blanc-Garin

Chauvat

2021

Genes

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“…Fast‐growing (e.g. S. elongatus UTEX 2973) and ‘non‐model’ species are also promising candidates for industrial applications (Yu et al , ; Gale et al , ; Mukherjee et al , ). Suicide constructs for making targeted genomic modifications by double homologous recombination can be transferred into cyanobacteria by natural transformation, conjugation or electroporation.…”

Section: Modifying Cyanobacterial Genomes Is Simple But Slowmentioning

confidence: 99%

Progress and challenges in engineering cyanobacteria as chassis for light‐driven biotechnology

Hitchcock

Hunter

Canniffe

2019

Microbial Biotechnology

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Summary Cyanobacteria are prokaryotic phototrophs that, in addition to being excellent model organisms for studying photosynthesis, have tremendous potential for light‐driven synthetic biology and biotechnology. These versatile and resilient microorganisms harness the energy of sunlight to oxidise water, generating chemical energy (ATP) and reductant (NADPH) that can be used to drive sustainable synthesis of high‐value natural products in genetically modified strains. In this commentary article for the Synthetic Microbiology Caucus we discuss the great progress that has been made in engineering cyanobacterial hosts as microbial cell factories for solar‐powered biosynthesis. We focus on some of the main areas where the synthetic biology and metabolic engineering tools in cyanobacteria are not as advanced as those in more widely used heterotrophic chassis, and go on to highlight key improvements that we feel are required to unlock the full power of cyanobacteria for future green biotechnology.

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“…These photoautotrophs are being genetically engineered to develop carbon‐neutral‐green cell factories for the production of various platform chemicals, fuels, and sensors . Metabolic models and 13 C flux analysis studies have helped gain a deeper understanding of cyanobacterial metabolism . Understanding the physiological characteristics of these strains would help optimize their productivity.…”

Section: Introductionmentioning

confidence: 99%

A method to compute instantaneous oxygen evolution rates in cyanobacterial cultures grown in shake flasks

Sengupta

Wangikar

2020

Engineering Reports

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Cyanobacteria have been attracting attention for various biotechnological applications due to their ability to carry out oxygenic photosynthesis. The oxygen evolution rate (OER) of cyanobacterial cultures is a key physiological parameter, which is typically measured offline by using oxygen electrodes. In situ measurement of OER has been reported in a photobioreactor fitted with a dissolved oxygen (DO) probe. Here, we show that the OER can be estimated from online measurements of the DO levels by using sensors fitted in shake flasks, which are widely used for preliminary characterization of microbial strains. We study how the DO levels change under diurnal light regime and different growth conditions in two strains of Synechococcus elongatus, namely, PCC 7942 and PCC 11801, in shake flasks. We use the DO levels coupled with the knowledge of the overall gas-liquid mass transfer coefficient for oxygen (k L a) to compute the OER.For the growth conditions tested, the cumulative oxygen evolved in a day correlated with the increase in biomass suggesting that the calculated OER, in turn, might provide an estimate of the organism's growth rate. We believe that the method may be widely applicable for the growth characterization of organisms that perform oxygenic photosynthesis. K E Y W O R D Sabiotic factors, cyanobacteria, dissolved oxygen profile, oxygen evolution rates, PreSens technology, shake flaskThis is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

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The role of systems biology in developing non-model cyanobacteria as hosts for chemical production

Cited by 25 publications

References 49 publications

Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications

Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications

Progress and challenges in engineering cyanobacteria as chassis for light‐driven biotechnology

A method to compute instantaneous oxygen evolution rates in cyanobacterial cultures grown in shake flasks

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