Halotolerant rhizobacteria isolated from a mangrove forest alleviate saline stress in Musa acuminata cv. Berangan.

Saline soils resulting from anthropogenic activity and climate change present a challenge to future food security. Towards addressing this, we isolated and characterized halotolerant bacteria from a Malaysian mangrove forest, and explored their effect on morpho-physiological and biochemical parameters of banana plantlets under salt stress. A total of 88 rhizobacterial and 16 endophytic bacterial isolates collected from the roots and rhizosphere of Rhizophora apiculata, Avicennia alba and Sonneratia alba, were found to tolerate up to 400 mM of sea salt. Based on best performance in multiple plant growth traits, three rhizobacterial strains RB1, RB3 and RB4 and three endophytic bacterial strains EB1, EB2 and EB3 were used for further analysis. The rhizobacterial strains were identified as Bacillus sp. and endophytic bacteria as Pseudomonas sp. based on 16 S rRNA gene sequence. SEM observation confirmed colonization of each strain on banana plantlet roots. When colonized plantlets were subjected to 90 mM salt and compared to uninoculated (control) and mock inoculated plants, improved plant growth was observed with each of the strains, especially with bacterial strains EB3 and RB3. Biochemical analysis of plantlets revealed that root colonization with EB3 and RB3 enhanced levels of plant chlorophyll (> 5-fold), carotenoid (> 2.85-fold) and proline (2.6-fold and 2.3-fold), while plantlets also showed reduced MDA content (0.45-fold and 0.51-fold), significantly reduced generation of ROS (0.23-fold and 0.47-fold) and lower levels of electrolyte leakage (0.77 and 0.51-fold). Antioxidant enzymes also showed enhanced activity with EB3 and RB3. Our results indicate that these halotolerant Bacillus and Pseudomonas strains from the mangrove have multifunctional plant growth promoting activity and can reduce salt stress in bananas. This data provides a reference for exploring halotolerant microbes from hypersaline environments to overcome salt stress in plants.

Beyond the PAR spectra: impact of light quality on the germination, flowering, and metabolite content of Stevia rebaudiana (Bertoni).

BACKGROUND: Stevia rebaudiana is a high value crop due to the strong commercial demand for its metabolites (steviol glycosides) but has limited geographical cultivation range. In non-native environments with different daylength and light quality, Stevia has low germination rates and early flowering resulting in lower biomass and poor yield of the desired metabolites. In this study, artificial lighting with light-emitting diodes (LEDs) was used to determine if different light quality within and outside of the photosynthetically active radiation (PAR) range can be used to improve germination rates and yields for production of steviol glycosides for the herbal supplement and food industry. RESULTS: Plants treated with red and blue light at an intensity of 130 µmol m-2  s-1 supplemented with 5% of UV-A light under a 16-h photoperiod produced the most desirable overall results with a high rate of germination, low percentage of early flowering, and high yields of dry leaf, stevioside and rebaudioside A, 175 days after planting. CONCLUSION: While red and blue light combinations are effective for plant growth, the use of supplemental non-PAR irradiation of UV-A wavelength significantly and desirably delayed flowering, enhanced germination, biomass, rebaudioside A and stevioside yields, while supplemental green light improved yield of biomass and rebaudioside A, but not stevioside. Overall, the combination of red, blue and UV-A light resulted in the best overall productivity for Stevia rebaudiana. © 2021 Society of Chemical Industry.

Epigenetic changes and their relationship to somaclonal variation: a need to monitor the micropropagation of plantation crops.

Chromatin modulation plays important roles in gene expression regulation and genome activities. In plants, epigenetic changes, including variations in histone modification and DNA methylation, are linked to alterations in gene expression. Despite the significance and potential of in vitro cell and tissue culture systems in fundamental research and marketable applications, these systems threaten the genetic and epigenetic networks of intact plant organs and tissues. Cell and tissue culture applications can lead to DNA variations, methylation alterations, transposon activation, and finally, somaclonal variations. In this review, we discuss the status of the current understanding of epigenomic changes that occur under in vitro conditions in plantation crops, including coconut, oil palm, rubber, cotton, coffee and tea. It is hoped that comprehensive knowledge of the molecular basis of these epigenomic variations will help researchers develop strategies to enhance the totipotent and embryogenic capabilities of tissue culture systems for plantation crops.

PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers.

Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intra-generic differences in plant genomes. Among these elements, microsatellites, or Simple Sequence Repeats (SSRs), have been widely demonstrated as powerful genetic markers for species and varieties discrimination. We present PlantFuncSSRs platform having more than 364 plant species with more than 2 million functional SSRs. They are provided with detailed annotations for easy functional browsing of SSRs and with information on primer pairs and associated functional domains. PlantFuncSSRs can be leveraged to identify functional-based genic variability among the species of interest, which might be of particular interest in developing functional markers in plants. This comprehensive on-line portal unifies mining of SSRs from first and next generation sequencing datasets, corresponding primer pairs and associated in-depth functional annotation such as gene ontology annotation, gene interactions and its identification from reference protein databases. PlantFuncSSRs is freely accessible at: http://www.bioinfocabd.upo.es/plantssr.

NAC transcription factor family genes are differentially expressed in rice during infections with Rice dwarf virus, Rice black-streaked dwarf virus, Rice grassy stunt virus, Rice ragged stunt virus, and Rice transitory yellowing virus.

Expression levels of the NAC gene family were studied in rice infected with Rice dwarf virus (RDV), Rice black-streaked dwarf virus (RBSDV), Rice grassy stunt virus (RGSV), Rice ragged stunt virus (RRSV), and Rice transitory yellowing virus (RTYV). Microarray analysis showed that 75 (68%) OsNAC genes were differentially regulated during infection with RDV, RBSDV, RGSV, and RRSV compared with the control. The number of OsNAC genes up-regulated was highest during RGSV infection, while the lowest number was found during RTYV infection. These phenomena correlate with the severity of the syndromes induced by the virus infections. Most of the genes in the NAC subgroups NAC22, SND, ONAC2, ANAC34, and ONAC3 were down-regulated for all virus infections. These OsNAC genes might be related to the health stage maintenance of the host plants. Interestingly, most of the genes in the subgroups TIP and SNAC were more highly expressed during RBSDV and RGSV infections. These results suggested that OsNAC genes might be related to the responses induced by the virus infection. All of the genes assigned to the TIP subgroups were highly expressed during RGSV infection when compared with the control. For RDV infection, the number of activated genes was greatest during infection with the S-strain, followed by the D84-strain and the O-strain, with seven OsNAC genes up-regulated during infection by all three strains. The Os12g03050 and Os11g05614 genes showed higher expression during infection with four of the five viruses, and Os11g03310, Os11g03370, and Os07g37920 genes showed high expression during at least three viral infections. We identified some duplicate genes that are classified as neofunctional and subfunctional according to their expression levels in different viral infections. A number of putative cis-elements were identified, which may help to clarify the function of these key genes in network pathways.

Transcriptome profiling shows gene regulation patterns in a flavonoid pathway in response to exogenous phenylalanine in Boesenbergia rotunda cell culture.

BACKGROUND: Panduratin A extracted from Boesenbergia rotunda is a flavonoid reported to possess a range of medicinal indications which include anti-dengue, anti-HIV, anti-cancer, antioxidant and anti-inflammatory properties. Boesenbergia rotunda is a plant from the Zingiberaceae family commonly used as a food ingredient and traditional medicine in Southeast Asia and China. Reports on the health benefits of secondary metabolites extracted from Boesenbergia rotunda over the last few years has resulted in rising demands for panduratin A. However large scale extraction has been hindered by the naturally low abundance of the compound and limited knowledge of its biosynthetic pathway. RESULTS: Transcriptome sequencing and digital gene expression (DGE) analysis of native and phenylalanine treated Boesenbergia rotunda cell suspension cultures were carried out to elucidate the key genes differentially expressed in the panduratin A biosynthetic pathway. Based on experiments that show increase in panduratin A production after 14 days post treatment with exogenous phenylalanine, an aromatic amino acid derived from the shikimic acid pathway, total RNA of untreated and 14 days post-phenylalanine treated cell suspension cultures were extracted and sequenced using next generation sequencing technology employing an Illumina-Solexa platform. The transcriptome data generated 101, 043 unigenes with 50, 932 (50.41%) successfully annotated in the public protein databases; including 49.93% (50, 447) in the non-redundant (NR) database, 34.63% (34, 989) in Swiss-Prot, 24,07% (24, 316) in Kyoto Encyclopedia of Genes and Genomes (KEGG) and 16.26% (16, 426) in Clusters of Orthologous Groups (COG). Through DGE analysis, we found that 14, 644 unigenes were up-regulated and 14, 379 unigenes down-regulated in response to exogenous phenylalanine treatment. In the phenylpropanoid pathway leading to the proposed panduratin A production, 2 up-regulated phenylalanine ammonia-lyase (PAL), 3 up-regulated 4-coumaroyl:coenzyme A ligase (4CL) and 1 up-regulated chalcone synthase (CHS) were found. CONCLUSIONS: This is the first report of Boesenbergia rotunda de novo transcriptome data that could serve as a reference for gene or enzyme functional studies in the Zingiberaceae family. Although enzymes that are directly involved in the panduratin A biosynthetic pathway were not completely elucidated, the data provides an overall picture of gene regulation patterns leading to panduratin A production.

Bcl-xL silencing induces alterations in hsa-miR-608 expression and subsequent cell death in A549 and SK-LU1 human lung adenocarcinoma cells.

Bcl-xL is an anti-apoptotic protein that is frequently found to be overexpressed in non-small cell lung cancer leading to an inhibition of apoptosis and poor prognosis. Recently, the role of miRNAs in regulating apoptosis and cell survival during tumorigenesis has become evident, with cancer cells showing perturbed expression of various miRNAs. In this study, we utilized miRNA microarrays to determine if miRNA dysregulation in bcl-xL silenced lung adenocarcinoma cells could be involved in regulating cell death. Short interfering RNA-based transfection of A549 and SK-LU1 lung adenocarcinoma cells was successful in inducing a reduction in bcl-xL expression levels, resulting in a decrease in cell viability. A total of 10 miRNAs were found to be significantly differentially expressed when compared between siRNA-transfected and non-transfected cells including hsa-miR-181a, hsa-miR-769-5p, hsa-miR-361-5p, hsa-miR-1304 and hsa-miR-608. When overexpression studies on hsa-miR-608 was performed via transfection of miRNA mimics, cell death was found to be induced in A549 and SK-LU1 cells in comparison to untreated cells. This effect was reversed when knockdown studies involving anti-sense inhibitors were introduced. Combination of siRNA based silencing of bcl-xL (siBcl-xL) followed by anti-sense inhibitor transfection led to a decrease in the apoptotic population of A549 and SK-LU1 cells in comparison to cells only treated with siBcl-xL, illustrating the connection between bcl-xL, hsa-miR-608 and cell death. Gene target prediction analysis implicated the PI3K/AKT, WNT, TGF-ß, and ERK signaling pathways as targets of bcl-xL induced miRNA alterations. We have demonstrated that bcl-xL silencing in A549 and SK-LU1 cells leads to the occurrence of cell death through the dysregulation of specific miRNAs. This study also provides a platform for anti-sense gene therapy whereby miRNA expression can be exploited to increase the apoptotic properties in lung adenocarcinoma cells.