Metabolic Engineering and Synthetic Biology of Cyanobacteria for Carbon Capture and Utilization

TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT

Since the introduction of the first transformer model with a unique self-attention mechanism, natural language processing (NLP) models have attained state-of-the-art (SOTA) performance on various tasks. As DNA is the blueprint of life, it can be viewed as an unusual language, with its characteristic lexicon and grammar. Therefore, NLP models may provide insights into the meaning of the sequential structure of DNA. In the current study, we employed and compared the performance of popular SOTA NLP models (i.e., XLNET, BERT, and a variant DNABERT trained on the human genome) to predict and analyze the promoters in freshwater cyanobacterium Synechocystis sp. PCC 6803 and the fastest growing cyanobacterium Synechococcus elongatus sp. UTEX 2973. These freshwater cyanobacteria are promising hosts for phototrophically producing value-added compounds from CO₂. Through a custom pipeline, promoters and non-promoters from Synechococcus elongatus sp. UTEX 2973 were used to train the model. The trained model achieved an AUROC score of 0.97 and F1 score of 0.92. During cross-validation with promoters from Synechocystis sp. PCC 6803, the model achieved an AUROC score of 0.96 and F1 score of 0.91. To increase accessibility, we developed an integrated platform (TSSNote-CyaPromBERT) to facilitate large dataset extraction, model training, and promoter prediction from public dRNA-seq datasets. Furthermore, various visualization tools have been incorporated to address the "black box" issue of deep learning and feature analysis. The learning transfer ability of large language models may help identify and analyze promoter regions for newly isolated strains with similar lineages.

A review of recent advances in engineering bacteria for enhanced CO2 capture and utilization

Carbon dioxide (CO₂) is emitted into the atmosphere due to some anthropogenic activities, such as the combustion of fossil fuels and industrial output. As a result, fears about catastrophic global warming and climate change have intensified. In the face of these challenges, conventional CO₂ capture technologies are typically ineffective, dangerous, and contribute to secondary pollution in the environment. Biological systems for CO₂ conversion, on the other hand, provide a potential path forward owing to its high application selectivity and adaptability. Moreover, many bacteria can use CO₂ as their only source of carbon and turn it into value-added products. The purpose of this review is to discuss recent significant breakthroughs in engineering bacteria to utilize CO₂ and other one-carbon compounds as substrate. In the same token, the paper also summarizes and presents aspects such as microbial CO₂ fixation pathways, engineered bacteria involved in CO₂ fixation, up-to-date genetic and metabolic engineering approaches for CO₂ fixation, and promising research directions for the production of value-added products from CO₂. This review's findings imply that using biological systems like modified bacteria to manage CO₂ has the added benefit of generating useful industrial byproducts like biofuels, pharmaceutical compounds, and bioplastics. The major downside, from an economic standpoint, thus far has been related to methods of cultivation. However, thanks to genetic engineering approaches, this can be addressed by large production yields. As a result, this review aids in the knowledge of various biological systems that can be used to construct a long-term CO₂ mitigation technology at an industrial scale, in this instance bacteria-based CO₂capture/utilization technology.

Green Chemistry, Biocatalysis, and the Chemical Industry of the Future

In the movement to decarbonize our economy and move away from fossil fuels we will need to harness the waste products of our activities, such as waste lignocellulose, methane, and carbon dioxide. Our wastes need to be integrated into a circular economy where used products are recycled into a manufacturing carbon cycle. Key to this will be the recycling of plastics at the resin and monomer levels. Biotechnology is well suited to a future chemical industry that must adapt to widely distributed and diverse biological chemical feedstocks. Our increasing mastery of biotechnology is allowing us to develop enzymes and organisms that can synthesize a widening selection of desirable bulk chemicals, including plastics, at commercially viable productivities. Integration of bioreactors with electrochemical systems will permit new production opportunities with enhanced productivities and the advantage of using a low-carbon electricity from renewable and sustainable sources.

Applications of synthetic light-driven microbial consortia for biochemicals production

Synthetic microbial consortia provide a versatile and efficient platform for biochemicals production through the labor division. Especially, microbial communities composed of phototrophs and heterotrophs offer a promising alternative, as they can directly convert carbon dioxide (CO₂) into chemicals. Within this system, photoautotrophic microbes can convert CO₂ into organic carbon for microbial growth and metabolites synthesis by the heterotrophic partners. In return, heterotrophs can provide additional CO₂ to support the growth of photoautotrophic microbes. However, the unmatched growing conditions, low stability and production efficiency of synthetic microbial consortia hinder their further applications. Thus, design and construction of mutualistic and stable synthetic light-driven microbial consortia are urgently needed. In this review, the progress of synthetic light-driven microbial consortia for chemicals production was comprehensively summarized. In addition, space-efficient synthetic light-driven microbial consortia in hydrogel system were reviewed. Perspectives on orderly distribution of light-driven microbial consortia associated with 3D printing technology in biomanufacturing were also addressed.

Yeast metabolic engineering for carbon dioxide fixation and its application

As numerous industrial bioprocesses rely on yeast fermentation, developing CO₂-fixing yeast strains can be an attractive option toward sustainable industrial processes and carbon neutrality. Recent studies have shown that the expression of ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) in yeasts, such as Saccharomyces cerevisiae and Kluyveromyces marxianus, enables mixotrophic CO₂ fixation and production of biofuels. Also, the expression of a synthetic Calvin-Benson-Bassham (CBB) cycle including RuBisCO in Pichia pastoris enables autotrophic growth on CO₂. This review highlights recent advances in metabolic engineering strategies to enable CO₂ fixation in yeasts. Also, we discuss the potentials of other natural and synthetic metabolic pathways independent of RuBisCO for developing CO₂-fixing yeast strains capable of producing value-added biochemicals.

Metabolic systems biology and multi-omics of cyanobacteria: Perspectives and future directions

Cyanobacteria are oxygenic photoautotrophs whose metabolism contains key biochemical pathways to fix atmospheric CO₂ and synthesize various metabolites. The development of bioengineering tools has enabled the manipulation of cyanobacterial chassis to produce various valuable bioproducts photosynthetically. However, effective utilization of cyanobacteria as photosynthetic cell factories needs a detailed understanding of their metabolism and its interaction with other cellular processes. Implementing systems and synthetic biology tools has generated a wealth of information on various metabolic pathways. However, to design effective engineering strategies for further improvement in growth, photosynthetic efficiency, and enhanced production of target biochemicals, in-depth knowledge of their carbon/nitrogen metabolism, pathway fluxe distribution, genetic regulation and integrative analyses are necessary. In this review, we discuss the recent advances in the development of genome-scale metabolic models (GSMMs), omics analyses (metabolomics, transcriptomics, proteomics, fluxomics), and integrative modeling approaches to showcase the current understanding of cyanobacterial metabolism.

Cyanobacteria as cell factories: the roles of host and pathway engineering and translational research

Cyanobacteria, a group of photoautotrophic prokaryotes, are attractive hosts for the sustainable production of chemicals from carbon dioxide and sunlight. However, the rates, yields, and titers have remained well below those needed for commercial deployment. We argue that the following areas will be central to the development of cyanobacterial cell factories: engineered and well-characterized host strains, model-guided pathway design, and advanced synthetic biology tools. Although several foundational studies report improved strain properties, translational research will be needed to develop engineered hosts and deploy them for metabolic engineering. Further, the recent developments in metabolic modeling and synthetic biology of cyanobacteria will enable nimble strategies for strain improvement with the complete cycle of design, build, test, and learn.

Biocontainment of Engineered Synechococcus elongatus PCC 7942 for Photosynthetic Production of α-Farnesene from CO2

Biocontainment systems have been developed to mitigate the concerns regarding biosafety and environmental risk because of the possible escape of genetically modified organisms into the environment following large-scale outdoor cultivation. Here, we present a biocontainment system entailing genetically modified Synechococcus elongatus PCC 7942, also engineered for α-farnesene production using a de-evolutionary strategy. In this approach, the gene cluster encoding the β-carboxysome and the associated carbon concentrating mechanism (CCM) were deleted in the α-farnesene-producing cyanobacteria, resulting in no cell growth and no α-farnesene production at ambient CO₂ concentrations (100% air bubbling). However, cell growth and α-farnesene production were detected in the CCM-deficient strains at high CO₂ concentrations (5% CO₂ [v/v], 10% CO₂ [v/v]), albeit at levels lower than those of the parental control. To overcome this limitation, the overexpression of carbonic anhydrase and bicarbonate transporter genes in the CCM-deficient strains restored cell growth and the production level of α-farnesene (5.0 ± 0.6 mg/L) to that of the parental control. The production of α-farnesene in the later strains strictly depended on CO₂ concentration in the photobioreactor and did not rely on a chemical induction process. Thus, next generation bio-solar cell factories could be promoted with the suggested biocontainment system.