Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications.
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SUBMITTER: Cassier-Chauvat C
PROVIDER: S-EPMC8066212 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Cyanobacteria are widely-diverse prokaryotes that colonize our planet. They use solar energy to assimilate huge amounts of atmospheric CO2 and produce a large part of the biomass and oxygen that sustain most life forms. Cyanobacteria are therefore increasingly studied for basic research objectives, as well as for the photosynthetic production of chemicals with industrial interests. One potential approach to reduce the cost of future bioproduction processes is to couple them with wastewater treatment, often polluted with urea, which in any case is cheaper than nitrate. As of yet, however, research has mostly focused on a very small number of model cyanobacteria growing on nitrate. Thus, the genetic inventory of the cyanobacterial phylum is still insufficiently employed to meaningfully select the right host for the right purpose. This review reports what is known about urea transport and catabolism in cyanobacteria, and what can be inferred from the comparative analysis of the publicly available genome sequence of the 308 cyanobacteria. We found that most cyanobacteria mostly harbor the genes encoding the urea catabolytic enzymes urease (ureABCDEFG), but not systematically, together with the urea transport (urtABCDE). These findings are consistent with the capacity of the few tested cyanobacteria that grow on urea as the sole nitrogen source. They also indicate that urease is important for the detoxification of internally generated urea (re-cycling its carbon and nitrogen). In contrast, several cyanobacteria have urtABCDE but not ureABCDEFG, suggesting that urtABCDE could operate in the transport of not only urea but also of other nutrients. Only four cyanobacteria appeared to have the genes encoding the urea carboxylase (uc) and allophanate hydrolase (ah) enzymes that sequentially catabolize urea. Three of these cyanobacteria belongs to the genera Gloeobacter and Gloeomargarita that have likely diverged early from other cyanobacteria, suggesting that the urea carboxylase and allophanate hydrolase enzymes appeared in cyanobacteria before urease.
| S-EPMC6737895 | biostudies-literature
Project description:Cyanobacteria are fascinating photosynthetic prokaryotes that are regarded as the ancestors of the plant chloroplast; the purveyors of oxygen and biomass for the food chain; and promising cell factories for an environmentally friendly production of chemicals. In colonizing most waters and soils of our planet, cyanobacteria are inevitably challenged by environmental stresses that generate DNA damages. Furthermore, many strains engineered for biotechnological purposes can use DNA recombination to stop synthesizing the biotechnological product. Hence, it is important to study DNA recombination and repair in cyanobacteria for both basic and applied research. This review reports what is known in a few widely studied model cyanobacteria and what can be inferred by mining the sequenced genomes of morphologically and physiologically diverse strains. We show that cyanobacteria possess many E. coli-like DNA recombination and repair genes, and possibly other genes not yet identified. E. coli-homolog genes are unevenly distributed in cyanobacteria, in agreement with their wide genome diversity. Many genes are extremely well conserved in cyanobacteria (mutMS, radA, recA, recFO, recG, recN, ruvABC, ssb, and uvrABCD), even in small genomes, suggesting that they encode the core DNA repair process. In addition to these core genes, the marine Prochlorococcus and Synechococcus strains harbor recBCD (DNA recombination), umuCD (mutational DNA replication), as well as the key SOS genes lexA (regulation of the SOS system) and sulA (postponing of cell division until completion of DNA reparation). Hence, these strains could possess an E. coli-type SOS system. In contrast, several cyanobacteria endowed with larger genomes lack typical SOS genes. For examples, the two studied Gloeobacter strains lack alkB, lexA, and sulA; and Synechococcus PCC7942 has neither lexA nor recCD. Furthermore, the Synechocystis PCC6803 lexA product does not regulate DNA repair genes. Collectively, these findings indicate that not all cyanobacteria have an E. coli-type SOS system. Also interestingly, several cyanobacteria possess multiple copies of E. coli-like DNA repair genes, such as Acaryochloris marina MBIC11017 (2 alkB, 3 ogt, 7 recA, 3 recD, 2 ssb, 3 umuC, 4 umuD, and 8 xerC), Cyanothece ATCC51142 (2 lexA and 4 ruvC), and Nostoc PCC7120 (2 ssb and 3 xerC).
| S-EPMC5101192 | biostudies-literature
Project description:Thermophilic cyanobacteria are prokaryotic photoautotrophic microorganisms capable of growth between 45 and 73 °C. They are typically found in hot springs where they serve as essential primary producers. Several key features make these robust photosynthetic microbes biotechnologically relevant. These are highly stable proteins and their complexes, the ability to actively transport and concentrate inorganic carbon and other nutrients, to serve as gene donors, microbial cell factories, and sources of bioactive metabolites. A thorough investigation of the recent progress in thermophilic cyanobacteria reveals a significant increase in the number of newly isolated and delineated organisms and wide application of thermophilic light-harvesting components in biohybrid devices. Yet despite these achievements, there are still deficiencies at the high-end of the biotechnological learning curve, notably in genetic engineering and gene editing. Thermostable proteins could be more widely employed, and an extensive pool of newly available genetic data could be better utilised. In this manuscript, we attempt to showcase the most important recent advances in thermophilic cyanobacterial biotechnology and provide an overview of the future direction of the field and challenges that need to be overcome before thermophilic cyanobacterial biotechnology can bridge the gap with highly advanced biotechnology of their mesophilic counterparts. KEY POINTS: • Increased interest in all aspects of thermophilic cyanobacteria in recent years • Light harvesting components remain the most biotechnologically relevant • Lack of reliable molecular biology tools hinders further development of the chassis.
| S-EPMC10957709 | biostudies-literature
Project description:Current industrial bioethanol production by yeast through fermentation generates carbon dioxide. Carbon neutral bioethanol production by cyanobacteria uses biological fixation (photosynthesis) of carbon dioxide or other waste inorganic carbon sources, whilst being sustainable and renewable. The first ethanologenic cyanobacterial process was developed over two decades ago using Synechococcus elongatus PCC 7942, by incorporating the recombinant pdc and adh genes from Zymomonas mobilis. Further engineering has increased bioethanol titres 24-fold, yet current levels are far below what is required for industrial application. At the heart of the problem is that the rate of carbon fixation cannot be drastically accelerated and carbon partitioning towards bioethanol production impacts on cell fitness. Key progress has been achieved by increasing the precursor pyruvate levels intracellularly, upregulating synthetic genes and knocking out pathways competing for pyruvate. Studies have shown that cyanobacteria accumulate high proportions of carbon reserves that are mobilised under specific environmental stresses or through pathway engineering to increase ethanol production. When used in conjunction with specific genetic knockouts, they supply significantly more carbon for ethanol production. This review will discuss the progress in generating ethanologenic cyanobacteria through chassis engineering, and exploring the impact of environmental stresses on increasing carbon flux towards ethanol production.
| S-EPMC8684110 | biostudies-literature
Project description:Antioxidant compounds from cyanobacteria may constitute a natural alternative to current synthetic antioxidants, which contain preservatives and suspected toxicity. In this work, we evaluate the antioxidant potential of cyanobacterial strains of distinct species/genus isolated from freshwater (n = 6), soil (n = 1) and wastewater (n = 1) environments. Lyophilized biomass obtained from in-vitro cultures of those strains was extracted with ethanol and methanol. The antioxidant potential was evaluated by chemical (DPPH scavenging method, β-carotene bleaching assay, determination of total phenolic and total flavonoid compounds) and biological (H2O2-exposed HEK293T cell line model) approach. Some strains showed high yields of antioxidant activity by the DPPH assay (up to 10.7% IP/20.7 TE μg/mL) and by the β-carotene bleaching assay (up to 828.94 AAC), as well as significant content in phenolic (123.16 mg EAG/g DW) and flavonoid (900.60 mg EQR/g DW) compounds. Normalization of data in a "per cell" or "per cell volume" base might facilitate the comparison between strains. Additionally, most of the cyanobacterial extracts conferred some degree of protection to HEK293T cells against the H2O2-induced cytotoxicity. Freshwater Aphanizomenon gracile (LMECYA 009) and Aphanizomenon flos-aquae (LMECYA 088), terrestrial Nostoc (LMECYA 291) and wastewater Planktothrix mougeotii (LEGE 06224) seem to be promising strains for further investigation on cyanobacteria antioxidant potential.
| S-EPMC7551995 | biostudies-literature
Project description:In this study, five cyanobacteria strains (Alkalinema aff. pantanalense LEGE15481, Cyanobium gracile LEGE12431, Nodosilinea (Leptolyngbya) antarctica LEGE13457, Cuspidothrix issatschenkoi LEGE03282 and Leptolyngbya-like sp. LEGE13412) from the Blue Biotechnology and Ecotoxicology Culture Collection (LEGE CC) of CIIMAR were explored for their biotechnological potential in the treatment of psoriasis. Different extracts were characterized for their pigment profile by HPLC-PDA. The antioxidant potential of the extracts was assessed against the superoxide anion radical (O2•-). Their anti-inflammatory and antiproliferative potential was assessed in vitro using the macrophages RAW 264.7 and the human keratinocytes HaCaT as cell-line models, respectively. Terrestrial and freshwater strains presented the highest carotenoid content (33193-63926 μg/g dry extract), with all-trans-β-carotene, zeaxanthin, echinenone and lutein derivatives being the most abundant carotenoids. Acetone was the most effective solvent for pigment extraction. The acetone extracts presented the lowest IC50 values (0.29-0.38 mg dry extract/mL) regarding O2•- scavenging, and revealed anti-inflammatory potential, with N. antarctica LEGE13457, A. pantanalense LEGE15481 and Leptolyngbya-like sp. LEGE13412 reducing the nitric oxide (NO) in RAW 264.7 cell culture medium in about 25% (p < 0.05). With the exception of A. pantanalense LEGE15481, all the extracts significantly reduced keratinocyte proliferation (p < 0.05), demonstrating a selective toxicity among the different cell lines. Overall, Leptolyngbya-like sp. LEGE13412 and N. antarctica LEGE13457 seem promising for further exploitation in the framework of psoriasis, due to their antioxidant, anti-inflammatory and antiproliferative potential.
| S-EPMC7074968 | biostudies-literature
Project description:Biosynthesis of NAD(P) cofactors is of special importance for cyanobacteria due to their role in photosynthesis and respiration. Despite significant progress in understanding NAD(P) biosynthetic machinery in some model organisms, relatively little is known about its implementation in cyanobacteria. We addressed this problem by a combination of comparative genome analysis with verification experiments in the model system of Synechocystis sp. strain PCC 6803. A detailed reconstruction of the NAD(P) metabolic subsystem using the SEED genomic platform (http://theseed.uchicago.edu/FIG/index.cgi) helped us accurately annotate respective genes in the entire set of 13 cyanobacterial species with completely sequenced genomes available at the time. Comparative analysis of operational variants implemented in this divergent group allowed us to elucidate both conserved (de novo and universal pathways) and variable (recycling and salvage pathways) aspects of this subsystem. Focused genetic and biochemical experiments confirmed several conjectures about the key aspects of this subsystem. (i) The product of the slr1691 gene, a homolog of Escherichia coli gene nadE containing an additional nitrilase-like N-terminal domain, is a NAD synthetase capable of utilizing glutamine as an amide donor in vitro. (ii) The product of the sll1916 gene, a homolog of E. coli gene nadD, is a nicotinic acid mononucleotide-preferring adenylyltransferase. This gene is essential for survival and cannot be compensated for by an alternative nicotinamide mononucleotide (NMN)-preferring adenylyltransferase (slr0787 gene). (iii) The product of the slr0788 gene is a nicotinamide-preferring phosphoribosyltransferase involved in the first step of the two-step non-deamidating utilization of nicotinamide (NMN shunt). (iv) The physiological role of this pathway encoded by a conserved gene cluster, slr0787-slr0788, is likely in the recycling of endogenously generated nicotinamide, as supported by the inability of this organism to utilize exogenously provided niacin. Positional clustering and the co-occurrence profile of the respective genes across a diverse collection of cellular organisms provide evidence of horizontal transfer events in the evolutionary history of this pathway.
| S-EPMC1446974 | biostudies-literature
Project description:Pepper (Capsicum spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant. The genus includes over 30 species, five of which (C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens) are domesticated and mainly grown for consumption as food and for non-food purposes (e.g., cosmetics). The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security, the growing consumers' demand for food. Furthermore, demographic trends and changes to climate require more efficient use of plant genetic resources in breeding programs. Increases in pepper consumption have been observed in the past 20 years, and for maintaining this trend, the development of new resistant and high yielding varieties is demanded. The range of pathogens afflicting peppers is very broad and includes fungi, viruses, bacteria, and insects. In this context, the large number of accessions of domesticated and wild species stored in the world seed banks represents a valuable resource for breeding in order to transfer traits related to resistance mechanisms to various biotic stresses. In the present review, we report comprehensive information on sources of resistance to a broad range of pathogens in pepper, revisiting the classical genetic studies and showing the contribution of genomics for the understanding of the molecular basis of resistance.
| S-EPMC7177692 | biostudies-literature
Project description:Natural transformation is the process by which bacteria actively take up and maintain extracellular DNA. This naturally occurring process is widely used as a genetic modification method in bacterial species, and is crucial for the efficient genetic modification of organisms in an industrial setting. Cyanobacteria are oxygenic photosynthetic microbes that are promising platforms for bioproduction of fuels, chemicals, and feedstocks. Using CO2 and sunlight alone, cyanobacteria can make these valuable bioproducts in a carbon-neutral manner. While genetic modifications have been performed in a number of cyanobacterial strains, natural transformation has been successfully demonstrated in only a handful of species. Even though thousands of cyanobacterial strains have been deposited in culture collections and hundreds of these species have had their genomes sequenced, only a few of these organisms have been experimentally transformed. Although there are many aspects of cyanobacterial biology that provide exciting opportunities for biological investigation, the absence of a rapid and straightforward genetic modification method such as natural transformation hinders research efforts to understand some of the fascinating nuances of cyanobacterial physiology. The ability to use natural transformation in more strains of cyanobacteria would facilitate the rapid employment of these organisms in bioproduction settings. This article discusses recent advances in the understanding of natural transformation in cyanobacteria. Additionally, it identifies gaps in the current knowledge about cyanobacterial natural transformation and provides an overview of how new genomic technologies may be implemented to understand this important process.
| S-EPMC6567925 | biostudies-literature
Project description:IntroductionThe search for life on distant exoplanets is expected to rely on atmospheric biosignatures detection, such as oxygen of biological origin. However, it is not demonstrated how much oxygenic photosynthesis, which on Earth depends on visible light, could work under spectral conditions simulating exoplanets orbiting the Habitable Zone of M-dwarf stars, which have low light emission in the visible and high light emission in the far-red/near-infrared. By utilizing cyanobacteria, the first organisms to evolve oxygenic photosynthesis on our planet, and a starlight simulator capable of accurately reproducing the emission spectrum of an M-dwarf in the range 350-900 nm, we could answer this question.MethodsWe performed experiments with the cyanobacterium Chlorogloeopsis fritschii PCC6912, capable of Far-Red Light Photoacclimation (FaRLiP), which allows the strain to harvest far-red in addition to visible light for photosynthesis, and Synechocystis sp. PCC6803, a species unable to perform this photoacclimation, comparing their responses when exposed to three simulated light spectra: M-dwarf, solar and far-red. We analysed growth and photosynthetic acclimation features in terms of pigment composition and photosystems organization. Finally, we determined the oxygen production of the strains directly exposed to the different spectra.ResultsBoth cyanobacteria were shown to grow and photosynthesize similarly under M-dwarf and solar light conditions: Synechocystis sp. by utilizing the few photons in the visible, C. fritschii by harvesting both visible and far-red light, activating the FaRLiP response.DiscussionOur results experimentally show that an M-dwarf light spectrum could support a biological oxygen production similar to that in solar light at the tested light intensities, suggesting the possibility to discover such atmospheric biosignatures on those exoplanets if other boundary conditions are met.
| S-EPMC9941696 | biostudies-literature