Ganoderma Fusions with High Yield of Ergothioneine and Comparative Analysis of Its Genomics

Ergothioneine (EGT), an exceptional antioxidant found ubiquitously across diverse living organisms, plays a pivotal role in various vital physiological regulatory functions. Its principal natural sources are mushrooms and animal liver tissues. Ganoderma spp., a traditional Chinese food and medicinal mushroom, boasts high concentrations of EGT. To advance the development of novel Ganoderma spp. strains with enhanced EGT yields, we employed an efficient Ganoderma spp. protoplasmic fusion system. Through molecular and biological characterization, we successfully generated seven novel fusion strains. Notably, fusion strain RS7 demonstrated a remarkable increase in mycelial EGT production (12.70 ± 1.85 mg/L), surpassing the parental strains FQ16 and FQ23 by 34.23% and 39.10%, respectively. Furthermore, in the context of the fruiting body, fusion strain RS11 displayed a notable 53.58% enhancement in EGT production (11.24 ± 1.96 mg/L) compared to its parental strains. Genomic analysis of the RS7, the strain with the highest levels of mycelial EGT production, revealed mutations in the gene EVM0005141 associated with EGT metabolism. These mutations led to a reduction in non-productive shunts, subsequently redirecting more substrate towards the EGT synthesis pathway. This redirection significantly boosted EGT production in the RS7 strain. The insights gained from this study provide valuable guidance for the commercial-scale production of EGT and the selective breeding of Ganoderma spp. strains.

Utilization of crop wild relatives for biotic and abiotic stress management in Indian mustard [Brassica juncea (L.) Czern. & Coss.]

Brassica juncea (L.) Czern. & Coss. (Indian mustard) is an economically important edible oil crop. Over the years, plant breeders have developed many elite varieties of B. juncea with better yield traits, but research work on the introgression of stress resilience traits has largely been lagging due to scarcity of resistant donors. Crop wild relatives (CWRs) are the weedy relatives of domesticated plant species which are left unutilized in their natural habitat due to the presence of certain undesirable alleles which hamper their yield potential, and thus, their further domestication. CWRs of B. juncea namely include Sinapis alba L. (White mustard), B. tournefortii Gouan. (African mustard), B. fruticulosa Cirillo (Twiggy turnip), Camelina sativa L. (Gold-of-pleasure), Diplotaxis tenuisiliqua Delile (Wall rocket), D. erucoides L. (White wall rocket), D. muralis L. (Annual wall rocket), Crambe abyssinica R.E.Fr. (Abyssinian mustard), Erucastrum gallicum Willd. (Common dogmustard), E. cardaminoides Webb ex Christ (Dogmustard), Capsella bursa-pastoris L. (Shepherds purse), Lepidium sativum L. (Garden Cress) etc. These CWRs have withstood several regimes of biotic and abiotic stresses over the past thousands of years which led them to accumulate many useful alleles contributing in resistance against various environmental stresses. Thus, CWRs could serve as resourceful gene pools for introgression of stress resilience traits into Indian mustard. This review summarizes research work on the introgression of resistance against Sclerotinia stem rot (caused by Sclerotinia sclerotiorum), Alternaria blight (caused by Alternaria brassicae), white rust (caused by Albugo candida), aphid attack, drought and high temperature from CWRs into B. juncea. However, various pre- and post-fertilization barriers due to different ploidy levels are major stumbling blocks in the success of such programmes, therefore, we also insightfully discuss how the advances made in -omics technology could be helpful in assisting various breeding programmes aiming at improvisation of stress resilience traits in B. juncea.

Tissue Culture in Ornamentals: Cultivation Factors, Propagation Techniques, and Its Application

Ornamentals come in a variety of shapes, sizes, and colors to suit a wide range of climates, landscapes, and gardening needs. Compared to demand, a shortage of plant materials and diversity force the search for solutions for their constant acquisition and improvement to increase their commercial value, respectively. In vitro cultures are a suitable solution to meet expectations using callus culture, somatic embryogenesis, protoplast culture, and the organogenesis of protocorm-like bodies; many of these techniques are commercially practiced. Factors such as culture media, explants, carbohydrates, plant growth regulators, and light are associated with the success of in vitro propagation. Techniques, especially embryo rescue and somatic hybridization, are widely used to improve ornamentals. The development of synthetic seed allows season-independent seed production and preservation in the long term. Despite the advantages of propagation and the improvement of ornamentals, many barriers still need to be resolved. In contrast to propagation and crop developmental studies, there is also a high scope for molecular studies, especially epigenetic changes caused by plant tissue culture of ornamentals. In this review, we have accumulated and discussed an overall update on cultivation factors, propagation techniques in ornamental plant tissue culture, in vitro plant improvement techniques, and future perspectives.

Generating Heterokaryotic Cells via Bacterial Cell-Cell Fusion

Fusion of cells is an important and common biological process that leads to the mixing of cellular contents and the formation of multinuclear cells. Cell fusion occurs when distinct membranes are brought into proximity of one another and merge to become one. Fusion holds promise for biotechnological innovations, for instance, for the discovery of urgently needed new antibiotics. Here, we used antibiotic-producing bacteria that can proliferate without their cell wall as a model to investigate cell-cell fusion. We found that fusion between genetically distinct cells yields heterokaryons that are viable, contain multiple selection markers, and show increased antimicrobial activity. The rate of fusion induced using physical and chemical methods was dependent on membrane fluidity, which is related to lipid composition as a function of cellular age. Finally, by using an innovative system of synthetic membrane-associated lipopeptides, we achieved targeted fusion between distinctly marked cells to further enhance fusion efficiency. These results provide a molecular handle to understand and control cell-cell fusion, which can be used in the future for the discovery of new drugs. IMPORTANCE Cell-cell fusion is instrumental in introducing different sets of genes in the same environment, which subsequently leads to diversity. There is need for new protocols to fuse cells of different types together for biotechnological applications like drug discovery. We present here wall-deficient cells as a platform for the same. We identify the fluidity of the membrane as an important characteristic for the process of fusion. We demonstrate a cell-specific approach for fusion using synthetically designed peptides yielding cells with modified antibiotic production profiles. Overall, wall-deficient cells can be a chassis for innovative metabolite production by providing an alternative method for cell-cell fusion.

Characterization of Non-selected Intermolecular Gene Conversion in the Polyploid Haloarchaeon Haloferax volcanii

Gene conversion is defined as the non-reciprocal transfer of genetic information from one site to a homologous, but not identical site of the genome. In prokaryotes, gene conversion can increase the variance of sequences, like in antigenic variation, but can also lead to a homogenization of sequences, like in the concerted evolution of multigene families. In contrast to these intramolecular mechanisms, the intermolecular gene conversion in polyploid prokaryotes, which leads to the equalization of the multiple genome copies, has hardly been studied. We have previously shown the intermolecular gene conversion in halophilic and methanogenic archaea is so efficient that it can be studied without selecting for conversion events. Here, we have established an approach to characterize unselected intermolecular gene conversion in Haloferax volcanii making use of two genes that encode enzymes involved in carotenoid biosynthesis. Heterozygous strains were generated by protoplast fusion, and gene conversion was quantified by phenotype analysis or/and PCR. It was verified that unselected gene conversion is extremely efficient and it was shown that gene conversion tracts are much longer than in antigenic variation or concerted evolution in bacteria. Two sites were nearly always co-converted when they were 600 bp apart, and more than 30% co-conversion even occurred when two sites were 5 kbp apart. The gene conversion frequency was independent from the extent of genome differences, and even a one nucleotide difference triggered conversion.

Use of Permanent Wall-Deficient Cells as a System for the Discovery of New-to-Nature Metabolites

Filamentous actinobacteria are widely used as microbial cell factories to produce valuable secondary metabolites, including the vast majority of clinically relevant antimicrobial compounds. Secondary metabolites are typically encoded by large biosynthetic gene clusters, which allow for a modular approach to generating diverse compounds through recombination. Protoplast fusion is a popular method for whole genome recombination that uses fusion of cells that are transiently wall-deficient. This process has been applied for both inter- and intraspecies recombination. An important limiting step in obtaining diverse recombinants from fused protoplasts is regeneration of the cell wall, because this forces the chromosomes from different parental lines to segregate, thereby preventing further recombination. Recently, several labs have gained insight into wall-deficient bacteria that have the ability to proliferate without their cell wall, known as L-forms. Unlike protoplasts, L-forms can stably maintain multiple chromosomes over many division cycles. Fusion of such L-forms would potentially allow cells to express genes from both parental genomes while also extending the time for recombination, both of which can contribute to an increased chemical diversity. Here, we present a perspective on how L-form fusion has the potential to become a platform for novel compound discovery and may thus help to overcome the antibiotic discovery void.

through two-step protoplast fusion for cellulase production enhancement

Fungal protoplast fusion is an approach to introduce novel characteristics into industrially important strains. Cellulases, essential enzymes with a wide range of biotechnological applications, are produced by many species of the filamentous fungi Trichoderma. In this study, a collection of 60 natural isolates were screened for Avicel and carboxymethyl cellulose degradation, and two cellulase producers of Trichoderma virens and Trichoderma harzianum were used for protoplast fusion. One of the resulting hybrids with improved cellulase activity, C1-3, was fused with the hyperproducer Trichoderma reesei Rut-C30. A new selected hybrid, F7, was increased in cellulase activity 1.8 and 5 times in comparison with Rut-C30 and C1-3, respectively. The increases in enzyme activity correlated with an upregulation of the cellulolytic genes cbh1, cbh2, egl3, and bgl1 in the parents. The amount of mRNA of cbh1 and cbh2 in F7 resembled that of Rut-C30 while the bgl1 mRNA level was similar to that of C1-3. AFLP (amplified fragment length polymorphism) fingerprinting and GC-MS (gas chromatography - mass spectrometry) analysis represented variations in parental strains and fusants. In conclusion, the results demonstrate that a 3-interspecific hybrid strain was isolated, with improved characteristics for cellulase degradation and showing genetic polymorphisms and differences in the volatile profile, suggesting reorganizations at the genetic level.

Encapsulation enhances protoplast fusant stability

A barrier to cost‐efficient biomanufacturing is the instability of engineered genetic elements, such as plasmids. Instability can also manifest at the whole‐genome level, when fungal dikaryons revert to parental species due to nuclear segregation during cell division. Here, we show that by encapsulating Saccharomyces cerevisiae‐Pichia stipitis dikaryons in an alginate matrix, we can limit cell division and preserve their expanded metabolic capabilities. As a proxy to cellulosic ethanol production, we tested the capacity of such cells to carry out ethanologenic fermentation of glucose and xylose, examining substrate use, ploidy, and cell viability in relation to planktonic fusants, as well as in relation to planktonic and encapsulated cell cultures consisting of mixtures of these species. Glucose and xylose consumption and ethanol production by encapsulated dikaryons were greater than planktonic controls. Simultaneous co‐fermentation did not occur; rather the order and kinetics of glucose and xylose catabolism by encapsulated dikaryons were similar to cultures where the two species were encapsulated together. Over repeated cycles of fed‐batch culture, encapsulated S. cerevisiae‐P. stipitis fusants exhibited a dramatic increase in genomic stability, relative to planktonic fusants. Encapsulation also increased the stability of antibiotic‐resistance plasmids used to mark each species and preserved a fixed ratio of S. cerevisiae to P. stipitis cells in mixed cultures. Our data demonstrate how encapsulating cells in an extracellular matrix restricts cell division and, thereby, preserves the stability and biological activity of entities ranging from genomes to plasmids to mixed populations, each of which can be essential to cost‐efficient biomanufacturing.

Molecular Characterization and Stress Tolerance Evaluation of New Allotetraploid Somatic Hybrids Between Carrizo Citrange and Citrus macrophylla W. rootstocks

Polyploidy is one of the main forces that drives the evolution of plants and provides great advantages for breeding. Somatic hybridization by protoplast fusion is used in citrus breeding programs. This method allows combining the whole parental genomes in a single genotype, adding complementary dominant characters, regardless of parental heterozygosity. It also contributes to surpass limitations imposed by reproductive biology and quickly generates progenies that combine the required traits. Two allotetraploid somatic hybrids recovered from the citrus rootstocks-Citrus macrophylla (CM) and Carrizo citrange (CC)-were characterized for morphology, genome composition using molecular markers (SNP, SSR, and InDel), and their tolerance to iron chlorosis, salinity, and Citrus tristeza virus (CTV). Both hybrids combine the whole parental genomes even though the loss of parental alleles was detected in most linkage groups. Mitochondrial genome was inherited from CM in both the hybrids, whereas recombination was observed for chloroplastic genome. Thus, somatic hybrids differ from each other in their genome composition, indicating that losses and rearrangements occurred during the fusion process. Both inherited the tolerance to stem pitting caused by CTV from CC, are tolerant to iron chlorosis such as CM, and have a higher tolerance to salinity than the sensitive CC. These hybrids have potential as improved rootstocks to grow citrus in areas with calcareous and saline soils where CTV is present, such as the Mediterranean region. The provided knowledge on the effects of somatic hybridization on the genome composition, anatomy, and physiology of citrus rootstocks will be key for breeding programs that aim to address current and future needs of the citrus industry.

Somatic hybridization provides segregating populations for the identification of causative mutations in sterile mutants of the moss Physcomitrella patens

Forward genetics is now straightforward in the moss Physcomitrella patens, and large mutant populations can be screened relatively easily. However, perturbation of development before the formation of gametes currently leaves no route to gene discovery. Somatic hybridization has previously been used to rescue sterile mutants and to assign P. patens mutations to complementation groups, but the cellular basis of the fusion process could not be monitored, and there was no tractable way to identify causative mutations. Here we use fluorescently tagged lines to generate somatic hybrids between Gransden (Gd) and Villersexel (Vx) strains of P. patens, and show that hybridization produces fertile diploid gametophytes that form phenotypically normal tetraploid sporophytes. Quantification of genetic variation between the two parental strains reveals single nucleotide polymorphisms at a frequency of 1/286 bp. Given that the genetic distinction between Gd and Vx strains exceeds that found between pairs of strains that are commonly used for genetic mapping in other plant species, the spore populations derived from hybrid sporophytes provide suitable material for bulk segregant analysis and gene identification by genome sequencing.

Expanding the Symbiodinium (Dinophyceae, Suessiales) Toolkit Through Protoplast Technology

Dinoflagellates within the genus Symbiodinium are photosymbionts of many tropical reef invertebrates, including corals, making them central to the health of coral reefs. Symbiodinium have therefore gained significant research attention, though studies have been constrained by technical limitations. In particular, the generation of viable cells with their cell walls removed (termed protoplasts) has enabled a wide range of experimental techniques for bacteria, fungi, plants, and algae such as ultrastructure studies, virus infection studies, patch clamping, genetic transformation, and protoplast fusion. However, previous studies have struggled to remove the cell walls from armored dinoflagellates, potentially due to the internal placement of their cell walls. Here, we produce the first Symbiodinium protoplasts from three genetically and physiologically distinct strains via incubation with cellulase and osmotic agents. Digestion of the cell walls was verified by a lack of Calcofluor White fluorescence signal and by cell swelling in hypotonic culture medium. Fused protoplasts were also observed, motivating future investigation into intra- and inter-specific somatic hybridization of Symbiodinium. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Generation of Symbiodinium protoplasts opens exciting, new avenues for researching these crucial symbiotic dinoflagellates, including genetic modification.

Highly toxic and broad-spectrum insecticidal local Bacillus strains engineered using protoplast fusion

Protoplast fusion was performed between a local Bacillus thuringiensis UV-resistant mutant 66/1a (Bt) and Bacillus sphaericus GHAI (Bs) to produce new Bacillus strains with a wider spectrum of action against different insects. Bt is characterized as sensitive to polymyxin and streptomycin and resistant to rifampicin and has shown 87% mortality against Spodoptera littoralis larvae at concentration of 1.5 × 10(7) cells/mL after 7 days of feeding; Bs is characterized as resistant to polymyxin and streptomycin and sensitive to rifampicin and has been shown to have 100% mortality against Culex pipiens after 1 day of feeding at the same concentration as that of Bt. Among a total of 64 Bt::Bs fusants produced on the selective medium containing polymyxin, streptomycin, and rifampicin, 17 fusants were selected because of their high mortality percentages against S. littoralis (Lepidoptera) and C. pipiens (Diptera). While Bt harboured 3 plasmids (600, 350, and 173 bp) and Bs had 2 plasmids (544 and 291 bp), all the selected fusants acquired plasmids from both parental strains. SDS-PAGE protein analysis of the 17 selected fusants and their parental strains confirmed that all fusant strains acquired and expressed many specific protein bands from the 2 parental strains, especially the larvicidal proteins to both lepidopteran and dipteran species with molecular masses of 65, 70, 80, 88, 100, and 135 kDa. Four protein bands with high molecular masses of 281, 263, 220, and 190 kDa, which existed in the Bt parental strain and did not exist in the Bs parental strain, and 2 other protein bands with high molecular masses of 185 and 180 kDa, which existed in the Bs parental strain and did not exist in the Bt parental strain, were expressed in most fusants. The results indicated the expression of some cry genes encoded for insecticidal crystal proteins from Bt and the binary toxin genes from Bs in all fusant strains. The recombinant fusants have more efficient and potential values for agricultural application compared with both the insecticidal Bt and the mosquitocidal Bs strains alone against S. littoralis and C. pipiens larvae, respectively.

Influence of protoplast fusion between two Trichoderma spp. on extracellular enzymes production and antagonistic activity

Biological control plays a crucial role in grapevine pathogens disease management. The cell-wall degrading enzymes chitinase, cellulase and β-glucanase have been suggested to be essential for the mycoparasitism activity of Trichoderma species against grapevine fungal pathogens. In order to develop a useful strain as a single source of these vital enzymes, it was intended to incorporate the characteristics of two parental fungicides tolerant mutants of Trichoderma belonging to the high chitinase producing species T. harzianum and the high cellulase producing species T. viride, by fusing their protoplasts. The phylogeny of the parental strains was carried out using a sequence of the 5.8S-ITS region. The BLAST of the obtained sequence identified these isolates as T. harzianum and T. viride. Protoplasts were isolated using lysing enzymes and were fused using polyethylene glycol. The fused protoplasts have been regenerated on protoplast regeneration minimal medium supplemented with two selective fungicides. Among the 40 fast growing fusants, 17 fusants were selected based on their enhanced growth on selective media for further studies. The fusant strains were growing 60%–70% faster than the parents up to third generation. All the 17 selected fusants exhibited morphological variations. Some fusant strains displayed threefold increased chitinase enzyme activity and twofold increase in β-glucanase enzyme activity compared to the parent strains. Most fusants showed powerful antagonistic activity against Macrophomin aphaseolina, Pythium ultimum and Sclerotium rolfsii pathogens. Fusant number 15 showed the highest inhibition percentage (92.8%) against M. phaseolina and P. ultimum, while fusant number 9 showed the highest inhibition percentage (98.2%) against the growth of S. rolfsii. A hyphal intertwining and degradation phenomenon was observed by scanning electron microscope. The Trichoderma antagonistic effect against pathogenic fungal mycelia was due to the mycoparasitism effect of the extracellular enzymes.

Green fluorescent protein as a visual marker in somatic hybridization

Using a transgenic citrus plant expressing Green Fluorescent Protein (GFP) as a parent in somatic fusion experiments, we investigated the suitability of GFP as an in vivo marker to follow the processes of protoplast fusion, regeneration and selection of hybrid plants. A high level of GFP expression was detected in transgenic citrus protoplasts, hybrid callus, embryos and plants. It is demonstrated that GFP can be used for the continuous monitoring of the fusion process, localization of hybrid colonies and callus, and selection of somatic hybrid embryos and plants.

A novel glutamine-RNA interaction identified by screening libraries in mammalian cells

The arginine-rich motif provides a versatile framework for RNA recognition in which few amino acids other than arginine are needed to mediate specific binding. Using a mammalian screening system based on transcriptional activation by HIV Tat, we identified novel arginine-rich peptides from combinatorial libraries that bind tightly to the Rev response element of HIV. Remarkably, a single glutamine, but not asparagine, within a stretch of polyarginine can mediate high-affinity binding. These results, together with the structure of a Rev peptide-Rev response element complex, suggest that the carboxamide groups of glutamine or asparagine are well-suited to hydrogen bond to G-A base pairs and begin to establish an RNA recognition code for the arginine-rich motif. The screening approach may provide a relatively general method for screening expression libraries in mammalian cells.

Characterization of Resistance in a Somatic Hybrid of Solanum bulbocastanum and S. tuberosum, to Meloidogyne chitwoodi

A somatic hybrid, CBP-233, between resistant Solanum bulbocastanum (SB-22) and susceptible S. tuberosum (R4) was tested for resistance to Meloidogyne chitwoodi race 1. One week after inoculation, only 0.04-0.4% of the initial inoculum (Pi, 5,000 eggs) as second stage-juveniles infected SB-22 and CBP-233 root systems, compared to 2% in R4. After 8 weeks, the number of M. chitwoodi in SB-22 and CBP-233 roots remained lower (0.3-1.5% of Pi) compared to R4, which increased from 2% to ca. 27%. Development of M. chitwoodi was delayed on SB-22 and CBP-233 by at least 2 weeks, and only half of the infective nematodes established feeding sites and matured in resistant clones compared to 99% in susceptible R4. Necrotic tissue surrounded nematodes that failed to develop in SB-22 and CBP-233. The reproductive factor (ratio of final number of eggs recovered from roots to Pi) was <0.01 for both SB-22 and CBP-233 and 46.8 for R4. Delaying inoculation of CBP-233 from 1 to 3 months after planting did not increase the chance or rate of tuber infection. Only a few M. chitwoodi developed to maturity on CBP-233 tubers and deposited a small number of eggs. SB-22 rarely produced tubers in these experiments, and like CBP-233 were resistant to M. chitwoodi. It appeared that the mechanisms of resistance to M. chitwoodi in roots and tubers of CBP-233 are similar.