Stable nuclear transformation of rhodophyte species Porphyridium purpureum: advanced molecular tools and an optimized method

Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs

Background

Group II introns are mobile genetic elements that can insert at specific target sequences, however, their origins are often challenging to reconstruct because of rapid sequence decay following invasion and spread into different sites. To advance understanding of group II intron spread, we studied the intron-rich mitochondrial genome (mitogenome) in the unicellular red alga, Porphyridium.

Results

Analysis of mitogenomes in three closely related species in this genus revealed they were 3–6-fold larger in size (56–132 kbp) than in other red algae, that have genomes of size 21–43 kbp. This discrepancy is explained by two factors, group II intron invasion and expansion of repeated sequences in large intergenic regions. Phylogenetic analysis demonstrates that many mitogenome group II intron families are specific to Porphyridium, whereas others are closely related to sequences in fungi and in the red alga-derived plastids of stramenopiles. Network analysis of intron-encoded proteins (IEPs) shows a clear link between plastid and mitochondrial IEPs in distantly related species, with both groups associated with prokaryotic sequences.

Conclusion

Our analysis of group II introns in Porphyridium mitogenomes demonstrates the dynamic nature of group II intron evolution, strongly supports the lateral movement of group II introns among diverse eukaryotes, and reveals their ability to proliferate, once integrated in mitochondrial DNA.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01200-3.

Physiological and transcriptome analysis elucidates the metabolic mechanism of versatile Porphyridium purpureum under nitrogen deprivation for exopolysaccharides accumulation

Porphyridium purpureum is a mesophilic, unicellular red alga rich in phycoerythrin, sulfate polysaccharides, and polyunsaturated fatty acids. Nitrogen deficiency inhibited the growth of P. purpureum and resulted in yellowing of the cells and thickening of the extracellular viscousness sheath. Under nitrogen stress, the contents of total lipids and exopolysaccharides in P. purpureum were increased by 65.2% and 188.0%, respectively. We demonstrate that the immediate response of P. purpureum to nitrogen deficiency is mediated by carbon flow to polysaccharide synthesis, while the synthesis of lipids is enhanced as a permanent energy storage substance at the later stage. Based on transcriptome annotation information, we elucidate the synthesis pathway of polysaccharides from P. purpureum from the perspective of glycosyl-donor interconversion, and demonstrate that the n-6 pathway is the main synthesis pathway of polyunsaturated fatty acids. This study not only provides a production strategy for polysaccharides and fatty acids by single-celled marine red algae P. purpureum, but also provides targets for further genetic modification.

Agrobacterium tumefaciens-Mediated Nuclear Transformation of a Biotechnologically Important Microalga-Euglena gracilis

Euglena gracilis (E. gracilis) is an attractive organism due to its evolutionary history and substantial potential to produce biochemicals of commercial importance. This study describes the establishment of an optimized protocol for the genetic transformation of E. gracilis mediated by Agrobacterium (A. tumefaciens). E. gracilis was found to be highly sensitive to hygromycin and zeocin, thus offering a set of resistance marker genes for the selection of transformants. A. tumefaciens-mediated transformation (ATMT) yielded hygromycin-resistant cells. However, hygromycin-resistant cells hosting the gus gene (encoding β-glucuronidase (GUS)) were found to be GUS-negative, indicating that the gus gene had explicitly been silenced. To circumvent transgene silencing, GUS was expressed from the nuclear genome as transcriptional fusions with the hygromycin resistance gene (hptII) (encoding hygromycin phosphotransferase II) with the foot and mouth disease virus (FMDV)-derived 2A self-cleaving sequence placed between the coding sequences. ATMT of Euglena with the hptII-2A–gus gene yielded hygromycin-resistant, GUS-positive cells. The transformation was verified by PCR amplification of the T-DNA region genes, determination of GUS activity, and indirect immunofluorescence assays. Cocultivation factors optimization revealed that a higher number of transformants was obtained when A. tumefaciens LBA4404 (A₆₀₀ = 1.0) and E. gracilis (A₇₅₀ = 2.0) cultures were cocultured for 48 h at 19 °C in an organic medium (pH 6.5) containing 50 µM acetosyringone. Transformation efficiency of 8.26 ± 4.9% was achieved under the optimized cocultivation parameters. The molecular toolkits and method presented here can be used to bioengineer E. gracilis for producing high-value products and fundamental studies.

Cytoskeletal diversification across 1 billion years: What red algae can teach us about the cytoskeleton, and vice versa

The cytoskeleton has a central role in eukaryotic biology, enabling cells to organize internally, polarize, and translocate. Studying cytoskeletal machinery across the tree of life can identify common elements, illuminate fundamental mechanisms, and provide insight into processes specific to less-characterized organisms. Red algae represent an ancient lineage that is diverse, ecologically significant, and biomedically relevant. Recent genomic analysis shows that red algae have a surprising paucity of cytoskeletal elements, particularly molecular motors. Here, we review the genomic and cell biological evidence and propose testable models of how red algal cells might perform processes including cell motility, cytokinesis, intracellular transport, and secretion, given their reduced cytoskeletons. In addition to enhancing understanding of red algae and lineages that evolved from red algal endosymbioses (e.g., apicomplexan parasites), these ideas may also provide insight into cytoskeletal processes in animal cells.

Efficient Agrobacterium tumefaciens-mediated stable genetic transformation of green microalgae, Chlorella sorokiniana

The green oleaginous microalgae, Chlorella sorokiniana, is a highly productive Chlorella species and a potential host for the production of biofuel, nutraceuticals, and recombinant therapeutic proteins. The lack of a stable and efficient genetic transformation system is the major bottleneck in improving this species. We report an efficient and stable Agrobacterium tumefaciens-mediated transformation system for the first time in C. sorokiniana. Cocultivation of C. sorokiniana cells (optical density at λ ₆₈₀ = 1.0) with Agrobacterium at a cell density of OD₆₀₀ = 0.6, on BG11 agar medium (pH 5.6) supplemented with 100 μM of acetosyringone, for three days at 25 ± 2 °C in the dark, resulted in significantly higher transformation efficiency (220 ± 5 hygromycin-resistant colonies per 10⁶ cells). Transformed cells primarily selected on BG11 liquid medium with 30 mg/L hygromycin followed by selecting homogenous transformants on BG11 agar medium with 75 mg/L hygromycin. PCR analysis confirmed the presence of hptII, and the absence of virG amplification ruled out the Agrobacterium contamination in transformed microalgal cells. Southern hybridization confirmed the integration of the hptII gene into the genome of C. sorokiniana. The qRT-PCR and Western blot analyses confirmed hptII and GUS gene expression in the transgenic cell lines. The specific growth rate, biomass doubling time, PSII activity, and fatty-acid profile of transformed cells were found similar to wild-type untransformed cells, clearly indicating the growth and basic metabolic processes not compromised by transgene expression. This protocol can facilitate opportunities for future production of biofuel, carotenoids, nutraceuticals, and therapeutic proteins.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02750-7.

Gene Delivery Technologies with Applications in Microalgal Genetic Engineering

Microalgae and cyanobacteria are photosynthetic microbes that can be grown with the simple inputs of water, carbon dioxide, (sun)light, and trace elements. Their engineering holds the promise of tailored bio-molecule production using sustainable, environmentally friendly waste carbon inputs. Although algal engineering examples are beginning to show maturity, severe limitations remain in the transformation of multigene expression cassettes into model species and DNA delivery into non-model hosts. This review highlights common and emerging DNA delivery methods used for other organisms that may find future applications in algal engineering.

Exploration of space to achieve scientific breakthroughs

Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.