N4‐methylcytidine ribosomal RNA methylation in chloroplasts is crucial for chloroplast function,development, and abscisic acid response in Arabidopsis

Although the essential role of messenger RNA methylation in the nucleus is increasingly understood, the nature of ribosomal RNA (rRNA) methyltransferases and the role of rRNA methylation in chloroplasts remain largely unknown. A recent study revealed that CMAL (for Chloroplast mr aW‐ Like) is a chloroplast‐localized rRNA methyltransferase that is responsible for N4‐methylcytidine (m⁴C) in 16S chloroplast rRNA in Arabidopsis thaliana. In this study, we further examined the role of CMAL in chloroplast biogenesis and function, development, and hormone response. The cmal mutant showed reduced chlorophyll biosynthesis, photosynthetic activity, and growth‐defect phenotypes, including severely stunted stems, fewer siliques, and lower seed yield. The cmal mutant was hypersensitive to chloroplast translation inhibitors, such as lincomycin and erythromycin, indicating that the m⁴C‐methylation defect in the 16S rRNA leads to a reduced translational activity in chloroplasts. Importantly, the stunted stem of the cmal mutant was partially rescued by exogenous gibberellic acid or auxin. The cmal mutant grew poorer than wild type, whereas the CMAL‐overexpressing transgenic Arabidopsis plants grew better than wild type in the presence of abscisic acid. Altogether, these results indicate that CMAL is an indispensable rRNA methyltransferase in chloroplasts and is crucial for chloroplast biogenesis and function, photosynthesis, and hormone response during plant growth and development.     

Telomeres and a repeat-rich chromosome encode effector gene clusters in plant pathogenic Colletotrichum fungi

Members of the Colletotrichum gloeosporioides species complex are causal agents of anthracnose in many commercially important plants. Closely related strains have different levels of pathogenicity on hosts despite their close phylogenetic relationship. To gain insight into the genetics underlying these differences, we generated and annotated whole-genome assemblies of multiple isolates of C. fructicola (Cf) and C. siamense (Cs), as well as three previously unsequenced species, C. aenigma (Ca), C. tropicale and C. viniferum with different pathogenicity on strawberry. Based on comparative genomics, we identified accessory regions with a high degree of conservation in strawberry-pathogenic Cf, Cs and Ca strains. These regions encode homologs of pathogenicity-related genes known as effectors, organized in syntenic gene clusters, with copy number variations in different strains of Cf, Cs and Ca. Analysis of highly contiguous assemblies of Cf, Cs and Ca revealed the association of related accessory effector gene clusters with telomeres and repeat-rich chromosomes and provided evidence of exchange between these two genomic compartments. In addition, expression analysis indicated that orthologues in syntenic gene clusters showed a tendency for correlated gene expression during infection. These data provide insight into mechanisms by which Colletotrichum genomes evolve, acquire and organize effectors.     

Optimization of Ionic Liquid Pretreatment of Mixed Softwood by Response Surface Methodology and Reutilization of Ionic Liquid from Hydrolysate

We investigated the feasibility of producing bioethanol from mixed softwood pretreated with the ionic liquid 1-butyl-3-methylimidazolium acetate ([Bmim]Ac). The optimal pretreatment conditions were determined by response surface methodology to be 100°C for 15 h, and the fermentable sugar yield was estimated to be 92.5%. Efficient pretreatment of softwood was maintained even after reutilizing [Bmim]Ac up to four times. Through the enzymatic saccharification and subsequent fermentation, bioethanol was produced with 0.42 g/g of yield and 0.24 g/L/h of productivity, which clearly suggests that efficient and economical bioethanol production can be achieved by optimizing pretreatment processes and reutilizing ionic liquid.     

EDC3 phosphorylation regulates growth and invasion through controlling P‐body formation and dynamics

Regulation of mRNA stability and translation plays a critical role in determining protein abundance within cells. Processing bodies (P‐bodies) are critical regulators of these processes. Here, we report that the Pim1 and 3 protein kinases bind to the P‐body protein enhancer of mRNA decapping 3 (EDC3) and phosphorylate EDC3 on serine (S)161, thereby modifying P‐body assembly. EDC3 phosphorylation is highly elevated in many tumor types, is reduced upon treatment of cells with kinase inhibitors, and blocks the localization of EDC3 to P‐bodies. Prostate cancer cells harboring an EDC3 S161A mutation show markedly decreased growth, migration, and invasion in tissue culture and in xenograft models. Consistent with these phenotypic changes, the expression of integrin β1 and α6 mRNA and protein is reduced in these mutated cells. These results demonstrate that EDC3 phosphorylation regulates multiple cancer‐relevant functions and suggest that modulation of P‐body activity may represent a new paradigm for cancer treatment.     

Chemical Composition,Antimicrobial, Nitric Oxide Inhibition and Cytotoxic Activity of Essential Oils from Zanthoxylum acanthopodium DC. Leaves and Stems from Vietnam

This study was aimed to investigate the chemical composition and biological activities of leaf and stem essential oils of Zanthoxylum acanthopodium DC. from Vietnam. Their chemical composition was analyzed by GC/MS. Antimicrobial activities were evaluated by microdilution broth assay. Anti-inflammatory activity was evaluated by the ability to inhibit nitric oxide production in macrophage cells. Cytotoxic activity was evaluated using the sulforhodamine B assay on three human cancer cell lines. Forty-four compounds were identified in the leaf oil, among which dehydroaromadendrane (23.4 %), (E)-carpacin (17.6 %), 2-tridecanone (12.2 %), and 9-methyl-2-decanone (11.8 %) were the most abundant. The stem oil contained fifty-five identified constituents, mainly γ-gurjunene (51.1 %) and butyl acetate (11.8 %). Both oils exhibited inhibitory effects on three bacterial strains, namely S. aureus, E. coli, P. aeruginosa and a fungal strain C. albican, while showed insignificant effects on B. subtilis, L. fermentum, and S. enterica. Both oils showed weak NO production inhibition in LPS-induced RAW264.7 cells, but exhibited potent cytotoxic activity against all three tested cell lines SK-LU-1, MCF-7, and HepG2 with the IC₅₀ values ranging from 16.03±0.77 to 35.60±1.62 μg/mL. This is the first report on the antimicrobial, anti-inflammatory and cytotoxic activities of essential oils from the leaves and stems of Z. acanthopodium.     

SMET: Systematic multiple enzyme targeting – a method to rationally design optimal strains for target chemical overproduction

Identifying multiple enzyme targets for metabolic engineering is very critical for redirecting cellular metabolism to achieve desirable phenotypes, e.g., overproduction of a target chemical. The challenge is to determine which enzymes and how much of these enzymes should be manipulated by adding, deleting, under-, and/or over-expressing associated genes. In this study, we report the development of a systematic multiple enzyme targeting method (SMET), to rationally design optimal strains for target chemical overproduction. The SMET method combines both elementary mode analysis and ensemble metabolic modeling to derive SMET metrics including l-values and c-values that can identify rate-limiting reaction steps and suggest which enzymes and how much of these enzymes to manipulate to enhance product yields, titers, and productivities. We illustrated, tested, and validated the SMET method by analyzing two networks, a simple network for concept demonstration and an Escherichia coli metabolic network for aromatic amino acid overproduction. The SMET method could systematically predict simultaneous multiple enzyme targets and their optimized expression levels, consistent with experimental data from the literature, without performing an iterative sequence of single-enzyme perturbation. The SMET method was much more efficient and effective than single-enzyme perturbation in terms of computation time and finding improved solutions.