New Phytol , IF:8.512 , 2021 Jan doi: 10.1111/nph.17179
Growth-Regulating Factor 5 (GRF5)-mediated gene regulatory network promotes leaf growth and expansion in poplar.
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, P.R. China.; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, P.R. China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin, 150040, P. R. China, Harbin.; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, P.R. China.; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, United States of America.
Although polyploid plants have larger leaves than their diploid counterparts, the molecular mechanisms underlying this difference (or trait) remain elusive. Differentially expressed genes (DEGs) between triploid and full-sib diploid poplar trees were identified from two transcriptomic data sets followed by a gene association study among DEGs to identify key leaf growth regulators. Yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay were employed to substantiate that PpnGRF5-1 directly regulated PpnCKX1. The interactions between PpnGRF5-1 and GRF-interacting factors were experimentally validated and a multilayered hierarchical regulatory network (ML-hGRN)-mediated by PpnGRF5-1 was constructed with Top-down GGM algorithm by combining RNA-seq data from its overexpression (OE) lines and DAP-seq data. PpnGRF5-1 is a negative regulator of PpnCKX1. OE of PpnGRF5-1 in diploid transgenic lines resulted in larger leaves resembling those of triploids, and significantly increased zeatin and isopentenyladenine in the apical buds and third leaves. PpnGRF5-1 also interacted with GIFs to increase its regulatory diversity and capacity. An ML-hGRN-mediated by PpnGRF5-1 was obtained and could largely elucidate larger leaves. PpnGRF5-1 and the ML-hGRN-mediated by PpnGRF5-1 were underlying the leaf growth and development.
PMID: 33423287
Elife , IF:7.08 , 2021 Jan , V10 doi: 10.7554/eLife.57467
Molecular basis for the adaptive evolution of environment-sensing by H-NS proteins.
Department of Chemistry, The University of Vermont, Burlington, United States.; King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal, Saudi Arabia.; King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Thuwal, Saudi Arabia.; Centre de Biochimie Structurale, CNRS, INSERM, Universite de Montpellier, Montpellier, France.
The DNA-binding protein H-NS is a pleiotropic gene regulator in gram-negative bacteria. Through its capacity to sense temperature and other environmental factors, H-NS allows pathogens like Salmonella to adapt their gene expression to their presence inside or outside warm-blooded hosts. To investigate how this sensing mechanism may have evolved to fit different bacterial lifestyles, we compared H-NS orthologs from bacteria that infect humans, plants, and insects, and from bacteria that live on a deep-sea hypothermal vent. The combination of biophysical characterization, high-resolution proton-less nuclear magnetic resonance spectroscopy, and molecular simulations revealed, at an atomistic level, how the same general mechanism was adapted to specific habitats and lifestyles. In particular, we demonstrate how environment-sensing characteristics arise from specifically positioned intra- or intermolecular electrostatic interactions. Our integrative approach clarified the exact modus operandi for H-NS-mediated environmental sensing and suggested that this sensing mechanism resulted from the exaptation of an ancestral protein feature.
PMID: 33410747
Sci Total Environ , IF:6.551 , 2021 Jan , V753 : P142194 doi: 10.1016/j.scitotenv.2020.142194
Plant litter decomposition in wetlands is closely associated with phyllospheric fungi as revealed by microbial community dynamics and co-occurrence network.
National Plateau Wetlands Research Center/Wetlands College, Southwest Forestry University, Kunming 650224, People's Republic of China; School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, People's Republic of China.; National Plateau Wetlands Research Center/Wetlands College, Southwest Forestry University, Kunming 650224, People's Republic of China.; National Plateau Wetlands Research Center/Wetlands College, Southwest Forestry University, Kunming 650224, People's Republic of China; College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China. Electronic address: hwang17@163.com.
Phyllospheric microbes play a crucial role in the biological decomposition of plant litter in wetland ecosystems. Previous studies have mainly focused on single stages of decomposition process, and to date there have been no reports on dynamic changes in the composition of phyllospheric microbes during the multiple stages of decomposition from living plant to death. Here we investigated fungal and bacterial community succession in the leaf litter of Schoenoplectus tabernaemontani, a wetland plant species using sequencing of the both fungal ITS and bacterial 16S genes. Our results revealed that, over the whole period of decomposition, the fungal communities underwent more distinct succession than did the bacterial communities. Proteobacteria dominated throughout the entire period, while, across different decomposition stages, the Ascomycete fungi were gradually replaced by the Ciliophora and Rozellomycota as the dominant fungi. Network analysis revealed higher degrees of species segregation and shorter average path lengths between species of fungi compared with species of bacteria. This suggests that fungal communities may harbor more niches and functional diversity and are potentially more susceptible to external interference than are bacterial communities. During decomposition, the contents of leaf cellulose, hemicellulose and lignin in the litter were significantly (p < 0.01) correlated with the fungal communities, and abiotic factors accounted for 89.8% of the total variation in the fungal communities. In contract, abiotic factors only explained 6.10% of the total variation in bacterial communities, suggesting external environments as drivers of fungal community succession. Overall, we provide evidence that the complex litter decay in wetlands is the result of a dynamic cross-kingdom succession, and this process is accompanied by distinct phyllospheric fungal community dynamics.
PMID: 33207455
Plant Cell Environ , IF:6.362 , 2021 Jan doi: 10.1111/pce.14003
More stories to tell: NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1, a salicylic acid receptor.
International Genome Center, Jiangsu University, Zhenjiang, P. R. China.; Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, P. R. China.; Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.; Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Lab of Biocontrol & Bacterial Molecular Biology, Nanjing, P. R. China.
Salicylic acid (SA) plays pivotal roles in plant defense against biotrophic and hemi-biotrophic pathogens. Tremendous progress has been made in the field of SA biosynthesis and SA signaling pathways over the past three decades. Among the key immune players in SA signaling pathway, NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1) functions as a master regulator of SA-mediated plant defense. The function of NPR1 as an SA receptor has been controversial; however, after years of arguments among several laboratories, NPR1 has finally been proven as one of the SA receptors. The function of NPR1 is strictly regulated via post-translational modifications and transcriptional regulation that were recently found. More recent advances in NPR1 biology, including novel functions of NPR1 and the structure of SA receptor proteins, have brought this field forward immensely. Therefore, based on these recent discoveries, this review acts to provide a full picture of how NPR1 functions in plant immunity and how NPR1 gene and NPR1 protein are regulated at multiple levels. Finally, we also discuss potential challenges in future studies of SA signaling pathway. This article is protected by copyright. All rights reserved.
PMID: 33495996
Epilepsia , IF:6.04 , 2021 Jan doi: 10.1111/epi.16811
Interictal electroencephalographic functional network topology in drug-resistant and well-controlled idiopathic generalized epilepsy.
Department of Neurology, Manchester Centre for Clinical Neurosciences, Salford, UK.; Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine, and Health, School of Biological Sciences, University of Manchester, Manchester, UK.; Manchester Academic Health Sciences Centre, Manchester, UK.; Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK.; Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK.
OBJECTIVE: The study aim was to compare interictal encephalographic (EEG) functional network topology between people with well-controlled idiopathic generalized epilepsy (WC-IGE) and drug-resistant IGE (DR-IGE). METHODS: Nineteen participants with WC-IGE, 18 with DR-IGE, and 20 controls underwent a resting state, 64-channel EEG. An artifact-free epoch was bandpass filtered into the frequency range of high and low extended alpha. Weighted functional connectivity matrices were calculated. Mean degree, degree distribution variance, characteristic path length (L), clustering coefficient, small world index (SWI), and betweenness centrality were measured. A Kruskal-Wallis H-test assessed effects across groups. Where significant differences were found, Bonferroni-corrected Mann-Whitney pairwise comparisons were calculated. RESULTS: In the low alpha band (6-9 Hz), there was a significant difference in L at the three-group level (p < .0001). This was lower in controls than both WC-IGE and DR-IGE (p < .0001 for both), with no difference in L between WC-IGE and DR-IGE. Mean degree (p = .031), degree distribution variance (p = .032), and SWI (p = .023) differed across the three groups in the high alpha band (10-12 Hz). Mean degree and degree distribution variance were lower in WC-IGE than controls (p = .029 for both), and SWI was higher in WC-IGE compared with controls (p = .038), with no differences in other pairwise comparisons. SIGNIFICANCE: IGE network topology is more regular in the low alpha frequency band, potentially reflecting a more vulnerable structure. WC-IGE network topology is different from controls in the high alpha band. This may reflect drug-induced network changes that have stabilized the WC-IGE network by rendering it less likely to synchronize. These results are of potential importance in advancing the understanding of mechanisms of epilepsy drug resistance and as a possible basis for a biomarker of DR-IGE.
PMID: 33501642
Antioxidants (Basel) , IF:5.014 , 2021 Jan , V10 (2) doi: 10.3390/antiox10020152
Function and Regulation of Chloroplast Peroxiredoxin IIE.
Department of Biochemistry and Physiology of Plants, Faculty of Biology, University of Bielefeld, 33615 Bielefeld, Germany.; Applied Biochemistry Group, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany.
Peroxiredoxins (PRX) are thiol peroxidases that are highly conserved throughout all biological kingdoms. Increasing evidence suggests that their high reactivity toward peroxides has a function not only in antioxidant defense but in particular in redox regulation of the cell. Peroxiredoxin IIE (PRX-IIE) is one of three PRX types found in plastids and has previously been linked to pathogen defense and protection from protein nitration. However, its posttranslational regulation and its function in the chloroplast protein network remained to be explored. Using recombinant protein, it was shown that the peroxidatic Cys121 is subjected to multiple posttranslational modifications, namely disulfide formation, S-nitrosation, S-glutathionylation, and hyperoxidation. Slightly oxidized glutathione fostered S-glutathionylation and inhibited activity in vitro. Immobilized recombinant PRX-IIE allowed trapping and subsequent identification of interaction partners by mass spectrometry. Interaction with the 14-3-3 upsilon protein was confirmed in vitro and was shown to be stimulated under oxidizing conditions. Interactions did not depend on phosphorylation as revealed by testing phospho-mimicry variants of PRX-IIE. Based on these data it is proposed that 14-3-3upsilon guides PRXIIE to certain target proteins, possibly for redox regulation. These findings together with the other identified potential interaction partners of type II PRXs localized to plastids, mitochondria, and cytosol provide a new perspective on the redox regulatory network of the cell.
PMID: 33494157
J Integr Plant Biol , IF:4.885 , 2021 Jan doi: 10.1111/jipb.13069
Maize Endosperm Development.
State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.; Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
Recent breakthroughs in transcriptome analysis and gene characterization have provided valuable resources and information about the maize endosperm developmental program. The high temporal-resolution transcriptome analysis has yielded unprecedented access to information about the genetic control of seed development. Detailed spatial transcriptome analysis using laser-capture microdissection has revealed the expression patterns of specific populations of genes in the four major endosperm compartments: the basal endosperm transfer layer (BETL), aleurone layer (AL), starchy endosperm (SE), and embryo-surrounding region (ESR). Although the overall picture of the transcriptional regulatory network of endosperm development remains fragmentary, there have been some exciting advances, such as the identification of OPAQUE11 (O11) as a central hub of the maize endosperm regulatory network connecting endosperm development, nutrient metabolism, and stress responses, and the discovery that the endosperm adjacent to scutellum (EAS) serves as a dynamic interface for endosperm-embryo crosstalk. In addition, several genes that function in BETL development, AL differentiation, and the endosperm cell cycle have been identified, such as ZmSWEET4c, Thk1, and Dek15, respectively. Here, we focus on current advances in understanding the molecular factors involved in BETL, AL, SE, ESR, and EAS development, including the specific transcriptional regulatory networks that function in each compartment during endosperm development. This article is protected by copyright. All rights reserved.
PMID: 33448626
Mol Plant Pathol , IF:4.326 , 2021 Jan doi: 10.1111/mpp.13032
Reconstruction and analysis of a genome-scale metabolic model for Agrobacterium tumefaciens.
College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China.
The plant pathogen Agrobacterium tumefaciens causes crown gall disease and is a widely used tool for generating transgenic plants owing to its virulence. The pathogenic process involves a shift from an independent to a living form within a host plant. However, comprehensive analyses of metabolites, genes, and reactions contributing to this complex process are lacking. To gain new insights about the pathogenicity from the viewpoints of physiology and cellular metabolism, a genome-scale metabolic model (GSMM) was reconstructed for A. tumefaciens. The model, referred to as iNX1344, contained 1,344 genes, 1,441 reactions, and 1,106 metabolites. It was validated by analyses of in silico cell growth on 39 unique carbon or nitrogen sources and the flux distribution of carbon metabolism. A. tumefaciens metabolic characteristics under three ecological niches were modelled. A high capacity to access and metabolize nutrients is more important for rhizosphere colonization than in the soil, and substantial metabolic changes were detected during the shift from the rhizosphere to tumour environments. Furthermore, by integrating transcriptome data for tumour conditions, significant alterations in central metabolic pathways and secondary metabolite metabolism were identified. Overall, the GSMM and constraint-based analysis could decode the physiological and metabolic features of A. tumefaciens as well as interspecific interactions with hosts, thereby improving our understanding of host adaptation and infection mechanisms.
PMID: 33433944
Microorganisms , IF:4.152 , 2021 Jan , V9 (1) doi: 10.3390/microorganisms9010161
Unraveling Mechanisms and Impact of Microbial Recruitment on Oilseed Rape (Brassica napus L.) and the Rhizosphere Mediated by Plant Growth-Promoting Rhizobacteria.
School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.; CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.; CSIRO Mineral Resources, Kensington, WA 6151, Australia.
Plant growth-promoting rhizobacteria (PGPR) are noticeably applied to enhance plant nutrient acquisition and improve plant growth and health. However, limited information is available on the compositional dynamics of rhizobacteria communities with PGPR inoculation. In this study, we investigated the effects of three PGPR strains, Stenotrophomonas rhizophila, Rhodobacter sphaeroides, and Bacillus amyloliquefaciens on the ecophysiological properties of Oilseed rape (Brassica napus L.), rhizosphere, and bulk soil; moreover, we assessed rhizobacterial community composition using high-throughput Illumina sequencing of 16S rRNA genes. Inoculation with S. rhizophila, R. sphaeroides, and B. amyloliquefaciens, significantly increased the plant total N (TN) (p < 0.01) content. R. sphaeroides and B. amyloliquefaciens selectively enhanced the growth of Pseudomonadacea and Flavobacteriaceae, whereas S. rhizophila could recruit diazotrophic rhizobacteria, members of Cyanobacteria and Actinobacteria, whose abundance was positively correlated with inoculation, and improved the transformation of organic nitrogen into inorganic nitrogen through the promotion of ammonification. Initial colonization by PGPR in the rhizosphere affected the rhizobacterial community composition throughout the plant life cycle. Network analysis indicated that PGPR had species-dependent effects on niche competition in the rhizosphere. These results provide a better understanding of PGPR-plant-rhizobacteria interactions, which is necessary to develop the application of PGPR.
PMID: 33445684
Plant Dis , IF:3.809 , 2021 Jan doi: 10.1094/PDIS-11-20-2492-RE
Effects of long-term bare fallow during the winter-wheat growth season on the soil chemical properties, fungal community composition and the occurrence of maize fungal diseases in North China.
Chinese Academy of Agricultural Sciences Institute of Plant Protection, 243827, Beijing, Beijing, China; yajiaowang515@163.com.; 437 Dongguan StreetBaoding, China, 071000; jilijing79@163.com.; Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, hebeibaoding, Baoding, China, 071000; alidd@163.com.; Hebei Academy of Agriculture and Forestry Sciences, 91600, Baoding, Hebei, China; wyx1209@163.com.; Hebei Academy of Agriculture and Forestry Sciences, 91600, Baoding, Hebei, China; licongcong2017@163.com.; Hebei Academy of Agricultural Sciences Institute of Plant Protection, Baoding, China; konglingxiao163@163.com.; Institutute of Plant Protection, Chinese Academy of Agricultural Science, Plant Pathology, Yuanmingyuan West Road No.2, Haidian District, Beijing, Beijing, China, 100094; wangxifeng@caas.cn.
On the North China Plain, one of the most water-deficient regions in China, bare fallow has been implemented over a large-scale area to conserve water during the growth season of water-intensive winter wheat since 2015. However, the effects of this bare fallow on fungal community and the occurrence of crop diseases are poorly understood. Here we measured soil chemical properties, fungal community composition and the occurrence of crop diseases after 15 years of long-term fallow (continuous maize or soybean) and non-fallow (maize-wheat rotation; soybean-wheat rotation) cropping systems. Bare fallow during the winter-wheat growth season significantly decreased soil organic matter, available nitrogen and phosphorus. It also changed the composition of soil fungal communities, i.e., increased relative abundances of some potentially pathogenic species of Lectera, Fusarium and Volutella but decreased beneficial Cladorrhium and Schizothecium. Meanwhile, the epidemic tendency of maize diseases changed correspondingly: the disease index of southern corn leaf blight and maize brown spot increased, but the incidence of stalk rot decreased compared with the non-fallow system. Soybean diseases were very mild regardless of the cropping system during the total experimental period. Network analysis demonstrated that the soil fungal diversity associated with maize diseases was affected by the decreased soil organic matter and available nitrogen and phosphorus. Our results suggest that bare fallow in winter-wheat season affected the soil chemical properties, fungal community and the occurrence of maize fungal diseases.
PMID: 33404273
Tree Physiol , IF:3.655 , 2021 Jan doi: 10.1093/treephys/tpaa180
UV-B induced molecular mechanisms of stress physiology responses in the major Northern Chinese conifer Pinus tabuliformis Carr.
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.; Department of Ecology and Environmental Science, UPSC, Umea University, Sweden.; Qigou State-owned Forest Farm, Pingquan, Hebei, 067509, China.; Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.; Department des Sciences du Bois et de la Foret, Faculte de Foresterie, de Geographie et Geomatique, Universite Laval Quebec, QC, G1V 0A6, Canada.
During their lifetimes, plants are exposed to different abiotic stress factors eliciting various physiological responses and triggering important defense processes. For UV-B radiation responses in forest trees, the genetics and molecular regulation remain to be elucidated. Here, we exposed Pinus tabuliformis Carr., a major conifer from Northern China, to short-term high-intensity UV-B and employed a systems biology approach to characterize the early physiological processes and the hierarchical gene regulation, which revealed a temporal transition from primary to secondary metabolism, the buildup of enhanced antioxidant capacity, and stress-signaling activation. Our findings showed that photosynthesis and biosynthesis of photosynthetic pigments were inhibited, while flavonoids and their related derivates biosynthesis as well as glutathione and glutathione S-transferase mediated antioxidant processes were enhanced. Likewise, stress related phytohormones (jasmonic acid, salicylic acid, and ethylene), kinase, and ROS signal transduction pathways were activated. Biological processes regulated by auxin and karrikin were, for the first time, found to be involved in plant defense against UV-B by promoting the biosynthesis of flavonoids and the improvement of antioxidant capacity in our research system. Our work evaluated the physiological and transcriptome perturbations in a conifer's response to UV-B, and generally, highlighted the necessity of a systems biology approach in addressing plant stress biology.
PMID: 33416074
Planta , IF:3.39 , 2021 Jan , V253 (2) : P26 doi: 10.1007/s00425-020-03544-6
Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice.
Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China.; Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China. yjhuang_cn@126.com.; Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China. zhaohai_wang@163.com.
MAIN CONCLUSION: Circular RNAs (circRNAs) identification, expression profiles, and construction of circRNA-parental gene relationships and circRNA-miRNA-mRNA ceRNA networks indicate that circRNAs are involved in flag leaf senescence of rice. Circular RNAs (circRNAs) are a class of 3'-5' head-to-tail covalently closed non-coding RNAs which have been proved to play important roles in various biological processes. However, no systematic identification of circRNAs associated with leaf senescence in rice has been studied. In this study, a genome-wide high-throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. Here, a total of 6612 circRNAs were identified, among which, 113 circRNAs were differentially expressed (DE) during the leaf senescence process. Moreover, 4601 (69.59%) circRNAs were derived from the exons or introns of their parental genes, while 2110 (71%) of the parental genes produced only one circRNA. The sequence alignment analysis showed that hundreds of rice circRNAs were conserved among different plant species. Gene Ontology (GO) enrichment analysis revealed that parental genes of DE circRNAs were enriched in many biological processes closely related to leaf senescence. Through weighted gene co-expression network analysis (WGCNA), six continuously down-expressed circRNAs, 18 continuously up-expressed circRNAs and 15 turn-point high-expressed circRNAs were considered to be highly associated with leaf senescence. Additionally, a total of 17 senescence-associated circRNAs were predicted to have parental genes, in which, regulations of three circRNAs to their parental genes were validated by qRT-PCR. The competing endogenous RNA (ceRNA) networks were also constructed. And a total of 11 senescence-associated circRNAs were predicted to act as miRNA sponges to regulate mRNAs, in which, regulation of two circRNAs to eight mRNAs was validated by qRT-PCR. It is discussed that senescence-associated circRNAs were involved in flag leaf senescence probably through mediating their parental genes and ceRNA networks, to participate in several well-studied senescence-associated processes, mainly including the processes of transcription, translation, and posttranslational modification (especially protein glycosylation), oxidation-reduction process, involvement of senescence-associated genes, hormone signaling pathway, proteolysis, and DNA damage repair. This study not only showed the systematic identification of circRNAs involved in leaf senescence of rice, but also laid a foundation for functional research on candidate circRNAs.
PMID: 33410920
BMC Microbiol , IF:2.989 , 2021 Jan , V21 (1) : P24 doi: 10.1186/s12866-020-02020-1
Berberine alters gut microbial function through modulation of bile acids.
Institute for Health Research and Policy, University of Illinois Chicago, Chicago, IL, USA.; Cancer Education and Career Development Program, University of Illinois, Chicago, IL, USA.; Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.; Structural and Computational Biology Research Unit, European Molecular Biology Laboratory, Heidelburg, Germany.; Center for Microbiome Analysis, George Mason University, Manassas, VA, USA.; Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, 152-0011, Japan.; School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu, Japan.; University of Illinois Chicago Research Resources Center, University of Illinois Chicago, Chicago, IL, USA.; Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.; Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA.; Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA.; Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.; Cancer Center of Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.; Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA. jmridlon@illinois.edu.; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA. jmridlon@illinois.edu.; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA. jmridlon@illinois.edu.; Cancer Center of Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA. jmridlon@illinois.edu.; Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA. jmridlon@illinois.edu.
BACKGROUND: Berberine (BBR) is a plant-based nutraceutical that has been used for millennia to treat diarrheal infections and in contemporary medicine to improve patient lipid profiles. Reduction in lipids, particularly cholesterol, is achieved partly through up-regulation of bile acid synthesis and excretion into the gastrointestinal tract (GI). The efficacy of BBR is also thought to be dependent on structural and functional alterations of the gut microbiome. However, knowledge of the effects of BBR on gut microbiome communities is currently lacking. Distinguishing indirect effects of BBR on bacteria through altered bile acid profiles is particularly important in understanding how dietary nutraceuticals alter the microbiome. RESULTS: Germfree mice were colonized with a defined minimal gut bacterial consortium capable of functional bile acid metabolism (Bacteroides vulgatus, Bacteroides uniformis, Parabacteroides distasonis, Bilophila wadsworthia, Clostridium hylemonae, Clostridium hiranonis, Blautia producta; B4PC2). Multi-omics (bile acid metabolomics, 16S rDNA sequencing, cecal metatranscriptomics) were performed in order to provide a simple in vivo model from which to identify network-based correlations between bile acids and bacterial transcripts in the presence and absence of dietary BBR. Significant alterations in network topology and connectivity in function were observed, despite similarity in gut microbial alpha diversity (P = 0.30) and beta-diversity (P = 0.123) between control and BBR treatment. BBR increased cecal bile acid concentrations, (P < 0.05), most notably deoxycholic acid (DCA) (P < 0.001). Overall, analysis of transcriptomes and correlation networks indicates both bacterial species-specific responses to BBR, as well as functional commonalities among species, such as up-regulation of Na(+)/H(+) antiporter, cell wall synthesis/repair, carbohydrate metabolism and amino acid metabolism. Bile acid concentrations in the GI tract increased significantly during BBR treatment and developed extensive correlation networks with expressed genes in the B4PC2 community. CONCLUSIONS: This work has important implications for interpreting the effects of BBR on structure and function of the complex gut microbiome, which may lead to targeted pharmaceutical interventions aimed to achieve the positive physiological effects previously observed with BBR supplementation.
PMID: 33430766
Integr Zool , IF:2.514 , 2021 Jan doi: 10.1111/1749-4877.12520
Weighted individual-resource networks in prey-predator systems: the role of prey availability on the emergence of modular structures.
Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Genova, Italy.; Italian National Research Council (CNR), Agriculture and Food Sciences Department (IBE), Institute of Bioeconomy - Biology, Roma, RM, Italy.
Ecological networks, usually depicting interactions among species, have been recently down-scaled to the individual level, permitting description of patterns of inter-individual resource variation that are usually hindered at the species level. Optimal diet theory (ODT) models, applied to prey-predator systems, predict different patterns of nestedness and modularity in the network, depending on the available resources and intra-specific competition. The effect of resource availability on the emergence of networks structures, and ODT framework, has not yet fully been clarified. Here, we analyzed the structural patterns of individual-resource networks in 3 species of Mediterranean salamanders, in relation to changes in prey availability. We used weighted individual-resource network metrics to interpret the observed patterns, according to 3 ODT models. We found significant nestedness recurring in our study system, indicating that both selective and opportunistic individuals occur in the same population. Prey diversity, rather than abundance, was apparently related to inter-individual resource variation and promoted the emergence of significant modularity within all networks. The observed patterns of nestedness and modularity, together with the variation in resource diversity and intra-specific competition, are in agreement with the distinct preferences model of ODT. These findings suggest that in the focal prey-predator systems, individuals were able to perceive changes in prey diversity and to exploit in different ways the variations in composition of available resources, shifting their diet assembly rules accordingly. Our findings also confirm that the use of weighted individual-resource networks, in prey-predator systems, allows to disclose dynamics that are masked at the species or population level.
PMID: 33415838
J Mol Model , IF:1.346 , 2021 Jan , V27 (1) : P14 doi: 10.1007/s00894-020-04651-7
Investigation of Alpinia calcarata constituent interactions with molecular targets of rheumatoid arthritis: docking, molecular dynamics, and network approach.
Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, Tamil Nadu, 620 024, India.; Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India.; Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, Tamil Nadu, 620 024, India. sanmug77@gmail.com.; Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India. mohane@bicpu.edu.in.
Rheumatoid arthritis (RA) is a systemic autoimmune disorder that commonly affects multiple joints of the body. Currently, there is no permanent cure to the disease, but it can be managed with several potent drugs that cause serious side effects on prolonged use. Traditional remedies are considered promising for the treatment of several diseases, particularly chronic conditions, because they have lower side effects compared to synthetic drugs. In folklore, the rhizome of Alpinia calcarata Roscoe (Zingiberaceae) is used as a major ingredient of herbal formulations to treat RA. Phytoconstituents reported in A. calcarata rhizomes are diterpenoids, sesquiterpenoid, flavonoids, phytosterol, and volatile oils. The present study is intended to understand the molecular-level interaction of phytoconstituents present in A. calcarata rhizomes with RA molecular targets using computational approaches. A total of 30 phytoconstituents reported from the plant were used to carry out docking with 36 known targets of RA. Based on the docking results, 4 flavonoids were found to be strongly interacting with the RA targets. Further, molecular dynamics simulation confirmed stable interaction of quercetin with 6 targets (JAK3, SYK, MMP2, TLR8, IRAK1, and JAK1), galangin with 2 targets (IRAK1 and JAK1), and kaempferol (IRAK1) with one target of RA. Moreover, the presence of these three flavonoids was confirmed in the A. calcarata rhizome extract using LC-MS analysis. The computational study suggests that flavonoids present in A. calcarata rhizome may be responsible for RA modulatory activity. Particularly, quercetin and galangin could be potential development candidates for the treatment of RA. Investigation of Alpinia calcarata constituent interactions with molecular targets of rheumatoid arthritis: docking, molecular dynamics, and network approach.
PMID: 33403456