Biotechnol Adv , IF:14.227 , 2022 Jul-Aug , V57 : P107947 doi: 10.1016/j.biotechadv.2022.107947
Data mining of Saccharomyces cerevisiae mutants engineered for increased tolerance towards inhibitors in lignocellulosic hydrolysates.
Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden. Electronic address: elenaca@chalmers.se.; Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden. Electronic address: lisbeth.olsson@chalmers.se.; Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden. Electronic address: jan.zrimec@nib.si.; Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden; Science for Life Laboratory, Stockholm, Sweden. Electronic address: aleksej.zelezniak@chalmers.se.; Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden. Electronic address: cecilia.geijer@chalmers.se.; Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden. Electronic address: yvonne.nygard@chalmers.se.
The use of renewable plant biomass, lignocellulose, to produce biofuels and biochemicals using microbial cell factories plays a fundamental role in the future bioeconomy. The development of cell factories capable of efficiently fermenting complex biomass streams will improve the cost-effectiveness of microbial conversion processes. At present, inhibitory compounds found in hydrolysates of lignocellulosic biomass substantially influence the performance of a cell factory and the economic feasibility of lignocellulosic biofuels and chemicals. Here, we present and statistically analyze data on Saccharomyces cerevisiae mutants engineered for altered tolerance towards the most common inhibitors found in lignocellulosic hydrolysates: acetic acid, formic acid, furans, and phenolic compounds. We collected data from 7971 experiments including single overexpression or deletion of 3955 unique genes. The mutants included in the analysis had been shown to display increased or decreased tolerance to individual inhibitors or combinations of inhibitors found in lignocellulosic hydrolysates. Moreover, the data included mutants grown on synthetic hydrolysates, in which inhibitors were added at concentrations that mimicked those of lignocellulosic hydrolysates. Genetic engineering aimed at improving inhibitor or hydrolysate tolerance was shown to alter the specific growth rate or length of the lag phase, cell viability, and vitality, block fermentation, and decrease product yield. Different aspects of strain engineering aimed at improving hydrolysate tolerance, such as choice of strain and experimental set-up are discussed and put in relation to their biological relevance. While successful genetic engineering is often strain and condition dependent, we highlight the conserved role of regulators, transporters, and detoxifying enzymes in inhibitor tolerance. The compiled meta-analysis can guide future engineering attempts and aid the development of more efficient cell factories for the conversion of lignocellulosic biomass.
PMID: 35314324
J Cachexia Sarcopenia Muscle , IF:12.91 , 2022 Apr , V13 (2) : P1262-1276 doi: 10.1002/jcsm.12903
MicroRNA regulatory networks associated with abnormal muscle repair in survivors of critical illness.
Keenan Research Centre for Biomedical Science, St Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.; Institute of Medical Science, University of Toronto, Toronto, ON, Canada.; University Health Network, Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, ON, Canada.; Department of Physical Therapy, University of Toronto, Toronto, ON, Canada.; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.; INSERM, Institute of Myology, Research Center in Myology, Sorbonne University, Paris, France.
BACKGROUND: Intensive care unit (ICU)-acquired weakness is characterized by muscle atrophy and impaired contractility that may persist after ICU discharge. Dysregulated muscle repair and regeneration gene co-expression networks are present in critical illness survivors with persistent muscle wasting and weakness. We aimed to identify microRNAs (miRs) regulating the gene networks and determine their role in the self-renewal of muscle in ICU survivors. METHODS: Muscle whole-transcriptome expression was assessed with microarrays in banked quadriceps biopsies obtained at 7 days and 6 months post-ICU discharge from critically ill patients (n = 15) in the RECOVER programme and healthy individuals (n = 8). We conducted an integrated miR-messenger RNA analysis to identify miR/gene pairs associated with muscle recovery post-critical illness and evaluated their impact on myoblast proliferation and differentiation in human AB1167 and murine C2C12 cell lines in vitro. Select target genes were validated with quantitative PCR. RESULTS: Twenty-two miRs were predicted to regulate the Day 7 post-ICU muscle transcriptome vs. controls. Thirty per cent of all differentially expressed genes shared a 3'UTR regulatory sequence for miR-424-3p/5p, which was 10-fold down-regulated in patients (P < 0.001) and correlated with quadriceps size (R = 0.86, P < 0.001), strength (R = 0.75, P = 0.007), and physical function (Functional Independence Measures motor subscore, R = 0.92, P < 0.001) suggesting its potential role as a master regulator of early recovery of muscle mass and strength following ICU discharge. Network analysis demonstrated enrichment for cellular respiration and muscle fate commitment/development related genes. At 6 months post-ICU discharge, a 14-miR expression signature, including miRs-490-3p and -744-5p, identified patients with muscle mass recovery vs. those with sustained atrophy. Constitutive overexpression of the novel miR-490-3p significantly inhibited AB1167 and C2C12 myoblast proliferation (cell count AB1167 miR-490-3p mimic or scrambled-miR transfected myoblasts 7926 +/- 4060 vs. 14 159 +/- 3515 respectively, P = 0.006; proportion Ki67-positive nuclei AB1167 miR-490-3p mimic or scrambled-miR transfected myoblasts 0.38 +/- 0.07 vs. 0.54 +/- 0.06 respectively, P < 0.001; proliferating cell nuclear antigen expression AB1167 miR-490-3p mimic or scrambled-miR transfected myoblasts 11.48 +/- 1.97 vs. 16.75 +/- 1.19 respectively, P = 0.040). Constitutive overexpression of miR-744-5p, a known regulator of myogenesis, significantly inhibited AB1167 and C2C12 myoblast differentiation (fusion index AB1167 miR-744-5p mimic or scrambled-miR transfected myoblasts 8.31 +/- 7.00% vs. 40.29 +/- 9.37% respectively, P < 0.001; myosin heavy chain expression miR-744-5p mimic or scrambled-miR transfected myoblasts 0.92 +/- 0.39 vs. 13.53 +/- 5.5 respectively, P = 0.01). CONCLUSIONS: Combined functional transcriptomics identified 36 miRs including miRs-424-3p/5p, -490-3p, and -744-5p as potential regulators of gene networks associated with recovery of muscle mass and strength following critical illness. MiR-490-3p is identified as a novel regulator of myogenesis.
PMID: 35092190
Food Chem , IF:7.514 , 2022 Mar , V372 : P131118 doi: 10.1016/j.foodchem.2021.131118
Regulatory effect of root restriction on aroma quality of Red Alexandria grape.
Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China.; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Institute of Agro-food Science and Technology/Key Laboratory of Agro-products, Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan 250100, China. Electronic address: fruit@sjtu.edu.cn.
To systematically study the impact of root restriction (RR) on the aroma quality of grape berry, in this study, free and bound compounds were investigated in 'Red Alexandria' grape skin and pulp produced with and without RR during development and ripening. Compared with the control, RR advanced the initiation of free-terpene synthesis and increased their concentrations at 14-18 weeks post-flowering (wpf) by promoting the conversion of bound terpenes to free terpenes. In addition, RR significantly regulated the aromatic series at 14-18 wpf and advanced the date of aroma maturation. Network analyses indicated that the correlations among bound compounds were more conserved than those among free compounds, and the skin network displayed tight coordination compared with the pulp network. Terpenes were highly intercorrelated and played a core role in these networks. Finally, 10 bound compounds in pulp were screened out as indicators of the developmental timing of grape.
PMID: 34600194
BMC Biol , IF:7.431 , 2022 Apr , V20 (1) : P83 doi: 10.1186/s12915-022-01273-8
Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response.
Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.; Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.; Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.; Present address: Ac-Planta Inc., 2-16-9 Yushima, Bunkyo-ku, Tokyo, 113-0034, Japan.; Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.; Present address: Department of Biological Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.; Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.; Present address: Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.; Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan. motoaki.seki@riken.jp.; Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. motoaki.seki@riken.jp.; Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK. Alessandra.Devoto@rhul.ac.uk.
BACKGROUND: Jasmonates (JAs) mediate trade-off between responses to both biotic and abiotic stress and growth in plants. The Arabidopsis thaliana HISTONE DEACETYLASE 6 is part of the CORONATINE INSENSITIVE1 receptor complex, co-repressing the HDA6/COI1-dependent acetic acid-JA pathway that confers plant drought tolerance. The decrease in HDA6 binding to target DNA mirrors histone H4 acetylation (H4Ac) changes during JA-mediated drought response, and mutations in HDA6 also cause depletion in the constitutive repressive marker H3 lysine 27 trimethylation (H3K27me3). However, the genome-wide effect of HDA6 on H4Ac and much of the impact of JAs on histone modifications and chromatin remodelling remain elusive. RESULTS: We performed high-throughput ChIP-Seq on the HDA6 mutant, axe1-5, and wild-type plants with or without methyl jasmonate (MeJA) treatment to assess changes in active H4ac and repressive H3K27me3 histone markers. Transcriptional regulation was investigated in parallel by microarray analysis in the same conditions. MeJA- and HDA6-dependent histone modifications on genes for specialized metabolism; linolenic acid and phenylpropanoid pathways; and abiotic and biotic stress responses were identified. H4ac and H3K27me3 enrichment also differentially affects JAs and HDA6-mediated genome integrity and gene regulatory networks, substantiating the role of HDA6 interacting with specific families of transposable elements in planta and highlighting further specificity of action as well as novel targets of HDA6 in the context of JA signalling for abiotic and biotic stress responses. CONCLUSIONS: The findings demonstrate functional overlap for MeJA and HDA6 in tuning plant developmental plasticity and response to stress at the histone modification level. MeJA and HDA6, nonetheless, maintain distinct activities on histone modifications to modulate genetic variability and to allow adaptation to environmental challenges.
PMID: 35399062
J Exp Bot , IF:6.992 , 2022 Apr , V73 (8) : P2487-2498 doi: 10.1093/jxb/erac044
Custom methods to identify conserved genetic modules applied to novel transcriptomic data from Amborella trichopoda.
Laboratoire Reproduction et Developpement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon-1, CNRS, INRA, Lyon, France.; Universite Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France.; Universite de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France.; UMR 1318 INRAe-AgroParisTech, Route de Saint Cyr, 78026 Versailles cedex, France.
We have devised a procedure for the inter-species comparison of transcriptomic data and used this procedure to reconstruct the expression dynamics of major genetic modules that were present at least 149 million years ago in the most recent common ancestor of living angiosperms. We began by using laser-assisted microdissection to generate novel transcriptomic data from female flower tissues of Amborella trichopoda, the likely sister to all other living angiosperms. We then employed a gene-expression clustering method, followed by a custom procedure to compare genetic modules on the basis of gene orthology between Amborella and the molecular-genetic model angiosperm Arabidopsis thaliana. Using this protocol, we succeeded in identifying nine major genetic modules that appear to have conserved their expression dynamics from an early stage in angiosperm evolution. The genes of these modules, representing over 5000 orthogroups, include around one third of those known to control female reproductive development in Arabidopsis. Our study constitutes a proof of concept for the comparison of transcriptomic data between widely diverged plant species and represents a first step in the large-scale analysis of gene expression dynamics in a macro-evolutionary context.
PMID: 35134938
J Exp Bot , IF:6.992 , 2022 Mar , V73 (5) : P1277-1287 doi: 10.1093/jxb/erab490
The epigenetic mechanisms regulating floral hub genes and their potential for manipulation.
Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
Gene regulatory networks formed by transcription factors play essential roles in the regulation of gene expression during plant reproductive development. These networks integrate endogenous, phytohormonal, and environmental cues. Molecular genetic, biochemical, and chemical analyses performed mainly in Arabidopsis have identified network hub genes and revealed the contributions of individual components to these networks. Here, I outline current understanding of key epigenetic regulatory circuits identified by research on plant reproduction, and highlight significant recent examples of genetic engineering and chemical applications to modulate the epigenetic regulation of gene expression. Furthermore, I discuss future prospects for applying basic plant science to engineer useful floral traits in a predictable manner as well as the potential side effects.
PMID: 34752611
Cell Biol Toxicol , IF:6.691 , 2022 Apr , V38 (2) : P325-345 doi: 10.1007/s10565-021-09599-9
Pyrrolizidine alkaloids cause cell cycle and DNA damage repair defects as analyzed by transcriptomics in cytochrome P450 3A4-overexpressing HepG2 clone 9 cells.
Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg University, Mainz, Germany.; Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), Heidelberg, Germany.; Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany.; Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg University, Mainz, Germany. efferth@uni-mainz.de.
Pyrrolizidine alkaloids (PAs) are a large group of highly toxic chemical compounds, which are found as cross-contaminants in numerous food products (e.g., honey), dietary supplements, herbal teas, and pharmaceutical herbal medicines. PA contaminations are responsible for serious hepatotoxicity and hepatocarcinogenesis. Health authorities have to set legal limit values to guarantee the safe consumption of plant-based nutritional and medical products without harmful health. Toxicological and chemical analytical methods are conventionally applied to determine legally permitted limit values for PAs. In the present investigation, we applied a highly sensitive transcriptomic approach to investigate the effect of low concentrations of five PAs (lasiocarpine, riddelliine, lycopsamine, echimidine, and monocrotaline) on human cytochrome P450 3A4-overexpressing HepG2 clone 9 hepatocytes. The transcriptomic profiling of deregulated gene expression indicated that the PAs disrupted important signaling pathways related to cell cycle regulation and DNA damage repair in the transfected hepatocytes, which may explain the carcinogenic PA effects. As PAs affected the expression of genes that involved in cell cycle regulation, we applied flow cytometric cell cycle analyses to verify the transcriptomic data. Interestingly, PA treatment led to an arrest in the S phase of the cell cycle, and this effect was more pronounced with more toxic PAs (i.e., lasiocarpine and riddelliine) than with the less toxic monocrotaline. Using immunofluorescence, high fractions of cells were detected with chromosome congression defects upon PA treatment, indicating mitotic failure. In conclusion, the tested PAs revealed threshold concentrations, above which crucial signaling pathways were deregulated resulting in cell damage and carcinogenesis. Cell cycle arrest and DNA damage repair point to the mutagenicity of PAs. The disturbance of chromosome congression is a novel mechanism of Pas, which may also contribute to PA-mediated carcinogenesis. Transcriptomic, cell cycle, and immunofluorescence analyses should supplement the standard techniques in toxicology to unravel the biological effects of PA exposure in liver cells as the primary target during metabolization of PAs.
PMID: 33884520
Int J Mol Sci , IF:5.923 , 2022 Mar , V23 (6) doi: 10.3390/ijms23062953
A Comparative Transcriptome and Metabolome Combined Analysis Reveals the Key Genes and Their Regulatory Model Responsible for Glucoraphasatin Accumulation in Radish Fleshy Taproots.
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.; Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.; Jinling Institute of Technology, College of Horticulture, Nanjing 210038, China.
Radish (Raphanus sativus L.) is rich in specific glucosinolates (GSLs), which benefit human health and special flavor formation. Although the basic GSLs metabolic pathway in Brassicaceae plants is clear, the regulating mechanism for specific glucosinolates content in radish fleshy taproots is not well understood. In this study, we discovered that there was a significant difference in the GSLs profiles and the content of various GSLs components. Glucoraphasatin (GRH) is the most predominant GSL in radish taproots of different genotypes as assessed by HPLC analysis. Further, we compared the taproot transcriptomes of three radish genotypes with high and low GSLs content by employing RNA-seq. Totally, we identified forty-one differentially expressed genes related to GSLs metabolism. Among them, thirteen genes (RsBCAT4, RsIPMDH1, RsMAM1a, RsMAM1b, RsCYP79F1, RsGSTF9, RsGGP1, RsSUR1, RsUGT74C1, RsST5b, RsAPK1, RsGSL-OH, and RsMYB28) were significantly higher co-expressed in the high content genotypes than in low content genotype. Notably, correlation analysis indicated that the expression level of RsMYB28, as an R2R3 transcription factor directly regulating aliphatic glucosinolate biosynthesis, was positively correlated with the GRH content. Co-expression network showed that RsMYB28 probably positively regulated the expression of the above genes, particularly RsSUR1, and consequently the synthesis of GRH. Moreover, the molecular mechanism of the accumulation of this 4-carbon (4C) GSL in radish taproots was explored. This study provides new perspectives on the GSLs accumulation mechanism and genetic improvements in radish taproots.
PMID: 35328374
J Fungi (Basel) , IF:5.816 , 2022 Mar , V8 (3) doi: 10.3390/jof8030299
Morel Production Associated with Soil Nitrogen-Fixing and Nitrifying Microorganisms.
Key Laboratory for Plant Diversity and Biotechnology of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.; Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand.; School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.; School of Chemical Engineering, Guizhou Institute of Technology, Guiyang 550003, China.; College of Life Science, Northwest Normal University, Lanzhou 730070, China.
True morels (Morchella, Pezizales) cultivated in soil are subject to complex influences from soil microbial communities. To explore the characteristics of soil microbial communities on morel cultivation, and evaluate whether these microbes are related to morel production, we collected 23 soil samples from four counties in Sichuan and Yunnan Provinces, China. Based on ITS and 16S rDNA amplicon sequencing, the alpha diversity analysis indicated that the biodiversity of morel cultivation soil showed a downward trend compared with the bare soil. The results also showed that there were no significant differences in soil microbial communities between OC (bare soil) and OO (after one-year suspension of sowing). This means that, after about one year of stopping sowing, the component and structure of soil that once cultivated morel would be restored. In co-occurrence networks, some noteworthy bacterial microbes involved in nitrogen fixation and nitrification have been identified in soils with high morel yields, such as Arthrobacter, Bradyhizobium, Devosia, Pseudarthrobacter, Pseudolabrys, and Nitrospira. In contrast, in soils with low or no morel yield, some pathogenic fungi accounted for a high proportion, including Gibberella, Microidium, Penicillium, Sarocladium, Streptomyces, and Trichoderma. This study provided valuable information for the isolation and culturing of some beneficial microbes for morel cultivation in further study and, potentially, to harness the power of the microbiome to improve morel production and health.
PMID: 35330300
Front Plant Sci , IF:5.753 , 2022 , V13 : P855486 doi: 10.3389/fpls.2022.855486
Transcriptome and Small RNA Sequencing Reveal the Mechanisms Regulating Harvest Index in Brassica napus.
Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.; Academy of Agricultural Sciences, Southwest University, Chongqing, China.; Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang, China.; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China.
Harvest index (HI), the ratio of harvested seed weight to total aboveground biomass weight, is an economically critical value reflecting the convergence of complex agronomic traits. HI values in rapeseed (Brassica napus) remain much lower than in other major crops, and the underlying regulatory network is largely unknown. In this study, we performed mRNA and small RNA sequencing to reveal the mechanisms shaping HI in B. napus during the seed-filling stage. A total of 8,410 differentially expressed genes (DEGs) between high-HI and low-HI accessions in four tissues (silique pericarp, seed, leaves, and stem) were identified. Combining with co-expression network, 72 gene modules were identified, and a key gene BnaSTY46 was found to participate in retarded establishment of photosynthetic capacity to influence HI. Further research found that the genes involved in circadian rhythms and response to stimulus may play important roles in HI and that their transcript levels were modulated by differentially expressed microRNAs (DEMs), and we identified 903 microRNAs (miRNAs), including 46 known miRNAs and 857 novel miRNAs. Furthermore, transporter activity-related genes were critical to enhancing HI in good cultivation environments. Of 903 miRNAs, we found that the bna-miR396-Bna.A06SRp34a/Bna.A01EMB3119 pair may control the seed development and the accumulation of storage compounds, thus contributing to higher HI. Our findings uncovered the underlying complex regulatory network behind HI and offer potential approaches to rapeseed improvement.
PMID: 35444672
Front Plant Sci , IF:5.753 , 2022 , V13 : P836213 doi: 10.3389/fpls.2022.836213
Multifarious and Interactive Roles of GRAS Transcription Factors During Arbuscular Mycorrhiza Development.
Department of Soil Microbiology and Symbiotic Systems, Zaidin Experimental Station (EEZ), CSIC, Granada, Spain.
Arbuscular mycorrhiza (AM) is a mutualistic symbiotic interaction between plant roots and AM fungi (AMF). This interaction is highly beneficial for plant growth, development and fitness, which has made AM symbiosis the focus of basic and applied research aimed at increasing plant productivity through sustainable agricultural practices. The creation of AM requires host root cells to undergo significant structural and functional modifications. Numerous studies of mycorrhizal plants have shown that extensive transcriptional changes are induced in the host during all stages of colonization. Advances have recently been made in identifying several plant transcription factors (TFs) that play a pivotal role in the transcriptional regulation of AM development, particularly those belonging to the GRAS TF family. There is now sufficient experimental evidence to suggest that GRAS TFs are capable to establish intra and interspecific interactions, forming a transcriptional regulatory complex that controls essential processes in the AM symbiosis. In this minireview, we discuss the integrative role of GRAS TFs in the regulation of the complex genetic re-programming determining AM symbiotic interactions. Particularly, research being done shows the relevance of GRAS TFs in the morphological and developmental changes required for the formation and turnover of arbuscules, the fungal structures where the bidirectional nutrient translocation occurs.
PMID: 35419017
Front Plant Sci , IF:5.753 , 2022 , V13 : P831204 doi: 10.3389/fpls.2022.831204
Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model.
Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.; Institute for Data Science and Informatics, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.; Department of Health Management and Informatics and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.; Division of Plant Sciences and Technology and Biochemistry Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.
Plant tissues are distinguished by their gene expression patterns, which can help identify tissue-specific highly expressed genes and their differential functional modules. For this purpose, large-scale soybean transcriptome samples were collected and processed starting from raw sequencing reads in a uniform analysis pipeline. To address the gene expression heterogeneity in different tissues, we utilized an adversarial deconfounding autoencoder (AD-AE) model to map gene expressions into a latent space and adapted a standard unsupervised autoencoder (AE) model to help effectively extract meaningful biological signals from the noisy data. As a result, four groups of 1,743, 914, 2,107, and 1,451 genes were found highly expressed specifically in leaf, root, seed and nodule tissues, respectively. To obtain key transcription factors (TFs), hub genes and their functional modules in each tissue, we constructed tissue-specific gene regulatory networks (GRNs), and differential correlation networks by using corrected and compressed gene expression data. We validated our results from the literature and gene enrichment analysis, which confirmed many identified tissue-specific genes. Our study represents the largest gene expression analysis in soybean tissues to date. It provides valuable targets for tissue-specific research and helps uncover broader biological patterns. Code is publicly available with open source at https://github.com/LingtaoSu/SoyMeta.
PMID: 35310659
Front Microbiol , IF:5.64 , 2022 , V13 : P799819 doi: 10.3389/fmicb.2022.799819
Integrated Analysis of the miRNAome and Transcriptome Reveals miRNA-mRNA Regulatory Networks in Catharanthus roseus Through Cuscuta campestris-Mediated Infection With "Candidatus Liberibacter asiaticus".
National Citrus Engineering Research Center, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China.
Citrus Huanglongbing (HLB) is the most devastating disease of citrus caused by the Gram-negative phloem-limited bacterium "Candidatus Liberibacter asiaticus" (CLas). It can be transmitted by the Asian citrus psyllid "Diaphorina citri," by grafting, and by the holoparasitic dodder. In this study, the non-natural host periwinkle (Catharanthus roseus) was infected via dodder (Cuscuta campestris) from CLas-infected citrus plants, and the asymptomatic leaves (AS) were subjected to transcriptomic and small-RNA profiling. The results were analyzed together with a transcriptome dataset from the NCBI repository that included leaves for which symptoms had just occurred (S) and yellowing leaves (Y). There were 3,675 differentially expressed genes (DEGs) identified in AS, and 6,390 more DEGs in S and further 2109 DEGs in Y. These DEGs were commonly enriched in photosystem, chloroplast, membrane, oxidation-reduction process, metal/zinc ion binding on GO. A total of 14,974 DEGs and 336 DE miRNAs (30 conserved and 301 novel) were identified. Through weighted gene co-expression network and nested network analyses, two critical nested miRNA-mRNA regulatory networks were identified with four conserved miRNAs. The primary miR164-NAC1 network is potentially involved in plant defense responses against CLas from the early infection stage to symptom development. The secondary network revealed the regulation of secondary metabolism and nutrient homeostasis through miR828-MYB94/miR1134-HSF4 and miR827-ATG8 regulatory networks, respectively. The findings discovered new potential mechanisms in periwinkle-CLas interactions, and its confirmation can be done in citrus-CLas system later on. The advantages of periwinkle plants in facilitating the quick establishment and greater multiplication of CLas, and shortening latency for disease symptom development make it a great surrogate for further studies, which could expedite our understanding of CLas pathogenesis.
PMID: 35308338
J Agric Food Chem , IF:5.279 , 2022 Mar , V70 (12) : P3719-3729 doi: 10.1021/acs.jafc.2c00231
Integrated Metabolo-transcriptomics Reveals the Defense Response of Homogentisic Acid in Wheat against Puccinia striiformis f. sp. tritici.
College of Plant Protection, Southwest University, Chongqing 400715, China.
Stripe rust is a widespread and harmful wheat disease caused by Puccinia striiformis f. sp. tritici (Pst) worldwide. Targeted metabolome and transcriptomics analyses of CYR23 infected leaves were performed to identify the differential metabolites and differentially expressed genes related to wheat disease resistance. We observed upregulation of 33 metabolites involved in the primary and secondary metabolism, especially for homogentisic acid (HGA), p-coumaroylagmatine, and saccharopine. These three metabolites were mainly involved in the phenylpropanoid metabolic pathway, hydroxycinnamic acid amides pathway, and saccharopine pathway. Combined with transcriptome data on non-compatible interaction, the synthesis-related genes of these three differential metabolites were all upregulated significantly. The gene regulatory network involved in response to Pst infection was constructed, which revealed that several transcription factor families including WRKYs, MYBs, and bZIPs were identified as potentially hubs in wheat resistance response against Pst. An in vitro test showed that HGA effectively inhibited the germination of stripe rust fungus urediniospores and reduced the occurrence of wheat stripe rust. The results of gene silencing and overexpression of HGA synthesis-related gene 4-hydroxyphenylpyruvate dioxygenase proved that HGA was involved in wheat disease resistance. These results provided a further understanding of the disease resistance of wheat and indicated that HGA can be developed as a potential agent against Pst.
PMID: 35293725
Front Mol Biosci , IF:5.246 , 2022 , V9 : P841373 doi: 10.3389/fmolb.2022.841373
Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation.
Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC-WHO), Lyon, France.; Toxalim (Research Centre in Food Toxicology), Universite de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France.; MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.; Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany.; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.; Bruker BioSpin GmbH, Ettlingen, Germany.; Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum Munchen, Neuherberg, Germany.; Metabolomics and Proteomics Core, Helmholtz Zentrum Munchen, Neuherberg, Germany.; Chair of Analytical Food Chemistry, TUM School of Life Sciences, Freising, Germany.
Both targeted and untargeted mass spectrometry-based metabolomics approaches are used to understand the metabolic processes taking place in various organisms, from prokaryotes, plants, fungi to animals and humans. Untargeted approaches allow to detect as many metabolites as possible at once, identify unexpected metabolic changes, and characterize novel metabolites in biological samples. However, the identification of metabolites and the biological interpretation of such large and complex datasets remain challenging. One approach to address these challenges is considering that metabolites are connected through informative relationships. Such relationships can be formalized as networks, where the nodes correspond to the metabolites or features (when there is no or only partial identification), and edges connect nodes if the corresponding metabolites are related. Several networks can be built from a single dataset (or a list of metabolites), where each network represents different relationships, such as statistical (correlated metabolites), biochemical (known or putative substrates and products of reactions), or chemical (structural similarities, ontological relations). Once these networks are built, they can subsequently be mined using algorithms from network (or graph) theory to gain insights into metabolism. For instance, we can connect metabolites based on prior knowledge on enzymatic reactions, then provide suggestions for potential metabolite identifications, or detect clusters of co-regulated metabolites. In this review, we first aim at settling a nomenclature and formalism to avoid confusion when referring to different networks used in the field of metabolomics. Then, we present the state of the art of network-based methods for mass spectrometry-based metabolomics data analysis, as well as future developments expected in this area. We cover the use of networks applications using biochemical reactions, mass spectrometry features, chemical structural similarities, and correlations between metabolites. We also describe the application of knowledge networks such as metabolic reaction networks. Finally, we discuss the possibility of combining different networks to analyze and interpret them simultaneously.
PMID: 35350714
Rice (N Y) , IF:4.783 , 2022 Mar , V15 (1) : P18 doi: 10.1186/s12284-022-00562-8
Genes and Their Molecular Functions Determining Seed Structure, Components, and Quality of Rice.
Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.; Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China. qqliu@yzu.edu.cn.; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China. qqliu@yzu.edu.cn.; Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China. qfli@yzu.edu.cn.; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China. qfli@yzu.edu.cn.
With the improvement of people's living standards and rice trade worldwide, the demand for high-quality rice is increasing. Therefore, breeding high quality rice is critical to meet the market demand. However, progress in improving rice grain quality lags far behind that of rice yield. This might be because of the complexity of rice grain quality research, and the lack of consensus definition and evaluation standards for high quality rice. In general, the main components of rice grain quality are milling quality (MQ), appearance quality (AQ), eating and cooking quality (ECQ), and nutritional quality (NQ). Importantly, all these quality traits are determined directly or indirectly by the structure and composition of the rice seeds. Structurally, rice seeds mainly comprise the spikelet hull, seed coat, aleurone layer, embryo, and endosperm. Among them, the size of spikelet hull is the key determinant of rice grain size, which usually affects rice AQ, MQ, and ECQ. The endosperm, mainly composed of starch and protein, is the major edible part of the rice seed. Therefore, the content, constitution, and physicochemical properties of starch and protein are crucial for multiple rice grain quality traits. Moreover, the other substances, such as lipids, minerals, vitamins, and phytochemicals, included in different parts of the rice seed, also contribute significantly to rice grain quality, especially the NQ. Rice seed growth and development are precisely controlled by many genes; therefore, cloning and dissecting these quality-related genes will enhance our knowledge of rice grain quality and will assist with the breeding of high quality rice. This review focuses on summarizing the recent progress on cloning key genes and their functions in regulating rice seed structure and composition, and their corresponding contributions to rice grain quality. This information will facilitate and advance future high quality rice breeding programs.
PMID: 35303197
BMC Med Res Methodol , IF:4.615 , 2022 Mar , V22 (1) : P62 doi: 10.1186/s12874-022-01544-6
Individual-specific networks for prediction modelling - A scoping review of methods.
Section for Clinical Biometrics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria.; Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.; BIO3 Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium.; Service de Biostatistique et d'Epidemiologie, Gustave Roussy, Oncostat U1018, Inserm, University Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif, France.; BIO3 Laboratory for Systems Genetics, GIGA-R Medical Genomics, University of Liege, Liege, Belgium.; Section for Clinical Biometrics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria. georg.heinze@meduniwien.ac.at.
BACKGROUND: Recent advances in biotechnology enable the acquisition of high-dimensional data on individuals, posing challenges for prediction models which traditionally use covariates such as clinical patient characteristics. Alternative forms of covariate representations for the features derived from these modern data modalities should be considered that can utilize their intrinsic interconnection. The connectivity information between these features can be represented as an individual-specific network defined by a set of nodes and edges, the strength of which can vary from individual to individual. Global or local graph-theoretical features describing the network may constitute potential prognostic biomarkers instead of or in addition to traditional covariates and may replace the often unsuccessful search for individual biomarkers in a high-dimensional predictor space. METHODS: We conducted a scoping review to identify, collate and critically appraise the state-of-art in the use of individual-specific networks for prediction modelling in medicine and applied health research, published during 2000-2020 in the electronic databases PubMed, Scopus and Embase. RESULTS: Our scoping review revealed the main application areas namely neurology and pathopsychology, followed by cancer research, cardiology and pathology (N = 148). Network construction was mainly based on Pearson correlation coefficients of repeated measurements, but also alternative approaches (e.g. partial correlation, visibility graphs) were found. For covariates measured only once per individual, network construction was mostly based on quantifying an individual's contribution to the overall group-level structure. Despite the multitude of identified methodological approaches for individual-specific network inference, the number of studies that were intended to enable the prediction of clinical outcomes for future individuals was quite limited, and most of the models served as proof of concept that network characteristics can in principle be useful for prediction. CONCLUSION: The current body of research clearly demonstrates the value of individual-specific network analysis for prediction modelling, but it has not yet been considered as a general tool outside the current areas of application. More methodological research is still needed on well-founded strategies for network inference, especially on adequate network sparsification and outcome-guided graph-theoretical feature extraction and selection, and on how networks can be exploited efficiently for prediction modelling.
PMID: 35249534
Front Genet , IF:4.599 , 2021 , V12 : P805771 doi: 10.3389/fgene.2021.805771
RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry.
Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States.; Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States.; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States.
Two hemibiotrophic pathogens, Colletotrichum acutatum (Ca) and C. gloeosporioides (Cg), cause anthracnose fruit rot and anthracnose crown rot in strawberry (Fragaria x ananassa Duchesne), respectively. Both Ca and Cg can initially infect through a brief biotrophic phase, which is associated with the production of intracellular primary hyphae that can infect host cells without causing cell death and establishing hemibiotrophic infection (HBI) or quiescent (latent infections) in leaf tissues. The Ca and Cg HBI in nurseries and subsequent distribution of asymptomatic infected transplants to fruit production fields is the major source of anthracnose epidemics in North Carolina. In the absence of complete resistance, strawberry varieties with good fruit quality showing rate-reducing resistance have frequently been used as a source of resistance to Ca and Cg. However, the molecular mechanisms underlying the rate-reducing resistance or susceptibility to Ca and Cg are still unknown. We performed comparative transcriptome analyses to examine how rate-reducing resistant genotype NCS 10-147 and susceptible genotype 'Chandler' respond to Ca and Cg and identify molecular events between 0 and 48 h after the pathogen-inoculated and mock-inoculated leaf tissues. Although plant response to both Ca and Cg at the same timepoint was not similar, more genes in the resistant interaction were upregulated at 24 hpi with Ca compared with those at 48 hpi. In contrast, a few genes were upregulated in the resistant interaction at 48 hpi with Cg. Resistance response to both Ca and Cg was associated with upregulation of MLP-like protein 44, LRR receptor-like serine/threonine-protein kinase, and auxin signaling pathway, whereas susceptibility was linked to modulation of the phenylpropanoid pathway. Gene regulatory network inference analysis revealed candidate transcription factors (TFs) such as GATA5 and MYB-10, and their downstream targets were upregulated in resistant interactions. Our results provide valuable insights into transcriptional changes during resistant and susceptible interactions, which can further facilitate assessing candidate genes necessary for resistance to two hemibiotrophic Colletotrichum spp. in strawberry.
PMID: 35360413
Genetics , IF:4.562 , 2022 Apr doi: 10.1093/genetics/iyac056
An interolog-based barley interactome as an integration framework for NLR immune signaling.
Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA.; Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA.; Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA.
The barley MLA nucleotide-binding leucine-rich-repeat (NLR) receptor and its orthologs confer recognition specificity to many fungal diseases, including powdery mildew, stem- and stripe rust. We used interolog inference to construct a barley protein interactome (HvInt) comprising 66133 edges and 7181 nodes, as a foundation to explore signaling networks associated with MLA. HvInt was compared to the experimentally validated Arabidopsis interactome of 11253 proteins and 73960 interactions, verifying that the two networks share scale-free properties, including a power-law distribution and small-world network. Then, by successive layering of defense-specific 'omics' datasets, HvInt was customized to model cellular response to powdery mildew infection. Integration of HvInt with expression quantitative trait loci (eQTL) enabled us to infer disease modules and responses associated with fungal penetration and haustorial development. Next, using HvInt and infection-time-course RNA sequencing of immune signaling mutants, we assembled resistant (R) and susceptible (S) subnetworks. The resulting differentially co-expressed (R-S) interactome is essential to barley immunity, facilitates the flow of signaling pathways and is linked to Mla through trans eQTL associations. Lastly, we anchored HvInt with new and previously identified interactors of the MLA coiled coli (CC) + nucleotide binding (NB) domains and extended these to additional MLA alleles, orthologs and NLR outgroups to predict receptor localization and conservation of signaling response. These results link genomic, transcriptomic, and physical interactions during MLA-specified immunity.
PMID: 35435213
Tree Physiol , IF:4.196 , 2022 Mar , V42 (3) : P664-683 doi: 10.1093/treephys/tpab114
SMRT and Illumina RNA sequencing reveal the complexity of terpenoid biosynthesis in Zanthoxylum armatum.
College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.; College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China.; Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing 400000, China.; Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.
Sichuan pepper (Zanthoxylum armatum DC) is a popular spice and is often prescribed in traditional Chinese medicine to treat vomiting, diarrhea, ascariasis and eczema, among other conditions. Volatile oils from Z. armatum leaves contain active ingredients, with terpenoids being one of the main components. In the present study, the combination of sequencing data of Z. armatum from PacBio single molecule real time (SMRT) and Illumina RNA sequencing (RNA-Seq) platforms facilitated an understanding of the gene regulatory network of terpenoid biosynthesis in pepper leaves. The leaves of three developmental stages from two Z. armatum cultivars, 'Rongchangwuci' (WC) and 'Zhuye' (ZY), were selected as test materials to construct sequencing libraries. A total of 143,122 predictions of unique coding sequences, 105,465 simple sequence repeats, 20,145 transcription factors and 4719 long non-coding RNAs (lncRNAs) were identified, and 142,829 transcripts were successfully annotated. The occurrence of alternative splicing events was verified by reverse transcription PCR, and quantitative real-time PCR was used to confirm the expression pattern of six randomly selected lncRNAs. A total of 96,931 differentially expressed genes were filtered from different samples. According to functional annotation, a total of 560 candidate genes were involved in terpenoid synthesis, of which 526 were differentially expressed genes (DEGs). To identify the key genes involved in terpenoid biosynthesis, the module genes in different samples, including structural and transcription factors genes, were analyzed using the weighted gene co-expression network method, and the co-expression network of genes was constructed. Thirty-one terpenoids were identified by gas chromatography-mass spectrometry. The correlation between 18 compounds with significantly different contents and genes with high connectivity in the module was jointly analyzed in both cultivars, yielding 12 candidate DEGs presumably involved in the regulation of terpenoid biosynthesis. Our findings showed that full-length transcriptome SMRT and Illumina RNA-Seq can play an important role in studying organisms without reference genomes and elucidating the gene regulation of a biosynthetic pathway.
PMID: 34448876
BMC Genomics , IF:3.969 , 2022 Mar , V23 (1) : P239 doi: 10.1186/s12864-022-08470-3
Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut.
College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 26000, China.; College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 26000, China. wangxiaohua19880721@126.com.; College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 26000, China. daishengjie@lyu.edu.cn.; Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture and Rural Affairs, Shandong Peanut Reasearch Instute, Qingdao, 266100, China.; College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 26000, China. liuzhening@lyu.edu.cn.
BACKGROUND: Peanut is the most essential oil and food crop globally due to its high oil and protein content. Root-knot nematode infects peanut roots, causing poor development and severely limiting peanut yields worldwide. The discovery of peanut genome identified a considerable number of genetic loci controlling the peanut root-knot nematode; however, the molecular mechanism of root-knot nematode remains unknown. RESULTS: The heterogeneous response to root-knot nematode stress in peanut roots was identified using whole-transcriptome RNA-seq. A total of 430 mRNAs, 111 miRNAs, 4453 lncRNAs, and 123 circRNAs were found to have differential expression between infected and non-infected peanuts. The expression profiles of the lncRNA/circRNA-miRNA-mRNA network were developed to understand the potential pathways that lead to root-knot nematodes in peanut roots. During root-knot nematodes stress, a total of 10 lncRNAs, 4 circRNAs, 5 miRNAs, and 13 mRNAs can create competing endogenous RNA and participate in the oxidation-reduction process as well as other biological metabolism processes in peanuts. The findings will highlight the role of peanut ceRNAs in response to root-knot nematodes. CONCLUSION: The GO classification and KEGG pathway enrichment study of core regulatory networks revealed that ceRNAs are involved in oxidation-reduction, peroxidase activity, lignin synthesis in the xylem, and flavonoid synthesis. Overall, these findings may help researchers better understand the role of non-coding RNAs in response to root-knot nematodes.
PMID: 35346027
Gene , IF:3.688 , 2022 Apr , V820 : P146114 doi: 10.1016/j.gene.2021.146114
Genome-wide evaluation of transcriptomic responses of human tissues to smoke: A systems biology study.
Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, Iran; Environmental Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.; Environmental Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran; Nutritional Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran. Electronic address: m_rashidi80@yahoo.com.; Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.; Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran.; Department of Immunology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.; Razi Herbal Medicines Research Center and Department of Pharmacognosy and Pharmaceutical Biotechnology, Faculty of Pharmacy, Lorestan University of Medical Sciences, Khorramabad, Iran.
The harmful compounds in various sources of smoke threaten human health. So far, many studies have investigated the effects of compounds of smoke on transcriptome changes in different human tissues. However, no study has been conducted on the effects of these compounds on transcriptome changes in different human tissues simultaneously. Hence, the present study was conducted to identify smoke-related genes (SRGs) and their response mechanisms to smoke in various human cells and tissues using systems biology based methods. A total of 6,484 SRGs were identified in the studied tissues, among which 4,095 SRGs were up-regulated and 2,389 SRGs were down-regulated. Totally, 459 SRGs were smoke-related transcription factors (SRTFs). Gene regulatory network analysis showed that the studied cells and tissues have different gene regulation and responses to compounds of smoke. The comparison of different tissues revealed no common SRG among the all studied tissues. However, the CYP1B1 gene was common among seven cells and tissues, and had the same expression trend. Network analysis showed that the CYP1B1 is a hub gene among SRGs in various cells and tissues. To the best of our knowledge, for the first time, our results showed that compounds of smoke induce and increase the expression of CYP1B1 key gene in all target and non-target tissues of human. Moreover, despite the specific characteristics of CYP1B1 gene and its identical expression trend in target and non-target tissues, it can be used as a biomarker for diagnosis and prognosis.
PMID: 35077830
Gene , IF:3.688 , 2022 Apr , V819 : P146233 doi: 10.1016/j.gene.2022.146233
Different gene co-expression patterns of aortic intima-media and adventitia in thoracic aortic aneurysm.
Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China. Electronic address: lcx_pumc@163.com.; Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China.; Department of Neurosurgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.; Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.; Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China. Electronic address: yuehongzheng@yahoo.com.
BACKGROUND: Due to permanent aortic dilation, thoracic aortic aneurysm (TAA) is a life-threatening disease. Once ruptured, TAA has a high lethality and disability rate. Although studies have focused on transcriptomic alterations in TAA, more detailed analysis is still lacking, especially the different aortic intima-media and adventitia roles. This study aimed to identify the different co-expression patterns between the aortic intima-media and the adventitia underlying the aortic dilation. METHODS: We analyzed the gene expression profiles obtained from Gene Expression Omnibus (GEO, GSE26155) database. With a false discovery rate (FDR) < 0.05 and |log2FC| >/= 1, 56 and 33 differential genes in the intima-media and adventitia, respectively, between the non-dilated and dilated status. Gene ontology (GO) and gene set enrichment analysis revealed that degranulation and activation of neutrophils play an essential role in the intima-media of dilated aortas. Through weighted gene co-expression network analysis (WGCNA), we identified essential co-expressed modules and hub genes to explore the biological functions of the dysregulated genes. RESULTS: Functional pathway analysis suggested that lipid metabolism, C-C motif chemokine pathways were significantly enriched in the adventitia, whereas ribosome proteins and related mRNA translation pathways were closely related to intima and media. Furthermore, the ssGSEA analysis indicated that macrophages, helper T cells, and neutrophils were higher in the intima-media of the dilated thoracic aorta. Finally, we validated the critical findings of the study with the murine model of TAA. CONCLUSION: This study identified and verified hub genes and pathways in aortic intima-media and adventitia prominently associated with aortic dilation, providing practical understanding in the perspective of searching for new molecular targets.
PMID: 35121027
J Plant Physiol , IF:3.549 , 2022 Apr , V271 : P153666 doi: 10.1016/j.jplph.2022.153666
Cropping practices manipulate soil bacterial structure and functions on the Qinghai-Tibet Plateau.
Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China.; Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China.; Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China. Electronic address: xqzhao@nwipb.cas.cn.; Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China. Electronic address: sxxu@nwipb.cas.cn.
There is an increasing awareness of the adverse environmental effects of the intensive practices used in modern crop farming, such as those that cause greenhouse gas emissions and nutrient leaching. Harnessing beneficial microbes by changing planting practices presents a promising strategy for optimizing plant growth and agricultural sustainability. However, the characteristics of soil microorganisms under different planting patterns remain uncertain. We conducted a study of soil bacterial structure and function under monoculture vs. polyculture planting regimes using 16S rRNA gene sequencing on the Qinghai-Tibet Plateau. We observed substantial variations in bacterial richness, diversity, and relative abundances of taxa between gramineous and leguminous monocultures, as well as between gramineae-legume polycultures. The number of operational taxonomic units and alpha and beta diversity were markedly higher in the leguminous monocultures than in the gramineous monocultures; conversely, network analysis revealed that the interactions among the bacterial genera in the gramineous monocultures were more complex than those in the other two planting regimes. Moreover, nitrogen fixation, soil detoxification, and productivity were increased under the gramineous monocultures; more importantly, low soil-borne diseases (e.g., animals parasitic or symbiont) also facilitated strongly suppressive effects toward soil-borne pathogens. Nevertheless, the gramineae-legume polycultures were prone to nitrate seepage contamination, and leguminous monocultures exhibited strong denitrification effects. These results revealed that the gramineous monoculture is a more promising cropping pattern on the Qinghai-Tibetan Plateau. Understanding the bacterial distribution patterns and interactions of crop-sensitive microbes presents a basis for developing microbial management strategies for smart farming.
PMID: 35303514
Fungal Genet Biol , IF:3.495 , 2022 Apr , V159 : P103673 doi: 10.1016/j.fgb.2022.103673
Distinctive carbon repression effects in the carbohydrate-selective wood decay fungus Rhodonia placenta.
Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, United States. Electronic address: zhan3437@umn.edu.; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States.; Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States. Electronic address: schillin@umn.edu.
Brown rot fungi dominate the carbon degradation of northern terrestrial conifers. These fungi adapted unique genetic inventories to degrade lignocellulose and to rapidly release a large quantity of carbohydrates for fungal catabolism. We know that brown rot involves "two-step" gene regulation to delay most hydrolytic enzyme expression until after harsh oxidative pretreatments. This implies the crucial role of concise gene regulation to brown rot efficacy, but the underlying regulatory mechanisms remain uncharacterized. Here, using the combined transcriptomic and enzyme analyses we investigated the roles of carbon catabolites in controlling gene expression in model brown rot fungus Rhodonia placenta. We identified co-regulated gene regulons as shared transcriptional responses to no-carbon controls, glucose, cellobiose, or aspen wood (Populus sp.). We found that cellobiose, a common inducing catabolite for fungi, induced expression of main chain-cleaving cellulases in GH5 and GH12 families (cellobiose vs. no-carbon > 4-fold, Padj < 0.05), whereas complex aspen was a universal inducer for Carbohydrate Active Enzymes (CAZymes) expression. Importantly, we observed the attenuated glucose-mediated repression effects on cellulases expression, but not on hemicellulases and lignin oxidoreductases, suggesting fungi might have adapted diverged regulatory routes to boost cellulase production for the fast carbohydrate release. Using carbon regulons, we further predicted the cis- and trans-regulatory elements and assembled a network model of the distinctive regulatory machinery of brown rot. These results offer mechanistic insights into the energy efficiency traits of a common group of decomposer fungi with enormous influence on the carbon cycle.
PMID: 35150839
Brain Sci , IF:3.394 , 2022 Mar , V12 (3) doi: 10.3390/brainsci12030378
A Preliminary Report of Network Electroencephalographic Measures in Primary Progressive Apraxia of Speech and Aphasia.
Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA.; Department of Neurology, Mayo Clinic, Scottsdale, AZ 85259, USA.; Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA.
The objective of this study was to characterize network-level changes in nonfluent/agrammatic Primary Progressive Aphasia (agPPA) and Primary Progressive Apraxia of Speech (PPAOS) with graph theory (GT) measures derived from scalp electroencephalography (EEG) recordings. EEGs of 15 agPPA and 7 PPAOS patients were collected during relaxed wakefulness with eyes closed (21 electrodes, 10-20 positions, 256 Hz sampling rate, 1-200 Hz bandpass filter). Eight artifact-free, non-overlapping 1024-point epochs were selected. Via Brainwave software, GT weighted connectivity and minimum spanning tree (MST) measures were calculated for theta and upper and lower alpha frequency bands. Differences in GT and MST measures between agPPA and PPAOS were assessed with Wilcoxon rank-sum tests. Of greatest interest, Spearman correlations were computed between behavioral and network measures in all frequency bands across all patients. There were no statistically significant differences in GT or MST measures between agPPA and PPAOS. There were significant correlations between several network and behavioral variables. The correlations demonstrate a relationship between reduced global efficiency and clinical symptom severity (e.g., parkinsonism, AOS). This preliminary, exploratory study demonstrates potential for EEG GT measures to quantify network changes associated with degenerative speech-language disorders.
PMID: 35326334
Virus Res , IF:3.303 , 2022 Apr , V311 : P198704 doi: 10.1016/j.virusres.2022.198704
Complex small RNA-mediated regulatory networks between viruses/viroids/satellites and host plants.
Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Plant Protection, China Agricultural University, Beijing 100193, China.; Chinese Academy of Inspection and Quarantine, Beijing 100176, China.; Chinese Academy of Inspection and Quarantine, Beijing 100176, China. Electronic address: zhusf@caiq.org.cn.
Host plants deploy the small RNA (sRNA)-directed RNA silencing pathway to resist invasion by acellular microorganisms (viruses/viroids/satellites), and, in turn, this pathway is exploited by pathogenic agents to create an environment conducive to infection. Previous known sRNA-RNA systems consist of host endogenous microRNAs (miRNAs) mediating the regulation of host mRNAs and virus/viroid/satellite-derived small interfering RNAs (vsiRNAs) targeting their genomic RNAs. However, more in-depth explorations have substantially expanded the understanding of the complexity of sRNA-RNA regulatory networks. Here, we review some recently discovered sRNA-mediated regulatory systems. Specifically, in addition to virus-encoded proteins acting as virulence factors, vsiRNAs can serve as important pathogenic determinants targeting host mRNAs and noncoding RNAs to promote virus/viroid/satellite infection and trigger symptoms that may be side effects of infection. Additionally, virus-activated but host-derived siRNAs (vasiRNAs) regulate endogenous plant gene expression related to virus resistance or pathogenicity. The inhibitory effect of miRNAs on plant endogenous mRNAs and viral RNAs (vRNAs) has also been identified. Furthermore, siRNA-based interregulation occurring between viruses and their parasite satellite RNAs (satRNAs) enables coexisting virus-satRNA-plant homoeostasis. Thus, the underlying mechanisms of plant-virus/viroid/satellite competition and symbiosis are largely obscured by these diverse sRNA-RNA combinations. Guided by the intricate regulatory network-based principle at the RNA level, practically applicable and feasible strategies have been developed for the management of plant viruses/viroids/satellites for which effective control measures are lacking.
PMID: 35139407
Brain Struct Funct , IF:3.27 , 2022 Apr , V227 (3) : P741-762 doi: 10.1007/s00429-021-02435-0
A hands-on tutorial on network and topological neuroscience.
Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Anatomy and Neurosciences, Amsterdam UMC, De Boelelaan 1117, Amsterdam, The Netherlands.; Institut Des Maladies Neurodegeneratives, UMR 5293, Universite de Bordeaux, CNRS, Bordeaux Neurocampus, 146 Rue Leo Saignat, 33000, Bordeaux, France.; Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Psychiatry, Amsterdam UMC, De Boelelaan 1117, Amsterdam, The Netherlands.; Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Anatomy and Neurosciences, Amsterdam UMC, De Boelelaan 1117, Amsterdam, The Netherlands. f.nobregasantos@amsterdamumc.nl.; Institute for Advanced Studies, University of Amsterdam, Oude Turfmarkt 147, 1012 GC, Amsterdam, The Netherlands. f.nobregasantos@amsterdamumc.nl.
The brain is an extraordinarily complex system that facilitates the optimal integration of information from different regions to execute its functions. With the recent advances in technology, researchers can now collect enormous amounts of data from the brain using neuroimaging at different scales and from numerous modalities. With that comes the need for sophisticated tools for analysis. The field of network neuroscience has been trying to tackle these challenges, and graph theory has been one of its essential branches through the investigation of brain networks. Recently, topological data analysis has gained more attention as an alternative framework by providing a set of metrics that go beyond pairwise connections and offer improved robustness against noise. In this hands-on tutorial, our goal is to provide the computational tools to explore neuroimaging data using these frameworks and to facilitate their accessibility, data visualisation, and comprehension for newcomers to the field. We will start by giving a concise (and by no means complete) overview of the field to introduce the two frameworks and then explain how to compute both well-established and newer metrics on resting-state functional magnetic resonance imaging. We use an open-source language (Python) and provide an accompanying publicly available Jupyter Notebook that uses the 1000 Functional Connectomes Project dataset. Moreover, we would like to highlight one part of our notebook dedicated to the realistic visualisation of high order interactions in brain networks. This pipeline provides three-dimensional (3-D) plots of pairwise and higher-order interactions projected in a brain atlas, a new feature tailor-made for network neuroscience.
PMID: 35142909
Appl Biochem Biotechnol , IF:2.926 , 2022 Apr , V194 (4) : P1479-1495 doi: 10.1007/s12010-021-03731-5
Bacterial Community Structure and Metabolic Function Succession During the Composting of Distilled Grain Waste.
College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, China.; College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, China. szy@scu.edu.cn.; Luzhou Laojiao Co., Ltd., Luzhou, 646000, China.; Solid-State Fermentation Resource Utilization Key Laboratory of Sichuan Province, Yibin University, Yibin, 644000, China.; Key Laboratory of Wuliangye-Flavor Liquor Solid-State Fermentation, China National Light Industry, Yibin, 644007, China.
Distilled grain waste (DGW) can be converted to organic fertilizer via aerobic composting process without inoculating exogenous microorganisms. To illustrate the material conversion mechanism, this study investigated the dynamic changes of bacterial community structure and metabolic function involved in DGW composting. Results showed that a significant increase in microbial community alpha diversity was observed during DGW composting. Moreover, unique community structures occurred at each composting stage. The dominant phyla were Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, Myxococcota, and Chloroflexi, whose abundance varied according to different composting stages. Keystone microbes can be selected as biomarkers for each stage, and Microbispora, Chryseolinea, Steroidobacter, Truepera, and Luteimonas indicating compost maturity. Co-occurrence network analysis revealed a significant relationship between keystone microbes and environmental factors. The carbohydrate and amino acid metabolism were confirmed as the primary metabolic pathways by metabolic function profiles. Furthermore, nitrogen metabolism pathway analysis indicated that denitrification and NH3 volatilization induced higher nitrogen loss during DGW composting. This study can provide new understanding of the microbiota for organic matter and nitrogen conversion in the composting process of DGW.
PMID: 34748150
Emerg Top Life Sci , 2022 Apr , V6 (2) : P137-139 doi: 10.1042/ETLS20220020
How 'omics technologies can drive plant engineering, ecosystem surveillance, human and animal health.
La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia.; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia.
'Omics describes a broad collection of research tools and techniques that enable researchers to collect data about biological systems at a very large, or near-complete, scale. These include sequencing of individual and community genomes (genomics, metagenomics), characterization and quantification of gene expression (transcriptomics), metabolite abundance (metabolomics), protein content (proteomics) and phosphorylation (phospho-proteomics), amongst many others. Though initially exploited as tools for fundamental discovery, 'omics techniques are now used extensively in applied and translational research, for example in plant and animal breeding, biomarker development and drug discovery. In this collection of reviews, we aimed to introduce readers to current and future applications of 'omics technologies to solve real-world problems.
PMID: 35403675
STAR Protoc , 2022 Mar , V3 (1) : P101208 doi: 10.1016/j.xpro.2022.101208
Gene coexpression analysis in Arabidopsis thaliana based on public microarray data.
Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.; biobank.cy Center of Excellence in Biobanking and Biomedical Research, University of Cyprus, 2029 Nicosia, Cyprus.
Coexpressed genes tend to participate in related biological processes. Gene coexpression analysis allows the discovery of functional gene partners or the assignment of biological roles to genes of unknown function. In this protocol, we describe the steps necessary to create a gene coexpression tree for Arabidopsis thaliana, using publicly available Affymetrix CEL microarray data. Because the computational analysis described here is highly dependent on sample quality, we detail an automatic quality control approach. For complete details on the use and execution of this protocol, please refer to Zogopoulos et al. (2021).
PMID: 35243384
STAR Protoc , 2022 Mar , V3 (1) : P101175 doi: 10.1016/j.xpro.2022.101175
TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets.
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.; Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada.; Department of Computer Science, Western University, London, ON N6A 5B7, Canada.; Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA.
Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning of large protein sequence phylogenetic datasets via the minimization of OTU redundancy. TreeTuner facilitates preliminary investigation of such datasets as well as more rigorous downstream analysis of specific subsets of OTUs. For complete details on the use and execution of this protocol, please refer to Maruyama et al. (2013) and Sibbald et al. (2019).
PMID: 35243369