Endophytic Bacillus spp. from medicinal plants inhibit mycelial growth of Sclerotinia sclerotiorum and promote plant growth

Plant growth promoting bacteria that are also capable of suppressing plant pathogenic fungi play an important role in sustainable agriculture. There is a critical need of conducting research to discover, characterize and evaluate efficacy of new strains of such bacteria in controlling highly aggressive plant pathogens. In this study, we isolated endophytic bacteria from medicinal plants of Bangladesh and evaluated their antagonistic capacity against an important phytopathogenic fungus Sclerotinia sclerotiorum. Growth promoting effects of those isolates on cucumber and rice seedlings also were assessed. Among 16 morphologically distinct isolates, BDR-2, BRtL-2, and BCL-1 significantly inhibited the growth of S. sclerotiorum through induction of characteristic morphological alterations in hyphae and reduction of mycelial dry weight. When cucumber and rice seeds were treated with these endophytic bacteria, seven isolates (BCL-1, BDL-1, BRtL-2, BRtL-3, BDR-1, BDR-2 and BBoS-1) enhanced seed germination, seedling vigor, seedling growth, and number of roots per plant at varying level compared to untreated controls. All isolates produced high levels of indole-3-acetic acid (6.3 to 63μg mL−1) in vitro. Two most potential isolates, BDR-2 and BRtL-2 were identified 34 as Bacillus amyloliquefaciens and B. subtilis, respectively based on the 16S rRNA gene sequencing. These results suggest that endophytic Bacillus species from native medicinal plants have great potential for using as natural plant growth promoter and biopesticides in sustainable crop production

NRF2 DLG Domain Mutations Identified in Japanese Liver Cancer Patients Affect the Transcriptional Activity in HCC Cell Lines

Geographically, East Asia had the highest liver cancer burden in 2017. Besides this, liver can-cer-related deaths were high in Japan, accounting for 3.90% of the global deaths. The develop-ment of liver cancer is influenced by several factors and genetic alteration is one of critical fac-tors among them. Therefore, a detailed mechanism driving the oncogenic transformation of liv-er cells needs to be elucidated. Recently, many researchers have focused on investigating the liver cancer genome and identified somatic mutations (MTs) of several transcription factors. In this line, next-generation sequencing of the cancer genome identified that oxidative stress-related transcription factor NRF2 (NFE2L2) is mutated in different cancers, including hepatocellular carcinoma (HCC). Here, we demonstrate NRF2 DLG mutations (NRF2 D29A and L30F), found in Japanese liver cancer patients, upregulate the transcriptional activity of NRF2 in HCC cell lines. Moreover, the transcriptional activity of NRF2 mutations is not suppressed by KEAP1, presumably because NRF2 MTs disturb proper NRF2-KEAP1 binding and block KEAP1-mediated degradation of NRF2. Additionally, we exhibit that both MTs upregulate the transcriptional activity of NRF2 on MMP9 promoter in Hepa1-6 and Huh7 cells, suggesting that MTs derived gain-of-function of NRF2 may be important for liver tumor progression. We also find ectopic overexpression of oncogenic BRAF WT and V600E increased the transcriptional ac-tivity of NRF2 WT on both 3xARE reporter and MMP9 promoter. Interestingly, NRF2 D29A and L30F MTs with oncogenic BRAF V600E MT synergistically upregulate the transcription activity of NRF2 on 3xARE reporter and MMP9 promoter in Hepa1-6 and Huh7 cells. In summary, our findings suggest that MTs in NRF2 have the pathogenic effect, and NRF2 MTs together with on-cogenic BRAF V600E MT synergistically cause more aberrant transcriptional activity. The high activity of NRF2 MTs in HCC with BRAF MT warrants further exploration of this pathway\u27s po-tential diagnostic, prognostic, and therapeutic utility in HCC

HNF1A POU Domain Mutations Found in Japanese Liver Cancer Patients Cause Downregulation of HNF4A Promoter Activity with Possible Disruption in Transcription Networks

Hepatocyte nuclear factor 1A (HNF1A) is the master regulator of liver homeostasis and organogenesis and regulates many aspects of hepatocyte functions. It acts as a tumor suppressor in the liver, evidenced by the increased proliferation in HNF1A knockout (KO) hepatocytes. Hence, we postulated that any loss-of-function variation in the gene structure or composition (mutation)could trigger dysfunction, including disrupted transcriptional networks in liver cells. From the International Cancer Genome Consortium (ICGC) database of cancer genomes, we identified several HNF1A mutations located in the functional Pit-Oct-Unc (POU) domain. In our biochemical analysis, we found that the HNF1A POU-domain mutations Y122C, R229Q and V259F suppressedHNF4A promoter activity and disrupted the binding of HNF1A to its target HNF4A promoter without any effect on the nuclear localization. Our results suggest that the decreased transcriptional activity of HNF1A mutants is due to impaired DNA binding. Through structural simulation analysis, we found that a V259F mutation was likely to affect DNA interaction by inducing large conformational changes in the N-terminal region of HNF1A. The results suggest that POU-domainmutations of HNF1A downregulate HNF4A gene expression. Therefore, to mimic the HNF1A mutation phenotype in transcription networks, we performed siRNA-mediated knockdown (KD) of HNF4A. Through RNA-Seq data analysis for the HNF4A KD, we found 748 differentially expressed genes (DEGs), of which 311 genes were downregulated (e.g., HNF1A, ApoB and SOAT2) and 437 genes were upregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) mapping revealed that the DEGs were involved in several signaling pathways (e.g., lipid and cholesterol metabolic pathways). Protein–protein network analysis suggested that the downregulated genes were related to lipid and cholesterol metabolism pathways, which are implicated in hepatocellularcarcinoma (HCC) development. Our study demonstrates that mutations of HNF1A in the POU domain result in the downregulation of HNF1A target genes, including HNF4A, and this may trigger HCC development through the disruption of HNF4A–HNF1A transcriptional networks

Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges

The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein9) genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses

Endophytic Bacillus spp. from medicinal plants inhibit mycelial growth of Sclerotinia sclerotiorum and promote plant growth

Plant growth-promoting bacteria that are also capable of suppressing plant pathogenic fungi play an important role in sustainable agriculture. There is a critical need for conducting research to discover, characterize and evaluate the efficacy of new strains of such bacteria in controlling highly aggressive plant pathogens. In this study, we isolated endophytic bacteria from medicinal plants of Bangladesh and evaluated their antagonistic capacity against an important phytopathogenic fungus Sclerotinia sclerotiorum. Growth-promoting effects of those isolates on cucumber and rice seedlings were also assessed. Among 16 morphologically distinct isolates, BDR-2, BRtL-2 and BCL-1 significantly inhibited the growth of S. sclerotiorum through induction of characteristic morphological alterations in hyphae and reduction of mycelial dry weight. When cucumber and rice seeds were treated with these endophytic bacteria, seven isolates (BCL-1, BDL-1, BRtL-2, BRtL-3, BDR-1, BDR-2 and BBoS-1) enhanced seed germination, seedling vigor, seedling growth and number of roots per plant at a varying level compared to untreated controls. All isolates produced high levels of indole-3-acetic acid (6 to 63 μg/mL) in vitro. Two most potential isolates, BDR-2 and BRtL-2, were identified as Bacillus amyloliquefaciens and B. subtilis, respectively, based on the 16S rRNA gene sequencing. These results suggest that endophytic Bacillus species from native medicinal plants have great potential for being used as natural plant growth promoter and biopesticides in sustainable crop production