Water Res , IF:11.236 , 2024 Apr , V253 : P121299 doi: 10.1016/j.watres.2024.121299
Unveiling intricate transformation pathways of emerging contaminants during wastewater treatment processes through simplified network analysis.
State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023 Jiangsu, China.; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400044, China.; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023 Jiangsu, China. Electronic address: weisi@nju.edu.cn.; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023 Jiangsu, China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400044, China. Electronic address: jjgeng@nju.edu.cn.
As the key stage for purifying wastewater, elimination of emerging contaminants (ECs) is found to be fairly low in wastewater treatment plants (WWTPs). However, less knowledge is obtained regarding the transformation pathways between various chemical structures of ECs under different treatment processes. This study unveiled the transformation pathways of ECs with different structures in 15 WWTPs distributed across China by simplified network analysis (SNA) we proposed. After treatment, the molecular weight of the whole component of wastewater decreased and the hydrophilicity increased. There are significant differences in the structure of eliminated, consistent and formed pollutants. Amino acids, peptides, and analogues (AAPAs) were detected most frequently and most removable. Benzenoids were refractory. Triazoles were often produced. The high-frequency reactions in different WWTPs were similar, (de)methylation and dehydration occurred most frequently. Different biological treatment processes performed similarly, while some advanced treatment processes differed, such as a significant increase of -13.976 (2HO reaction) paired mass distances (PMDs) in the chlorine alone process. Further, the common structural transformation was uncovered. 4 anti-hypertensive drugs, including irbesartan, valsartan, olmesartan, and losartan, were identified, along with 22 transformation products (TPs) of them. OH(2) and H(2)O PMDs occurred most frequently and in 80.81 % of the parent-transformation product pairs, the intensity of the product was higher than parent in effluents, whose risk should be considered in future assessment activity. Together our results provide a macrography perspective on the transformation processes of ECs in WWTPs. In the future, selectively adopting wastewater treatment technology according to structures is conductive for eliminating recalcitrant ECs in WWTPs.
PMID: 38387265
Proc Natl Acad Sci U S A , IF:11.205 , 2024 Apr , V121 (18) : Pe2322751121 doi: 10.1073/pnas.2322751121
Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes.
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907.; Center for Plant Biology, Purdue University, West Lafayette, IN 47907.; United States Department of Agriculture-Agricultural Research Service Crop Production and Pest Control Research Unit, West Lafayette, IN 47907.
Organ-specific gene expression datasets that include hundreds to thousands of experiments allow the reconstruction of organ-level gene regulatory networks (GRNs). However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here, we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, and seed in Arabidopsis thaliana. A GRN inference approach was used to determine the: i. influential transcription factors (TFs) in each organ and, ii. most influential TFs for specific biological processes in that organ. These genome-wide, organ-delimited GRNs (OD-GRNs), recalled many known regulators of organ development and processes operating in those organs. Importantly, many previously unknown TF regulators were uncovered as potential regulators of these processes. As a proof-of-concept, we focused on experimentally validating the predicted TF regulators of lipid biosynthesis in seeds, an important food and biofuel trait. Of the top 20 predicted TFs, eight are known regulators of seed oil content, e.g., WRI1, LEC1, FUS3. Importantly, we validated our prediction of MybS2, TGA4, SPL12, AGL18, and DiV2 as regulators of seed lipid biosynthesis. We elucidated the molecular mechanism of MybS2 and show that it induces purple acid phosphatase family genes and lipid synthesis genes to enhance seed lipid content. This general approach has the potential to be extended to any species with sufficiently large gene expression datasets to find unique regulators of any trait-of-interest.
PMID: 38652750
J Hazard Mater , IF:10.588 , 2024 May , V469 : P134085 doi: 10.1016/j.jhazmat.2024.134085
Plant growth-promoting bacteria improve the Cd phytoremediation efficiency of soils contaminated with PE-Cd complex pollution by influencing the rhizosphere microbiome of sorghum.
International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China.; International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China. Electronic address: 17657311626@163.com.; International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China. Electronic address: zhaojin_chen@163.com.
Composite pollution by microplastics and heavy metals poses a potential threat to the soilplant system and has received increasing attention. Plant growth-promoting bacteria (PGPB) have good application potential for the remediation of combined microplastic and heavy metal pollution, but few related studies exist. The present study employed a pot experiment to investigate the effects of inoculation with the PGPB Bacillus sp. SL-413 and Enterobacter sp. VY-1 on sorghum growth and Cd accumulation under conditions of combined cadmium (Cd) and polyethylene (PE) pollution. Cd+PE composite contamination led to a significant reduction in sorghum length and biomass due to increased toxicity. Inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 alleviated the stress caused by Cd+PE complex pollution, and the dry weight of sorghum increased by 25.7% to 46.1% aboveground and by 12.3% to 45.3% belowground. Bacillus sp. SL-413 and Enterobacter sp. VY-1 inoculation increased the Cd content and accumulation in sorghum and improved the phytoremediation efficiency of Cd. The inoculation treatment effectively alleviated the nutrient stress caused by the reduction in soil mineral nutrients due to Cd+PE composite pollution. The composition of the soil bacterial communities was also affected by the Cd, Cd+PE and bacterial inoculation treatments, which affected the diversity of the soil bacterial communities. Network analyses indicated that bacterial inoculation regulated the interaction of rhizospheric microorganisms and increased the stability of soil bacterial communities. The Mantel test showed that the changes in the soil bacterial community and function due to inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 were important factors influencing sorghum growth and Cd remediation efficiency. The results of this study will provide new evidence for the research on joint plantmicrobe remediation of heavy metal and microplastic composite pollution.
PMID: 38522197
New Phytol , IF:10.151 , 2024 Apr doi: 10.1111/nph.19734
Isotopically nonstationary metabolic flux analysis of plants: recent progress and future opportunities.
Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA.; United States Department of Agriculture, Agriculture Research Service, 975 North Warson Road, St Louis, MO, 63132, USA.
Metabolic flux analysis (MFA) is a valuable tool for quantifying cellular phenotypes and to guide plant metabolic engineering. By introducing stable isotopic tracers and employing mathematical models, MFA can quantify the rates of metabolic reactions through biochemical pathways. Recent applications of isotopically nonstationary MFA (INST-MFA) to plants have elucidated nonintuitive metabolism in leaves under optimal and stress conditions, described coupled fluxes for fast-growing algae, and produced a synergistic multi-organ flux map that is a first in MFA for any biological system. These insights could not be elucidated through other approaches and show the potential of INST-MFA to correct an oversimplified understanding of plant metabolism.
PMID: 38628036
New Phytol , IF:10.151 , 2024 Apr doi: 10.1111/nph.19737
Genome-wide association study and network analysis of in vitro transformation in Populus trichocarpa support key roles of diverse phytohormone pathways and cross talk.
Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.; School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA.; Statistics Department, Oregon State University, Corvallis, OR, 97331, USA.; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.; Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA.
Wide variation in amenability to transformation and regeneration (TR) among many plant species and genotypes presents a challenge to the use of genetic engineering in research and breeding. To help understand the causes of this variation, we performed association mapping and network analysis using a population of 1204 wild trees of Populus trichocarpa (black cottonwood). To enable precise and high-throughput phenotyping of callus and shoot TR, we developed a computer vision system that cross-referenced complementary red, green, and blue (RGB) and fluorescent-hyperspectral images. We performed association mapping using single-marker and combined variant methods, followed by statistical tests for epistasis and integration of published multi-omic datasets to identify likely regulatory hubs. We report 409 candidate genes implicated by associations within 5 kb of coding sequences, and epistasis tests implicated 81 of these candidate genes as regulators of one another. Gene ontology terms related to protein-protein interactions and transcriptional regulation are overrepresented, among others. In addition to auxin and cytokinin pathways long established as critical to TR, our results highlight the importance of stress and wounding pathways. Potential regulatory hubs of signaling within and across these pathways include GROWTH REGULATORY FACTOR 1 (GRF1), PHOSPHATIDYLINOSITOL 4-KINASE beta1 (PI-4Kbeta1), and OBF-BINDING PROTEIN 1 (OBP1).
PMID: 38650352
New Phytol , IF:10.151 , 2024 May , V242 (3) : P1307-1323 doi: 10.1111/nph.19660
Genetic underpinnings of arthropod community distributions in Populus trichocarpa.
Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.; Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.; The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA.; Computational Systems Biology Group, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.; Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, 80309, USA.; Department of Biology, Georgetown University, Washington, DC, 20057, USA.
Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.
PMID: 38488269
New Phytol , IF:10.151 , 2024 Apr , V242 (2) : P786-796 doi: 10.1111/nph.19591
Sorghum SbGhd7 is a major regulator of floral transition and directly represses genes crucial for flowering activation.
Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA.; Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA.; National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY, 11973, USA.; College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Department of Soil and Crop Science, University of Georgia, Athens, GA, 30602, USA.; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.; Key Laboratory of Tropical Plant Resources and Sustainable Use, Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
Molecular genetic understanding of flowering time regulation is crucial for sorghum development. GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (SbGhd7) is one of the six classical loci conferring photoperiod sensitivity of sorghum flowering. However, its functions remain poorly studied. The molecular functions of SbGhd7 were characterized. The gene regulatory network controlled by SbGhd7 was constructed and validated. The biological roles of SbGhd7 and its major targets were studied. SbGhd7 overexpression (OE) completely prevented sorghum flowering. Additionally, we show that SbGhd7 is a major negative regulator of flowering, binding to the promoter motif TGAATG(A/T)(A/T/C) and repressing transcription of the major florigen FLOWERING LOCUS T 10 (SbFT10) and floral activators EARLY HEADING DATE (SbEhd1), FLAVIN-BINDING, KELCH REPEAT, F-BOX1 (SbFKF1) and EARLY FLOWERING 3 (SbELF3). Reinforcing the direct effect of SbGhd7, SbEhd1 OE activated the promoters of three functional florigens (SbFT1, SbFT8 and SbFT10), dramatically accelerating flowering. Our studies demonstrate that SbGhd7 is a major repressor of sorghum flowering by directly and indirectly targeting genes for flowering activation. The mechanism appears ancient. Our study extends the current model of floral transition regulation in sorghum and provides a framework for a comprehensive understanding of sorghum photoperiod response.
PMID: 38451101
Metab Eng , IF:9.783 , 2024 Mar , V83 : P86-101 doi: 10.1016/j.ymben.2024.03.009
Resource allocation modeling for autonomous prediction of plant cell phenotypes.
Universite Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France. Electronic address: anne.goelzer@inrae.fr.; Universite Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.; Universite Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France. Electronic address: vincent.fromion@inrae.fr.
Predicting the plant cell response in complex environmental conditions is a challenge in plant biology. Here we developed a resource allocation model of cellular and molecular scale for the leaf photosynthetic cell of Arabidopsis thaliana, based on the Resource Balance Analysis (RBA) constraint-based modeling framework. The RBA model contains the metabolic network and the major macromolecular processes involved in the plant cell growth and survival and localized in cellular compartments. We simulated the model for varying environmental conditions of temperature, irradiance, partial pressure of CO(2) and O(2), and compared RBA predictions to known resource distributions and quantitative phenotypic traits such as the relative growth rate, the C:N ratio, and finally to the empirical characteristics of CO(2) fixation given by the well-established Farquhar model. In comparison to other standard constraint-based modeling methods like Flux Balance Analysis, the RBA model makes accurate quantitative predictions without the need for empirical constraints. Altogether, we show that RBA significantly improves the autonomous prediction of plant cell phenotypes in complex environmental conditions, and provides mechanistic links between the genotype and the phenotype of the plant cell.
PMID: 38561149
Sci Total Environ , IF:7.963 , 2024 Jun , V927 : P171301 doi: 10.1016/j.scitotenv.2024.171301
Impact of harmful algal bloom severity on bacterial communities in a full-scale biological filtration system for drinking water treatment.
Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH 43606, United States of America.; Water Infrastructure Division, Center for Environmental Solutions and Emergency Response, U.S. Environmental Protection Agency, Cincinnati, OH 45268, United States of America.; Carollo Engineers' Research and Development Practice, Costa Mesa, CA 92626, United States of America.; City of Toledo Colins Park Water Treatment, Toledo, OH 43605, United States of America.; Department of Civil and Environmental Engineering, University of Toledo, Mail Stop 307, 3006 Nitschke Hall, Toledo, OH 43606, United States of America; Department of Chemical and Engineering, University of Toledo, Mail Stop 307, 3048 Nitschke Hall, Toledo, OH 43606, United States of America. Electronic address: Youngwoo.Seo@utoledo.edu.
The occurrence of harmful algal blooms (HABs) in freshwater environments has been expanded worldwide with growing frequency and severity. HABs can pose a threat to public water supplies, raising concerns about safety of treated water. Many studies have provided valuable information about the impacts of HABs and management strategies on the early-stage treatment processes (e.g., pre-oxidation and coagulation/flocculation) in conventional drinking water treatment plants (DWTPs). However, the potential effect of HAB-impacted water in the granular media filtration has not been well studied. Biologically-active filters (BAFs), which are used in drinking water treatment and rely largely on bacterial community interactions, have not been examined during HABs in full-scale DWTPs. In this study, we assessed the bacterial community structure of BAFs, functional profiles, assembly processes, and bio-interactions in the community during both severe and mild HABs. Our findings indicate that bacterial diversity in BAFs significantly decreases during severe HABs due to the predominance of bloom-associated bacteria (e.g., Spingopyxis, Porphyrobacter, and Sphingomonas). The excitation-emission matrix combined with parallel factor analysis (EEM-PARAFAC) confirmed that filter influent affected by the severe HAB contained a higher portion of protein-like substances than filter influent samples during a mild bloom. In addition, BAF community functions showed increases in metabolisms associated with intracellular algal organic matter (AOM), such as lipids and amino acids, during severe HABs. Further ecological process and network analyses revealed that severe HAB, accompanied by the abundance of bloom-associated taxa and increased nutrient availability, led to not only strong stochastic processes in the assembly process, but also a bacterial community with lower complexity in BAFs. Overall, this study provides deeper insights into BAF bacterial community structure, function, and assembly in response to HABs.
PMID: 38423320
Sci Total Environ , IF:7.963 , 2024 Apr , V919 : P170801 doi: 10.1016/j.scitotenv.2024.170801
Quality variation and salt-alkali-tolerance mechanism of Cynomorium songaricum: Interacting from microbiome-transcriptome-metabolome.
Key lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China.; Center for Biotechnology & Microbiology, University of Peshawar, 25000 Peshawar, Pakistan.; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China. Electronic address: peixjin@163.com.; Key lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China. Electronic address: lfhuang@implad.ac.cn.
Addressing soil salinization and implementing sustainable practices for cultivating cash crops on saline-alkali land is a prominent global challenge. Cynomorium songaricum is an important salt-alkali tolerant medicinal plant capable of adapting to saline-alkali environments. In this study, two typical ecotypes of C. songaricum from the desert-steppe (DS) and saline-alkali land (SAL) habitats were selected. Through the integration of multi-omics with machine learning, the rhizosphere microbial communities, genetic maps, and metabolic profiles of two ecotypes were created and the crucial factors for the adaptation of C. songaricum to saline-alkali stress were identified, including 7 keystone OTUs (i.e. Novosphingobium sp., Sinorhizobium meliloti, and Glycomyces sp.), 5 core genes (cell wall-related genes), and 10 most important metabolites (i.e. cucurbitacin D and 3-Hydroxybutyrate) were identified. Our results indicated that under saline-alkali environments, the microbial competition might become more intense, and the microbial community network had the simple but stable structure, accompanied by the changes in the gene expression related to cell wall for adaptation. However, this regulation led to the reduction in active ingredients, such as the accumulation of flavonoids and organic acid, and enhanced the synthesis of bitter substances (cucurbitacin D), resulting in the decrease in the quality of C. songaricum. Therefore, compared to the SAL ecotype, the DS was more suitable for the subsequent development of medicinal and edible products of C. songaricum. Furthermore, to explore the reasons for this quality variation, we constructed a comprehensive microbial-genetic-metabolic regulatory network, revealing that the metabolism of C. songaricum was primarily influenced by genetic factors. These findings not only offer new insights for future research into plant salt-alkali tolerance strategies but also provide a crucial understanding for cultivating high-quality medicinal plants.
PMID: 38340858
Plant Cell Physiol , IF:4.927 , 2024 Apr doi: 10.1093/pcp/pcae037
Multiple roles of brassinosteroid signaling in vascular development.
College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan.; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.; Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Kobe 657-8501, Japan.; Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043, Japan.
Brassinosteroids (BRs) are plant steroid hormones that control growth and stress responses. In the context of development, BRs play diverse roles in controlling cell differentiation and tissue patterning. The vascular system, which is essential for transporting water and nutrients throughout the plant body, initially establishes a tissue pattern during primary development and then dramatically increases the number of vascular cells during secondary development. This complex developmental process is properly regulated by a network consisting of various hormonal signalling pathways. Genetic studies have revealed that mutants defective in BR biosynthesis or the BR signalling cascade exhibit a multifaceted vascular development phenotype. Furthermore, BR crosstalk with other plant hormones, including peptide hormones, coordinately regulates vascular development. Recently, the involvement of BR in vascular development, especially in xylem differentiation, has also been suggested in plant species other than the model plant Arabidopsis thaliana. In this review, we briefly summarize the recent findings on the roles of BR in primary and secondary vascular development in Arabidopsis and other species.
PMID: 38590039
Plant Physiol Biochem , IF:4.27 , 2024 Apr , V210 : P108609 doi: 10.1016/j.plaphy.2024.108609
Integrated omics approach reveals the molecular pathways activated in tomato by Kocuria rhizophila, a soil plant growth-promoting bacterium.
University Mediterranea of Reggio Calabria, AGRARIA Department, Localita Feo di Vito, 89122, Reggio Calabria, Italy.; National Research Council, Institute of Biosciences and Bioresources (IBBR), Via Ugo La Malfa 153, 90146, Palermo, Italy; University of Palermo, SAAF Department, Viale Delle Scienze, 90128, Palermo, Italy.; University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy.; National Research Council, Institute of Biosciences and Bioresources (IBBR), Via Ugo La Malfa 153, 90146, Palermo, Italy.; National Research Council, Proteomics, Metabolomics and Mass Spectrometry Laboratory (ISPAAM), Piazzale E. Fermi 1, 80055, Portici, (Napoli), Italy.; Mugavero Teresa S.A.S., Corso Umberto e Margherita 1B, 90018, Termini Imerese, (Palermo), Italy.; University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy.; National Research Council, Institute of Biosciences and Bioresources (IBBR), Via Ugo La Malfa 153, 90146, Palermo, Italy. Electronic address: francesco.mercati@cnr.it.
Plant microbial biostimulants application has become a promising and eco-friendly agricultural strategy to improve crop yields, reducing chemical inputs for more sustainable cropping systems. The soil dwelling bacterium Kocuria rhizophila was previously characterized as Plant Growth Promoting Bacteria (PGPB) for its multiple PGP traits, such as indole-3-acetic acid production, phosphate solubilization capability and salt and drought stress tolerance. Here, we evaluated by a multi-omics approach, the PGP activity of K. rhizophila on tomato, revealing the molecular pathways by which it promotes plant growth. Transcriptomic analysis showed several up-regulated genes mainly related to amino acid metabolism, cell wall organization, lipid and secondary metabolism, together with a modulation in the DNA methylation profile, after PGPB inoculation. In agreement, proteins involved in photosynthesis, cell division, and plant growth were highly accumulated by K. rhizophila. Furthermore, "amino acid and peptides", "monosaccharides", and "TCA" classes of metabolites resulted the most affected by PGPB treatment, as well as dopamine, a catecholamine neurotransmitter mediating plant growth through S-adenosylmethionine decarboxylase (SAMDC), a gene enhancing the vegetative growth, up-regulated in tomato by K. rhizophila treatment. Interestingly, eight gene modules well correlated with differentially accumulated proteins (DAPs) and metabolites (DAMs), among which two modules showed the highest correlation with nine proteins, including a nucleoside diphosphate kinase, and cytosolic ascorbate peroxidase, as well as with several amino acids and metabolites involved in TCA cycle. Overall, our findings highlighted that sugars and amino acids, energy regulators, involved in tomato plant growth, were strongly modulated by the K. rhizophila-plant interaction.
PMID: 38615442
Tree Physiol , IF:4.196 , 2024 Apr doi: 10.1093/treephys/tpae040
Transcriptional dynamics reveals the asymmetrical events underlying graft union formation in pecan (Carya illinoinensis).
Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China.; Jiangsu Engineering Research Center for the Germplasm Innovation and Utilization of Pecan.
Grafting is a widely used technique for pecan propagation, however, the background molecular events underlying grafting are still poorly understood. In our study, the graft partners during pecan graft union formation were separately sampled for RNA-seq, and the transcriptional dynamics were described via weighted gene co-expression network analysis (WGCNA). To reveal the main events underlying grafting, the correlations between modules and grafting traits were analyzed. Functional annotation showed that during the entire graft process, signal transduction was activated in the scion, while mRNA splicing was induced in the rootstock. At 2 DAG, the main processes occurred in the scion were associated with protein synthesis and processing, while the primary processes happened in the rootstock were energy release-related. During the period of 7-14 DAG, defense response was a critical process worked in the scion, however, the main process functioned in the rootstock was photosynthesis. From 22 to 32 DAG, the principal processes taken place in the scion were jasmonic acid biosynthesis and defense response, whereas the highly activated processes associated with the rootstock were auxin biosynthesis and plant-type secondary cell wall biogenesis. Detection of hydrogen peroxide contents as well as peroxidase and beta-1,3-glucanase activities showed that their levels were increased in the scion not the rootstock at certain time points after grafting. Our study reveals that the scion and rootstock might response asymmetrically to grafting in pecan, and the scion was likely associated with stress response, while the rootstock was probably involved in energy supply and xylem bridge differentiation during graft union formation.
PMID: 38598328
Planta , IF:4.116 , 2024 Apr , V259 (5) : P120 doi: 10.1007/s00425-024-04390-6
Transcriptome and small RNA analysis unveils novel insights into the C(4) gene regulation in sugarcane.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China.; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Department of Plant Biology, The University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China. zjisen@gxu.edu.cn.
This study reveals miRNA indirect regulation of C(4) genes in sugarcane through transcription factors, highlighting potential key regulators like SsHAM3a. C(4) photosynthesis is crucial for the high productivity and biomass of sugarcane, however, the miRNA regulation of C(4) genes in sugarcane remains elusive. We have identified 384 miRNAs along the leaf gradients, including 293 known miRNAs and 91 novel miRNAs. Among these, 86 unique miRNAs exhibited differential expression patterns, and we identified 3511 potential expressed targets of these differentially expressed miRNAs (DEmiRNAs). Analyses using Pearson correlation coefficient (PCC) and Gene Ontology (GO) enrichment revealed that targets of miRNAs with positive correlations are integral to chlorophyll-related photosynthetic processes. In contrast, negatively correlated pairs are primarily associated with metabolic functions. It is worth noting that no C(4) genes were predicted as targets of DEmiRNAs. Our application of weighted gene co-expression network analysis (WGCNA) led to a gene regulatory network (GRN) suggesting miRNAs might indirectly regulate C(4) genes via transcription factors (TFs). The GRAS TF SsHAM3a emerged as a potential regulator of C(4) genes, targeted by miR171y and miR171am, and exhibiting a negative correlation with miRNA expression along the leaf gradient. This study sheds light on the complex involvement of miRNAs in regulating C(4) genes, offering a foundation for future research into enhancing sugarcane's photosynthetic efficiency.
PMID: 38607398
J Sci Food Agric , IF:3.638 , 2024 May , V104 (7) : P4109-4127 doi: 10.1002/jsfa.13293
Integrative metabolome and transcriptome profiling provide insights into elucidation of the synthetic mechanisms of phenolic compounds in Yunnan hulled wheat (Triticum aestivum ssp. yunnanense King).
College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.; College of Tropical Crops, Yunnan Agricultural University, Kunming, China.; Agricultural Technology Extension Station of Lincang, Lincang, China.; Jiangshu Lixiahe Institue of Agriculture Science, Yangzhou, China.
BACKGROUND: Yunnan hulled wheat grains (YHWs) have abundant phenolic compounds (PCs). However, a systematic elucidation of the phenolic characteristics and molecular basis in YHWs is currently lacking. The aim of the study, for the first time, was to conduct metabolomic and transcriptomic analyses of YHWs at different developmental stages. RESULTS: A total of five phenolic metabolite classes (phenolic acids, flavonoids, quinones, lignans and coumarins, and tannins) and 361 PCs were identified, with flavonoids and phenolic acids being the most abundant components. The relative abundance of the identified PCs showed a dynamic decreasing pattern with grain development, and the most significant differences in accumulation were between the enlargement and mature stage, which is consistent with the gene regulation patterns of the corresponding phenolic biosynthesis pathway. Through co-expression and co-network analysis, PAL, HCT, CCR, F3H, CHS, CHI and bZIP were identified and predicted as candidate key enzymes and transcription factors. CONCLUSION: The results broaden our understanding of PC accumulation in wheat whole grains, especially the differential transfer between immature and mature grains. The identified PCs and potential regulatory factors provide important information for future in-depth research on the biosynthesis of PCs and the improvement of wheat nutritional quality. (c) 2024 Society of Chemical Industry.
PMID: 38308467
Enzyme Microb Technol , IF:3.493 , 2024 Jun , V177 : P110429 doi: 10.1016/j.enzmictec.2024.110429
Towards consolidated bioprocessing of biomass and plastic substrates for semi-synthetic production of bio-poly(ethylene furanoate) (PEF) polymer using omics-guided construction of artificial microbial consortia.
Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), UKM, Bangi, Selangor 43600, Malaysia.; Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia; Centre for Sustainable Process Technology (CESPRO), Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia.; BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.; Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), UKM, Bangi, Selangor 43600, Malaysia. Electronic address: bazliramzi@ukm.edu.my.
Poly(ethylene furanoate) (PEF) plastic is a 100% renewable polyester that is currently being pursued for commercialization as the next-generation bio-based plastic. This is in line with growing demand for circular bioeconomy and new plastics economy that is aimed at minimizing plastic waste mismanagement and lowering carbon footprint of plastics. However, the current catalytic route for the synthesis of PEF is impeded with technical challenges including high cost of pretreatment and catalyst refurbishment. On the other hand, the semi-biosynthetic route of PEF plastic production is of increased biotechnological interest. In particular, the PEF monomers (Furan dicarboxylic acid and ethylene glycol) can be synthesized via microbial-based biorefinery and purified for subsequent catalyst-mediated polycondensation into PEF. Several bioengineering and bioprocessing issues such as efficient substrate utilization and pathway optimization need to be addressed prior to establishing industrial-scale production of the monomers. This review highlights current advances in semi-biosynthetic production of PEF monomers using consolidated waste biorefinery strategies, with an emphasis on the employment of omics-driven systems biology approaches in enzyme discovery and pathway construction. The roles of microbial protein transporters will be discussed, especially in terms of improving substrate uptake and utilization from lignocellulosic biomass, as well as from depolymerized plastic waste as potential bio-feedstock. The employment of artificial bioengineered microbial consortia will also be highlighted to provide streamlined systems and synthetic biology strategies for bio-based PEF monomer production using both plant biomass and plastic-derived substrates, which are important for circular and new plastics economy advances.
PMID: 38537325
Plant Commun , 2024 Apr : P100920 doi: 10.1016/j.xplc.2024.100920
Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses.
Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 121, SI-1000 Ljubljana, Slovenia. Electronic address: carissa.bleker@nib.si.; Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 121, SI-1000 Ljubljana, Slovenia.; Plant Cell Biology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany.; Department of Knowledge Technologies, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia.; Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, AT-1030 Vienna, Austria.; Mass spectrometry unit, Core Facility Shared Services, University of Vienna, Djerassiplatz 1, AT-1030 Vienna, Austria.
Stress Knowledge Map (SKM, https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs describing current knowledge of biochemical, signalling, and regulatory molecular interactions in plants: a highly curated model of plant stress signalling (PSS, 543 reactions) and a large comprehensive knowledge network (CKN, 488,390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entrypoint for plant stress response investigations and the related growth trade-offs as well as interactive exploration of current knowledge. PSS is also formulated as qualitative and quantitative models for systems biology, and thus represents a starting point of a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation, design of validation experiments, or to gain new insights into experimental observations in plant biology.
PMID: 38616489
Cureus , 2024 Apr , V16 (4) : Pe57430 doi: 10.7759/cureus.57430
Bibliometric Analysis and Visualization of Clinical Trials on the Therapeutic Potential of Essential Oils (1967-2024).
Dentistry, Karnavati Scientific Research Center, Karnavati School of Dentistry, Karnavati University, Gandhinagar, IND.; Therapeutics, Karnavati Scientific Research Center, Karnavati School of Dentistry, Karnavati University, Gandhinagar, IND.; Pharmacology and Therapeutics, National Defence University of Malaysia, Kuala Lumpur, MYS.; Periodontology and Implantology, Karnavati Scientific Research Center, Karnavati School of Dentistry, Karnavati University, Gandhinagar, IND.
Essential oils, aromatic compounds extracted from various parts of plants, have garnered significant attention in recent years due to their diverse therapeutic properties and potential applications in healthcare. This analysis delves into the publication trends, productivity patterns, most relevant contributors, coauthorship networks, most frequently used keywords, and their co-occurrence, topic trends, thematic evolution, and collaboration between various countries in clinical trials exploring the therapeutic potential of essential oils. Six hundred sixty-one clinical trials were selected from the PubMed database for analysis, authored by 2959 authors, and published across 359 sources. The analysis identified Horrobin DF as the most contributing author based on the number of published clinical trials, followed by Kasper S, McGuire JA, and Schlafke S. Lotka's law underscores the distribution of authors' productivity, revealing a small number of highly productive authors. Coauthorship analysis identifies significant collaborations among authors and institutions, with prominent contributors like Siegfried Kasper and institutions like Shiraz University of Medical Sciences. Furthermore, the analysis highlights leading journals like Complementary Therapies in Clinical Practice and the Journal of Alternative and Complementary Medicine. Using keyword clustering, connections between various subjects and their chronological presence are uncovered, offering insights into the changing research landscape. The thematic examination exposes changes in research emphasis over time, progressing from fundamental studies on essential oil components to broader utilization and focused inquiries into oils and therapeutic domains. Analysis of the countries of corresponding authors revealed that Iran has the highest number of multiple-country publications. Moreover, international collaboration trends have been unveiled. Together, these analyses furnish holistic understandings of keyword relationships, thematic shifts, and global partnerships in essential oil research, presenting valuable perspectives on trends and focal points within this domain.
PMID: 38572180
J Biomol Struct Dyn , 2024 Apr , V42 (7) : P3382-3395 doi: 10.1080/07391102.2023.2213341
Computational investigation of phytochemicals identified from medicinal plant extracts against tuberculosis.
Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.; Sygnature Discovery, Nottingham, United Kingdom.
Tuberculosis (TB) is still one of the world's most challenging infectious diseases and the emergence of drug-resistant Mycobacterium tuberculosis poses a significant threat to the treatment of TB. Identifying new medications based on local traditional remedies has become more essential. Gas Chromatography-Mass spectrometry (GC-MS) (Perkin-Elmer, MA, USA) was used to identify potential bioactive components in Solanum surattense, Piper longum, and Alpinia galanga plants sections. The fruits and rhizomes' chemical compositions were analyzed using solvents like petroleum ether, chloroform, ethyl acetate, and methanol. A total of 138 phytochemicals were identified, further categorized and finalized with 109 chemicals. The phytochemicals were docked with selected proteins (ethA, gyrB, and rpoB) using AutoDock Vina. The top complexes were selected and preceded with molecular dynamics simulation. It was found that the rpoB-sclareol complex is very stable, which means it could be further explored. The compounds were further studied for ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties. Sclareol has obeyed all the rules and it might be a potential chemical to treat TB.Communicated by Ramaswamy H. Sarma.
PMID: 37211911