Biotechnology, Biochemistry, Genetics and Molecular Biology, Plant Science, Agricultural and Biological Sciences
14
Scopus Publications
Scopus Publications
Deciphering the metabolic details of L-lysine toxicity in cyanobacteria Andreas M Enkerlin, Ute A Hoffmann, Johanna Rapp, Rui Miao, Johannes Postma, Michael Feldbrügge, Hannes Link, Elton P Hudson, Khaled A Selim Plant Physiology, 2026 L-lysine (Lys) has been explored as a potential cyanobactericide due to its inhibitory effects on cyanobacterial growth at micromolar concentrations, comparable to many antibiotics. Here, we investigated the early metabolic and physiological responses of the model cyanobacterium Synechocystis sp. PCC 6803 to Lys exposure. Physiological analyses revealed cell enlargement, oxidative stress, and photosynthesis inhibition, leading to growth arrest. Metabolomic profiling indicated disruptions in peptidoglycan biosynthesis, evidenced by the accumulation of L-/D-alanine, meso-diaminopimelate, and D-Ala-D-Ala, suggesting interference with cell wall integrity. Furthermore, levels of energy metabolites and other amino acids, including tyrosine, tryptophan, valine, and iso-/leucine, were significantly altered, implying broader metabolic impacts of Lys toxicity. To explore potential resistance mechanisms, we used a CRISPRi-based genetic screen to identify key genes involved in relieving Lys toxicity. The Bgt permease system, responsible for basic amino acid uptake, was essential for acquiring Lys resistance, as a bgtA mutant exhibited normal growth on elevated Lys concentrations, thereby validating our CRISPRi screen. Additionally, UirR, a DNA-binding response regulator, and genes linked to c-di-AMP signaling seemed implicated in Lys metabolism. Deletion of the c-di-AMP synthase gene increased Lys sensitivity, supporting a role for c-di-AMP in cell wall homeostasis and osmotic stress regulation. Altogether, our findings explored the early metabolic responses and physiological consequences of Lys exposure in Synechocystis, demonstrating its effects on peptidoglycan biosynthesis, amino acid metabolism, and nucleotide biosynthesis. This, as well as the identification of key genetic factors contributing to Lys resistance, provides insights into cyanobacterial physiology and the potential application of Lys in bloom-control strategies.
Absence of alka(e)nes triggers profound remodeling of glycerolipid and carotenoid composition in cyanobacteria membrane Rui Miao, Bertrand Légeret, Stéphan Cuine, Adrien Burlacot, Peter Lindblad, Yonghua Li-Beisson, Fred Beisson, Gilles Peltier Plant Physiology, 2024 Alka(e)nes are produced by many living organisms and exhibit diverse physiological roles, reflecting a high functional versatility. Alka(e)nes serve as waterproof wax in plants, communicating pheromones for insects, and microbial signaling molecules in some bacteria. Although alka(e)nes have been found in cyanobacteria and algal chloroplasts, their importance for photosynthetic membranes has remained elusive. In this study, we investigated the consequences of the absence of alka(e)nes on membrane lipid composition and photosynthesis using the cyanobacterium Synechocystis PCC6803 as a model organism. By following the dynamics of membrane lipids and the photosynthetic performance in strains defected and altered in alka(e)ne biosynthesis, we show that drastic changes in the glycerolipid contents occur in the absence of alka(e)nes, including a decrease in the membrane carotenoid content, a decrease in some digalactosyldiacylglycerol (DGDG) species and a parallel increase in monogalactosyldiacylglycerol (MGDG) species. These changes are associated with a higher susceptibility of photosynthesis and growth to high light in alka(e)ne-deficient strains. All these phenotypes are reversed by expressing an algal photoenzyme producing alka(e)nes from fatty acids. Therefore, alkenes, despite their low abundance, are an essential component of the lipid composition of membranes. The profound remodeling of lipid composition that results from their absence suggests that they play an important role in one or more membrane properties in cyanobacteria. Moreover, the lipid compensatory mechanism observed is not sufficient to restore normal functioning of the photosynthetic membranes, particularly under high-light intensity. We conclude that alka(e)nes play a crucial role in maintaining the lipid homeostasis of thylakoid membranes, thereby contributing to the proper functioning of photosynthesis, particularly under elevated light intensities.
CRISPR interference screens reveal growth–robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions Rui Miao, Michael Jahn, Kiyan Shabestary, Gilles Peltier, Elton P Hudson Plant Cell, 2023 Barcoded mutant libraries are a powerful tool for elucidating gene function in microbes, particularly when screened in multiple growth conditions. Here, we screened a pooled CRISPR interference library of the model cyanobacterium Synechocystis sp. PCC 6803 in 11 bioreactor-controlled conditions, spanning multiple light regimes and carbon sources. This gene repression library contained 21,705 individual mutants with high redundancy over all open reading frames and noncoding RNAs. Comparison of the derived gene fitness scores revealed multiple instances of gene repression being beneficial in 1 condition while generally detrimental in others, particularly for genes within light harvesting and conversion, such as antennae components at high light and PSII subunits during photoheterotrophy. Suboptimal regulation of such genes likely represents a tradeoff of reduced growth speed for enhanced robustness to perturbation. The extensive data set assigns condition-specific importance to many previously unannotated genes and suggests additional functions for central metabolic enzymes. Phosphoribulokinase, glyceraldehyde-3-phosphate dehydrogenase, and the small protein CP12 were critical for mixotrophy and photoheterotrophy, which implicates the ternary complex as important for redirecting metabolic flux in these conditions in addition to inactivation of the Calvin cycle in the dark. To predict the potency of sgRNA sequences, we applied machine learning on sgRNA sequences and gene repression data, which showed the importance of C enrichment and T depletion proximal to the PAM site. Fitness data for all genes in all conditions are compiled in an interactive web application.
Cycling between growth and production phases increases cyanobacteria bioproduction of lactate Kiyan Shabestary, Hugo Pineda Hernández, Rui Miao, Emil Ljungqvist, Olivia Hallman, Emil Sporre, Filipe Branco dos Santos, Elton P. Hudson Metabolic Engineering, 2021 Decoupling growth from product synthesis is a promising strategy to increase carbon partitioning and maximize productivity in cell factories. However, reduction in both substrate uptake rate and metabolic activity in the production phase are an underlying problem for upscaling. Here, we used CRISPR interference to repress growth in lactate-producing Synechocystis sp. PCC 6803. Carbon partitioning to lactate in the production phase exceeded 90%, but CO2 uptake was severely reduced compared to uptake during the growth phase. We characterized strains during the onset of growth arrest using transcriptomics and proteomics. Multiple genes involved in ATP homeostasis were regulated once growth was inhibited, which suggests an alteration of energy charge that may lead to reduced substrate uptake. In order to overcome the reduced metabolic activity and take advantage of increased carbon partitioning, we tested a novel production strategy that involved alternating growth arrest and recovery by periodic addition of an inducer molecule to activate CRISPRi. Using this strategy, we maintained lactate biosynthesis in Synechocystis for 30 days in a constant light turbidostat cultivation. Cumulative lactate titers were also increased by 100% compared to a constant growth-arrest regime, and reached 1 g/L. Further, the cultivation produced lactate for 30 days, compared to 20 days for the non-growth arrest cultivation. Periodic growth arrest could be applicable for other products, and in cyanobacteria, could be linked to internal circadian rhythms that persist in constant light.
Engineering cyanobacteria for photosynthetic butanol production Xufeng Liu, Hao Xie, Stamatina Roussou, Rui Miao, Peter Lindblad Photosynthesis Biotechnological Applications with Microalgae, 2021 Cyanobacteria are photoautotrophic microorganisms that can be engineered to convert CO2 and water into fuels and chemicals via photosynthesis using solar energy in direct processes. Based on knowledge and progress in fermentative heterotrophic biobutanol production, cyanobacteria have been engineered to produce photosynthetic butanol from sunlight, water and CO2. This chapter discusses the present status of engineering cyanobacteria for photosynthetic isobutanol and 1-butanol production. Special focus is on recent advances in introducing enzymes and pathways, redirecting carbon toward the product, importance of five regions in the genetic constructs and optimization of the cultivation system. Also included are recent contributions addressing butanol tolerance, recovery of the produced photosynthetic butanol, life cycle assessment on environmental impacts, energy demand of photosynthetic butanol production and public acceptance of genetically engineered algae/cyanobacteria for biofuel production.
Current processes and future challenges of photoautotrophic production of acetyl-CoA-derived solar fuels and chemicals in cyanobacteria Rui Miao, Hao Xie, Xufeng Liu, Pia Lindberg, Peter Lindblad Current Opinion in Chemical Biology, 2020 The production of fuels and other valuable chemicals via biological routes has gained significant attention during last decades. Cyanobacteria are prokaryotes that convert solar energy to chemical compounds in vivo in direct processes. Intensive studies have been carried out with the aim of engineering cyanobacteria as microfactories for solar fuel and chemical production. Engineered strains of photosynthetic cyanobacteria can produce different compounds on a proof-of-concept level, but few products show titers comparable with those achieved in heterotrophic organisms. Efficient genetic engineering tools and metabolic modeling can accelerate the development of solar fuel and chemical production in cyanobacteria. This review addresses the most recent approaches to produce solar fuels and chemicals in engineered cyanobacteria with a focus on acetyl-CoA-dependent products.
Improved lipid production via fatty acid biosynthesis and free fatty acid recycling in engineered Synechocystis sp. PCC 6803 Kamonchanock Eungrasamee, Rui Miao, Aran Incharoensakdi, Peter Lindblad, Saowarath Jantaro Biotechnology for Biofuels, 2019 Cyanobacteria are potential sources for third generation biofuels. Their capacity for biofuel production has been widely improved using metabolically engineered strains. In this study, we employed metabolic engineering design with target genes involved in selected processes including the fatty acid synthesis (a cassette of accD, accA, accC and accB encoding acetyl-CoA carboxylase, ACC), phospholipid hydrolysis (lipA encoding lipase A), alkane synthesis (aar encoding acyl-ACP reductase, AAR), and recycling of free fatty acid (FFA) (aas encoding acyl–acyl carrier protein synthetase, AAS) in the unicellular cyanobacterium Synechocystis sp. PCC 6803. To enhance lipid production, engineered strains were successfully obtained including an aas-overexpressing strain (OXAas), an aas-overexpressing strain with aar knockout (OXAas/KOAar), and an accDACB-overexpressing strain with lipA knockout (OXAccDACB/KOLipA). All engineered strains grew slightly slower than wild-type (WT), as well as with reduced levels of intracellular pigment levels of chlorophyll a and carotenoids. A higher lipid content was noted in all the engineered strains compared to WT cells, especially in OXAas, with maximal content and production rate of 34.5% w/DCW and 41.4 mg/L/day, respectively, during growth phase at day 4. The OXAccDACB/KOLipA strain, with an impediment of phospholipid hydrolysis to FFA, also showed a similarly high content of total lipid of about 32.5% w/DCW but a lower production rate of 31.5 mg/L/day due to a reduced cell growth. The knockout interruptions generated, upon a downstream flow from intermediate fatty acyl-ACP, an induced unsaturated lipid production as observed in OXAas/KOAar and OXAccDACB/KOLipA strains with 5.4% and 3.1% w/DCW, respectively. Among the three metabolically engineered Synechocystis strains, the OXAas with enhanced free fatty acid recycling had the highest efficiency to increase lipid production.
Enhancement of photosynthetic isobutanol production in engineered cells of Synechocystis PCC 6803 Rui Miao, Hao Xie, Peter Lindblad Biotechnology for Biofuels, 2018 Cyanobacteria, oxygenic photoautotrophic prokaryotes, can be engineered to produce various valuable chemicals from solar energy and CO2 in direct processes. The concept of photosynthetic production of isobutanol, a promising chemical and drop-in biofuel, has so far been demonstrated for Synechocystis PCC 6803 and Synechococcus elongatus PCC 7942. In Synechocystis PCC 6803, a heterologous expression of α-ketoisovalerate decarboxylase (Kivd) from Lactococcus lactis resulted in an isobutanol and 3-methyl-1-butanol producing strain. Kivd was identified as a bottleneck in the metabolic pathway and its activity was further improved by reducing the size of its substrate-binding pocket with a single replacement of serine-286 to threonine (KivdS286T). However, isobutanol production still remained low. In the present study, we report on how cultivation conditions significantly affect the isobutanol production in Synechocystis PCC 6803. A HCl-titrated culture grown under medium light (50 μmol photons m−2 s−1) showed the highest isobutanol production with an in-flask titer of 194 mg l−1 after 10 days and 435 mg l−1 at day 40. This corresponds to a cumulative isobutanol production of 911 mg l−1, with a maximal production rate of 43.6 mg l−1 day−1 observed between days 4 and 6. Additional metabolic bottlenecks in the isobutanol biosynthesis pathway were further addressed. The expression level of KivdS286T was significantly affected when co-expressed with another gene downstream in a single operon and in a convergent oriented operon. Moreover, the expression of the ADH encoded by codon-optimized slr1192 and co-expression of IlvC and IlvD were identified as potential approaches to further enhance isobutanol production in Synechocystis PCC 6803. The present study demonstrates the importance of a suitable cultivation condition to enhance isobutanol production in Synechocystis PCC 6803. Chemostat should be used to further increase both the total titer as well as the rate of production. Furthermore, identified bottleneck, Kivd, should be expressed at the highest level to further enhance isobutanol production.
Engineering cyanobacteria for biofuel production Rui Miao, Adam Wegelius, Claudia Durall, Feiyan Liang, Namita Khanna, Peter Lindblad Modern Topics in the Phototrophic Prokaryotes Environmental and Applied Aspects, 2017
